--- _id: '2719' abstract: - lang: eng text: Prediction of the evolutionary process is a long standing problem both in the theory of evolutionary biology and evolutionary computation (EC). It has long been realized that heritable variation is crucial to both the response to selection and the success of genetic algorithms. However, not all variation contributes in the same way to the response. Quantitative genetics has developed a large body of work trying to estimate and understand how different components of the variance in fitness in the population contribute to the response to selection. We illustrate how to apply some concepts of quantitative genetics to the analysis of genetic algorithms. In particular, we derive estimates for the short term prediction of the response to selection and we use variance decomposition to gain insight on local aspects of the landscape. Finally, we propose a new population based genetic algorithm that uses these methods to improve its operation. author: - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Paixao T, Barton NH. A variance decomposition approach to the analysis of genetic algorithms. In: Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation. ACM; 2013:845-852. doi:10.1145/2463372.2463470' apa: 'Paixao, T., & Barton, N. H. (2013). A variance decomposition approach to the analysis of genetic algorithms. In Proceedings of the 15th annual conference on Genetic and evolutionary computation (pp. 845–852). Amsterdam, Netherlands: ACM. https://doi.org/10.1145/2463372.2463470' chicago: Paixao, Tiago, and Nicholas H Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, 845–52. ACM, 2013. https://doi.org/10.1145/2463372.2463470. ieee: T. Paixao and N. H. Barton, “A variance decomposition approach to the analysis of genetic algorithms,” in Proceedings of the 15th annual conference on Genetic and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 845–852. ista: 'Paixao T, Barton NH. 2013. A variance decomposition approach to the analysis of genetic algorithms. Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 845–852.' mla: Paixao, Tiago, and Nicholas H. Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–52, doi:10.1145/2463372.2463470. short: T. Paixao, N.H. Barton, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–852. conference: end_date: 2013-07-10 location: Amsterdam, Netherlands name: 'GECCO: Genetic and evolutionary computation conference' start_date: 2013-07-06 date_created: 2018-12-11T11:59:15Z date_published: 2013-07-01T00:00:00Z date_updated: 2021-01-12T06:59:15Z day: '01' department: - _id: NiBa - _id: CaGu doi: 10.1145/2463372.2463470 ec_funded: 1 language: - iso: eng month: '07' oa_version: None page: 845 - 852 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Proceedings of the 15th annual conference on Genetic and evolutionary computation publication_status: published publisher: ACM publist_id: '4173' quality_controlled: '1' scopus_import: 1 status: public title: A variance decomposition approach to the analysis of genetic algorithms type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2817' abstract: - lang: eng text: The basic idea of evolutionary game theory is that payoff determines reproductive rate. Successful individuals have a higher payoff and produce more offspring. But in evolutionary and ecological situations there is not only reproductive rate but also carrying capacity. Individuals may differ in their exposure to density limiting effects. Here we explore an alternative approach to evolutionary game theory by assuming that the payoff from the game determines the carrying capacity of individual phenotypes. Successful strategies are less affected by density limitation (crowding) and reach higher equilibrium abundance. We demonstrate similarities and differences between our framework and the standard replicator equation. Our equation is defined on the positive orthant, instead of the simplex, but has the same equilibrium points as the replicator equation. Linear stability analysis produces the classical conditions for asymptotic stability of pure strategies, but the stability properties of internal equilibria can differ in the two frameworks. For example, in a two-strategy game with an internal equilibrium that is always stable under the replicator equation, the corresponding equilibrium can be unstable in the new framework resulting in a limit cycle. author: - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Novak S, Chatterjee K, Nowak M. Density games. Journal of Theoretical Biology. 2013;334:26-34. doi:10.1016/j.jtbi.2013.05.029 apa: Novak, S., Chatterjee, K., & Nowak, M. (2013). Density games. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2013.05.029 chicago: Novak, Sebastian, Krishnendu Chatterjee, and Martin Nowak. “Density Games.” Journal of Theoretical Biology. Elsevier, 2013. https://doi.org/10.1016/j.jtbi.2013.05.029. ieee: S. Novak, K. Chatterjee, and M. Nowak, “Density games,” Journal of Theoretical Biology, vol. 334. Elsevier, pp. 26–34, 2013. ista: Novak S, Chatterjee K, Nowak M. 2013. Density games. Journal of Theoretical Biology. 334, 26–34. mla: Novak, Sebastian, et al. “Density Games.” Journal of Theoretical Biology, vol. 334, Elsevier, 2013, pp. 26–34, doi:10.1016/j.jtbi.2013.05.029. short: S. Novak, K. Chatterjee, M. Nowak, Journal of Theoretical Biology 334 (2013) 26–34. date_created: 2018-12-11T11:59:45Z date_published: 2013-10-07T00:00:00Z date_updated: 2021-01-12T06:59:55Z day: '07' ddc: - '000' department: - _id: NiBa - _id: KrCh doi: 10.1016/j.jtbi.2013.05.029 ec_funded: 1 file: - access_level: open_access checksum: 3c29059ab03a4b8f97a07646b817ddbb content_type: application/pdf creator: system date_created: 2018-12-12T10:14:54Z date_updated: 2020-07-14T12:45:49Z file_id: '5110' file_name: IST-2016-400-v1+1_1-s2.0-S0022519313002609-main.pdf file_size: 834604 relation: main_file file_date_updated: 2020-07-14T12:45:49Z has_accepted_license: '1' intvolume: ' 334' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '10' oa: 1 oa_version: Published Version page: 26 - 34 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '3984' pubrep_id: '400' quality_controlled: '1' scopus_import: 1 status: public title: Density games tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 334 year: '2013' ... --- _id: '2823' abstract: - lang: eng text: The primary goal of restoration is to create self-sustaining ecological communities that are resilient to periodic disturbance. Currently, little is known about how restored communities respond to disturbance events such as fire and how this response compares to remnant vegetation. Following the 2003 fires in south-eastern Australia we examined the post-fire response of revegetation plantings and compared this to remnant vegetation. Ten burnt and 10 unburnt (control) sites were assessed for each of three types of vegetation (direct seeding revegetation, revegetation using nursery seedlings (tubestock) and remnant woodland). Sixty sampling sites were surveyed 6months after fire to quantify the initial survival of mid- and overstorey plant species in each type of vegetation. Three and 5years after fire all sites were resurveyed to assess vegetation structure, species diversity and vigour, as well as indicators of soil function. Overall, revegetation showed high (>60%) post-fire survival, but this varied among species depending on regeneration strategy (obligate seeder or resprouter). The native ground cover, mid- and overstorey in both types of plantings showed rapid recovery of vegetation structure and cover within 3years of fire. This recovery was similar to the burnt remnant woodlands. Non-native (exotic) ground cover initially increased after fire, but was no different in burnt and unburnt sites 5years after fire. Fire had no effect on species richness, but burnt direct seeding sites had reduced species diversity (Simpson's Diversity Index) while diversity was higher in burnt remnant woodlands. Indices of soil function in all types of vegetation had recovered to levels found in unburnt sites 5years after fire. These results indicate that even young revegetation (stands <10years old) showed substantial recovery from disturbance by fire. This suggests that revegetation can provide an important basis for restoring woodland communities in the fire-prone Australian environment. author: - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: Susie full_name: Wilson, Susie last_name: Wilson - first_name: David full_name: Freudenberger, David last_name: Freudenberger - first_name: Nick full_name: Nicholls, Nick last_name: Nicholls - first_name: Lori full_name: Gould, Lori last_name: Gould - first_name: Sarah full_name: Hnatiuk, Sarah last_name: Hnatiuk - first_name: Jeni full_name: Delandre, Jeni last_name: Delandre citation: ama: Pickup M, Wilson S, Freudenberger D, et al. Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. 2013;38(3):300-312. doi:10.1111/j.1442-9993.2012.02404.x apa: Pickup, M., Wilson, S., Freudenberger, D., Nicholls, N., Gould, L., Hnatiuk, S., & Delandre, J. (2013). Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1442-9993.2012.02404.x chicago: Pickup, Melinda, Susie Wilson, David Freudenberger, Nick Nicholls, Lori Gould, Sarah Hnatiuk, and Jeni Delandre. “Post-Fire Recovery of Revegetated Woodland Communities in South-Eastern Australia.” Austral Ecology. Wiley-Blackwell, 2013. https://doi.org/10.1111/j.1442-9993.2012.02404.x. ieee: M. Pickup et al., “Post-fire recovery of revegetated woodland communities in south-eastern Australia,” Austral Ecology, vol. 38, no. 3. Wiley-Blackwell, pp. 300–312, 2013. ista: Pickup M, Wilson S, Freudenberger D, Nicholls N, Gould L, Hnatiuk S, Delandre J. 2013. Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. 38(3), 300–312. mla: Pickup, Melinda, et al. “Post-Fire Recovery of Revegetated Woodland Communities in South-Eastern Australia.” Austral Ecology, vol. 38, no. 3, Wiley-Blackwell, 2013, pp. 300–12, doi:10.1111/j.1442-9993.2012.02404.x. short: M. Pickup, S. Wilson, D. Freudenberger, N. Nicholls, L. Gould, S. Hnatiuk, J. Delandre, Austral Ecology 38 (2013) 300–312. date_created: 2018-12-11T11:59:47Z date_published: 2013-05-01T00:00:00Z date_updated: 2021-01-12T06:59:58Z day: '01' department: - _id: NiBa doi: 10.1111/j.1442-9993.2012.02404.x intvolume: ' 38' issue: '3' language: - iso: eng month: '05' oa_version: None page: 300 - 312 publication: Austral Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '3978' quality_controlled: '1' scopus_import: 1 status: public title: Post-fire recovery of revegetated woodland communities in south-eastern Australia type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 38 year: '2013' ... --- _id: '2842' abstract: - lang: eng text: 'We outline two approaches to inference of neighbourhood size, N, and dispersal rate, σ2, based on either allele frequencies or on the lengths of sequence blocks that are shared between genomes. Over intermediate timescales (10-100 generations, say), populations that live in two dimensions approach a quasi-equilibrium that is independent of both their local structure and their deeper history. Over such scales, the standardised covariance of allele frequencies (i.e. pairwise FS T) falls with the logarithm of distance, and depends only on neighbourhood size, N, and a ''local scale'', κ; the rate of gene flow, σ2, cannot be inferred. We show how spatial correlations can be accounted for, assuming a Gaussian distribution of allele frequencies, giving maximum likelihood estimates of N and κ. Alternatively, inferences can be based on the distribution of the lengths of sequence that are identical between blocks of genomes: long blocks (>0.1 cM, say) tell us about intermediate timescales, over which we assume a quasi-equilibrium. For large neighbourhood size, the distribution of long blocks is given directly by the classical Wright-Malécot formula; this relationship can be used to infer both N and σ2. With small neighbourhood size, there is an appreciable chance that recombinant lineages will coalesce back before escaping into the distant past. For this case, we show that if genomes are sampled from some distance apart, then the distribution of lengths of blocks that are identical in state is geometric, with a mean that depends on N and σ2.' author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge - first_name: Jerome full_name: Kelleher, Jerome last_name: Kelleher - first_name: Amandine full_name: Véber, Amandine last_name: Véber citation: ama: 'Barton NH, Etheridge A, Kelleher J, Véber A. Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. 2013;87(1):105-119. doi:10.1016/j.tpb.2013.03.001' apa: 'Barton, N. H., Etheridge, A., Kelleher, J., & Véber, A. (2013). Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2013.03.001' chicago: 'Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber. “Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence Blocks.” Theoretical Population Biology. Elsevier, 2013. https://doi.org/10.1016/j.tpb.2013.03.001.' ieee: 'N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks,” Theoretical Population Biology, vol. 87, no. 1. Elsevier, pp. 105–119, 2013.' ista: 'Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. 87(1), 105–119.' mla: 'Barton, Nicholas H., et al. “Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence Blocks.” Theoretical Population Biology, vol. 87, no. 1, Elsevier, 2013, pp. 105–19, doi:10.1016/j.tpb.2013.03.001.' short: N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population Biology 87 (2013) 105–119. date_created: 2018-12-11T11:59:53Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T07:00:09Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1016/j.tpb.2013.03.001 ec_funded: 1 file: - access_level: open_access checksum: 9bf9d9a6fd03dd9df50906891f393bf8 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:33Z date_updated: 2020-07-14T12:45:50Z file_id: '5288' file_name: IST-2016-558-v1+1_inference_revised3101NB.pdf file_size: 1554712 relation: main_file - access_level: open_access checksum: 2bceddb76edacd0cd5fad73051e2a928 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:34Z date_updated: 2020-07-14T12:45:50Z file_id: '5289' file_name: IST-2016-558-v1+2_inference_revised3101NBApp.pdf file_size: 822964 relation: main_file file_date_updated: 2020-07-14T12:45:50Z has_accepted_license: '1' intvolume: ' 87' issue: '1' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 105 - 119 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Theoretical Population Biology publication_status: published publisher: Elsevier publist_id: '3953' pubrep_id: '558' quality_controlled: '1' scopus_import: 1 status: public title: 'Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 87 year: '2013' ... --- _id: '2910' abstract: - lang: eng text: "Coalescent simulation has become an indispensable tool in population genetics and many complex evolutionary scenarios have been incorporated into the basic algorithm. Despite many years of intense interest in spatial structure, however, there are no available methods to simulate the ancestry of a sample of genes that occupy a spatial continuum. This is mainly due to the severe technical problems encountered by the classical model of isolation\r\nby distance. A recently introduced model solves these technical problems and provides a solid theoretical basis for the study of populations evolving in continuous space. We present a detailed algorithm to simulate the coalescent process in this model, and provide an efficient implementation of a generalised version of this algorithm as a freely available Python module." author: - first_name: Jerome full_name: Kelleher, Jerome last_name: Kelleher - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge citation: ama: Kelleher J, Barton NH, Etheridge A. Coalescent simulation in continuous space. Bioinformatics. 2013;29(7):955-956. doi:10.1093/bioinformatics/btt067 apa: Kelleher, J., Barton, N. H., & Etheridge, A. (2013). Coalescent simulation in continuous space. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btt067 chicago: Kelleher, Jerome, Nicholas H Barton, and Alison Etheridge. “Coalescent Simulation in Continuous Space.” Bioinformatics. Oxford University Press, 2013. https://doi.org/10.1093/bioinformatics/btt067. ieee: J. Kelleher, N. H. Barton, and A. Etheridge, “Coalescent simulation in continuous space,” Bioinformatics, vol. 29, no. 7. Oxford University Press, pp. 955–956, 2013. ista: Kelleher J, Barton NH, Etheridge A. 2013. Coalescent simulation in continuous space. Bioinformatics. 29(7), 955–956. mla: Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space.” Bioinformatics, vol. 29, no. 7, Oxford University Press, 2013, pp. 955–56, doi:10.1093/bioinformatics/btt067. short: J. Kelleher, N.H. Barton, A. Etheridge, Bioinformatics 29 (2013) 955–956. date_created: 2018-12-11T12:00:17Z date_published: 2013-02-07T00:00:00Z date_updated: 2021-01-12T07:00:38Z day: '07' ddc: - '570' department: - _id: NiBa doi: 10.1093/bioinformatics/btt067 ec_funded: 1 file: - access_level: open_access checksum: a3b54d7477fac923815ac082403d9bd0 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:04Z date_updated: 2020-07-14T12:45:52Z file_id: '5189' file_name: IST-2016-556-v1+1_bioinformatics-2013.pdf file_size: 170197 relation: main_file file_date_updated: 2020-07-14T12:45:52Z has_accepted_license: '1' intvolume: ' 29' issue: '7' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 955 - 956 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Bioinformatics publication_status: published publisher: Oxford University Press publist_id: '3833' pubrep_id: '556' quality_controlled: '1' scopus_import: 1 status: public title: Coalescent simulation in continuous space type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2013' ... --- _id: '2909' abstract: - lang: eng text: "We survey a class of models for spatially structured populations\r\nwhich we have called spatial Λ-Fleming–Viot processes. They arise from a flexible\r\nframework for modelling in which the key innovation is that random genetic drift\r\nis driven by a Poisson point process of spatial ‘events’. We demonstrate how this\r\novercomes some of the obstructions to modelling populations which evolve in two-\r\n(and higher-) dimensional spatial continua, how its predictions match phenomena\r\nobserved in data and how it fits with classical models. Finally we outline some\r\ndirections for future research." article_processing_charge: No author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge - first_name: Amandine full_name: Véber, Amandine last_name: Véber citation: ama: Barton NH, Etheridge A, Véber A. Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. 2013;2013(1). doi:10.1088/1742-5468/2013/01/P01002 apa: Barton, N. H., Etheridge, A., & Véber, A. (2013). Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd. https://doi.org/10.1088/1742-5468/2013/01/P01002 chicago: Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “Modelling Evolution in a Spatial Continuum.” Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd., 2013. https://doi.org/10.1088/1742-5468/2013/01/P01002. ieee: N. H. Barton, A. Etheridge, and A. Véber, “Modelling evolution in a spatial continuum,” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 1. IOP Publishing Ltd., 2013. ista: Barton NH, Etheridge A, Véber A. 2013. Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. 2013(1). mla: Barton, Nicholas H., et al. “Modelling Evolution in a Spatial Continuum.” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 1, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/01/P01002. short: N.H. Barton, A. Etheridge, A. Véber, Journal of Statistical Mechanics Theory and Experiment 2013 (2013). date_created: 2018-12-11T12:00:17Z date_published: 2013-01-16T00:00:00Z date_updated: 2021-01-12T07:00:37Z day: '16' ddc: - '570' department: - _id: NiBa doi: 10.1088/1742-5468/2013/01/P01002 ec_funded: 1 file: - access_level: open_access checksum: ce8a4424385b3086138a1e054e16e0e3 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:52Z date_updated: 2020-07-14T12:45:52Z file_id: '5242' file_name: IST-2016-557-v1+1_BEVrevised.pdf file_size: 702583 relation: main_file file_date_updated: 2020-07-14T12:45:52Z has_accepted_license: '1' intvolume: ' 2013' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Journal of Statistical Mechanics Theory and Experiment publication_status: published publisher: IOP Publishing Ltd. publist_id: '3834' pubrep_id: '557' quality_controlled: '1' scopus_import: 1 status: public title: Modelling evolution in a spatial continuum type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 2013 year: '2013' ... --- _id: '2908' abstract: - lang: eng text: 'Hybridization is an almost inevitable component of speciation, and its study can tell us much about that process. However, hybridization itself may have a negligible influence on the origin of species: on the one hand, universally favoured alleles spread readily across hybrid zones, whilst on the other, spatially heterogeneous selection causes divergence despite gene flow. Thus, narrow hybrid zones or occasional hybridisation may hardly affect the process of divergence.' author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Barton NH. Does hybridisation influence speciation?  . Journal of Evolutionary Biology. 2013;26(2):267-269. doi:10.1111/jeb.12015 apa: Barton, N. H. (2013). Does hybridisation influence speciation?  . Journal of Evolutionary Biology. Wiley-Blackwell. https://doi.org/10.1111/jeb.12015 chicago: Barton, Nicholas H. “Does Hybridisation Influence Speciation?  .” Journal of Evolutionary Biology. Wiley-Blackwell, 2013. https://doi.org/10.1111/jeb.12015. ieee: N. H. Barton, “Does hybridisation influence speciation?  ,” Journal of Evolutionary Biology, vol. 26, no. 2. Wiley-Blackwell, pp. 267–269, 2013. ista: Barton NH. 2013. Does hybridisation influence speciation?  . Journal of Evolutionary Biology. 26(2), 267–269. mla: Barton, Nicholas H. “Does Hybridisation Influence Speciation?  .” Journal of Evolutionary Biology, vol. 26, no. 2, Wiley-Blackwell, 2013, pp. 267–69, doi:10.1111/jeb.12015. short: N.H. Barton, Journal of Evolutionary Biology 26 (2013) 267–269. date_created: 2018-12-11T12:00:17Z date_published: 2013-01-17T00:00:00Z date_updated: 2021-01-12T07:00:37Z day: '17' ddc: - '576' department: - _id: NiBa doi: 10.1111/jeb.12015 file: - access_level: open_access checksum: 716e88714c3411cd0bd70928b14ea692 content_type: text/rtf creator: system date_created: 2018-12-12T10:09:38Z date_updated: 2020-07-14T12:45:52Z file_id: '4762' file_name: IST-2013-111-v1+1_Hybridisation_and_speciation_revised.rtf file_size: 13339 relation: main_file - access_level: open_access checksum: 957fd07c71c1b1eac2c65ae3311aca78 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:39Z date_updated: 2020-07-14T12:45:52Z file_id: '4763' file_name: IST-2017-111-v1+2_Hybridisation_and_speciation_revised.pdf file_size: 103437 relation: main_file file_date_updated: 2020-07-14T12:45:52Z has_accepted_license: '1' intvolume: ' 26' issue: '2' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 267 - 269 publication: Journal of Evolutionary Biology publication_status: published publisher: Wiley-Blackwell publist_id: '3835' pubrep_id: '111' quality_controlled: '1' scopus_import: 1 status: public title: 'Does hybridisation influence speciation? ' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2013' ... --- _id: '2907' abstract: - lang: eng text: 'Sex and recombination are among the most striking features of the living world, and they play a crucial role in allowing the evolution of complex adaptation. The sharing of genomes through the sexual union of different individuals requires elaborate behavioral and physiological adaptations. At the molecular level, the alignment of two DNA double helices, followed by their precise cutting and rejoining, is an extraordinary feat. Sex and recombination have diverse—and often surprising—evolutionary consequences: distinct sexes, elaborate mating displays, selfish genetic elements, and so on.' author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Barton NH. Recombination and sex. In: The Princeton Guide to Evolution. Princeton University Press; 2013:328-333.' apa: Barton, N. H. (2013). Recombination and sex. In The Princeton Guide to Evolution (pp. 328–333). Princeton University Press. chicago: Barton, Nicholas H. “Recombination and Sex.” In The Princeton Guide to Evolution, 328–33. Princeton University Press, 2013. ieee: N. H. Barton, “Recombination and sex,” in The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–333. ista: 'Barton NH. 2013.Recombination and sex. In: The Princeton Guide to Evolution. , 328–333.' mla: Barton, Nicholas H. “Recombination and Sex.” The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–33. short: N.H. Barton, in:, The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–333. date_created: 2018-12-11T12:00:16Z date_published: 2013-11-04T00:00:00Z date_updated: 2021-01-12T07:00:37Z day: '04' ddc: - '576' department: - _id: NiBa file: - access_level: open_access checksum: 8332ca9cb40f7e66d1006b175ce36b60 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: system date_created: 2018-12-12T10:16:47Z date_updated: 2020-07-14T12:45:52Z file_id: '5237' file_name: IST-2013-119-v1+1_IV.4_Recombination_and_Sex_Barton_1-13-13-e.docx file_size: 79838 relation: main_file - access_level: open_access checksum: 849f418620fb78d6ba23bb4f488ee93f content_type: application/pdf creator: system date_created: 2018-12-12T10:16:48Z date_updated: 2020-07-14T12:45:52Z file_id: '5238' file_name: IST-2017-119-v1+2_Barton_Recombination_Sex.pdf file_size: 144131 relation: main_file file_date_updated: 2020-07-14T12:45:52Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version page: 328 - 333 publication: The Princeton Guide to Evolution publication_identifier: isbn: - '9780691149776' publication_status: published publisher: Princeton University Press publist_id: '3839' pubrep_id: '119' quality_controlled: '1' status: public title: Recombination and sex type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '450' abstract: - lang: eng text: Understanding the relative importance of heterosis and outbreeding depression over multiple generations is a key question in evolutionary biology and is essential for identifying appropriate genetic sources for population and ecosystem restoration. Here we use 2455 experimental crosses between 12 population pairs of the rare perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational (F1, F2, F3) fitness outcomes of inter-population hybridization. We detected no evidence of outbreeding depression, with inter-population hybrids and backcrosses showing either similar fitness or significant heterosis for fitness components across the three generations. Variation in heterosis among population pairs was best explained by characteristics of the foreign source or home population, and was greatest when the source population was large, with high genetic diversity and low inbreeding, and the home population was small and inbred. Our results indicate that the primary consideration for maximizing progeny fitness following population augmentation or restoration is the use of seed from large, genetically diverse populations. article_number: '2058' author: - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: David full_name: Rowell, David last_name: Rowell - first_name: Andrew full_name: Young, Andrew last_name: Young citation: ama: Pickup M, Field D, Rowell D, Young A. