[{"issue":"15","publist_id":"3577","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. "}],"type":"journal_article","author":[{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David"},{"first_name":"Spencer","last_name":"Barrett","full_name":"Barrett, Spencer"}],"volume":21,"oa_version":"None","date_created":"2018-12-11T12:01:31Z","date_updated":"2021-01-12T07:41:13Z","_id":"3122","year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley-Blackwell","intvolume":" 21","department":[{"_id":"NiBa"}],"publication_status":"published","title":"Disassortative mating and the maintenance of sexual polymorphism in painted maple","status":"public","day":"01","month":"08","scopus_import":1,"date_published":"2012-08-01T00:00:00Z","doi":"10.1111/j.1365-294X.2012.05643.x","language":[{"iso":"eng"}],"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","ista":"Field D, Barrett S. 2012. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 21(15), 3640–3643.","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.","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","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.","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."},"publication":"Molecular Ecology","page":"3640 - 3643","quality_controlled":"1"},{"month":"06","doi":"10.1371/journal.pgen.1002740","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"file_date_updated":"2020-07-14T12:46:01Z","ec_funded":1,"publist_id":"3566","article_number":"e1002740","author":[{"full_name":"Weissman, Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Weissman"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"date_created":"2018-12-11T12:01:34Z","date_updated":"2021-01-12T07:41:17Z","volume":8,"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.","year":"2012","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","day":"07","has_accepted_license":"1","scopus_import":1,"date_published":"2012-06-07T00:00:00Z","publication":"PLoS Genetics","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","ista":"Weissman D, Barton NH. 2012. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 8(6), e1002740.","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","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.","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).","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."},"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."}],"issue":"6","type":"journal_article","pubrep_id":"114","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":1284801,"access_level":"open_access","file_name":"IST-2013-114-v1+1_WeissmanBarton2012.pdf","checksum":"729a4becda7d786c4c3db8f9a1f77953","date_created":"2018-12-12T10:08:00Z","date_updated":"2020-07-14T12:46:01Z","file_id":"4659","relation":"main_file"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3131","title":"Limits to the rate of adaptive substitution in sexual populations","status":"public","ddc":["570","576"],"intvolume":" 8"},{"language":[{"iso":"eng"}],"doi":"10.1186/1745-6150-7-6","quality_controlled":"1","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"02","date_created":"2018-12-11T12:01:46Z","date_updated":"2021-01-12T07:41:31Z","volume":7,"author":[{"orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","last_name":"Vladar","first_name":"Harold","full_name":"Vladar, Harold"}],"publication_status":"published","publisher":"BioMed Central","department":[{"_id":"NiBa"}],"acknowledgement":"The author was supported by the ERC-2009-AdG Grant for project 250152 SELECTIONINFORMATION. ","year":"2012","file_date_updated":"2020-07-14T12:46:02Z","ec_funded":1,"publist_id":"3518","article_number":"6","date_published":"2012-02-10T00:00:00Z","publication":"Biology Direct","citation":{"short":"H. de Vladar, Biology Direct 7 (2012).","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.","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.","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","ieee":"H. de Vladar, “Amino acid fermentation at the origin of the genetic code,” Biology Direct, vol. 7. BioMed Central, 2012.","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","ista":"de Vladar H. 2012. Amino acid fermentation at the origin of the genetic code. Biology Direct. 7, 6."},"day":"10","has_accepted_license":"1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":4099536,"creator":"system","file_name":"IST-2012-99-v1+1_1745-6150-7-6.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:02Z","date_created":"2018-12-12T10:15:44Z","checksum":"e511e401e239ef608a7fd79b21a06d78","relation":"main_file","file_id":"5166"}],"pubrep_id":"99","ddc":["570","576"],"title":"Amino acid fermentation at the origin of the genetic code","status":"public","intvolume":" 7","_id":"3166","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","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)"}],"type":"journal_article"},{"quality_controlled":"1","page":"387 - 405","publication":"Life on Earth and other planetary bodies","citation":{"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","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.","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","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.","short":"H. de Vladar, J. Chela Flores, in:, Life on Earth and Other Planetary Bodies, Springer, 2012, pp. 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."},"language":[{"iso":"eng"}],"date_published":"2012-01-01T00:00:00Z","doi":"10.1007/978-94-007-4966-5_22","month":"01","day":"01","title":"Can the evolution of multicellularity be anticipated in the exploration of the solar system?","status":"public","publication_status":"published","intvolume":" 24","publisher":"Springer","department":[{"_id":"NiBa"}],"year":"2012","_id":"3277","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:42:20Z","date_created":"2018-12-11T12:02:25Z","oa_version":"None","volume":24,"author":[{"full_name":"de Vladar, Harold","orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","last_name":"de Vladar","first_name":"Harold"},{"last_name":"Chela Flores","first_name":"Julian","full_name":"Chela Flores, Julian"}],"alternative_title":["Cellular Origin, Life in Extreme Habitats and Astrobiology"],"type":"book_chapter","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."}],"publist_id":"3369"},{"publist_id":"7322","file_date_updated":"2020-07-14T12:46:35Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","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","year":"2012","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"publication_status":"published","author":[{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","first_name":"Melinda","last_name":"Pickup","full_name":"Pickup, Melinda"},{"full_name":"Field, David","last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rowell","first_name":"David","full_name":"Rowell, David"},{"last_name":"Young","first_name":"Andrew","full_name":"Young, Andrew"}],"volume":5,"date_created":"2018-12-11T11:46:48Z","date_updated":"2021-01-12T08:01:06Z","month":"12","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"quality_controlled":"1","doi":"10.1111/j.1752-4571.2012.00284.x","language":[{"iso":"eng"}],"type":"journal_article","issue":"8","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."