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. 2013;280(1750). doi:10.1098/rspb.2012.2058 apa: Pickup, M., Field, D., Rowell, D., & Young, A. (2013). Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2012.2058 chicago: Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2013. https://doi.org/10.1098/rspb.2012.2058. ieee: M. Pickup, D. Field, D. Rowell, and A. Young, “Source population characteristics affect heterosis following genetic rescue of fragmented plant populations,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 280, no. 1750. Royal Society, The, 2013. ista: Pickup M, Field D, Rowell D, Young A. 2013. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. 280(1750), 2058. mla: Pickup, Melinda, et al. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 280, no. 1750, 2058, Royal Society, The, 2013, doi:10.1098/rspb.2012.2058. short: M. Pickup, D. Field, D. Rowell, A. Young, Proceedings of the Royal Society of London Series B Biological Sciences 280 (2013). date_created: 2018-12-11T11:46:32Z date_published: 2013-01-07T00:00:00Z date_updated: 2021-01-12T07:57:25Z day: '07' department: - _id: NiBa doi: 10.1098/rspb.2012.2058 external_id: pmid: - '23173202' intvolume: ' 280' issue: '1750' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574427/ month: '01' oa: 1 oa_version: Submitted Version pmid: 1 publication: Proceedings of the Royal Society of London Series B Biological Sciences publication_status: published publisher: Royal Society, The publist_id: '7372' quality_controlled: '1' status: public title: Source population characteristics affect heterosis following genetic rescue of fragmented plant populations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 280 year: '2013' ... --- _id: '2944' abstract: - lang: eng text: 'We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction.' acknowledged_ssus: - _id: ScienComp acknowledgement: This study has made use of the computational resources provided by IST Austria and the Edinburgh Compute and Data Facility (ECDF; http://www.ecdf.ed.ac.uk). The ECDF is partially supported by the eDIKT initiative (http://www.edikt.org.uk). S.A. acknowledges financial support by IST Austria, the Janggen-Pöhn Foundation, St. Gallen, the Roche Research Foundation, Basel, the University of Edinburgh in the form of a Torrance Studentship, and the Austrian Science Fund (FWF P21305-N13). author: - first_name: Simon full_name: Aeschbacher, Simon id: 2D35326E-F248-11E8-B48F-1D18A9856A87 last_name: Aeschbacher - first_name: Andreas full_name: Futschik, Andreas last_name: Futschik - first_name: Mark full_name: Beaumont, Mark last_name: Beaumont citation: ama: 'Aeschbacher S, Futschik A, Beaumont M. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 2013;22(4):987-1002. doi:10.1111/mec.12165' apa: 'Aeschbacher, S., Futschik, A., & Beaumont, M. (2013). Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12165' chicago: 'Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” Molecular Ecology. Wiley-Blackwell, 2013. https://doi.org/10.1111/mec.12165.' ieee: 'S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ,” Molecular Ecology, vol. 22, no. 4. Wiley-Blackwell, pp. 987–1002, 2013.' ista: 'Aeschbacher S, Futschik A, Beaumont M. 2013. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 22(4), 987–1002.' mla: 'Aeschbacher, Simon, et al. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” Molecular Ecology, vol. 22, no. 4, Wiley-Blackwell, 2013, pp. 987–1002, doi:10.1111/mec.12165.' short: S. Aeschbacher, A. Futschik, M. Beaumont, Molecular Ecology 22 (2013) 987–1002. date_created: 2018-12-11T12:00:28Z date_published: 2013-02-01T00:00:00Z date_updated: 2023-02-23T14:07:19Z day: '01' department: - _id: NiBa doi: 10.1111/mec.12165 intvolume: ' 22' issue: '4' language: - iso: eng month: '02' oa_version: None page: 987 - 1002 publication: Molecular Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '3788' quality_controlled: '1' related_material: record: - id: '9758' relation: research_data status: public scopus_import: 1 status: public title: 'Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2013' ... --- _id: '9754' abstract: - lang: eng text: Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate among recent, non-equilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida) which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning theWestern Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model, and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources. article_processing_charge: No author: - first_name: Jack full_name: Hearn, Jack last_name: Hearn - first_name: Graham full_name: Stone, Graham last_name: Stone - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Konrad full_name: Lohse, Konrad last_name: Lohse - first_name: Lynsey full_name: Bunnefeld, Lynsey last_name: Bunnefeld citation: ama: 'Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. 2013. doi:10.5061/dryad.r3r60' apa: 'Hearn, J., Stone, G., Barton, N. H., Lohse, K., & Bunnefeld, L. (2013). Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. Dryad. https://doi.org/10.5061/dryad.r3r60' chicago: 'Hearn, Jack, Graham Stone, Nicholas H Barton, Konrad Lohse, and Lynsey Bunnefeld. “Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies.” Dryad, 2013. https://doi.org/10.5061/dryad.r3r60.' ieee: 'J. Hearn, G. Stone, N. H. Barton, K. Lohse, and L. Bunnefeld, “Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies.” Dryad, 2013.' ista: 'Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. 2013. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies, Dryad, 10.5061/dryad.r3r60.' mla: 'Hearn, Jack, et al. Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies. Dryad, 2013, doi:10.5061/dryad.r3r60.' short: J. Hearn, G. Stone, N.H. Barton, K. Lohse, L. Bunnefeld, (2013). date_created: 2021-07-30T08:31:22Z date_published: 2013-10-01T00:00:00Z date_updated: 2023-02-23T10:31:17Z day: '01' department: - _id: NiBa doi: 10.5061/dryad.r3r60 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.r3r60 month: '10' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '2170' relation: used_in_publication status: public status: public title: 'Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2013' ... --- _id: '2917' abstract: - lang: eng text: 'The search for extra-terrestrial intelligence (SETI) has been performed principally as a one-way survey, listening of radio frequencies across the Milky Way and other galaxies. However, scientists have engaged in an active messaging only rarely. This suggests the simple rationale that if other civilizations exist and take a similar approach to ours, namely listening but not broadcasting, the result is a silent universe. A simple game theoretical model, the prisoner''s dilemma, explains this situation: each player (civilization) can passively search (defect), or actively search and broadcast (cooperate). In order to maximize the payoff (or, equivalently, minimize the risks) the best strategy is not to broadcast. In fact, the active search has been opposed on the basis that it might be dangerous to expose ourselves. However, most of these ideas have not been based on objective arguments, and ignore accounting of the possible gains and losses. Thus, the question stands: should we perform an active search? I develop a game-theoretical framework where civilizations can be of different types, and explicitly apply it to a situation where societies are either interested in establishing a two-way communication or belligerent and in urge to exploit ours. The framework gives a quantitative solution (a mixed-strategy), which is how frequent we should perform the active SETI. This frequency is roughly proportional to the inverse of the risk, and can be extremely small. However, given the immense amount of stars being scanned, it supports active SETI. The model is compared with simulations, and the possible actions are evaluated through the San Marino scale, measuring the risks of messaging.' author: - first_name: Harold full_name: Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: Vladar orcid: 0000-0002-5985-7653 citation: ama: de Vladar H. The game of active search for extra terrestrial intelligence Breaking the Great Silence . International Journal of Astrobiology. 2012;12(1):53-62. doi:10.1017/S1473550412000407 apa: de Vladar, H. (2012). The game of active search for extra terrestrial intelligence Breaking the Great Silence . International Journal of Astrobiology. Cambridge University Press. https://doi.org/10.1017/S1473550412000407 chicago: Vladar, Harold de. “The Game of Active Search for Extra Terrestrial Intelligence Breaking the Great Silence .” International Journal of Astrobiology. Cambridge University Press, 2012. https://doi.org/10.1017/S1473550412000407. ieee: H. de Vladar, “The game of active search for extra terrestrial intelligence Breaking the Great Silence ,” International Journal of Astrobiology, vol. 12, no. 1. Cambridge University Press, pp. 53–62, 2012. ista: de Vladar H. 2012. The game of active search for extra terrestrial intelligence Breaking the Great Silence . International Journal of Astrobiology. 12(1), 53–62. mla: de Vladar, Harold. “The Game of Active Search for Extra Terrestrial Intelligence Breaking the Great Silence .” International Journal of Astrobiology, vol. 12, no. 1, Cambridge University Press, 2012, pp. 53–62, doi:10.1017/S1473550412000407. short: H. de Vladar, International Journal of Astrobiology 12 (2012) 53–62. date_created: 2018-12-11T12:00:19Z date_published: 2012-11-06T00:00:00Z date_updated: 2021-01-12T07:00:41Z day: '06' department: - _id: NiBa doi: 10.1017/S1473550412000407 intvolume: ' 12' issue: '1' language: - iso: eng month: '11' oa_version: None page: 53 - 62 publication: International Journal of Astrobiology publication_status: published publisher: Cambridge University Press publist_id: '3821' quality_controlled: '1' scopus_import: 1 status: public title: 'The game of active search for extra terrestrial intelligence Breaking the Great Silence ' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2012' ... --- _id: '2962' abstract: - lang: eng text: The choice of summary statistics is a crucial step in approximate Bayesian computation (ABC). Since statistics are often not sufficient, this choice involves a trade-off between loss of information and reduction of dimensionality. The latter may increase the efficiency of ABC. Here, we propose an approach for choosing summary statistics based on boosting, a technique from the machine learning literature. We consider different types of boosting and compare them to partial least squares regression as an alternative. To mitigate the lack of sufficiency, we also propose an approach for choosing summary statistics locally, in the putative neighborhood of the true parameter value. We study a demographic model motivated by the re-introduction of Alpine ibex (Capra ibex) into the Swiss Alps. The parameters of interest are the mean and standard deviation across microsatellites of the scaled ancestral mutation rate (θanc = 4 Ne u), and the proportion of males obtaining access to matings per breeding season (ω). By simulation, we assess the properties of the posterior distribution obtained with the various methods. According to our criteria, ABC with summary statistics chosen locally via boosting with the L2-loss performs best. Applying that method to the ibex data, we estimate θanc ≈ 1.288, and find that most of the variation across loci of the ancestral mutation rate u is between 7.7×10−4 and 3.5×10−3 per locus per generation. The proportion of males with access to matings is estimated to ω ≈ 0.21, which is in good agreement with recent independent estimates. acknowledged_ssus: - _id: ScienComp author: - first_name: Simon full_name: Aeschbacher, Simon id: 2D35326E-F248-11E8-B48F-1D18A9856A87 last_name: Aeschbacher - first_name: Mark full_name: Beaumont, Mark last_name: Beaumont - first_name: Andreas full_name: Futschik, Andreas last_name: Futschik citation: ama: Aeschbacher S, Beaumont M, Futschik A. A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. 2012;192(3):1027-1047. doi:10.1534/genetics.112.143164 apa: Aeschbacher, S., Beaumont, M., & Futschik, A. (2012). A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.112.143164 chicago: Aeschbacher, Simon, Mark Beaumont, and Andreas Futschik. “A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation.” Genetics. Genetics Society of America, 2012. https://doi.org/10.1534/genetics.112.143164. ieee: S. Aeschbacher, M. Beaumont, and A. Futschik, “A novel approach for choosing summary statistics in approximate Bayesian computation,” Genetics, vol. 192, no. 3. Genetics Society of America, pp. 1027–1047, 2012. ista: Aeschbacher S, Beaumont M, Futschik A. 2012. A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. 192(3), 1027–1047. mla: Aeschbacher, Simon, et al. “A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation.” Genetics, vol. 192, no. 3, Genetics Society of America, 2012, pp. 1027–47, doi:10.1534/genetics.112.143164. short: S. Aeschbacher, M. Beaumont, A. Futschik, Genetics 192 (2012) 1027–1047. date_created: 2018-12-11T12:00:34Z date_published: 2012-11-01T00:00:00Z date_updated: 2021-01-12T07:40:05Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.112.143164 external_id: pmid: - '22960215' intvolume: ' 192' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522150/ month: '11' oa: 1 oa_version: Submitted Version page: 1027 - 1047 pmid: 1 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '3763' quality_controlled: '1' scopus_import: 1 status: public title: A novel approach for choosing summary statistics in approximate Bayesian computation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 192 year: '2012' ... --- _id: '3122' abstract: - lang: eng text: 'Since Darwin''s pioneering research on plant reproductive biology (e.g. Darwin 1877), understanding the mechanisms maintaining the diverse sexual strategies of plants has remained an important challenge for evolutionary biologists. In some species, populations are sexually polymorphic and contain two or more mating morphs (sex phenotypes). Differences in morphology or phenology among the morphs influence patterns of non-random mating. In these populations, negative frequency-dependent selection arising from disassortative (intermorph) mating is usually required for the evolutionary maintenance of sexual polymorphism, but few studies have demonstrated the required patterns of non-random mating. In the current issue of Molecular Ecology, Shang (2012) make an important contribution to our understanding of how disassortative mating influences sex phenotype ratios in Acer pictum subsp. mono (painted maple), a heterodichogamous, deciduous tree of eastern China. They monitored sex expression in 97 adults and used paternity analysis of open-pollinated seed to examine disassortative mating among three sex phenotypes. Using a deterministic ''pollen transfer'' model, Shang et al. present convincing evidence that differences in the degree of disassortative mating in progeny arrays of the sex phenotypes can explain their uneven frequencies in the adult population. This study provides a useful example of how the deployment of genetic markers, demographic monitoring and modelling can be integrated to investigate the maintenance of sexual diversity in plants. ' author: - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: Spencer full_name: Barrett, Spencer last_name: Barrett citation: ama: Field D, Barrett S. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 2012;21(15):3640-3643. doi:10.1111/j.1365-294X.2012.05643.x apa: Field, D., & Barrett, S. (2012). Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05643.x chicago: Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05643.x. ieee: D. Field and S. Barrett, “Disassortative mating and the maintenance of sexual polymorphism in painted maple,” Molecular Ecology, vol. 21, no. 15. Wiley-Blackwell, pp. 3640–3643, 2012. ista: Field D, Barrett S. 2012. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 21(15), 3640–3643. mla: Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology, vol. 21, no. 15, Wiley-Blackwell, 2012, pp. 3640–43, doi:10.1111/j.1365-294X.2012.05643.x. short: D. Field, S. Barrett, Molecular Ecology 21 (2012) 3640–3643. date_created: 2018-12-11T12:01:31Z date_published: 2012-08-01T00:00:00Z date_updated: 2021-01-12T07:41:13Z day: '01' department: - _id: NiBa doi: 10.1111/j.1365-294X.2012.05643.x intvolume: ' 21' issue: '15' language: - iso: eng month: '08' oa_version: None page: 3640 - 3643 publication: Molecular Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '3577' quality_controlled: '1' scopus_import: 1 status: public title: Disassortative mating and the maintenance of sexual polymorphism in painted maple type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2012' ... --- _id: '3131' abstract: - lang: eng text: 'In large populations, many beneficial mutations may be simultaneously available and may compete with one another, slowing adaptation. By finding the probability of fixation of a favorable allele in a simple model of a haploid sexual population, we find limits to the rate of adaptive substitution, Λ, that depend on simple parameter combinations. When variance in fitness is low and linkage is loose, the baseline rate of substitution is Λ 0=2NU〈s〉 is the population size, U is the rate of beneficial mutations per genome, and 〈s〉 is their mean selective advantage. Heritable variance ν in log fitness due to unlinked loci reduces Λ by e -4ν under polygamy and e -8ν under monogamy. With a linear genetic map of length R Morgans, interference is yet stronger. We use a scaling argument to show that the density of adaptive substitutions depends on s, N, U, and R only through the baseline density: Λ/R=F(Λ 0/R). Under the approximation that the interference due to different sweeps adds up, we show that Λ/R~(Λ 0/R)/(1+2Λ 0/R), implying that interference prevents the rate of adaptive substitution from exceeding one per centimorgan per 200 generations. Simulations and numerical calculations confirm the scaling argument and confirm the additive approximation for Λ 0/R 1; for higher Λ 0/R, the rate of adaptation grows above R/2, but only very slowly. We also consider the effect of sweeps on neutral diversity and show that, while even occasional sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become more common-diversity can be maintained even in populations experiencing very strong interference. Our results indicate that for some organisms the rate of adaptive substitution may be primarily recombination-limited, depending only weakly on the mutation supply and the strength of selection.' acknowledgement: "The work was funded by ERC grant 250152.\r\nWe thank B. Charlesworth, O. Hallatschek, W. G. Hill, R. A. Neher, S. P. Otto, and the anonymous reviewers for their helpful suggestions." article_number: e1002740 author: - first_name: Daniel full_name: Weissman, Daniel id: 2D0CE020-F248-11E8-B48F-1D18A9856A87 last_name: Weissman - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Weissman D, Barton NH. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 2012;8(6). doi:10.1371/journal.pgen.1002740 apa: Weissman, D., & Barton, N. H. (2012). Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002740 chicago: Weissman, Daniel, and Nicholas H Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002740. ieee: D. Weissman and N. H. Barton, “Limits to the rate of adaptive substitution in sexual populations,” PLoS Genetics, vol. 8, no. 6. Public Library of Science, 2012. ista: Weissman D, Barton NH. 2012. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 8(6), e1002740. mla: Weissman, Daniel, and Nicholas H. Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” PLoS Genetics, vol. 8, no. 6, e1002740, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002740. short: D. Weissman, N.H. Barton, PLoS Genetics 8 (2012). date_created: 2018-12-11T12:01:34Z date_published: 2012-06-07T00:00:00Z date_updated: 2021-01-12T07:41:17Z day: '07' ddc: - '570' - '576' department: - _id: NiBa doi: 10.1371/journal.pgen.1002740 ec_funded: 1 file: - access_level: open_access checksum: 729a4becda7d786c4c3db8f9a1f77953 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:00Z date_updated: 2020-07-14T12:46:01Z file_id: '4659' file_name: IST-2013-114-v1+1_WeissmanBarton2012.pdf file_size: 1284801 relation: main_file file_date_updated: 2020-07-14T12:46:01Z has_accepted_license: '1' intvolume: ' 8' issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: PLoS Genetics publication_status: published publisher: Public Library of Science publist_id: '3566' pubrep_id: '114' quality_controlled: '1' scopus_import: 1 status: public title: Limits to the rate of adaptive substitution in sexual populations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2012' ... --- _id: '3166' abstract: - lang: eng text: 'There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments into a proto-code that optimises the energetic yield. Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors. Reviewers: this article was reviewed by Prof. William Martin, Prof. Eors Szathmary (nominated by Dr. Gaspar Jekely) and Dr. Adam Kun (nominated by Dr. Sandor Pongor)' acknowledgement: 'The author was supported by the ERC-2009-AdG Grant for project 250152 SELECTIONINFORMATION. ' article_number: '6' author: - first_name: Harold full_name: Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: Vladar orcid: 0000-0002-5985-7653 citation: ama: de Vladar H. Amino acid fermentation at the origin of the genetic code. Biology Direct. 2012;7. doi:10.1186/1745-6150-7-6 apa: de Vladar, H. (2012). Amino acid fermentation at the origin of the genetic code. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-7-6 chicago: Vladar, Harold de. “Amino Acid Fermentation at the Origin of the Genetic Code.” Biology Direct. BioMed Central, 2012. https://doi.org/10.1186/1745-6150-7-6. ieee: H. de Vladar, “Amino acid fermentation at the origin of the genetic code,” Biology Direct, vol. 7. BioMed Central, 2012. ista: de Vladar H. 2012. Amino acid fermentation at the origin of the genetic code. Biology Direct. 7, 6. mla: de Vladar, Harold. “Amino Acid Fermentation at the Origin of the Genetic Code.” Biology Direct, vol. 7, 6, BioMed Central, 2012, doi:10.1186/1745-6150-7-6. short: H. de Vladar, Biology Direct 7 (2012). date_created: 2018-12-11T12:01:46Z date_published: 2012-02-10T00:00:00Z date_updated: 2021-01-12T07:41:31Z day: '10' ddc: - '570' - '576' department: - _id: NiBa doi: 10.1186/1745-6150-7-6 ec_funded: 1 file: - access_level: open_access checksum: e511e401e239ef608a7fd79b21a06d78 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:44Z date_updated: 2020-07-14T12:46:02Z file_id: '5166' file_name: IST-2012-99-v1+1_1745-6150-7-6.pdf file_size: 4099536 relation: main_file file_date_updated: 2020-07-14T12:46:02Z has_accepted_license: '1' intvolume: ' 7' language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Biology Direct publication_status: published publisher: BioMed Central publist_id: '3518' pubrep_id: '99' quality_controlled: '1' status: public title: Amino acid fermentation at the origin of the genetic code tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2012' ... --- _id: '3277' abstract: - lang: eng text: The problem of the origin of metazoa is becoming more urgent in the context of astrobiology. By now it is clear that clues to the understanding of this crucial transition in the evolution of life can arise in a fourth pathway besides the three possibilities in the quest for simplicity outlined by Bonner in his classical book. In other words, solar system exploration seems to be one way in the long-term to elucidate the simplicity of evolutionary development. We place these ideas in the context of different inheritance systems, namely the genotypic and phenotypic replicators with limited or unlimited heredity, and ask which of these can support multicellular development, and to which degree of complexity. However, the quest for evidence on the evolution of biotas from planets around other stars does not seem to be feasible with present technology with direct visualization of living organisms on exoplanets. But this may be attempted on the Galilean moons of Jupiter where there is a possibility of detecting reliable biomarkers in the next decade with the Europa Jupiter System Mission, in view of recent progress by landing micropenetrators on planetary, or satellite surfaces. Mars is a second possibility in the inner Solar System, in spite of the multiple difficulties faced by the fleet of past, present and future missions. We discuss a series of preliminary ideas for elucidating the origin of metazoan analogues with available instrumentation in potential payloads of feasible space missions to the Galilean moons. alternative_title: - Cellular Origin, Life in Extreme Habitats and Astrobiology author: - first_name: Harold full_name: de Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: de Vladar orcid: 0000-0002-5985-7653 - first_name: Julian full_name: Chela Flores, Julian last_name: Chela Flores citation: ama: 'de Vladar H, Chela Flores J. Can the evolution of multicellularity be anticipated in the exploration of the solar system? In: Life on Earth and Other Planetary Bodies. Vol 24. Springer; 2012:387-405. doi:10.1007/978-94-007-4966-5_22' apa: de Vladar, H., & Chela Flores, J. (2012). Can the evolution of multicellularity be anticipated in the exploration of the solar system? In Life on Earth and other planetary bodies (Vol. 24, pp. 387–405). Springer. https://doi.org/10.1007/978-94-007-4966-5_22 chicago: Vladar, Harold de, and Julian Chela Flores. “Can the Evolution of Multicellularity Be Anticipated in the Exploration of the Solar System?” In Life on Earth and Other Planetary Bodies, 24:387–405. Springer, 2012. https://doi.org/10.1007/978-94-007-4966-5_22. ieee: H. de Vladar and J. Chela Flores, “Can the evolution of multicellularity be anticipated in the exploration of the solar system?,” in Life on Earth and other planetary bodies, vol. 24, Springer, 2012, pp. 387–405. ista: 'de Vladar H, Chela Flores J. 2012.Can the evolution of multicellularity be anticipated in the exploration of the solar system? In: Life on Earth and other planetary bodies. Cellular Origin, Life in Extreme Habitats and Astrobiology, vol. 24, 387–405.' mla: de Vladar, Harold, and Julian Chela Flores. “Can the Evolution of Multicellularity Be Anticipated in the Exploration of the Solar System?” Life on Earth and Other Planetary Bodies, vol. 24, Springer, 2012, pp. 387–405, doi:10.1007/978-94-007-4966-5_22. short: H. de Vladar, J. Chela Flores, in:, Life on Earth and Other Planetary Bodies, Springer, 2012, pp. 387–405. date_created: 2018-12-11T12:02:25Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T07:42:20Z day: '01' department: - _id: NiBa doi: 10.1007/978-94-007-4966-5_22 intvolume: ' 24' language: - iso: eng month: '01' oa_version: None page: 387 - 405 publication: Life on Earth and other planetary bodies publication_status: published publisher: Springer publist_id: '3369' quality_controlled: '1' status: public title: Can the evolution of multicellularity be anticipated in the exploration of the solar system? type: book_chapter user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2012' ... --- _id: '498' abstract: - lang: eng text: Understanding patterns and correlates of local adaptation in heterogeneous landscapes can provide important information in the selection of appropriate seed sources for restoration. We assessed the extent of local adaptation of fitness components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides (Asteraceae) and examined whether spatial scale (0.7-600 km), environmental distance, quantitative (QST) and neutral (FST) genetic differentiation, and size of the local and foreign populations could predict patterns of adaptive differentiation. Local adaptation varied among populations and fitness components. Including all population pairs, local adaptation was observed for seedling survival, but not for biomass, while foreign genotype advantage was observed for reproduction (number of inflorescences). Among population pairs, local adaptation increased with QST and local population size for biomass. QST was associated with environmental distance, suggesting ecological selection for phenotypic divergence. However, low FST and variation in population structure in small populations demonstrates the interaction of gene flow and drift in constraining local adaptation in R. leptorrhynchoides. Our study indicates that for species in heterogeneous landscapes, collecting seed from large populations from similar environments to candidate sites is likely to provide the most appropriate seed sources for restoration. acknowledgement: "We thank Graham Pickup, David Steer, Linda Broadhurst, Lan Li and Carole Elliott for technical assistance. The New\r\nSouth Wales Department of Environment and Climate Change, ACT Parks, Conservation and Lands and the\r\nDepartment of Sustainability and Environment in Victoria provided permits for seed and soil collection. We thank\r\nSpencer C. H. Barrett for comments that improved the quality of the manuscript.\r\n" author: - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: David full_name: Rowell, David last_name: Rowell - first_name: Andrew full_name: Young, Andrew last_name: Young citation: ama: 'Pickup M, Field D, Rowell D, Young A. Predicting local adaptation in fragmented plant populations: Implications for restoration genetics. Evolutionary Applications. 2012;5(8):913-924. doi:10.1111/j.1752-4571.2012.00284.x' apa: 'Pickup, M., Field, D., Rowell, D., & Young, A. (2012). Predicting local adaptation in fragmented plant populations: Implications for restoration genetics. Evolutionary Applications. Wiley-Blackwell. https://doi.org/10.1111/j.1752-4571.2012.00284.x' chicago: 'Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Predicting Local Adaptation in Fragmented Plant Populations: Implications for Restoration Genetics.” Evolutionary Applications. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1752-4571.2012.00284.x.' ieee: 'M. Pickup, D. Field, D. Rowell, and A. Young, “Predicting local adaptation in fragmented plant populations: Implications for restoration genetics,” Evolutionary Applications, vol. 5, no. 8. Wiley-Blackwell, pp. 913–924, 2012.' ista: 'Pickup M, Field D, Rowell D, Young A. 2012. Predicting local adaptation in fragmented plant populations: Implications for restoration genetics. Evolutionary Applications. 5(8), 913–924.' mla: 'Pickup, Melinda, et al. “Predicting Local Adaptation in Fragmented Plant Populations: Implications for Restoration Genetics.” Evolutionary Applications, vol. 5, no. 8, Wiley-Blackwell, 2012, pp. 913–24, doi:10.1111/j.1752-4571.2012.00284.x.' short: M. Pickup, D. Field, D. Rowell, A. Young, Evolutionary Applications 5 (2012) 913–924. date_created: 2018-12-11T11:46:48Z date_published: 2012-12-01T00:00:00Z date_updated: 2021-01-12T08:01:06Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1111/j.1752-4571.2012.00284.x file: - access_level: open_access checksum: 233007138606aca5a2f75f7ae1742f43 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:33Z date_updated: 2020-07-14T12:46:35Z file_id: '4821' file_name: IST-2018-942-v1+1_Pickup_et_al-2012-Evolutionary_Applications.pdf file_size: 396136 relation: main_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' intvolume: ' 5' issue: '8' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '12' oa: 1 oa_version: Published Version page: 913 - 924 publication: Evolutionary Applications publication_status: published publisher: Wiley-Blackwell publist_id: '7322' pubrep_id: '942' quality_controlled: '1' status: public title: 'Predicting local adaptation in fragmented plant populations: Implications for restoration genetics' tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2012' ... --- _id: '9758' abstract: - lang: eng text: 'We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction.' article_processing_charge: No author: - first_name: Simon full_name: Aeschbacher, Simon id: 2D35326E-F248-11E8-B48F-1D18A9856A87 last_name: Aeschbacher - first_name: Andreas full_name: Futschik, Andreas last_name: Futschik - first_name: Mark full_name: Beaumont, Mark last_name: Beaumont citation: ama: 'Aeschbacher S, Futschik A, Beaumont M. Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. 2012. doi:10.5061/dryad.274b1' apa: 'Aeschbacher, S., Futschik, A., & Beaumont, M. (2012). Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. Dryad. https://doi.org/10.5061/dryad.274b1' chicago: 'Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Data from: Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates.” Dryad, 2012. https://doi.org/10.5061/dryad.274b1.' ieee: 'S. Aeschbacher, A. Futschik, and M. Beaumont, “Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates.” Dryad, 2012.' ista: 'Aeschbacher S, Futschik A, Beaumont M. 2012. Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates, Dryad, 10.5061/dryad.274b1.' mla: 'Aeschbacher, Simon, et al. Data from: Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. Dryad, 2012, doi:10.5061/dryad.274b1.' short: S. Aeschbacher, A. Futschik, M. Beaumont, (2012). date_created: 2021-07-30T12:36:39Z date_published: 2012-11-14T00:00:00Z date_updated: 2023-02-23T11:05:19Z day: '14' department: - _id: NiBa doi: 10.5061/dryad.274b1 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.274b1 month: '11' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '2944' relation: used_in_publication status: public status: public title: 'Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2012' ... --- _id: '2968' abstract: - lang: eng text: Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, Cecidostiba semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and-using triplet alignments of intronic loci-quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times. © 2012 Blackwell Publishing Ltd. acknowledgement: "This work was supported by funding from the UK Natural Environment Research Council to KL (NE/I020288/1) and GS (NE/H000038/1, NE/E014453/1, NER/B/504406/1, NER/B/S2003/00856) and a grant from the European Research Council (250152) to NB.\r\nWe thank Majide Tavakoli, Juli Pujade-Villar and Pablo-Fuentes Utrilla for contributing specimens. Mike Hickerson and three anonymous reviewers gave helpful comments on earlier versions of the manuscript. " author: - first_name: Konrad full_name: Lohse, Konrad last_name: Lohse - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: George full_name: Melika, George last_name: Melika - first_name: Graham full_name: Stone, Graham last_name: Stone citation: ama: Lohse K, Barton NH, Melika G, Stone G. A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. 2012;21(18):4605-4617. doi:10.1111/j.1365-294X.2012.05700.x apa: Lohse, K., Barton, N. H., Melika, G., & Stone, G. (2012). A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05700.x chicago: Lohse, Konrad, Nicholas H Barton, George Melika, and Graham Stone. “A Likelihood Based Comparison of Population Histories in a Parasitoid Guild.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05700.x. ieee: K. Lohse, N. H. Barton, G. Melika, and G. Stone, “A likelihood based comparison of population histories in a parasitoid guild,” Molecular Ecology, vol. 21, no. 18. Wiley-Blackwell, pp. 4605–4617, 2012. ista: Lohse K, Barton NH, Melika G, Stone G. 2012. A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. 21(18), 4605–4617. mla: Lohse, Konrad, et al. “A Likelihood Based Comparison of Population Histories in a Parasitoid Guild.” Molecular Ecology, vol. 21, no. 18, Wiley-Blackwell, 2012, pp. 4605–17, doi:10.1111/j.1365-294X.2012.05700.x. short: K. Lohse, N.H. Barton, G. Melika, G. Stone, Molecular Ecology 21 (2012) 4605–4617. date_created: 2018-12-11T12:00:36Z date_published: 2012-09-01T00:00:00Z date_updated: 2023-05-30T13:07:47Z day: '01' ddc: - '570' - '579' department: - _id: NiBa doi: 10.1111/j.1365-294X.2012.05700.x ec_funded: 1 file: - access_level: open_access checksum: c14ee4cb2a8ba9575bfd8a9bb7a883bb content_type: application/pdf creator: system date_created: 2018-12-12T10:17:47Z date_updated: 2020-07-14T12:45:57Z file_id: '5304' file_name: IST-2014-296-v1+1_4_wasps_revised3.pdf file_size: 235820 relation: main_file - access_level: open_access checksum: f00afc5b887c8222014b57375b8caece content_type: application/pdf creator: system date_created: 2018-12-12T10:17:48Z date_updated: 2020-07-14T12:45:57Z file_id: '5305' file_name: IST-2014-296-v1+2_4_wasps_Supporting2.pdf file_size: 41975 relation: main_file file_date_updated: 2020-07-14T12:45:57Z has_accepted_license: '1' intvolume: ' 21' issue: '18' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 4605 - 4617 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Molecular Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '3746' pubrep_id: '296' quality_controlled: '1' related_material: record: - id: '13075' relation: research_data status: public scopus_import: 1 status: public title: A likelihood based comparison of population histories in a parasitoid guild type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2012' ... --- _id: '13075' abstract: - lang: eng text: Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, C. semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and - using triplet alignments of intronic loci - quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times. article_processing_charge: No author: - first_name: Konrad full_name: Lohse, Konrad last_name: Lohse - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Graham full_name: Stone, Graham last_name: Stone - first_name: George full_name: Melika, George last_name: Melika citation: ama: 'Lohse K, Barton NH, Stone G, Melika G. Data from: A likelihood-based comparison of population histories in a parasitoid guild. 2012. doi:10.5061/DRYAD.0G0FS' apa: 'Lohse, K., Barton, N. H., Stone, G., & Melika, G. (2012). Data from: A likelihood-based comparison of population histories in a parasitoid guild. Dryad. https://doi.org/10.5061/DRYAD.0G0FS' chicago: 'Lohse, Konrad, Nicholas H Barton, Graham Stone, and George Melika. “Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild.” Dryad, 2012. https://doi.org/10.5061/DRYAD.0G0FS.' ieee: 'K. Lohse, N. H. Barton, G. Stone, and G. Melika, “Data from: A likelihood-based comparison of population histories in a parasitoid guild.” Dryad, 2012.' ista: 'Lohse K, Barton NH, Stone G, Melika G. 2012. Data from: A likelihood-based comparison of population histories in a parasitoid guild, Dryad, 10.5061/DRYAD.0G0FS.' mla: 'Lohse, Konrad, et al. Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild. Dryad, 2012, doi:10.5061/DRYAD.0G0FS.' short: K. Lohse, N.H. Barton, G. Stone, G. Melika, (2012). date_created: 2023-05-23T17:01:02Z date_published: 2012-06-08T00:00:00Z date_updated: 2023-05-30T13:07:48Z day: '08' ddc: - '570' department: - _id: NiBa doi: 10.5061/DRYAD.0G0FS license: https://creativecommons.org/publicdomain/zero/1.0/ main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.0g0fs month: '06' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '2968' relation: used_in_publication status: public status: public title: 'Data from: A likelihood-based comparison of population histories in a parasitoid guild' tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '3372' abstract: - lang: eng text: Nowak et al.1 argue that inclusive fitness theory has been of little value in explaining the natural world, and that it has led to negligible progress in explaining the evolution of eusociality. However, we believe that their arguments are based upon a misunderstanding of evolutionary theory and a misrepresentation of the empirical literature. We will focus our comments on three general issues. author: - first_name: Patrick full_name: Abbot, Patrick last_name: Abbot - first_name: Jun full_name: Abe, Jun last_name: Abe - first_name: John full_name: Alcock, John last_name: Alcock - first_name: Samuel full_name: Alizon, Samuel last_name: Alizon - first_name: Joao full_name: Alpedrinha, Joao last_name: Alpedrinha - first_name: Malte full_name: Andersson, Malte last_name: Andersson - first_name: Jean full_name: Andre, Jean last_name: Andre - first_name: Minus full_name: Van Baalen, Minus last_name: Van Baalen - first_name: Francois full_name: Balloux, Francois last_name: Balloux - first_name: Sigal full_name: Balshine, Sigal last_name: Balshine - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Leo full_name: Beukeboom, Leo last_name: Beukeboom - first_name: Jay full_name: Biernaskie, Jay last_name: Biernaskie - first_name: Trine full_name: Bilde, Trine last_name: Bilde - first_name: Gerald full_name: Borgia, Gerald last_name: Borgia - first_name: Michael full_name: Breed, Michael last_name: Breed - first_name: Sam full_name: Brown, Sam last_name: Brown - first_name: Redouan full_name: Bshary, Redouan last_name: Bshary - first_name: Angus full_name: Buckling, Angus last_name: Buckling - first_name: Nancy full_name: Burley, Nancy last_name: Burley - first_name: Max full_name: Burton Chellew, Max last_name: Burton Chellew - first_name: Michael full_name: Cant, Michael last_name: Cant - first_name: Michel full_name: Chapuisat, Michel last_name: Chapuisat - first_name: Eric full_name: Charnov, Eric last_name: Charnov - first_name: Tim full_name: Clutton Brock, Tim last_name: Clutton Brock - first_name: Andrew full_name: Cockburn, Andrew last_name: Cockburn - first_name: Blaine full_name: Cole, Blaine last_name: Cole - first_name: Nick full_name: Colegrave, Nick last_name: Colegrave - first_name: Leda full_name: Cosmides, Leda last_name: Cosmides - first_name: Iain full_name: Couzin, Iain last_name: Couzin - first_name: Jerry full_name: Coyne, Jerry last_name: Coyne - first_name: Scott full_name: Creel, Scott last_name: Creel - first_name: Bernard full_name: Crespi, Bernard last_name: Crespi - first_name: Robert full_name: Curry, Robert last_name: Curry - first_name: Sasha full_name: Dall, Sasha last_name: Dall - first_name: Troy full_name: Day, Troy last_name: Day - first_name: Janis full_name: Dickinson, Janis last_name: Dickinson - first_name: Lee full_name: Dugatkin, Lee last_name: Dugatkin - first_name: Claire full_name: El Mouden, Claire last_name: El Mouden - first_name: Stephen full_name: Emlen, Stephen last_name: Emlen - first_name: Jay full_name: Evans, Jay last_name: Evans - first_name: Regis full_name: Ferriere, Regis last_name: Ferriere - first_name: Jeremy full_name: Field, Jeremy last_name: Field - first_name: Susanne full_name: Foitzik, Susanne last_name: Foitzik - first_name: Kevin full_name: Foster, Kevin last_name: Foster - first_name: William full_name: Foster, William last_name: Foster - first_name: Charles full_name: Fox, Charles last_name: Fox - first_name: Juergen full_name: Gadau, Juergen last_name: Gadau - first_name: Sylvain full_name: Gandon, Sylvain last_name: Gandon - first_name: Andy full_name: Gardner, Andy last_name: Gardner - first_name: Michael full_name: Gardner, Michael last_name: Gardner - first_name: Thomas full_name: Getty, Thomas last_name: Getty - first_name: Michael full_name: Goodisman, Michael last_name: Goodisman - first_name: Alan full_name: Grafen, Alan last_name: Grafen - first_name: Rick full_name: Grosberg, Rick last_name: Grosberg - first_name: Christina full_name: Grozinger, Christina last_name: Grozinger - first_name: Pierre full_name: Gouyon, Pierre last_name: Gouyon - first_name: Darryl full_name: Gwynne, Darryl last_name: Gwynne - first_name: Paul full_name: Harvey, Paul last_name: Harvey - first_name: Ben full_name: Hatchwell, Ben last_name: Hatchwell - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze - first_name: Heikki full_name: Helantera, Heikki last_name: Helantera - first_name: Ken full_name: Helms, Ken last_name: Helms - first_name: Kim full_name: Hill, Kim last_name: Hill - first_name: Natalie full_name: Jiricny, Natalie last_name: Jiricny - first_name: Rufus full_name: Johnstone, Rufus last_name: Johnstone - first_name: Alex full_name: Kacelnik, Alex last_name: Kacelnik - first_name: E Toby full_name: Kiers, E Toby last_name: Kiers - first_name: Hanna full_name: Kokko, Hanna last_name: Kokko - first_name: Jan full_name: Komdeur, Jan last_name: Komdeur - first_name: Judith full_name: Korb, Judith last_name: Korb - first_name: Daniel full_name: Kronauer, Daniel last_name: Kronauer - first_name: Rolf full_name: Kümmerli, Rolf last_name: Kümmerli - first_name: Laurent full_name: Lehmann, Laurent last_name: Lehmann - first_name: Timothy full_name: Linksvayer, Timothy last_name: Linksvayer - first_name: Sébastien full_name: Lion, Sébastien last_name: Lion - first_name: Bruce full_name: Lyon, Bruce last_name: Lyon - first_name: James full_name: Marshall, James last_name: Marshall - first_name: Richard full_name: Mcelreath, Richard last_name: Mcelreath - first_name: Yannis full_name: Michalakis, Yannis last_name: Michalakis - first_name: Richard full_name: Michod, Richard last_name: Michod - first_name: Douglas full_name: Mock, Douglas last_name: Mock - first_name: Thibaud full_name: Monnin, Thibaud last_name: Monnin - first_name: Robert full_name: Montgomerie, Robert last_name: Montgomerie - first_name: Allen full_name: Moore, Allen last_name: Moore - first_name: Ulrich full_name: Mueller, Ulrich last_name: Mueller - first_name: Ronald full_name: Noë, Ronald last_name: Noë - first_name: Samir full_name: Okasha, Samir last_name: Okasha - first_name: Pekka full_name: Pamilo, Pekka last_name: Pamilo - first_name: Geoff full_name: Parker, Geoff last_name: Parker - first_name: Jes full_name: Pedersen, Jes last_name: Pedersen - first_name: Ido full_name: Pen, Ido last_name: Pen - first_name: David full_name: Pfennig, David last_name: Pfennig - first_name: David full_name: Queller, David last_name: Queller - first_name: Daniel full_name: Rankin, Daniel last_name: Rankin - first_name: Sarah full_name: Reece, Sarah last_name: Reece - first_name: Hudson full_name: Reeve, Hudson last_name: Reeve - first_name: Max full_name: Reuter, Max last_name: Reuter - first_name: Gilbert full_name: Roberts, Gilbert last_name: Roberts - first_name: Simon full_name: Robson, Simon last_name: Robson - first_name: Denis full_name: Roze, Denis last_name: Roze - first_name: Francois full_name: Rousset, Francois last_name: Rousset - first_name: Olav full_name: Rueppell, Olav last_name: Rueppell - first_name: Joel full_name: Sachs, Joel last_name: Sachs - first_name: Lorenzo full_name: Santorelli, Lorenzo last_name: Santorelli - first_name: Paul full_name: Schmid Hempel, Paul last_name: Schmid Hempel - first_name: Michael full_name: Schwarz, Michael last_name: Schwarz - first_name: Tom full_name: Scott Phillips, Tom last_name: Scott Phillips - first_name: Janet full_name: Shellmann Sherman, Janet last_name: Shellmann Sherman - first_name: Paul full_name: Sherman, Paul last_name: Sherman - first_name: David full_name: Shuker, David last_name: Shuker - first_name: Jeff full_name: Smith, Jeff last_name: Smith - first_name: Joseph full_name: Spagna, Joseph last_name: Spagna - first_name: Beverly full_name: Strassmann, Beverly last_name: Strassmann - first_name: Andrew full_name: Suarez, Andrew last_name: Suarez - first_name: Liselotte full_name: Sundström, Liselotte last_name: Sundström - first_name: Michael full_name: Taborsky, Michael last_name: Taborsky - first_name: Peter full_name: Taylor, Peter last_name: Taylor - first_name: Graham full_name: Thompson, Graham last_name: Thompson - first_name: John full_name: Tooby, John last_name: Tooby - first_name: Neil full_name: Tsutsui, Neil last_name: Tsutsui - first_name: Kazuki full_name: Tsuji, Kazuki last_name: Tsuji - first_name: Stefano full_name: Turillazzi, Stefano last_name: Turillazzi - first_name: Francisco full_name: Úbeda, Francisco last_name: Úbeda - first_name: Edward full_name: Vargo, Edward last_name: Vargo - first_name: Bernard full_name: Voelkl, Bernard last_name: Voelkl - first_name: Tom full_name: Wenseleers, Tom last_name: Wenseleers - first_name: Stuart full_name: West, Stuart last_name: West - first_name: Mary full_name: West Eberhard, Mary last_name: West Eberhard - first_name: David full_name: Westneat, David last_name: Westneat - first_name: Diane full_name: Wiernasz, Diane last_name: Wiernasz - first_name: Geoff full_name: Wild, Geoff last_name: Wild - first_name: Richard full_name: Wrangham, Richard last_name: Wrangham - first_name: Andrew full_name: Young, Andrew last_name: Young - first_name: David full_name: Zeh, David last_name: Zeh - first_name: Jeanne full_name: Zeh, Jeanne last_name: Zeh - first_name: Andrew full_name: Zink, Andrew last_name: Zink citation: ama: Abbot P, Abe J, Alcock J, et al. Inclusive fitness theory and eusociality. Nature. 2011;471(7339):E1-E4. doi:10.1038/nature09831 apa: Abbot, P., Abe, J., Alcock, J., Alizon, S., Alpedrinha, J., Andersson, M., … Zink, A. (2011). Inclusive fitness theory and eusociality. Nature. Nature Publishing Group. https://doi.org/10.1038/nature09831 chicago: Abbot, Patrick, Jun Abe, John Alcock, Samuel Alizon, Joao Alpedrinha, Malte Andersson, Jean Andre, et al. “Inclusive Fitness Theory and Eusociality.” Nature. Nature Publishing Group, 2011. https://doi.org/10.1038/nature09831. ieee: P. Abbot et al., “Inclusive fitness theory and eusociality,” Nature, vol. 471, no. 7339. Nature Publishing Group, pp. E1–E4, 2011. ista: Abbot P et al. 2011. Inclusive fitness theory and eusociality. Nature. 471(7339), E1–E4. mla: Abbot, Patrick, et al. “Inclusive Fitness Theory and Eusociality.” Nature, vol. 471, no. 7339, Nature Publishing Group, 2011, pp. E1–4, doi:10.1038/nature09831. short: P. Abbot, J. Abe, J. Alcock, S. Alizon, J. Alpedrinha, M. Andersson, J. Andre, M. Van Baalen, F. Balloux, S. Balshine, N.H. Barton, L. Beukeboom, J. Biernaskie, T. Bilde, G. Borgia, M. Breed, S. Brown, R. Bshary, A. Buckling, N. Burley, M. Burton Chellew, M. Cant, M. Chapuisat, E. Charnov, T. Clutton Brock, A. Cockburn, B. Cole, N. Colegrave, L. Cosmides, I. Couzin, J. Coyne, S. Creel, B. Crespi, R. Curry, S. Dall, T. Day, J. Dickinson, L. Dugatkin, C. El Mouden, S. Emlen, J. Evans, R. Ferriere, J. Field, S. Foitzik, K. Foster, W. Foster, C. Fox, J. Gadau, S. Gandon, A. Gardner, M. Gardner, T. Getty, M. Goodisman, A. Grafen, R. Grosberg, C. Grozinger, P. Gouyon, D. Gwynne, P. Harvey, B. Hatchwell, J. Heinze, H. Helantera, K. Helms, K. Hill, N. Jiricny, R. Johnstone, A. Kacelnik, E.T. Kiers, H. Kokko, J. Komdeur, J. Korb, D. Kronauer, R. Kümmerli, L. Lehmann, T. Linksvayer, S. Lion, B. Lyon, J. Marshall, R. Mcelreath, Y. Michalakis, R. Michod, D. Mock, T. Monnin, R. Montgomerie, A. Moore, U. Mueller, R. Noë, S. Okasha, P. Pamilo, G. Parker, J. Pedersen, I. Pen, D. Pfennig, D. Queller, D. Rankin, S. Reece, H. Reeve, M. Reuter, G. Roberts, S. Robson, D. Roze, F. Rousset, O. Rueppell, J. Sachs, L. Santorelli, P. Schmid Hempel, M. Schwarz, T. Scott Phillips, J. Shellmann Sherman, P. Sherman, D. Shuker, J. Smith, J. Spagna, B. Strassmann, A. Suarez, L. Sundström, M. Taborsky, P. Taylor, G. Thompson, J. Tooby, N. Tsutsui, K. Tsuji, S. Turillazzi, F. Úbeda, E. Vargo, B. Voelkl, T. Wenseleers, S. West, M. West Eberhard, D. Westneat, D. Wiernasz, G. Wild, R. Wrangham, A. Young, D. Zeh, J. Zeh, A. Zink, Nature 471 (2011) E1–E4. date_created: 2018-12-11T12:02:57Z date_published: 2011-03-23T00:00:00Z date_updated: 2021-01-12T07:43:02Z day: '23' department: - _id: NiBa doi: 10.1038/nature09831 external_id: pmid: - '21430721' intvolume: ' 471' issue: '7339' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836173/ month: '03' oa: 1 oa_version: Submitted Version page: E1 - E4 pmid: 1 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '3237' quality_controlled: '1' scopus_import: 1 status: public title: Inclusive fitness theory and eusociality type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 471 year: '2011' ... --- _id: '3394' abstract: - lang: eng text: 'Random genetic drift shifts clines in space, alters their width, and distorts their shape. Such random fluctuations complicate inferences from cline width and position. Notably, the effect of genetic drift on the expected shape of the cline is opposite to the naive (but quite common) misinterpretation of classic results on the expected cline. While random drift on average broadens the overall cline in expected allele frequency, it narrows the width of any particular cline. The opposing effects arise because locally, drift drives alleles to fixation—but fluctuations in position widen the expected cline. The effect of genetic drift can be predicted from standardized variance in allele frequencies, averaged across the habitat: 〈F〉. A cline maintained by spatially varying selection (step change) is expected to be narrower by a factor of relative to the cline in the absence of drift. The expected cline is broader by the inverse of this factor. In a tension zone maintained by underdominance, the expected cline width is narrower by about 1 – 〈F〉relative to the width in the absence of drift. Individual clines can differ substantially from the expectation, and we give quantitative predictions for the variance in cline position and width. The predictions apply to clines in almost one-dimensional circumstances such as hybrid zones in rivers, deep valleys, or along a coast line and give a guide to what patterns to expect in two dimensions.' author: - first_name: Jitka full_name: Polechova, Jitka id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Polechova J, Barton NH. Genetic drift widens the expected cline but narrows the expected cline width. Genetics. 2011;189(1):227-235. doi:10.1534/genetics.111.129817 apa: Polechova, J., & Barton, N. H. (2011). Genetic drift widens the expected cline but narrows the expected cline width. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.111.129817 chicago: Polechova, Jitka, and Nicholas H Barton. “Genetic Drift Widens the Expected Cline but Narrows the Expected Cline Width.” Genetics. Genetics Society of America, 2011. https://doi.org/10.1534/genetics.111.129817. ieee: J. Polechova and N. H. Barton, “Genetic drift widens the expected cline but narrows the expected cline width,” Genetics, vol. 189, no. 1. Genetics Society of America, pp. 227–235, 2011. ista: Polechova J, Barton NH. 2011. Genetic drift widens the expected cline but narrows the expected cline width. Genetics. 189(1), 227–235. mla: Polechova, Jitka, and Nicholas H. Barton. “Genetic Drift Widens the Expected Cline but Narrows the Expected Cline Width.” Genetics, vol. 189, no. 1, Genetics Society of America, 2011, pp. 227–35, doi:10.1534/genetics.111.129817. short: J. Polechova, N.H. Barton, Genetics 189 (2011) 227–235. date_created: 2018-12-11T12:03:05Z date_published: 2011-09-01T00:00:00Z date_updated: 2021-01-12T07:43:11Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.111.129817 ec_funded: 1 intvolume: ' 189' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176109/ month: '09' oa: 1 oa_version: Submitted Version page: 227 - 235 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '3213' quality_controlled: '1' scopus_import: 1 status: public title: Genetic drift widens the expected cline but narrows the expected cline width type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 189 year: '2011' ... --- _id: '3390' abstract: - lang: eng text: 'What determines the genetic contribution that an individual makes to future generations? With biparental reproduction, each individual leaves a ''pedigree'' of descendants, determined by the biparental relationships in the population. The pedigree of an individual constrains the lines of descent of each of its genes. An individual''s reproductive value is the expected number of copies of each of its genes that is passed on to distant generations conditional on its pedigree. For the simplest model of biparental reproduction analogous to the Wright-Fisher model, an individual''s reproductive value is determined within ~10 generations, independent of population size. Partial selfing and subdivision do not greatly slow this convergence. Our central result is that the probability that a gene will survive is proportional to the reproductive value of the individual that carries it, and that conditional on survival, after a few tens of generations, the distribution of the number of surviving copies is the same for all individuals, whatever their reproductive value. These results can be generalized to the joint distribution of surviving blocks of ancestral genome. Selection on unlinked loci in the genetic background may greatly increase the variance in reproductive value, but the above results nevertheless still hold. The almost linear relationship between survival probability and reproductive value also holds for weakly favored alleles. Thus, the influence of the complex pedigree of descendants on an individual''s genetic contribution to the population can be summarized through a single number: its reproductive value.' author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge citation: ama: Barton NH, Etheridge A. The relation between reproductive value and genetic contribution. Genetics. 2011;188(4):953-973. doi:10.1534/genetics.111.127555 apa: Barton, N. H., & Etheridge, A. (2011). The relation between reproductive value and genetic contribution. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.111.127555 chicago: Barton, Nicholas H, and Alison Etheridge. “The Relation between Reproductive Value and Genetic Contribution.” Genetics. Genetics Society of America, 2011. https://doi.org/10.1534/genetics.111.127555. ieee: N. H. Barton and A. Etheridge, “The relation between reproductive value and genetic contribution,” Genetics, vol. 188, no. 4. Genetics Society of America, pp. 953–973, 2011. ista: Barton NH, Etheridge A. 2011. The relation between reproductive value and genetic contribution. Genetics. 188(4), 953–973. mla: Barton, Nicholas H., and Alison Etheridge. “The Relation between Reproductive Value and Genetic Contribution.” Genetics, vol. 188, no. 4, Genetics Society of America, 2011, pp. 953–73, doi:10.1534/genetics.111.127555. short: N.H. Barton, A. Etheridge, Genetics 188 (2011) 953–973. date_created: 2018-12-11T12:03:04Z date_published: 2011-08-01T00:00:00Z date_updated: 2021-01-12T07:43:09Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.111.127555 ec_funded: 1 intvolume: ' 188' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176105/ month: '08' oa: 1 oa_version: Submitted Version page: 953 - 973 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '3217' quality_controlled: '1' scopus_import: 1 status: public title: The relation between reproductive value and genetic contribution type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 188 year: '2011' ... --- _id: '3391' abstract: - lang: eng text: 'Evolutionary biology shares many concepts with statistical physics: both deal with populations, whether of molecules or organisms, and both seek to simplify evolution in very many dimensions. Often, methodologies have undergone parallel and independent development, as with stochastic methods in population genetics. Here, we discuss aspects of population genetics that have embraced methods from physics: non-equilibrium statistical mechanics, travelling waves and Monte-Carlo methods, among others, have been used to study polygenic evolution, rates of adaptation and range expansions. These applications indicate that evolutionary biology can further benefit from interactions with other areas of statistical physics; for example, by following the distribution of paths taken by a population through time' author: - first_name: Harold full_name: de Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: de Vladar orcid: 0000-0002-5985-7653 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: de Vladar H, Barton NH. The contribution of statistical physics to evolutionary biology. Trends in Ecology and Evolution. 2011;26(8):424-432. doi:10.1016/j.tree.2011.04.002 apa: de Vladar, H., & Barton, N. H. (2011). The contribution of statistical physics to evolutionary biology. Trends in Ecology and Evolution. Cell Press. https://doi.org/10.1016/j.tree.2011.04.002 chicago: Vladar, Harold de, and Nicholas H Barton. “The Contribution of Statistical Physics to Evolutionary Biology.” Trends in Ecology and Evolution. Cell Press, 2011. https://doi.org/10.1016/j.tree.2011.04.002. ieee: H. de Vladar and N. H. Barton, “The contribution of statistical physics to evolutionary biology,” Trends in Ecology and Evolution, vol. 26, no. 8. Cell Press, pp. 424–432, 2011. ista: de Vladar H, Barton NH. 2011. The contribution of statistical physics to evolutionary biology. Trends in Ecology and Evolution. 26(8), 424–432. mla: de Vladar, Harold, and Nicholas H. Barton. “The Contribution of Statistical Physics to Evolutionary Biology.” Trends in Ecology and Evolution, vol. 26, no. 8, Cell Press, 2011, pp. 424–32, doi:10.1016/j.tree.2011.04.002. short: H. de Vladar, N.H. Barton, Trends in Ecology and Evolution 26 (2011) 424–432. date_created: 2018-12-11T12:03:04Z date_published: 2011-08-01T00:00:00Z date_updated: 2021-01-12T07:43:10Z day: '01' department: - _id: NiBa doi: 10.1016/j.tree.2011.04.002 ec_funded: 1 intvolume: ' 26' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1104.2854 month: '08' oa: 1 oa_version: Submitted Version page: 424 - 432 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Trends in Ecology and Evolution publication_status: published publisher: Cell Press publist_id: '3216' quality_controlled: '1' scopus_import: 1 status: public title: The contribution of statistical physics to evolutionary biology type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2011' ... --- _id: '3784' abstract: - lang: eng text: Advanced stages of Scyllarus phyllosoma larvae were collected by demersal trawling during fishery research surveys in the western Mediterranean Sea in 2003–2005. Nucleotide sequence analysis of the mitochondrial 16S rDNA gene allowed the final-stage phyllosoma of Scyllarus arctus to be identified among these larvae. Its morphology is described and illustrated. This constitutes the second complete description of a Scyllaridae phyllosoma with its specific identity being validated by molecular techniques (the first was S. pygmaeus). These results also solved a long lasting taxonomic anomaly of several species assigned to the ancient genus Phyllosoma Leach, 1814. Detailed examination indicated that the final-stage phyllosoma of S. arctus shows closer affinities with the American scyllarid Scyllarus depressus or with the Australian Scyllarus sp. b (sensu Phillips et al., 1981) than to its sympatric species S. pygmaeus. article_processing_charge: No article_type: original author: - first_name: Ferran full_name: Palero, Ferran id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87 last_name: Palero orcid: 0000-0002-0343-8329 - first_name: Guillermo full_name: Guerao, Guillermo last_name: Guerao - first_name: Paul full_name: Clark, Paul last_name: Clark - first_name: Pere full_name: Abello, Pere last_name: Abello citation: ama: 'Palero F, Guerao G, Clark P, Abello P. Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description. Journal of the Marine Biological Association of the United Kingdom. 2011;91(2):485-492. doi:10.1017/S0025315410000287' apa: 'Palero, F., Guerao, G., Clark, P., & Abello, P. (2011). Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description. Journal of the Marine Biological Association of the United Kingdom. Cambridge University Press. https://doi.org/10.1017/S0025315410000287' chicago: 'Palero, Ferran, Guillermo Guerao, Paul Clark, and Pere Abello. “Scyllarus Arctus (Crustacea: Decapoda: Scyllaridae) Final Stage Phyllosoma Identified by DNA Analysis, with Morphological Description.” Journal of the Marine Biological Association of the United Kingdom. Cambridge University Press, 2011. https://doi.org/10.1017/S0025315410000287.' ieee: 'F. Palero, G. Guerao, P. Clark, and P. Abello, “Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description,” Journal of the Marine Biological Association of the United Kingdom, vol. 91, no. 2. Cambridge University Press, pp. 485–492, 2011.' ista: 'Palero F, Guerao G, Clark P, Abello P. 2011. Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description. Journal of the Marine Biological Association of the United Kingdom. 91(2), 485–492.' mla: 'Palero, Ferran, et al. “Scyllarus Arctus (Crustacea: Decapoda: Scyllaridae) Final Stage Phyllosoma Identified by DNA Analysis, with Morphological Description.” Journal of the Marine Biological Association of the United Kingdom, vol. 91, no. 2, Cambridge University Press, 2011, pp. 485–92, doi:10.1017/S0025315410000287.' short: F. Palero, G. Guerao, P. Clark, P. Abello, Journal of the Marine Biological Association of the United Kingdom 91 (2011) 485–492. date_created: 2018-12-11T12:05:09Z date_published: 2011-03-01T00:00:00Z date_updated: 2021-01-12T07:52:10Z day: '01' department: - _id: NiBa doi: 10.1017/S0025315410000287 intvolume: ' 91' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://digital.csic.es/bitstream/10261/32783/3/Palero_et_al_2011.pdf month: '03' oa: 1 oa_version: Published Version page: 485 - 492 publication: Journal of the Marine Biological Association of the United Kingdom publication_status: published publisher: Cambridge University Press publist_id: '2443' quality_controlled: '1' scopus_import: 1 status: public title: 'Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 91 year: '2011' ... --- _id: '3290' abstract: - lang: eng text: 'Analysis of genomic data requires an efficient way to calculate likelihoods across very large numbers of loci. We describe a general method for finding the distribution of genealogies: we allow migration between demes, splitting of demes [as in the isolation-with-migration (IM) model], and recombination between linked loci. These processes are described by a set of linear recursions for the generating function of branch lengths. Under the infinite-sites model, the probability of any configuration of mutations can be found by differentiating this generating function. Such calculations are feasible for small numbers of sampled genomes: as an example, we show how the generating function can be derived explicitly for three genes under the two-deme IM model. This derivation is done automatically, using Mathematica. Given data from a large number of unlinked and nonrecombining blocks of sequence, these results can be used to find maximum-likelihood estimates of model parameters by tabulating the probabilities of all relevant mutational configurations and then multiplying across loci. The feasibility of the method is demonstrated by applying it to simulated data and to a data set previously analyzed by Wang and Hey (2010) consisting of 26,141 loci sampled from Drosophila simulans and D. melanogaster. Our results suggest that such likelihood calculations are scalable to genomic data as long as the numbers of sampled individuals and mutations per sequence block are small.' author: - first_name: Konrad full_name: Lohse, Konrad last_name: Lohse - first_name: Richard full_name: Harrison, Richard last_name: Harrison - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Lohse K, Harrison R, Barton NH. A general method for calculating likelihoods under the coalescent process. Genetics. 2011;189(3):977-987. doi:10.1534/genetics.111.129569 apa: Lohse, K., Harrison, R., & Barton, N. H. (2011). A general method for calculating likelihoods under the coalescent process. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.111.129569 chicago: Lohse, Konrad, Richard Harrison, and Nicholas H Barton. “A General Method for Calculating Likelihoods under the Coalescent Process.” Genetics. Genetics Society of America, 2011. https://doi.org/10.1534/genetics.111.129569. ieee: K. Lohse, R. Harrison, and N. H. Barton, “A general method for calculating likelihoods under the coalescent process,” Genetics, vol. 189, no. 3. Genetics Society of America, pp. 977–987, 2011. ista: Lohse K, Harrison R, Barton NH. 2011. A general method for calculating likelihoods under the coalescent process. Genetics. 189(3), 977–987. mla: Lohse, Konrad, et al. “A General Method for Calculating Likelihoods under the Coalescent Process.” Genetics, vol. 189, no. 3, Genetics Society of America, 2011, pp. 977–87, doi:10.1534/genetics.111.129569. short: K. Lohse, R. Harrison, N.H. Barton, Genetics 189 (2011) 977–987. date_created: 2018-12-11T12:02:29Z date_published: 2011-11-01T00:00:00Z date_updated: 2021-01-12T07:42:26Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.111.129569 ec_funded: 1 intvolume: ' 189' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213358/ month: '11' oa: 1 oa_version: Submitted Version page: 977 - 987 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '3355' quality_controlled: '1' scopus_import: 1 status: public title: A general method for calculating likelihoods under the coalescent process type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 189 year: '2011' ... --- _id: '3380' abstract: - lang: eng text: Linkage between markers and genes that affect a phenotype of interest may be determined by examining differences in marker allele frequency in the extreme progeny of a cross between two inbred lines. This strategy is usually employed when pooling is used to reduce genotyping costs. When the cross progeny are asexual, the extreme progeny may be selected by multiple generations of asexual reproduction and selection. We analyse this method of measuring phenotype in asexual progeny and examine the changes in marker allele frequency due to selection over many generations. Stochasticity in marker frequency in the selected population arises due to the finite initial population size. We derive the distribution of marker frequency as a result of selection at a single major locus, and show that in order to avoid spurious changes in marker allele frequency in the selected population, the initial population size should be in the low to mid hundreds. article_processing_charge: No article_type: original author: - first_name: Sayanthan full_name: Logeswaran, Sayanthan last_name: Logeswaran - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Logeswaran S, Barton NH. Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. Genetical Research. 2011;93(3):221-232. doi:10.1017/S0016672311000115 apa: Logeswaran, S., & Barton, N. H. (2011). Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. Genetical Research. Cambridge University Press. https://doi.org/10.1017/S0016672311000115 chicago: Logeswaran, Sayanthan, and Nicholas H Barton. “Mapping Mendelian Traits in Asexual Progeny Using Changes in Marker Allele Frequency.” Genetical Research. Cambridge University Press, 2011. https://doi.org/10.1017/S0016672311000115. ieee: S. Logeswaran and N. H. Barton, “Mapping Mendelian traits in asexual progeny using changes in marker allele frequency,” Genetical Research, vol. 93, no. 3. Cambridge University Press, pp. 221–232, 2011. ista: Logeswaran S, Barton NH. 2011. Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. Genetical Research. 93(3), 221–232. mla: Logeswaran, Sayanthan, and Nicholas H. Barton. “Mapping Mendelian Traits in Asexual Progeny Using Changes in Marker Allele Frequency.” Genetical Research, vol. 93, no. 3, Cambridge University Press, 2011, pp. 221–32, doi:10.1017/S0016672311000115. short: S. Logeswaran, N.H. Barton, Genetical Research 93 (2011) 221–232. date_created: 2018-12-11T12:03:00Z date_published: 2011-05-18T00:00:00Z date_updated: 2021-01-12T07:43:05Z day: '18' department: - _id: NiBa doi: 10.1017/S0016672311000115 intvolume: ' 93' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://www.pure.ed.ac.uk/ws/files/8144621/GR_2011_Barton.pdf month: '05' oa: 1 oa_version: Published Version page: 221 - 232 publication: Genetical Research publication_status: published publisher: Cambridge University Press publist_id: '3227' quality_controlled: '1' scopus_import: 1 status: public title: Mapping Mendelian traits in asexual progeny using changes in marker allele frequency type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 93 year: '2011' ... --- _id: '3778' author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Barton NH. Estimating linkage disequilibria. Heredity. 2011;106(2):205-206. doi:10.1038/hdy.2010.67 apa: Barton, N. H. (2011). Estimating linkage disequilibria. Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2010.67 chicago: Barton, Nicholas H. “Estimating Linkage Disequilibria.” Heredity. Nature Publishing Group, 2011. https://doi.org/10.1038/hdy.2010.67. ieee: N. H. Barton, “Estimating linkage disequilibria,” Heredity, vol. 106, no. 2. Nature Publishing Group, pp. 205–206, 2011. ista: Barton NH. 2011. Estimating linkage disequilibria. Heredity. 106(2), 205–206. mla: Barton, Nicholas H. “Estimating Linkage Disequilibria.” Heredity, vol. 106, no. 2, Nature Publishing Group, 2011, pp. 205–06, doi:10.1038/hdy.2010.67. short: N.H. Barton, Heredity 106 (2011) 205–206. date_created: 2018-12-11T12:05:07Z date_published: 2011-02-01T00:00:00Z date_updated: 2021-01-12T07:52:08Z day: '01' department: - _id: NiBa doi: 10.1038/hdy.2010.67 external_id: pmid: - '20502479' intvolume: ' 106' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3183869/ month: '02' oa: 1 oa_version: Submitted Version page: 205 - 206 pmid: 1 publication: Heredity publication_status: published publisher: Nature Publishing Group publist_id: '2449' scopus_import: 1 status: public title: Estimating linkage disequilibria type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 106 year: '2011' ... --- _id: '3395' abstract: - lang: eng text: Defining population structure and genetic diversity levels is of the utmost importance for developing efficient conservation strategies. Overfishing has caused mean annual catches of the European spiny lobster (Palinurus elephas) to decrease alarmingly along its distribution area. In this context, there is a need for comprehensive studies aiming to evaluate the genetic health of the exploited populations. The present study is based on a set of ten nuclear markers amplified in 331 individuals from ten different localities covering most of P. elephas distribution area. Samples from Atlantic and Mediterranean basins showed small but significant differences, indicating that P. elephas populations do not behave as a single panmictic unit but form two partially-overlapping groups. Despite intense overfishing, our dataset did not recover a recent bottleneck signal, and instead showed a large and stable historical effective size. This result could be accounted for by specific life-history traits (reproduction and longevity) and the limitations of molecular markers in covering recent timescales for nontemporal samples. The findings of the present study emphasize the need to integrate information on effective population sizes and life-history parameters when evaluating population connectivity levels from genetic data. acknowledgement: This work was supported by a pre-doctoral fellowship awarded by the Autonomous Government of Catalonia to F.P. (2006FIC-00082). Research was funded by projects FBBVA-BIOCON 08-187/09, CGL2006-13423, and CTM2007-66635. The authors are part of the research group 2009SGR-636, 2009SGR-655, and 2009SGR-1364 of the Generalitat de Catalunya. F.P. acknowledges EU-Synthesys grant (GB-TAF-4474). article_processing_charge: No author: - first_name: Ferran full_name: Palero, Ferran id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87 last_name: Palero orcid: 0000-0002-0343-8329 - first_name: Pere full_name: Abello, Pere last_name: Abello - first_name: Enrique full_name: Macpherson, Enrique last_name: Macpherson - first_name: Mark full_name: Beaumont, Mark last_name: Beaumont - first_name: Marta full_name: Pascual, Marta last_name: Pascual citation: ama: Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas. Biological Journal of the Linnean Society. 2011;104(2):407-418. doi:10.1111/j.1095-8312.2011.01728.x apa: Palero, F., Abello, P., Macpherson, E., Beaumont, M., & Pascual, M. (2011). Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas. Biological Journal of the Linnean Society. Wiley-Blackwell. https://doi.org/10.1111/j.1095-8312.2011.01728.x chicago: Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta Pascual. “Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster Palinurus Elephas.” Biological Journal of the Linnean Society. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1095-8312.2011.01728.x. ieee: F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas,” Biological Journal of the Linnean Society, vol. 104, no. 2. Wiley-Blackwell, pp. 407–418, 2011. ista: Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas. Biological Journal of the Linnean Society. 104(2), 407–418. mla: Palero, Ferran, et al. “Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster Palinurus Elephas.” Biological Journal of the Linnean Society, vol. 104, no. 2, Wiley-Blackwell, 2011, pp. 407–18, doi:10.1111/j.1095-8312.2011.01728.x. short: F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, Biological Journal of the Linnean Society 104 (2011) 407–418. date_created: 2018-12-11T12:03:06Z date_published: 2011-09-14T00:00:00Z date_updated: 2023-02-23T14:07:31Z day: '14' department: - _id: NiBa doi: 10.1111/j.1095-8312.2011.01728.x intvolume: ' 104' issue: '2' language: - iso: eng month: '09' oa_version: None page: 407 - 418 publication: Biological Journal of the Linnean Society publication_status: published publisher: Wiley-Blackwell publist_id: '3212' quality_controlled: '1' related_material: record: - id: '9762' relation: research_data status: public scopus_import: '1' status: public title: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 104 year: '2011' ... --- _id: '9762' abstract: - lang: eng text: Defining population structure and genetic diversity levels is of the utmost importance for developing efficient conservation strategies. Overfishing has caused mean annual catches of the European spiny lobster (Palinurus elephas) to decrease alarmingly along its distribution area. In this context, there is a need for comprehensive studies to evaluate the genetic health of the exploited populations. The present work is based on a set of 10 nuclear markers amplified in 331 individuals from 10 different localities covering most of P. elephas distribution area. Samples from Atlantic and Mediterranean basins showed small but significant differences, indicating that P. elephas populations do not behave as a single panmictic unit but form two partially-overlapping groups. Despite intense overfishing, our dataset did not recover a recent bottleneck signal, and showed a large and stable historical effective size instead. This result could be accounted for by specific life history traits (reproduction and longevity) and the limitations of molecular markers in covering very recent timescales for non temporal samples. Our study emphasizes the necessity of integrating information on effective population sizes and life history parameters when evaluating population connectivity levels from genetic data. article_processing_charge: No author: - first_name: Ferran full_name: Palero, Ferran id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87 last_name: Palero orcid: 0000-0002-0343-8329 - first_name: Pere full_name: Abello, Pere last_name: Abello - first_name: Enrique full_name: Macpherson, Enrique last_name: Macpherson - first_name: Mark full_name: Beaumont, Mark last_name: Beaumont - first_name: Marta full_name: Pascual, Marta last_name: Pascual citation: ama: 'Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas). 2011. doi:10.5061/dryad.299h8' apa: 'Palero, F., Abello, P., Macpherson, E., Beaumont, M., & Pascual, M. (2011). Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas). IST Austria. https://doi.org/10.5061/dryad.299h8' chicago: 'Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta Pascual. “Data from: Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster (Palinurus Elephas).” IST Austria, 2011. https://doi.org/10.5061/dryad.299h8.' ieee: 'F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas).” IST Austria, 2011.' ista: 'Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas), IST Austria, 10.5061/dryad.299h8.' mla: 'Palero, Ferran, et al. Data from: Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster (Palinurus Elephas). IST Austria, 2011, doi:10.5061/dryad.299h8.' short: F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, (2011). date_created: 2021-08-02T07:11:19Z date_published: 2011-05-12T00:00:00Z date_updated: 2023-02-23T11:25:25Z day: '12' department: - _id: NiBa doi: 10.5061/dryad.299h8 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.299h8 month: '05' oa: 1 oa_version: Published Version publisher: IST Austria related_material: record: - id: '3395' relation: used_in_publication status: public status: public title: 'Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas)' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2011' ... --- _id: '3375' abstract: - lang: eng text: 'By exploiting an analogy between population genetics and statistical mechanics, we study the evolution of a polygenic trait under stabilizing selection, mutation and genetic drift. This requires us to track only four macroscopic variables, instead of the distribution of all the allele frequencies that influence the trait. These macroscopic variables are the expectations of: the trait mean and its square, the genetic variance, and of a measure of heterozygosity, and are derived from a generating function that is in turn derived by maximizing an entropy measure. These four macroscopics are enough to accurately describe the dynamics of the trait mean and of its genetic variance (and in principle of any other quantity). Unlike previous approaches that were based on an infinite series of moments or cumulants, which had to be truncated arbitrarily, our calculations provide a well-defined approximation procedure. We apply the framework to abrupt and gradual changes in the optimum, as well as to changes in the strength of stabilizing selection. Our approximations are surprisingly accurate, even for systems with as few as five loci. We find that when the effects of drift are included, the expected genetic variance is hardly altered by directional selection, even though it fluctuates in any particular instance. We also find hysteresis, showing that even after averaging over the microscopic variables, the macroscopic trajectories retain a memory of the underlying genetic states.' article_processing_charge: No article_type: original author: - first_name: Harold full_name: de Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: de Vladar orcid: 0000-0002-5985-7653 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: de Vladar H, Barton NH. The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. Journal of the Royal Society Interface. 2011;8(58):720-739. doi:10.1098/rsif.2010.0438 apa: de Vladar, H., & Barton, N. H. (2011). The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. Journal of the Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2010.0438 chicago: Vladar, Harold de, and Nicholas H Barton. “The Statistical Mechanics of a Polygenic Character under Stabilizing Selection Mutation and Drift.” Journal of the Royal Society Interface. The Royal Society, 2011. https://doi.org/10.1098/rsif.2010.0438. ieee: H. de Vladar and N. H. Barton, “The statistical mechanics of a polygenic character under stabilizing selection mutation and drift,” Journal of the Royal Society Interface, vol. 8, no. 58. The Royal Society, pp. 720–739, 2011. ista: de Vladar H, Barton NH. 2011. The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. Journal of the Royal Society Interface. 8(58), 720–739. mla: de Vladar, Harold, and Nicholas H. Barton. “The Statistical Mechanics of a Polygenic Character under Stabilizing Selection Mutation and Drift.” Journal of the Royal Society Interface, vol. 8, no. 58, The Royal Society, 2011, pp. 720–39, doi:10.1098/rsif.2010.0438. short: H. de Vladar, N.H. Barton, Journal of the Royal Society Interface 8 (2011) 720–739. date_created: 2018-12-11T12:02:58Z date_published: 2011-05-01T00:00:00Z date_updated: 2023-10-18T06:39:05Z day: '01' department: - _id: NiBa doi: 10.1098/rsif.2010.0438 ec_funded: 1 external_id: pmid: - '21084341' intvolume: ' 8' issue: '58' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061091/ month: '05' oa: 1 oa_version: Submitted Version page: 720 - 739 pmid: 1 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Journal of the Royal Society Interface publication_status: published publisher: The Royal Society publist_id: '3232' quality_controlled: '1' scopus_import: '1' status: public title: The statistical mechanics of a polygenic character under stabilizing selection mutation and drift type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2011' ... --- _id: '3393' abstract: - lang: eng text: 'Unlike unconditionally advantageous “Fisherian” variants that tend to spread throughout a species range once introduced anywhere, “bistable” variants, such as chromosome translocations, have two alternative stable frequencies, absence and (near) fixation. Analogous to populations with Allee effects, bistable variants tend to increase locally only once they become sufficiently common, and their spread depends on their rate of increase averaged over all frequencies. Several proposed manipulations of insect populations, such as using Wolbachia or “engineered underdominance” to suppress vector-borne diseases, produce bistable rather than Fisherian dynamics. We synthesize and extend theoretical analyses concerning three features of their spatial behavior: rate of spread, conditions to initiate spread from a localized introduction, and wave stopping caused by variation in population densities or dispersal rates. Unlike Fisherian variants, bistable variants tend to spread spatially only for particular parameter combinations and initial conditions. Wave initiation requires introduction over an extended region, while subsequent spatial spread is slower than for Fisherian waves and can easily be halted by local spatial inhomogeneities. We present several new results, including robust sufficient conditions to initiate (and stop) spread, using a one-parameter cubic approximation applicable to several models. The results have both basic and applied implications.' article_processing_charge: No article_type: original author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Michael full_name: Turelli, Michael last_name: Turelli citation: ama: 'Barton NH, Turelli M. Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects. American Naturalist. 2011;178(3):E48-E75. doi:10.1086/661246' apa: 'Barton, N. H., & Turelli, M. (2011). Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects. American Naturalist. The University of Chicago Press. https://doi.org/10.1086/661246' chicago: 'Barton, Nicholas H, and Michael Turelli. “Spatial Waves of Advance with Bistable Dynamics: Cytoplasmic and Genetic Analogues of Allee Effects.” American Naturalist. The University of Chicago Press, 2011. https://doi.org/10.1086/661246.' ieee: 'N. H. Barton and M. Turelli, “Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects,” American Naturalist, vol. 178, no. 3. The University of Chicago Press, pp. E48–E75, 2011.' ista: 'Barton NH, Turelli M. 2011. Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects. American Naturalist. 178(3), E48–E75.' mla: 'Barton, Nicholas H., and Michael Turelli. “Spatial Waves of Advance with Bistable Dynamics: Cytoplasmic and Genetic Analogues of Allee Effects.” American Naturalist, vol. 178, no. 3, The University of Chicago Press, 2011, pp. E48–75, doi:10.1086/661246.' short: N.H. Barton, M. Turelli, American Naturalist 178 (2011) E48–E75. date_created: 2018-12-11T12:03:05Z date_published: 2011-09-01T00:00:00Z date_updated: 2023-10-18T08:01:43Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1086/661246 file: - access_level: open_access checksum: 7fd22a2ef3321a6fca6a439b3be5d8f4 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:31Z date_updated: 2020-07-14T12:46:11Z file_id: '4692' file_name: IST-2016-554-v1+1_BartonTurelli2011_copy.pdf file_size: 629130 relation: main_file file_date_updated: 2020-07-14T12:46:11Z has_accepted_license: '1' intvolume: ' 178' issue: '3' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: E48 - E75 publication: American Naturalist publication_identifier: eissn: - 1537-5323 issn: - 0003-0147 publication_status: published publisher: The University of Chicago Press publist_id: '3214' pubrep_id: '554' quality_controlled: '1' scopus_import: '1' status: public title: 'Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 178 year: '2011' ... --- _id: '3303' abstract: - lang: eng text: 'Biological traits result in part from interactions between different genetic loci. This can lead to sign epistasis, in which a beneficial adaptation involves a combination of individually deleterious or neutral mutations; in this case, a population must cross a “fitness valley” to adapt. Recombination can assist this process by combining mutations from different individuals or retard it by breaking up the adaptive combination. Here, we analyze the simplest fitness valley, in which an adaptation requires one mutation at each of two loci to provide a fitness benefit. We present a theoretical analysis of the effect of recombination on the valley-crossing process across the full spectrum of possible parameter regimes. We find that low recombination rates can speed up valley crossing relative to the asexual case, while higher recombination rates slow down valley crossing, with the transition between the two regimes occurring when the recombination rate between the loci is approximately equal to the selective advantage provided by the adaptation. In large populations, if the recombination rate is high and selection against single mutants is substantial, the time to cross the valley grows exponentially with population size, effectively meaning that the population cannot acquire the adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing time by up to several orders of magnitude relative to that in an asexual population. ' acknowledgement: "This work was supported in part by a Robert N. Noyce Stanford Graduate Fellowship and European Research Council grant 250152 (to D.B.W.) and by National Institutes of Health grant GM 28016 (to M.W.F.).\r\nWe thank Michael Desai for many ideas and discussions and are grateful to Joanna Masel and an anonymous reviewer for their helpful suggestions. " author: - first_name: Daniel full_name: Weissman, Daniel id: 2D0CE020-F248-11E8-B48F-1D18A9856A87 last_name: Weissman - first_name: Marcus full_name: Feldman, Marcus last_name: Feldman - first_name: Daniel full_name: Fisher, Daniel last_name: Fisher citation: ama: Weissman D, Feldman M, Fisher D. The rate of fitness-valley crossing in sexual populations. Genetics. 2010;186(4):1389-1410. doi:10.1534/genetics.110.123240 apa: Weissman, D., Feldman, M., & Fisher, D. (2010). The rate of fitness-valley crossing in sexual populations. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.110.123240 chicago: Weissman, Daniel, Marcus Feldman, and Daniel Fisher. “The Rate of Fitness-Valley Crossing in Sexual Populations.” Genetics. Genetics Society of America, 2010. https://doi.org/10.1534/genetics.110.123240. ieee: D. Weissman, M. Feldman, and D. Fisher, “The rate of fitness-valley crossing in sexual populations,” Genetics, vol. 186, no. 4. Genetics Society of America, pp. 1389–1410, 2010. ista: Weissman D, Feldman M, Fisher D. 2010. The rate of fitness-valley crossing in sexual populations. Genetics. 186(4), 1389–1410. mla: Weissman, Daniel, et al. “The Rate of Fitness-Valley Crossing in Sexual Populations.” Genetics, vol. 186, no. 4, Genetics Society of America, 2010, pp. 1389–410, doi:10.1534/genetics.110.123240. short: D. Weissman, M. Feldman, D. Fisher, Genetics 186 (2010) 1389–1410. date_created: 2018-12-11T12:02:33Z date_published: 2010-12-01T00:00:00Z date_updated: 2021-01-12T07:42:31Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.110.123240 ec_funded: 1 intvolume: ' 186' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998319/ month: '12' oa: 1 oa_version: Submitted Version page: 1389 - 1410 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '3337' quality_controlled: '1' scopus_import: 1 status: public title: The rate of fitness-valley crossing in sexual populations type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 186 year: '2010' ... --- _id: '3604' abstract: - lang: eng text: We investigated temporal changes in hybridization and introgression between native red deer (Cervus elaphus) and invasive Japanese sika (Cervus nippon) on the Kintyre Peninsula, Scotland, over 15 years, through analysis of 1513 samples of deer at 20 microsatellite loci and a mtDNA marker. We found no evidence that either the proportion of recent hybrids, or the levels of introgression had changed over the study period. Nevertheless, in one population where the two species have been in contact since ∼1970, 44% of individuals sampled during the study were hybrids. This suggests that hybridization between these species can proceed fairly rapidly. By analysing the number of alleles that have introgressed from polymorphic red deer into the genetically homogenous sika population, we reconstructed the haplotypes of red deer alleles introduced by backcrossing. Five separate hybridization events could account for all the recently hybridized sika-like individuals found across a large section of the Peninsula. Although we demonstrate that low rates of F1 hybridization can lead to substantial introgression, the progress of hybridization and introgression appears to be unpredictable over the short timescales. author: - first_name: Helen full_name: Senn, Helen last_name: Senn - first_name: Simon full_name: Goodman, Simon last_name: Goodman - first_name: Graeme full_name: Swanson, Graeme last_name: Swanson - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Josephine full_name: Pemberton, Josephine last_name: Pemberton citation: ama: Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. Molecular Ecology. 2010;19(5):910-924. doi:10.1111/j.1365-294X.2009.04497.x apa: Senn, H., Goodman, S., Swanson, G., Barton, N. H., & Pemberton, J. (2010). Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2009.04497.x chicago: Senn, Helen, Simon Goodman, Graeme Swanson, Nicholas H Barton, and Josephine Pemberton. “Investigating Temporal Changes in Hybridisation and Introgression between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on the Kintyre Peninsula, Scotland.” Molecular Ecology. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1365-294X.2009.04497.x. ieee: H. Senn, S. Goodman, G. Swanson, N. H. Barton, and J. Pemberton, “Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland,” Molecular Ecology, vol. 19, no. 5. Wiley-Blackwell, pp. 910–924, 2010. ista: Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. 2010. Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. Molecular Ecology. 19(5), 910–924. mla: Senn, Helen, et al. “Investigating Temporal Changes in Hybridisation and Introgression between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on the Kintyre Peninsula, Scotland.” Molecular Ecology, vol. 19, no. 5, Wiley-Blackwell, 2010, pp. 910–24, doi:10.1111/j.1365-294X.2009.04497.x. short: H. Senn, S. Goodman, G. Swanson, N.H. Barton, J. Pemberton, Molecular Ecology 19 (2010) 910–924. date_created: 2018-12-11T12:04:12Z date_published: 2010-03-01T00:00:00Z date_updated: 2021-01-12T07:44:36Z day: '01' department: - _id: NiBa doi: 10.1111/j.1365-294X.2009.04497.x intvolume: ' 19' issue: '5' language: - iso: eng month: '03' oa_version: None page: 910 - 924 publication: Molecular Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '2779' quality_controlled: '1' scopus_import: 1 status: public title: Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2010' ... --- _id: '3783' abstract: - lang: eng text: MICROSATELIGHT is a Perl/Tk pipeline with a graphical user interface that facilitates several tasks when scoring microsatellites. It implements new subroutines in R and PERL and takes advantage of features provided by previously developed freeware. MICROSATELIGHT takes raw genotype data and automates the peak identification through PeakScanner. The PeakSelect subroutine assigns peaks to different microsatellite markers according to their multiplex group, fluorochrome type, and size range. After peak selection, binning of alleles can be carried out 1) automatically through AlleloBin or 2) by manual bin definition through Binator. In both cases, several features for quality checking and further binning improvement are provided. The genotype table can then be converted into input files for several population genetics programs through CREATE. Finally, Hardy–Weinberg equilibrium tests and confidence intervals for null allele frequency can be obtained through GENEPOP. MICROSATELIGHT is the only freely available public-domain software that facilitates full multiplex microsatellite scoring, from electropherogram files to user-defined text files to be used with population genetics software. MICROSATELIGHT has been created for the Windows XP operating system and has been successfully tested under Windows 7. It is available at http://sourceforge.net/projects/microsatelight/. acknowledgement: "Ministerio de Educación y Ciencia (CGL2006-13423, CTM2007-66635). M.P. and FP are part of the research group 2009SGR-636 of the Generalitat de Catalunya. F.P. acknowledges an EU-Synthesys grant (GB-TAF-4474).\r\n\r\nThanks to José Gabriel Segarra-Moragues (Centro de Investigaciones sobre Desertificación) for sending us pictures with several types of stuttering and Pedro Simões and Gemma Calàbria (Universitat de Barcelona) for testing this software. Finally, thanks are due to 2 anonymous referees for their valuable comments. These comments certainly helped to improve the manuscript." author: - first_name: Ferran full_name: Palero, Ferran id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87 last_name: Palero orcid: 0000-0002-0343-8329 - first_name: Fernando full_name: González Candelas, Fernando last_name: González Candelas - first_name: Marta full_name: Pascual, Marta last_name: Pascual citation: ama: Palero F, González Candelas F, Pascual M. Microsatelight – Pipeline to expedite microsatellite analysis. Journal of Heredity. 2010;102(2):247-249. doi:10.1093/jhered/esq111 apa: Palero, F., González Candelas, F., & Pascual, M. (2010). Microsatelight – Pipeline to expedite microsatellite analysis. Journal of Heredity. Oxford University Press. https://doi.org/10.1093/jhered/esq111 chicago: Palero, Ferran, Fernando González Candelas, and Marta Pascual. “Microsatelight – Pipeline to Expedite Microsatellite Analysis.” Journal of Heredity. Oxford University Press, 2010. https://doi.org/10.1093/jhered/esq111. ieee: F. Palero, F. González Candelas, and M. Pascual, “Microsatelight – Pipeline to expedite microsatellite analysis,” Journal of Heredity, vol. 102, no. 2. Oxford University Press, pp. 247–249, 2010. ista: Palero F, González Candelas F, Pascual M. 2010. Microsatelight – Pipeline to expedite microsatellite analysis. Journal of Heredity. 102(2), 247–249. mla: Palero, Ferran, et al. “Microsatelight – Pipeline to Expedite Microsatellite Analysis.” Journal of Heredity, vol. 102, no. 2, Oxford University Press, 2010, pp. 247–49, doi:10.1093/jhered/esq111. short: F. Palero, F. González Candelas, M. Pascual, Journal of Heredity 102 (2010) 247–249. date_created: 2018-12-11T12:05:09Z date_published: 2010-12-02T00:00:00Z date_updated: 2021-01-12T07:52:10Z day: '02' department: - _id: NiBa doi: 10.1093/jhered/esq111 intvolume: ' 102' issue: '2' language: - iso: eng month: '12' oa_version: None page: 247 - 249 publication: Journal of Heredity publication_status: published publisher: Oxford University Press publist_id: '2444' quality_controlled: '1' scopus_import: 1 status: public title: Microsatelight – Pipeline to expedite microsatellite analysis type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 102 year: '2010' ... --- _id: '4134' abstract: - lang: eng text: 'All species are restricted in their distribution. Currently, ecological models can only explain such limits if patches vary in quality, leading to asymmetrical dispersal, or if genetic variation is too low at the margins for adaptation. However, population genetic models suggest that the increase in genetic variance resulting from dispersal should allow adaptation to almost any ecological gradient. Clearly therefore, these models miss something that prevents evolution in natural populations. We developed an individual-based simulation to explore stochastic effects in these models. At high carrying capacities, our simulations largely agree with deterministic predictions. However, when carrying capacity is low, the population fails to establish for a wide range of parameter values where adaptation was expected from previous models. Stochastic or transient effects appear critical around the boundaries in parameter space between simulation behaviours. Dispersal, gradient steepness, and population density emerge as key factors determining adaptation on an ecological gradient. ' acknowledgement: We are very grateful to Nick Barton. author: - first_name: Jon full_name: Bridle, Jon last_name: Bridle - first_name: Jitka full_name: Polechova, Jitka id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 - first_name: Masakado full_name: Kawata, Masakado last_name: Kawata - first_name: Roger full_name: Butlin, Roger last_name: Butlin citation: ama: Bridle J, Polechova J, Kawata M, Butlin R. Why is adaptation prevented at ecological margins? New insights from individual-based simulations. Ecology Letters. 2010;13(4):485-494. doi:10.1111/j.1461-0248.2010.01442.x apa: Bridle, J., Polechova, J., Kawata, M., & Butlin, R. (2010). Why is adaptation prevented at ecological margins? New insights from individual-based simulations. Ecology Letters. Wiley-Blackwell. https://doi.org/10.1111/j.1461-0248.2010.01442.x chicago: Bridle, Jon, Jitka Polechova, Masakado Kawata, and Roger Butlin. “Why Is Adaptation Prevented at Ecological Margins? New Insights from Individual-Based Simulations.” Ecology Letters. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1461-0248.2010.01442.x. ieee: J. Bridle, J. Polechova, M. Kawata, and R. Butlin, “Why is adaptation prevented at ecological margins? New insights from individual-based simulations,” Ecology Letters, vol. 13, no. 4. Wiley-Blackwell, pp. 485–494, 2010. ista: Bridle J, Polechova J, Kawata M, Butlin R. 2010. Why is adaptation prevented at ecological margins? New insights from individual-based simulations. Ecology Letters. 13(4), 485–494. mla: Bridle, Jon, et al. “Why Is Adaptation Prevented at Ecological Margins? New Insights from Individual-Based Simulations.” Ecology Letters, vol. 13, no. 4, Wiley-Blackwell, 2010, pp. 485–94, doi:10.1111/j.1461-0248.2010.01442.x. short: J. Bridle, J. Polechova, M. Kawata, R. Butlin, Ecology Letters 13 (2010) 485–494. date_created: 2018-12-11T12:07:08Z date_published: 2010-03-15T00:00:00Z date_updated: 2021-01-12T07:54:45Z day: '15' department: - _id: NiBa doi: 10.1111/j.1461-0248.2010.01442.x ec_funded: 1 intvolume: ' 13' issue: '4' language: - iso: eng month: '03' oa_version: None page: 485 - 494 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Ecology Letters publication_status: published publisher: Wiley-Blackwell publist_id: '1987' quality_controlled: '1' scopus_import: 1 status: public title: Why is adaptation prevented at ecological margins? New insights from individual-based simulations type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2010' ... --- _id: '4243' abstract: - lang: eng text: We investigate a new model for populations evolving in a spatial continuum. This model can be thought of as a spatial version of the Lambda-Fleming-Viot process. It explicitly incorporates both small scale reproduction events and large scale extinction-recolonisation events. The lineages ancestral to a sample from a population evolving according to this model can be described in terms of a spatial version of the Lambda-coalescent. Using a technique of Evans (1997), we prove existence and uniqueness in law for the model. We then investigate the asymptotic behaviour of the genealogy of a finite number of individuals sampled uniformly at random (or more generally `far enough apart') from a two-dimensional torus of sidelength L as L tends to infinity. Under appropriate conditions (and on a suitable timescale) we can obtain as limiting genealogical processes a Kingman coalescent, a more general Lambda-coalescent or a system of coalescing Brownian motions (with a non-local coalescence mechanism). author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge - first_name: Amandine full_name: Véber, Amandine last_name: Véber citation: ama: Barton NH, Etheridge A, Véber A. A new model for evolution in a spatial continuum. Electronic Journal of Probability. 2010;15(7):162-216. doi:10.1214/EJP.v15-741 apa: Barton, N. H., Etheridge, A., & Véber, A. (2010). A new model for evolution in a spatial continuum. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/EJP.v15-741 chicago: Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “A New Model for Evolution in a Spatial Continuum.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2010. https://doi.org/10.1214/EJP.v15-741. ieee: N. H. Barton, A. Etheridge, and A. Véber, “A new model for evolution in a spatial continuum,” Electronic Journal of Probability, vol. 15, no. 7. Institute of Mathematical Statistics, pp. 162–216, 2010. ista: Barton NH, Etheridge A, Véber A. 2010. A new model for evolution in a spatial continuum. Electronic Journal of Probability. 15(7), 162–216. mla: Barton, Nicholas H., et al. “A New Model for Evolution in a Spatial Continuum.” Electronic Journal of Probability, vol. 15, no. 7, Institute of Mathematical Statistics, 2010, pp. 162–216, doi:10.1214/EJP.v15-741. short: N.H. Barton, A. Etheridge, A. Véber, Electronic Journal of Probability 15 (2010) 162–216. date_created: 2018-12-11T12:07:48Z date_published: 2010-02-03T00:00:00Z date_updated: 2021-01-12T07:55:34Z day: '03' ddc: - '576' department: - _id: NiBa doi: 10.1214/EJP.v15-741 file: - access_level: open_access checksum: bab577546dd4e8f882e9a9dd645cd01e content_type: application/pdf creator: system date_created: 2018-12-12T10:15:21Z date_updated: 2020-07-14T12:46:26Z file_id: '5140' file_name: IST-2015-369-v1+1_741-2535-1-PB.pdf file_size: 450171 relation: main_file file_date_updated: 2020-07-14T12:46:26Z has_accepted_license: '1' intvolume: ' 15' issue: '7' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 162 - 216 publication: Electronic Journal of Probability publication_status: published publisher: Institute of Mathematical Statistics publist_id: '1863' pubrep_id: '369' quality_controlled: '1' scopus_import: 1 status: public title: A new model for evolution in a spatial continuum tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2010' ... --- _id: '3776' abstract: - lang: eng text: 'The prevalence of recombination in eukaryotes poses one of the most puzzling questions in biology. The most compelling general explanation is that recombination facilitates selection by breaking down the negative associations generated by random drift (i.e. Hill-Robertson interference, HRI). I classify the effects of HRI owing to: deleterious mutation, balancing selection and selective sweeps on: neutral diversity, rates of adaptation and the mutation load. These effects are mediated primarily by the density of deleterious mutations and of selective sweeps. Sequence polymorphism and divergence suggest that these rates may be high enough to cause significant interference even in genomic regions of high recombination. However, neither seems able to generate enough variance in fitness to select strongly for high rates of recombination. It is plausible that spatial and temporal fluctuations in selection generate much more fitness variance, and hence selection for recombination, than can be explained by uniformly deleterious mutations or species-wide selective sweeps.' acknowledgement: "Royal Society and Wolfson Foundation for their support\r\nWe would like to thank Brian Charlesworth and Sally Otto for their helpful comments." author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Barton NH. Genetic linkage and natural selection. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2010;365(1552):2559-2569. doi:10.1098/rstb.2010.0106 apa: Barton, N. H. (2010). Genetic linkage and natural selection. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society. https://doi.org/10.1098/rstb.2010.0106 chicago: Barton, Nicholas H. “Genetic Linkage and Natural Selection.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, 2010. https://doi.org/10.1098/rstb.2010.0106. ieee: N. H. Barton, “Genetic linkage and natural selection,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1552. Royal Society, pp. 2559–2569, 2010. ista: Barton NH. 2010. Genetic linkage and natural selection. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1552), 2559–2569. mla: Barton, Nicholas H. “Genetic Linkage and Natural Selection.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1552, Royal Society, 2010, pp. 2559–69, doi:10.1098/rstb.2010.0106. short: N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 2559–2569. date_created: 2018-12-11T12:05:06Z date_published: 2010-08-27T00:00:00Z date_updated: 2021-01-12T07:52:07Z day: '27' ddc: - '570' department: - _id: NiBa doi: 10.1098/rstb.2010.0106 file: - access_level: open_access checksum: 4d8aade10db030124ab158b622e337e0 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:40Z date_updated: 2020-07-14T12:46:15Z file_id: '5093' file_name: IST-2016-555-v1+1_RS2009_revised.pdf file_size: 250255 relation: main_file file_date_updated: 2020-07-14T12:46:15Z has_accepted_license: '1' intvolume: ' 365' issue: '1552' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 2559 - 2569 publication: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences publication_status: published publisher: Royal Society publist_id: '2450' pubrep_id: '555' quality_controlled: '1' scopus_import: 1 status: public title: Genetic linkage and natural selection type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 365 year: '2010' ... --- _id: '3773' abstract: - lang: eng text: If distinct biological species are to coexist in sympatry, they must be reproductively isolated and must exploit different limiting resources. A two-niche Levene model is analysed, in which habitat preference and survival depend on underlying additive traits. The population genetics of preference and viability are equivalent. However, there is a linear trade-off between the chances of settling in either niche, whereas viabilities may be constrained arbitrarily. With a convex trade-off, a sexual population evolves a single generalist genotype, whereas with a concave trade-off, disruptive selection favours maximal variance. A pure habitat preference evolves to global linkage equilibrium if mating occurs in a single pool, but remarkably, evolves to pairwise linkage equilibrium within niches if mating is within those niches--independent of the genetics. With a concave trade-off, the population shifts sharply between a unimodal distribution with high gene flow and a bimodal distribution with strong isolation, as the underlying genetic variance increases. However, these alternative states are only simultaneously stable for a narrow parameter range. A sharp threshold is only seen if survival in the 'wrong' niche is low; otherwise, strong isolation is impossible. Gene flow from divergent demes makes speciation much easier in parapatry than in sympatry. acknowledgement: "The author thanks the Werner-Gren Foundation and the Royal Swedish Academy of Sciences for organizing the symposium on the ‘Origin of Species’. He also thanks Reinhard Bürger, and two anonymous referees, for their helpful comments.\r\n" author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Barton NH. What role does natural selection play in speciation? Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2010;365(1547):1825-1840. doi:10.1098/rstb.2010.0001 apa: Barton, N. H. (2010). What role does natural selection play in speciation? Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society. https://doi.org/10.1098/rstb.2010.0001 chicago: Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, 2010. https://doi.org/10.1098/rstb.2010.0001. ieee: N. H. Barton, “What role does natural selection play in speciation?,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1547. Royal Society, pp. 1825–1840, 2010. ista: Barton NH. 2010. What role does natural selection play in speciation? Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1547), 1825–1840. mla: Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1547, Royal Society, 2010, pp. 1825–40, doi:10.1098/rstb.2010.0001. short: N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1825–1840. date_created: 2018-12-11T12:05:05Z date_published: 2010-06-12T00:00:00Z date_updated: 2021-01-12T07:52:06Z day: '12' department: - _id: NiBa doi: 10.1098/rstb.2010.0001 external_id: pmid: - '20439284' intvolume: ' 365' issue: '1547' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pubmed/20439284 month: '06' oa: 1 oa_version: Submitted Version page: 1825 - 1840 pmid: 1 publication: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences publication_status: published publisher: Royal Society publist_id: '2455' quality_controlled: '1' scopus_import: 1 status: public title: What role does natural selection play in speciation? type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 365 year: '2010' ... --- _id: '3777' abstract: - lang: eng text: 'Under the classical view, selection depends more or less directly on mutation: standing genetic variance is maintained by a balance between selection and mutation, and adaptation is fuelled by new favourable mutations. Recombination is favoured if it breaks negative associations among selected alleles, which interfere with adaptation. Such associations may be generated by negative epistasis, or by random drift (leading to the Hill-Robertson effect). Both deterministic and stochastic explanations depend primarily on the genomic mutation rate, U. This may be large enough to explain high recombination rates in some organisms, but seems unlikely to be so in general. Random drift is a more general source of negative linkage disequilibria, and can cause selection for recombination even in large populations, through the chance loss of new favourable mutations. The rate of species-wide substitutions is much too low to drive this mechanism, but local fluctuations in selection, combined with gene flow, may suffice. These arguments are illustrated by comparing the interaction between good and bad mutations at unlinked loci under the infinitesimal model.' acknowledgement: I would like to thank W. G. Hill and L. Loewe for organizing this special issue, and the Royal Society and Wolfson Foundation for their support. Also, A. Kondrashov and L. Loewe gave very helpful comments that helped improve the manuscript. author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Barton NH. Mutation and the evolution of recombination. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2010;365(1544):1281-1294. doi:10.1098/rstb.2009.0320 apa: Barton, N. H. (2010). Mutation and the evolution of recombination. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society. https://doi.org/10.1098/rstb.2009.0320 chicago: Barton, Nicholas H. “Mutation and the Evolution of Recombination.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, 2010. https://doi.org/10.1098/rstb.2009.0320. ieee: N. H. Barton, “Mutation and the evolution of recombination,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1544. Royal Society, pp. 1281–1294, 2010. ista: Barton NH. 2010. Mutation and the evolution of recombination. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1544), 1281–1294. mla: Barton, Nicholas H. “Mutation and the Evolution of Recombination.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1544, Royal Society, 2010, pp. 1281–94, doi:10.1098/rstb.2009.0320. short: N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1281–1294. date_created: 2018-12-11T12:05:07Z date_published: 2010-04-27T00:00:00Z date_updated: 2021-01-12T07:52:07Z day: '27' department: - _id: NiBa doi: 10.1098/rstb.2009.0320 external_id: pmid: - '20308104' intvolume: ' 365' issue: '1544' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pubmed/20308104 month: '04' oa: 1 oa_version: Submitted Version page: 1281 - 1294 pmid: 1 publication: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences publication_status: published publisher: Royal Society publist_id: '2451' quality_controlled: '1' scopus_import: 1 status: public title: Mutation and the evolution of recombination type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 365 year: '2010' ... --- _id: '3774' abstract: - lang: eng text: 1. Hybridisation with an invasive species has the potential to alter the phenotype and hence the ecology of a native counterpart. 2. Here data from populations of native red deer Cervus elaphus and invasive sika deer Cervus nippon in Scotland is used to assess the extent to which hybridisation between them is causing phenotypic change. This is done by regression of phenotypic traits against genetic hybrid scores. 3. Hybridisation is causing increases in the body weight of sika-like deer and decreases in the body weight of red-like females. Hybridisation is causing increases in jaw length and increases in incisor arcade breadth in sika-like females. Hybridisation is also causing decreases in incisor arcade breadth in red-like females. 4. There is currently no evidence that hybridisation is causing changes in the kidney fat weight or pregnancy rates of either population. 5. Increased phenotypic similarity between the two species is likely to lead to further hybridisation. The ecological consequences of this are difficult to predict. acknowledgement: "This project was funded through a NERC studentship to HVS which was CASE partnered by the Macaulay Institute.\r\nWe thank the Forestry Commission Scotland rangers for all their help with providing the larder data for and samples from red and sika deer, Stephen Senn and Jarrod Hadfield for statistical advice and Steve Albon for helpful comments on the manuscript." author: - first_name: Helen full_name: Senn, Helen last_name: Senn - first_name: Graeme full_name: Swanson, Graeme last_name: Swanson - first_name: Simon full_name: Goodman, Simon last_name: Goodman - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Josephine full_name: Pemberton, Josephine last_name: Pemberton citation: ama: Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. Phenotypic correlates of hybridisation between red and sika deer (genus Cervus). Journal of Animal Ecology. 2010;79(2):414-425. doi:10.1111/j.1365-2656.2009.01633.x apa: Senn, H., Swanson, G., Goodman, S., Barton, N. H., & Pemberton, J. (2010). Phenotypic correlates of hybridisation between red and sika deer (genus Cervus). Journal of Animal Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-2656.2009.01633.x chicago: Senn, Helen, Graeme Swanson, Simon Goodman, Nicholas H Barton, and Josephine Pemberton. “Phenotypic Correlates of Hybridisation between Red and Sika Deer (Genus Cervus).” Journal of Animal Ecology. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1365-2656.2009.01633.x. ieee: H. Senn, G. Swanson, S. Goodman, N. H. Barton, and J. Pemberton, “Phenotypic correlates of hybridisation between red and sika deer (genus Cervus),” Journal of Animal Ecology, vol. 79, no. 2. Wiley-Blackwell, pp. 414–425, 2010. ista: Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. 2010. Phenotypic correlates of hybridisation between red and sika deer (genus Cervus). Journal of Animal Ecology. 79(2), 414–425. mla: Senn, Helen, et al. “Phenotypic Correlates of Hybridisation between Red and Sika Deer (Genus Cervus).” Journal of Animal Ecology, vol. 79, no. 2, Wiley-Blackwell, 2010, pp. 414–25, doi:10.1111/j.1365-2656.2009.01633.x. short: H. Senn, G. Swanson, S. Goodman, N.H. Barton, J. Pemberton, Journal of Animal Ecology 79 (2010) 414–425. date_created: 2018-12-11T12:05:06Z date_published: 2010-03-01T00:00:00Z date_updated: 2021-01-12T07:52:06Z day: '01' department: - _id: NiBa doi: 10.1111/j.1365-2656.2009.01633.x external_id: pmid: - '20002231' intvolume: ' 79' issue: '2' language: - iso: eng month: '03' oa_version: None page: 414 - 425 pmid: 1 publication: Journal of Animal Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '2453' quality_controlled: '1' scopus_import: 1 status: public title: Phenotypic correlates of hybridisation between red and sika deer (genus Cervus) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 79 year: '2010' ... --- _id: '3772' article_number: e1000987 author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Barton NH. Understanding adaptation in large populations. PLoS Genetics. 2010;6(6). doi:10.1371/journal.pgen.1000987 apa: Barton, N. H. (2010). Understanding adaptation in large populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1000987 chicago: Barton, Nicholas H. “Understanding Adaptation in Large Populations.” PLoS Genetics. Public Library of Science, 2010. https://doi.org/10.1371/journal.pgen.1000987. ieee: N. H. Barton, “Understanding adaptation in large populations,” PLoS Genetics, vol. 6, no. 6. Public Library of Science, 2010. ista: Barton NH. 2010. Understanding adaptation in large populations. PLoS Genetics. 6(6), e1000987. mla: Barton, Nicholas H. “Understanding Adaptation in Large Populations.” PLoS Genetics, vol. 6, no. 6, e1000987, Public Library of Science, 2010, doi:10.1371/journal.pgen.1000987. short: N.H. Barton, PLoS Genetics 6 (2010). date_created: 2018-12-11T12:05:05Z date_published: 2010-06-17T00:00:00Z date_updated: 2021-01-12T07:52:05Z day: '17' ddc: - '570' - '576' department: - _id: NiBa doi: 10.1371/journal.pgen.1000987 file: - access_level: open_access checksum: 5c14de2680ab483cb835096c99ee734d content_type: application/pdf creator: system date_created: 2018-12-12T10:14:24Z date_updated: 2020-07-14T12:46:15Z file_id: '5075' file_name: IST-2016-524-v1+1_journal.pgen.1000987.PDF file_size: 349965 relation: main_file file_date_updated: 2020-07-14T12:46:15Z has_accepted_license: '1' intvolume: ' 6' issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: PLoS Genetics publication_status: published publisher: Public Library of Science publist_id: '2454' pubrep_id: '524' quality_controlled: '1' scopus_import: 1 status: public title: Understanding adaptation in large populations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2010' ... --- _id: '3787' abstract: - lang: eng text: DNA samples were extracted from ethanol and formalin-fixed decapod crustacean tissue using a new method based on Tetramethylsilane (TMS)-Chelex. It is shown that neither an indigestible matrix of cross-linked protein nor soluble PCR inhibitors impede PCR success when dealing with formalin-fixed material. Instead, amplification success from formalin-fixed tissue appears to depend on the presence of unmodified DNA in the extracted sample. A staining method that facilitates the targeting of samples with a high content of unmodified DNA is provided. acknowledgement: "The authors would like to thank two anonymous reviewers for their remarks, which helped to improve the manuscript. This project was supported by the Marine Biodiversity and Ecosystem Functioning Network of Excellence MarBEF (Contract no. GOCE-CT-2003-505446) of the 6th European Framework Programme(FP6), the Zoology Research Fund, Department of Zoology, NHM, London, a Research Grant from the Royal Society to S.T., and a pre-doctoral fellowship awarded by the Autonomous Government of Catalonia to F.P.(2006FIC-00082). This research received support from the SYNTHESYS Project http://www.synthesys. info/ which is financed by European Community Research Infrastructure Action under the FP6 “Structuring the European Research Area” Programme. Many thanks are due to J. Fortuño for suggesting TMS as an alternative to critical point drying, P.Crabb for helping with the UV-light photography setting and our colleagues/friends in the Whale Basement Molecular Laboratories, Department of Zoology NHM \r\n\r\n" author: - first_name: Ferran full_name: Palero, Ferran id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87 last_name: Palero orcid: 0000-0002-0343-8329 - first_name: Sally full_name: Hall, Sally last_name: Hall - first_name: Paul full_name: Clark, Paul last_name: Clark - first_name: David full_name: Johnston, David last_name: Johnston - first_name: Jackie full_name: Mackenzie Dodds, Jackie last_name: Mackenzie Dodds - first_name: Sven full_name: Thatje, Sven last_name: Thatje citation: ama: 'Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia Marina. 2010;74(3):465-470. doi:10.3989/scimar.2010.74n3465' apa: 'Palero, F., Hall, S., Clark, P., Johnston, D., Mackenzie Dodds, J., & Thatje, S. (2010). DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia Marina. Consejo Superior de Investigaciones Científicas. https://doi.org/10.3989/scimar.2010.74n3465' chicago: 'Palero, Ferran, Sally Hall, Paul Clark, David Johnston, Jackie Mackenzie Dodds, and Sven Thatje. “DNA Extraction from Formalin-Fixed Tissue: New Light from the Deep Sea.” Scientia Marina. Consejo Superior de Investigaciones Científicas, 2010. https://doi.org/10.3989/scimar.2010.74n3465.' ieee: 'F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, and S. Thatje, “DNA extraction from formalin-fixed tissue: new light from the deep sea,” Scientia Marina, vol. 74, no. 3. Consejo Superior de Investigaciones Científicas, pp. 465–470, 2010.' ista: 'Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. 2010. DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia Marina. 74(3), 465–470.' mla: 'Palero, Ferran, et al. “DNA Extraction from Formalin-Fixed Tissue: New Light from the Deep Sea.” Scientia Marina, vol. 74, no. 3, Consejo Superior de Investigaciones Científicas, 2010, pp. 465–70, doi:10.3989/scimar.2010.74n3465.' short: F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, S. Thatje, Scientia Marina 74 (2010) 465–470. date_created: 2018-12-11T12:05:10Z date_published: 2010-09-01T00:00:00Z date_updated: 2021-01-12T07:52:11Z day: '01' department: - _id: NiBa doi: 10.3989/scimar.2010.74n3465 intvolume: ' 74' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://eprints.soton.ac.uk/68731/ month: '09' oa: 1 oa_version: Submitted Version page: 465 - 470 publication: Scientia Marina publication_status: published publisher: Consejo Superior de Investigaciones Científicas publist_id: '2440' quality_controlled: '1' scopus_import: 1 status: public title: 'DNA extraction from formalin-fixed tissue: new light from the deep sea' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 74 year: '2010' ... --- _id: '3786' abstract: - lang: eng text: Four rare palinurid phyllosoma larvae, one mid-stage and three final stage, were found among the unclassified collections in the Crustacea Section, Natural History Museum, London. Detailed morphological analysis of the larvae indicated that they belong to several Palinustus species given the presence of incipient blunt-horns, length of antennula, length ratio of segments of antennular peduncle, distribution of pereiopod spines, and shape of uropods and telson. Moreover, the size of the final-stage larvae agrees with that expected given the size of the recently described puerulus stage of Palinustus mossambicus. This constitutes the first description of a complete phyllosoma assigned to Palinustus species. The phyllosoma described in the present study include the largest Palinuridae larva ever found. article_processing_charge: No article_type: original author: - first_name: Ferran full_name: Palero, Ferran id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87 last_name: Palero orcid: 0000-0002-0343-8329 - first_name: Guillermo full_name: Guerao, Guillermo last_name: Guerao - first_name: Paul full_name: Clark, Paul last_name: Clark - first_name: Pere full_name: Abello, Pere last_name: Abello citation: ama: 'Palero F, Guerao G, Clark P, Abello P. Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description. Zootaxa. 2010;2403(1):42-58. doi:10.11646/zootaxa.2403.1.4' apa: 'Palero, F., Guerao, G., Clark, P., & Abello, P. (2010). Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description. Zootaxa. Magnolia Press. https://doi.org/10.11646/zootaxa.2403.1.4' chicago: 'Palero, Ferran, Guillermo Guerao, Paul Clark, and Pere Abello. “Final-Stage Phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The First Complete Description.” Zootaxa. Magnolia Press, 2010. https://doi.org/10.11646/zootaxa.2403.1.4.' ieee: 'F. Palero, G. Guerao, P. Clark, and P. Abello, “Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description,” Zootaxa, vol. 2403, no. 1. Magnolia Press, pp. 42–58, 2010.' ista: 'Palero F, Guerao G, Clark P, Abello P. 2010. Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description. Zootaxa. 2403(1), 42–58.' mla: 'Palero, Ferran, et al. “Final-Stage Phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The First Complete Description.” Zootaxa, vol. 2403, no. 1, Magnolia Press, 2010, pp. 42–58, doi:10.11646/zootaxa.2403.1.4.' short: F. Palero, G. Guerao, P. Clark, P. Abello, Zootaxa 2403 (2010) 42–58. date_created: 2018-12-11T12:05:10Z date_published: 2010-03-19T00:00:00Z date_updated: 2022-03-21T08:22:58Z day: '19' department: - _id: NiBa doi: 10.11646/zootaxa.2403.1.4 intvolume: ' 2403' issue: '1' language: - iso: eng month: '03' oa_version: None page: 42 - 58 publication: Zootaxa publication_status: published publisher: Magnolia Press publist_id: '2441' quality_controlled: '1' scopus_import: '1' status: public title: 'Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2403 year: '2010' ... --- _id: '474' abstract: - lang: eng text: 'Classical models of gene flow fail in three ways: they cannot explain large-scale patterns; they predict much more genetic diversity than is observed; and they assume that loosely linked genetic loci evolve independently. We propose a new model that deals with these problems. Extinction events kill some fraction of individuals in a region. These are replaced by offspring from a small number of parents, drawn from the preexisting population. This model of evolution forwards in time corresponds to a backwards model, in which ancestral lineages jump to a new location if they are hit by an event, and may coalesce with other lineages that are hit by the same event. We derive an expression for the identity in allelic state, and show that, over scales much larger than the largest event, this converges to the classical value derived by Wright and Malécot. However, rare events that cover large areas cause low genetic diversity, large-scale patterns, and correlations in ancestry between unlinked loci.' acknowledgement: This work has made use of the resources provided by the Edinburgh Compute and Data Facility (ECDF). The ECDF is partially supported by the eDIKT initiative. NHB is supported in part by EPSRC Grant EP/E066070/1; JK is supported by EPSRC Grant EP/E066070/1; and AME is supported in part by EPSRC Grant EP/E065945/1. author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Jerome full_name: Kelleher, Jerome last_name: Kelleher - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge citation: ama: 'Barton NH, Kelleher J, Etheridge A. A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. Evolution. 2010;64(9):2701-2715. doi:10.1111/j.1558-5646.2010.01019.x' apa: 'Barton, N. H., Kelleher, J., & Etheridge, A. (2010). A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.1558-5646.2010.01019.x' chicago: 'Barton, Nicholas H, Jerome Kelleher, and Alison Etheridge. “A New Model for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.” Evolution. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1558-5646.2010.01019.x.' ieee: 'N. H. Barton, J. Kelleher, and A. Etheridge, “A new model for extinction and recolonization in two dimensions: Quantifying phylogeography,” Evolution, vol. 64, no. 9. Wiley-Blackwell, pp. 2701–2715, 2010.' ista: 'Barton NH, Kelleher J, Etheridge A. 2010. A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. Evolution. 64(9), 2701–2715.' mla: 'Barton, Nicholas H., et al. “A New Model for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.” Evolution, vol. 64, no. 9, Wiley-Blackwell, 2010, pp. 2701–15, doi:10.1111/j.1558-5646.2010.01019.x.' short: N.H. Barton, J. Kelleher, A. Etheridge, Evolution 64 (2010) 2701–2715. date_created: 2018-12-11T11:46:40Z date_published: 2010-09-01T00:00:00Z date_updated: 2021-01-12T08:00:52Z day: '01' department: - _id: NiBa doi: 10.1111/j.1558-5646.2010.01019.x intvolume: ' 64' issue: '9' language: - iso: eng month: '09' oa_version: None page: 2701 - 2715 publication: Evolution publication_status: published publisher: Wiley-Blackwell publist_id: '2780' quality_controlled: '1' scopus_import: 1 status: public title: 'A new model for extinction and recolonization in two dimensions: Quantifying phylogeography' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 64 year: '2010' ... --- _id: '3779' abstract: - lang: eng text: Crosses between closely related species give two contrasting results. One result is that species hybrids may be inferior to their parents, for example, being less fertile [1]. The other is that F1 hybrids may display superior performance (heterosis), for example with increased vigour [2]. Although various hypotheses have been proposed to account for these two aspects of hybridisation, their biological basis is still poorly understood [3]. To gain further insights into this issue, we analysed the role that variation in gene expression may play. We took a conserved trait, flower asymmetry in Antirrhinum, and determined the extent to which the underlying regulatory genes varied in expression among closely related species. We show that expression of both genes analysed, CYC and RAD, varies significantly between species because of cis-acting differences. By making a quantitative genotype-phenotype map, using a range of mutant alleles, we demonstrate that the species lie on a plateau in gene expression-morphology space, so that the variation has no detectable phenotypic effect. However, phenotypic differences can be revealed by shifting genotypes off the plateau through genetic crosses. Our results can be readily explained if genomes are free to evolve within an effectively neutral zone in gene expression space. The consequences of this drift will be negligible for individual loci, but when multiple loci across the genome are considered, we show that the variation may have significant effects on phenotype and fitness, causing a significant drift load. By considering these consequences for various gene-expression-fitness landscapes, we conclude that F1 hybrids might be expected to show increased performance with regard to conserved traits, such as basic physiology, but reduced performance with regard to others. Thus, our study provides a new way of explaining how various aspects of hybrid performance may arise through natural variation in gene activity. acknowledgement: "This was supported by a Marie Curie grant for early stage training and the BBSRC-John Innes Centre PhD Rotation Program.\r\nWe would like to thank X. Feng and A. Hudson for assistance with introgressions and genotyping; A. Green, A. Bangham and J. Pateman for advice and assistance on shape model procedures; F. Alderson and S.Mitchell from JIC horticultural services; P.J. Wittkopp for protocols and advice on pyrosequencing; and R. Sablowski for discussions and comments.\r\n" article_number: e1000429 author: - first_name: Ulises full_name: Rosas, Ulises last_name: Rosas - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Lucy full_name: Copsey, Lucy last_name: Copsey - first_name: Pierre full_name: Barbier De Reuille, Pierre last_name: Barbier De Reuille - first_name: Enrico full_name: Coen, Enrico last_name: Coen citation: ama: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Cryptic variation between species and the basis of hybrid performance. PLoS Biology. 2010;8(7). doi:10.1371/journal.pbio.1000429 apa: Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., & Coen, E. (2010). Cryptic variation between species and the basis of hybrid performance. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000429 chicago: Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille, and Enrico Coen. “Cryptic Variation between Species and the Basis of Hybrid Performance.” PLoS Biology. Public Library of Science, 2010. https://doi.org/10.1371/journal.pbio.1000429. ieee: U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Cryptic variation between species and the basis of hybrid performance,” PLoS Biology, vol. 8, no. 7. Public Library of Science, 2010. ista: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Cryptic variation between species and the basis of hybrid performance. PLoS Biology. 8(7), e1000429. mla: Rosas, Ulises, et al. “Cryptic Variation between Species and the Basis of Hybrid Performance.” PLoS Biology, vol. 8, no. 7, e1000429, Public Library of Science, 2010, doi:10.1371/journal.pbio.1000429. short: U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, PLoS Biology 8 (2010). date_created: 2018-12-11T12:05:07Z date_published: 2010-07-20T00:00:00Z date_updated: 2023-02-23T14:07:34Z day: '20' ddc: - '576' department: - _id: NiBa doi: 10.1371/journal.pbio.1000429 file: - access_level: open_access checksum: ee1ce2fb283a6b4127544ae532d0b4a1 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:11Z date_updated: 2020-07-14T12:46:15Z file_id: '5060' file_name: IST-2015-366-v1+1_journal.pbio.1000429.pdf file_size: 1089530 relation: main_file file_date_updated: 2020-07-14T12:46:15Z has_accepted_license: '1' intvolume: ' 8' issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: PLoS Biology publication_status: published publisher: Public Library of Science publist_id: '2448' pubrep_id: '366' quality_controlled: '1' related_material: record: - id: '9764' relation: research_data status: public scopus_import: 1 status: public title: Cryptic variation between species and the basis of hybrid performance tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2010' ... --- _id: '9764' article_processing_charge: No author: - first_name: Ulises full_name: Rosas, Ulises last_name: Rosas - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Lucy full_name: Copsey, Lucy last_name: Copsey - first_name: Pierre full_name: Barbier De Reuille, Pierre last_name: Barbier De Reuille - first_name: Enrico full_name: Coen, Enrico last_name: Coen citation: ama: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Heterosis and the drift load. 2010. doi:10.1371/journal.pbio.1000429.s003 apa: Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., & Coen, E. (2010). Heterosis and the drift load. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000429.s003 chicago: Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille, and Enrico Coen. “Heterosis and the Drift Load.” Public Library of Science, 2010. https://doi.org/10.1371/journal.pbio.1000429.s003. ieee: U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Heterosis and the drift load.” Public Library of Science, 2010. ista: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Heterosis and the drift load, Public Library of Science, 10.1371/journal.pbio.1000429.s003. mla: Rosas, Ulises, et al. Heterosis and the Drift Load. Public Library of Science, 2010, doi:10.1371/journal.pbio.1000429.s003. short: U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, (2010). date_created: 2021-08-02T09:45:39Z date_published: 2010-07-20T00:00:00Z date_updated: 2023-02-23T11:42:17Z day: '20' department: - _id: NiBa doi: 10.1371/journal.pbio.1000429.s003 month: '07' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '3779' relation: used_in_publication status: public status: public title: Heterosis and the drift load type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2010' ... --- _id: '3785' abstract: - lang: eng text: Most fisheries involving spiny lobsters of the genus Palinurus have been over exploited during the last decades, so there is a raising concern about management decisions for these valuable resources. A total of 13 microsatellite DNA loci recently developed in Palinurus elephas were assayed in order to assess genetic diversity levels in every known species of the genus. Microsatellite markers gave amplifications and showed polymorphism in all species, with gene diversity values varying from 0.65060.077 SD (Palinurus barbarae) to 0.79260.051 SD (Palinurus elephas). Most importantly, when depth distribution was taken into account, shallower waters pecies consistently showed larger historical effective population sizes than their deeper-water counterparts. This could explain why deeper-water species are more sensitive to overfishing, and would indicate that overexploitation may have a larger impact on their long-term genetic diversity. article_processing_charge: No author: - first_name: Ferran full_name: Palero, Ferran id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87 last_name: Palero orcid: 0000-0002-0343-8329 - first_name: Pere full_name: Abello, Pere last_name: Abello - first_name: E. full_name: Macpherson, E. last_name: Macpherson - first_name: C. full_name: Matthee, C. last_name: Matthee - first_name: Marta full_name: Pascual, Marta last_name: Pascual citation: ama: 'Palero F, Abello P, Macpherson E, Matthee C, Pascual M. Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata). Journal of Crustacean Biology. 2010;30(4):658-663. doi:10.1651/09-3192.1' apa: 'Palero, F., Abello, P., Macpherson, E., Matthee, C., & Pascual, M. (2010). Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata). Journal of Crustacean Biology. Oxford University Press. https://doi.org/10.1651/09-3192.1' chicago: 'Palero, Ferran, Pere Abello, E. Macpherson, C. Matthee, and Marta Pascual. “Genetic Diversity Levels in Fishery-Exploited Spiny Lobsters of the Genus Palinurus (Decapoda: Achelata).” Journal of Crustacean Biology. Oxford University Press, 2010. https://doi.org/10.1651/09-3192.1.' ieee: 'F. Palero, P. Abello, E. Macpherson, C. Matthee, and M. Pascual, “Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata),” Journal of Crustacean Biology, vol. 30, no. 4. Oxford University Press, pp. 658–663, 2010.' ista: 'Palero F, Abello P, Macpherson E, Matthee C, Pascual M. 2010. Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata). Journal of Crustacean Biology. 30(4), 658–663.' mla: 'Palero, Ferran, et al. “Genetic Diversity Levels in Fishery-Exploited Spiny Lobsters of the Genus Palinurus (Decapoda: Achelata).” Journal of Crustacean Biology, vol. 30, no. 4, Oxford University Press, 2010, pp. 658–63, doi:10.1651/09-3192.1.' short: F. Palero, P. Abello, E. Macpherson, C. Matthee, M. Pascual, Journal of Crustacean Biology 30 (2010) 658–663. date_created: 2018-12-11T12:05:09Z date_published: 2010-10-01T00:00:00Z date_updated: 2023-10-16T09:51:05Z day: '01' department: - _id: NiBa doi: 10.1651/09-3192.1 intvolume: ' 30' issue: '4' language: - iso: eng month: '10' oa_version: None page: 658 - 663 publication: Journal of Crustacean Biology publication_identifier: eissn: - 1937-240X issn: - 0278-0372 publication_status: published publisher: Oxford University Press publist_id: '2442' quality_controlled: '1' scopus_import: '1' status: public title: 'Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata)' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2010' ... --- _id: '3780' abstract: - lang: eng text: Why are sinistral snails so rare? Two main hypotheses are that selection acts against the establishment of new coiling morphs, because dextral and sinistral snails have trouble mating, or else a developmental constraint prevents the establishment of sinistrals. We therefore used an isolate of the snail Lymnaea stagnalis, in which sinistrals are rare, and populations of Partula suturalis, in which sinistrals are common, as well as a mathematical model, to understand the circumstances by which new morphs evolve. The main finding is that the sinistral genotype is associated with reduced egg viability in L. stagnalis, but in P. suturalis individuals of sinistral and dextral genotype appear equally fecund, implying a lack of a constraint. As positive frequency-dependent selection against the rare chiral morph in P. suturalis also operates over a narrow range (< 3%), the results suggest a model for chiral evolution in snails in which weak positive frequency-dependent selection may be overcome by a negative frequency-dependent selection, such as reproductive character displacement. In snails, there is not always a developmental constraint. As the direction of cleavage, and thus the directional asymmetry of the entire body, does not generally vary in other Spiralia (annelids, echiurans, vestimentiferans, sipunculids and nemerteans), it remains an open question as to whether this is because of a constraint and/or because most taxa do not have a conspicuous external asymmetry (like a shell) upon which selection can act. acknowledgement: We owe a great debt to Jim Murray for his many contributions to the study of Partula, in the field, in the laboratory, in the interpretation of data, and in generating new ideas about evolution. With pleasure and respect we dedicate this paper to him. Jim Murray played a leading role in making the collections used here. We are very grateful also to Ann Clarke and Elizabeth Murray for help with collecting, to Lorna Stewart for snail dissections, to Joris Koene for the gift of snails, to Natasha Constant for entering the data, and Takahiro Asami, Edmund Gittenberger and Gerhard Falkner for establishing the sinistral stock of L. stagnalis. Comments from an anonymous referee, A. Richard Palmer and the editorial board improved the manuscript. Work in the field was supported by the Royal Society, The Carnegie Trust, the Percy Sladen Trust and the National Science Foundation. The Science Research Council (B/SR/4144), the National Science Foundation (GB-4188), the Royal Society and the University of Nottingham supported work in the laboratory. author: - first_name: Angus full_name: Davison, Angus last_name: Davison - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Bryan full_name: Clarke, Bryan last_name: Clarke citation: ama: 'Davison A, Barton NH, Clarke B. The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails. Journal of Evolutionary Biology. 2009;22(8):1624-1635. doi:10.1111/j.1420-9101.2009.01770.x' apa: 'Davison, A., Barton, N. H., & Clarke, B. (2009). The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/j.1420-9101.2009.01770.x' chicago: 'Davison, Angus, Nicholas H Barton, and Bryan Clarke. “The Effect of Chirality Phenotype and Genotype on the Fecundity and Viability of Partula Suturalis and Lymnaea Stagnalis: Implications for the Evolution of Sinistral Snails.” Journal of Evolutionary Biology. Wiley, 2009. https://doi.org/10.1111/j.1420-9101.2009.01770.x.' ieee: 'A. Davison, N. H. Barton, and B. Clarke, “The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails,” Journal of Evolutionary Biology, vol. 22, no. 8. Wiley, pp. 1624–1635, 2009.' ista: 'Davison A, Barton NH, Clarke B. 2009. The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails. Journal of Evolutionary Biology. 22(8), 1624–1635.' mla: 'Davison, Angus, et al. “The Effect of Chirality Phenotype and Genotype on the Fecundity and Viability of Partula Suturalis and Lymnaea Stagnalis: Implications for the Evolution of Sinistral Snails.” Journal of Evolutionary Biology, vol. 22, no. 8, Wiley, 2009, pp. 1624–35, doi:10.1111/j.1420-9101.2009.01770.x.' short: A. Davison, N.H. Barton, B. Clarke, Journal of Evolutionary Biology 22 (2009) 1624–1635. date_created: 2018-12-11T12:05:08Z date_published: 2009-08-01T00:00:00Z date_updated: 2021-01-12T07:52:09Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/j.1420-9101.2009.01770.x file: - access_level: open_access checksum: f70c15c6ab9306121d4153a3be0d2346 content_type: application/pdf creator: dernst date_created: 2019-02-22T09:21:44Z date_updated: 2020-07-14T12:46:15Z file_id: '6044' file_name: Davison_JEB_v31_2009.pdf file_size: 2583812 relation: main_file file_date_updated: 2020-07-14T12:46:15Z has_accepted_license: '1' intvolume: ' 22' issue: '8' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 1624 - 1635 publication: Journal of Evolutionary Biology publication_status: published publisher: Wiley publist_id: '2447' pubrep_id: '553' quality_controlled: '1' scopus_import: 1 status: public title: 'The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2009' ... --- _id: '4136' abstract: - lang: eng text: 'Populations living in a spatially and temporally changing environment can adapt to the changing optimum and/or migrate toward favorable habitats. Here we extend previous analyses with a static optimum to allow the environment to vary in time as well as in space. The model follows both population dynamics and the trait mean under stabilizing selection, and the outcomes can be understood by comparing the loads due to genetic variance, dispersal, and temporal change. With fixed genetic variance, we obtain two regimes: (1) adaptation that is uniform along the environmental gradient and that responds to the moving optimum as expected for panmictic populations and when the spatial gradient is sufficiently steep, and (2) a population with limited range that adapts more slowly than the environmental optimum changes in both time and space; the population therefore becomes locally extinct and migrates toward suitable habitat. We also use a population‐genetic model with many loci to allow genetic variance to evolve, and we show that the only solution now has uniform adaptation.' article_processing_charge: No article_type: original author: - first_name: Jitka full_name: Polechova, Jitka id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Glenn full_name: Marion, Glenn last_name: Marion citation: ama: 'Polechova J, Barton NH, Marion G. Species’ range: Adaptation in space and time. American Naturalist. 2009;174(5):E186-E204. doi:10.1086/605958' apa: 'Polechova, J., Barton, N. H., & Marion, G. (2009). Species’ range: Adaptation in space and time. American Naturalist. University of Chicago Press. https://doi.org/10.1086/605958' chicago: 'Polechova, Jitka, Nicholas H Barton, and Glenn Marion. “Species’ Range: Adaptation in Space and Time.” American Naturalist. University of Chicago Press, 2009. https://doi.org/10.1086/605958.' ieee: 'J. Polechova, N. H. Barton, and G. Marion, “Species’ range: Adaptation in space and time,” American Naturalist, vol. 174, no. 5. University of Chicago Press, pp. E186–E204, 2009.' ista: 'Polechova J, Barton NH, Marion G. 2009. Species’ range: Adaptation in space and time. American Naturalist. 174(5), E186–E204.' mla: 'Polechova, Jitka, et al. “Species’ Range: Adaptation in Space and Time.” American Naturalist, vol. 174, no. 5, University of Chicago Press, 2009, pp. E186–204, doi:10.1086/605958.' short: J. Polechova, N.H. Barton, G. Marion, American Naturalist 174 (2009) E186–E204. date_created: 2018-12-11T12:07:09Z date_published: 2009-11-05T00:00:00Z date_updated: 2021-01-12T07:54:46Z day: '05' ddc: - '570' department: - _id: NiBa doi: 10.1086/605958 external_id: pmid: - ' 19788353' intvolume: ' 174' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://www.doi.org/10.1086/605958 month: '11' oa: 1 oa_version: Published Version page: E186 - E204 pmid: 1 publication: American Naturalist publication_status: published publisher: University of Chicago Press publist_id: '1986' pubrep_id: '552' quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1086/659642 scopus_import: 1 status: public title: 'Species'' range: Adaptation in space and time' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 174 year: '2009' ... --- _id: '4242' abstract: - lang: eng text: 'Felsenstein distinguished two ways by which selection can directly strengthen isolation. First, a modifier that strengthens prezygotic isolation can be favored everywhere. This fits with the traditional view of reinforcement as an adaptation to reduce deleterious hybridization by strengthening assortative mating. Second, selection can favor association between different incompatibilities, despite recombination. We generalize this “two allele” model to follow associations among any number of incompatibilities, which may include both assortment and hybrid inviability. Our key argument is that this process, of coupling between incompatibilities, may be quite different from the usual view of reinforcement: strong isolation can evolve through the coupling of any kind of incompatibility, whether prezygotic or postzygotic. Single locus incompatibilities become coupled because associations between them increase the variance in compatibility, which in turn increases mean fitness if there is positive epistasis. Multiple incompatibilities, each maintained by epistasis, can become coupled in the same way. In contrast, a single-locus incompatibility can become coupled with loci that reduce the viability of haploid hybrids because this reduces harmful recombination. We obtain simple approximations for the limits of tight linkage, and strong assortment, and show how assortment alleles can invade through associations with other components of reproductive isolation.' acknowledgement: "This work was supported by a Royal Society/Wolfson Research Merit award, and by a grant from the Natural Environment Research Council.\r\nWe are very grateful for insightful comments from S. P. Otto, and for helpful suggestions from the referees and the Associate Editor, Maria Servedio." author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Maria full_name: De Cara, Maria last_name: De Cara citation: ama: Barton NH, De Cara M. The evolution of strong reproductive isolation. Evolution; International Journal of Organic Evolution. 2009;63(5):1171-1190. doi:10.1111/j.1558-5646.2009.00622.x apa: Barton, N. H., & De Cara, M. (2009). The evolution of strong reproductive isolation. Evolution; International Journal of Organic Evolution. Wiley. https://doi.org/10.1111/j.1558-5646.2009.00622.x chicago: Barton, Nicholas H, and Maria De Cara. “The Evolution of Strong Reproductive Isolation.” Evolution; International Journal of Organic Evolution. Wiley, 2009. https://doi.org/10.1111/j.1558-5646.2009.00622.x. ieee: N. H. Barton and M. De Cara, “The evolution of strong reproductive isolation,” Evolution; International Journal of Organic Evolution, vol. 63, no. 5. Wiley, pp. 1171–1190, 2009. ista: Barton NH, De Cara M. 2009. The evolution of strong reproductive isolation. Evolution; International Journal of Organic Evolution. 63(5), 1171–1190. mla: Barton, Nicholas H., and Maria De Cara. “The Evolution of Strong Reproductive Isolation.” Evolution; International Journal of Organic Evolution, vol. 63, no. 5, Wiley, 2009, pp. 1171–90, doi:10.1111/j.1558-5646.2009.00622.x. short: N.H. Barton, M. De Cara, Evolution; International Journal of Organic Evolution 63 (2009) 1171–1190. date_created: 2018-12-11T12:07:48Z date_published: 2009-05-01T00:00:00Z date_updated: 2021-01-12T07:55:33Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/j.1558-5646.2009.00622.x file: - access_level: open_access checksum: 1920d2e25ef335833764256c1a47bbfb content_type: application/pdf creator: system date_created: 2018-12-12T10:11:46Z date_updated: 2020-07-14T12:46:25Z file_id: '4903' file_name: IST-2016-551-v1+1_BartonDeCaraRevNew.pdf file_size: 720913 relation: main_file - access_level: open_access checksum: c1c51bbc10d4f328fc96fc5b0e5dc25d content_type: application/pdf creator: system date_created: 2018-12-12T10:11:47Z date_updated: 2020-07-14T12:46:25Z file_id: '4904' file_name: IST-2016-551-v1+2_BartonDeCaraRevNewSI.pdf file_size: 290160 relation: main_file file_date_updated: 2020-07-14T12:46:25Z has_accepted_license: '1' intvolume: ' 63' issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 1171 - 1190 publication: Evolution; International Journal of Organic Evolution publication_status: published publisher: Wiley publist_id: '1866' pubrep_id: '551' quality_controlled: '1' scopus_import: 1 status: public title: The evolution of strong reproductive isolation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 63 year: '2009' ... --- _id: '3675' abstract: - lang: eng text: "Sex and recombination have long been seen as adaptations that facilitate natural selection by generating favorable variations. If recombination is to aid selection, there must be negative linkage disequilibria—favorable alleles must be found together less often than expected by chance. These negative linkage disequilibria can be generated directly by selection, but this must involve negative epistasis of just the right strength, which is not expected, from either experiment or theory. Random drift provides a more general source of negative associations: Favorable mutations almost always arise on different genomes, and negative associations tend to persist, precisely because they shield variation from selection.\r\n\r\nWe can understand how recombination aids adaptation by determining the maximum possible rate of adaptation. With unlinked loci, this rate increases only logarithmically with the influx of favorable mutations. With a linear genome, a scaling argument shows that in a large population, the rate of adaptive substitution depends only on the expected rate in the absence of interference, divided by the total rate of recombination. A two-locus approximation predicts an upper bound on the rate of substitution, proportional to recombination rate.\r\n\r\nIf associations between linked loci do impede adaptation, there can be substantial selection for modifiers that increase recombination. Whether this can account for the maintenance of high rates of sex and recombination depends on the extent of selection. It is clear that the rate of species-wide substitutions is typically far too low to generate appreciable selection for recombination. However, local sweeps within a subdivided population may be effective." acknowledgement: Royal Society and the Engineering and Physical Sciences for support (GR/ T11753/01) author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Barton NH. Why sex and recombination? . In: Cold Spring Harbor Symposia on Quantitative Biology. Vol 74. Cold Spring Harbor Laboratory Press; 2009:187-195. doi:10.1101/sqb.2009.74.030' apa: Barton, N. H. (2009). Why sex and recombination? . In Cold Spring Harbor Symposia on Quantitative Biology (Vol. 74, pp. 187–195). Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/sqb.2009.74.030 chicago: Barton, Nicholas H. “Why Sex and Recombination? .” In Cold Spring Harbor Symposia on Quantitative Biology, 74:187–95. Cold Spring Harbor Laboratory Press, 2009. https://doi.org/10.1101/sqb.2009.74.030. ieee: N. H. Barton, “Why sex and recombination? ,” in Cold Spring Harbor Symposia on Quantitative Biology, vol. 74, Cold Spring Harbor Laboratory Press, 2009, pp. 187–195. ista: 'Barton NH. 2009.Why sex and recombination? . In: Cold Spring Harbor Symposia on Quantitative Biology. vol. 74, 187–195.' mla: Barton, Nicholas H. “Why Sex and Recombination? .” Cold Spring Harbor Symposia on Quantitative Biology, vol. 74, Cold Spring Harbor Laboratory Press, 2009, pp. 187–95, doi:10.1101/sqb.2009.74.030. short: N.H. Barton, in:, Cold Spring Harbor Symposia on Quantitative Biology, Cold Spring Harbor Laboratory Press, 2009, pp. 187–195. date_created: 2018-12-11T12:04:33Z date_published: 2009-11-10T00:00:00Z date_updated: 2021-01-12T07:45:04Z day: '10' department: - _id: NiBa doi: 10.1101/sqb.2009.74.030 intvolume: ' 74' language: - iso: eng month: '11' oa_version: None page: 187 - 195 publication: Cold Spring Harbor Symposia on Quantitative Biology publication_status: published publisher: Cold Spring Harbor Laboratory Press publist_id: '2708' quality_controlled: '1' scopus_import: 1 status: public title: 'Why sex and recombination? ' type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 74 year: '2009' ... --- _id: '3775' abstract: - lang: eng text: There is a close analogy between statistical thermodynamics and the evolution of allele frequencies under mutation, selection and random drift. Wright's formula for the stationary distribution of allele frequencies is analogous to the Boltzmann distribution in statistical physics. Population size, 2N, plays the role of the inverse temperature, 1/kT, and determines the magnitude of random fluctuations. Log mean fitness, View the MathML source, tends to increase under selection, and is analogous to a (negative) energy; a potential function, U, increases under mutation in a similar way. An entropy, SH, can be defined which measures the deviation from the distribution of allele frequencies expected under random drift alone; the sum View the MathML source gives a free fitness that increases as the population evolves towards its stationary distribution. Usually, we observe the distribution of a few quantitative traits that depend on the frequencies of very many alleles. The mean and variance of such traits are analogous to observable quantities in statistical thermodynamics. Thus, we can define an entropy, SΩ, which measures the volume of allele frequency space that is consistent with the observed trait distribution. The stationary distribution of the traits is View the MathML source; this applies with arbitrary epistasis and dominance. The entropies SΩ, SH are distinct, but converge when there are so many alleles that traits fluctuate close to their expectations. Populations tend to evolve towards states that can be realised in many ways (i.e., large SΩ), which may lead to a substantial drop below the adaptive peak; we illustrate this point with a simple model of genetic redundancy. This analogy with statistical thermodynamics brings together previous ideas in a general framework, and justifies a maximum entropy approximation to the dynamics of quantitative traits. acknowledgement: "This work was supported by a Royal Society/Wolfson Award, and by grants EP/T11753/01, EP/C546318/01 from the EPSRC.\r\nWe are grateful to M. Cates, H.P. de Vladar and G. Sella, and to two anonymous referees, for their helpful comments." author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Jason full_name: Coe, Jason last_name: Coe citation: ama: Barton NH, Coe J. On the application of statistical physics to evolutionary biology. Journal of Theoretical Biology. 2009;259(2):317-324. doi:10.1016/j.jtbi.2009.03.019 apa: Barton, N. H., & Coe, J. (2009). On the application of statistical physics to evolutionary biology. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2009.03.019 chicago: Barton, Nicholas H, and Jason Coe. “On the Application of Statistical Physics to Evolutionary Biology.” Journal of Theoretical Biology. Elsevier, 2009. https://doi.org/10.1016/j.jtbi.2009.03.019. ieee: N. H. Barton and J. Coe, “On the application of statistical physics to evolutionary biology,” Journal of Theoretical Biology, vol. 259, no. 2. Elsevier, pp. 317–324, 2009. ista: Barton NH, Coe J. 2009. On the application of statistical physics to evolutionary biology. Journal of Theoretical Biology. 259(2), 317–324. mla: Barton, Nicholas H., and Jason Coe. “On the Application of Statistical Physics to Evolutionary Biology.” Journal of Theoretical Biology, vol. 259, no. 2, Elsevier, 2009, pp. 317–24, doi:10.1016/j.jtbi.2009.03.019. short: N.H. Barton, J. Coe, Journal of Theoretical Biology 259 (2009) 317–324. date_created: 2018-12-11T12:05:06Z date_published: 2009-07-21T00:00:00Z date_updated: 2021-01-12T07:52:06Z day: '21' department: - _id: NiBa doi: 10.1016/j.jtbi.2009.03.019 intvolume: ' 259' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://hal.archives-ouvertes.fr/hal-00554594/document month: '07' oa: 1 oa_version: Submitted Version page: 317 - 324 publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '2452' quality_controlled: '1' scopus_import: 1 status: public title: On the application of statistical physics to evolutionary biology type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 259 year: '2009' ... --- _id: '4231' abstract: - lang: eng text: The evolution of quantitative characters depends on the frequencies of the alleles involved, yet these frequencies cannot usually be measured. Previous groups have proposed an approximation to the dynamics of quantitative traits, based on an analogy with statistical mechanics. We present a modified version of that approach, which makes the analogy more precise and applies quite generally to describe the evolution of allele frequencies. We calculate explicitly how the macroscopic quantities (i.e., quantities that depend on the quantitative trait) depend on evolutionary forces, in a way that is independent of the microscopic details. We first show that the stationary distribution of allele frequencies under drift, selection, and mutation maximizes a certain measure of entropy, subject to constraints on the expectation of observable quantities. We then approximate the dynamical changes in these expectations, assuming that the distribution of allele frequencies always maximizes entropy, conditional on the expected values. When applied to directional selection on an additive trait, this gives a very good approximation to the evolution of the trait mean and the genetic variance, when the number of mutations per generation is sufficiently high (4Nμ > 1). We show how the method can be modified for small mutation rates (4Nμ → 0). We outline how this method describes epistatic interactions as, for example, with stabilizing selection. acknowledgement: "N.B. was supported by the Engineering and Physical Sciences Research Council (GR/T11753 and GR/T19537) and by the Royal Society.\r\nWe are grateful to Ellen Baake for helping to initiate this project and for her comments on this manuscript. We also thank Michael Turelli for his comments on the manuscript and I. Pen for discussions and support in this project. This project was a result of a collaboration supported by the European Science Foundation grant “Integrating population genetics and conservation biology.” " author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Harold full_name: De Vladar, Harold last_name: De Vladar citation: ama: Barton NH, De Vladar H. Statistical mechanics and the evolution of polygenic quantitative traits. Genetics. 2009;181(3):997-1011. doi:10.1534/genetics.108.099309 apa: Barton, N. H., & De Vladar, H. (2009). Statistical mechanics and the evolution of polygenic quantitative traits. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.108.099309 chicago: Barton, Nicholas H, and Harold De Vladar. “Statistical Mechanics and the Evolution of Polygenic Quantitative Traits.” Genetics. Genetics Society of America, 2009. https://doi.org/10.1534/genetics.108.099309. ieee: N. H. Barton and H. De Vladar, “Statistical mechanics and the evolution of polygenic quantitative traits,” Genetics, vol. 181, no. 3. Genetics Society of America, pp. 997–1011, 2009. ista: Barton NH, De Vladar H. 2009. Statistical mechanics and the evolution of polygenic quantitative traits. Genetics. 181(3), 997–1011. mla: Barton, Nicholas H., and Harold De Vladar. “Statistical Mechanics and the Evolution of Polygenic Quantitative Traits.” Genetics, vol. 181, no. 3, Genetics Society of America, 2009, pp. 997–1011, doi:10.1534/genetics.108.099309. short: N.H. Barton, H. De Vladar, Genetics 181 (2009) 997–1011. date_created: 2018-12-11T12:07:44Z date_published: 2009-03-01T00:00:00Z date_updated: 2021-01-12T07:55:29Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.108.099309 intvolume: ' 181' issue: '3' language: - iso: eng month: '03' oa_version: None page: 997 - 1011 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '1882' quality_controlled: '1' scopus_import: 1 status: public title: Statistical mechanics and the evolution of polygenic quantitative traits type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 181 year: '2009' ... --- _id: '517' article_processing_charge: No author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Barton NH. Identity and coalescence in structured populations: A commentary on “Inbreeding coefficients and coalescence times” by Montgomery Slatkin. Genetics Research. 2008;89(5-6):475-477. doi:10.1017/S0016672308009683' apa: 'Barton, N. H. (2008). Identity and coalescence in structured populations: A commentary on “Inbreeding coefficients and coalescence times” by Montgomery Slatkin. Genetics Research. Cambridge University Press. https://doi.org/10.1017/S0016672308009683' chicago: 'Barton, Nicholas H. “Identity and Coalescence in Structured Populations: A Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery Slatkin.” Genetics Research. Cambridge University Press, 2008. https://doi.org/10.1017/S0016672308009683.' ieee: 'N. H. Barton, “Identity and coalescence in structured populations: A commentary on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin,” Genetics Research, vol. 89, no. 5–6. Cambridge University Press, pp. 475–477, 2008.' ista: 'Barton NH. 2008. Identity and coalescence in structured populations: A commentary on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin. Genetics Research. 89(5–6), 475–477.' mla: 'Barton, Nicholas H. “Identity and Coalescence in Structured Populations: A Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery Slatkin.” Genetics Research, vol. 89, no. 5–6, Cambridge University Press, 2008, pp. 475–77, doi:10.1017/S0016672308009683.' short: N.H. Barton, Genetics Research 89 (2008) 475–477. date_created: 2018-12-11T11:46:55Z date_published: 2008-10-29T00:00:00Z date_updated: 2024-02-14T09:51:09Z day: '29' department: - _id: NiBa doi: 10.1017/S0016672308009683 intvolume: ' 89' issue: 5-6 language: - iso: eng month: '10' oa_version: None page: 475 - 477 publication: Genetics Research publication_status: published publisher: Cambridge University Press publist_id: '7302' quality_controlled: '1' scopus_import: '1' status: public title: 'Identity and coalescence in structured populations: A commentary on ''Inbreeding coefficients and coalescence times'' by Montgomery Slatkin' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 89 year: '2008' ...