}],"_id":"498","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 5","status":"public","title":"Predicting local adaptation in fragmented plant populations: Implications for restoration genetics","ddc":["576"],"pubrep_id":"942","file":[{"creator":"system","content_type":"application/pdf","file_size":396136,"file_name":"IST-2018-942-v1+1_Pickup_et_al-2012-Evolutionary_Applications.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:35Z","date_created":"2018-12-12T10:10:33Z","checksum":"233007138606aca5a2f75f7ae1742f43","file_id":"4821","relation":"main_file"}],"oa_version":"Published Version","has_accepted_license":"1","day":"01","citation":{"short":"M. Pickup, D. Field, D. Rowell, A. Young, Evolutionary Applications 5 (2012) 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.","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.","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","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.","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","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."},"publication":"Evolutionary Applications","page":"913 - 924","date_published":"2012-12-01T00:00:00Z"},{"day":"14","month":"11","article_processing_charge":"No","citation":{"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.","short":"S. Aeschbacher, A. Futschik, M. Beaumont, (2012).","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.","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.","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","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.","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"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.274b1"}],"oa":1,"doi":"10.5061/dryad.274b1","date_published":"2012-11-14T00:00:00Z","type":"research_data_reference","abstract":[{"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.","lang":"eng"}],"_id":"9758","year":"2012","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates","status":"public","publisher":"Dryad","department":[{"_id":"NiBa"}],"author":[{"first_name":"Simon","last_name":"Aeschbacher","id":"2D35326E-F248-11E8-B48F-1D18A9856A87","full_name":"Aeschbacher, Simon"},{"full_name":"Futschik, Andreas","first_name":"Andreas","last_name":"Futschik"},{"last_name":"Beaumont","first_name":"Mark","full_name":"Beaumont, Mark"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"2944"}]},"date_created":"2021-07-30T12:36:39Z","date_updated":"2023-02-23T11:05:19Z","oa_version":"Published Version"},{"publication_status":"published","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"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. ","year":"2012","date_updated":"2023-05-30T13:07:47Z","date_created":"2018-12-11T12:00:36Z","volume":21,"author":[{"first_name":"Konrad","last_name":"Lohse","full_name":"Lohse, Konrad"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"last_name":"Melika","first_name":"George","full_name":"Melika, George"},{"full_name":"Stone, Graham","first_name":"Graham","last_name":"Stone"}],"related_material":{"record":[{"id":"13075","status":"public","relation":"research_data"}]},"file_date_updated":"2020-07-14T12:45:57Z","publist_id":"3746","ec_funded":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/j.1365-294X.2012.05700.x","month":"09","ddc":["570","579"],"title":"A likelihood based comparison of population histories in a parasitoid guild","status":"public","intvolume":" 21","_id":"2968","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"IST-2014-296-v1+1_4_wasps_revised3.pdf","creator":"system","content_type":"application/pdf","file_size":235820,"file_id":"5304","relation":"main_file","checksum":"c14ee4cb2a8ba9575bfd8a9bb7a883bb","date_created":"2018-12-12T10:17:47Z","date_updated":"2020-07-14T12:45:57Z"},{"creator":"system","content_type":"application/pdf","file_size":41975,"access_level":"open_access","file_name":"IST-2014-296-v1+2_4_wasps_Supporting2.pdf","checksum":"f00afc5b887c8222014b57375b8caece","date_updated":"2020-07-14T12:45:57Z","date_created":"2018-12-12T10:17:48Z","file_id":"5305","relation":"main_file"}],"pubrep_id":"296","type":"journal_article","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."}],"issue":"18","page":"4605 - 4617","publication":"Molecular Ecology","citation":{"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.","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.","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","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.","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.","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"},"date_published":"2012-09-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1"},{"month":"06","day":"08","article_processing_charge":"No","tmp":{"short":"CC0 (1.0)","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)"},"oa":1,"citation":{"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).","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.","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","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.","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.","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"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.0g0fs"}],"date_published":"2012-06-08T00:00:00Z","doi":"10.5061/DRYAD.0G0FS","type":"research_data_reference","abstract":[{"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.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13075","year":"2012","ddc":["570"],"title":"Data from: A likelihood-based comparison of population histories in a parasitoid guild","status":"public","department":[{"_id":"NiBa"}],"publisher":"Dryad","author":[{"last_name":"Lohse","first_name":"Konrad","full_name":"Lohse, Konrad"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"last_name":"Stone","first_name":"Graham","full_name":"Stone, Graham"},{"first_name":"George","last_name":"Melika","full_name":"Melika, George"}],"related_material":{"record":[{"id":"2968","relation":"used_in_publication","status":"public"}]},"date_created":"2023-05-23T17:01:02Z","date_updated":"2023-05-30T13:07:48Z","oa_version":"Published Version"},{"type":"journal_article","issue":"7339","abstract":[{"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.","lang":"eng"}],"intvolume":" 471","status":"public","title":"Inclusive fitness theory and eusociality","_id":"3372","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","scopus_import":1,"day":"23","page":"E1 - E4","citation":{"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.","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.","ama":"Abbot P, Abe J, Alcock J, et al. Inclusive fitness theory and eusociality. Nature. 2011;471(7339):E1-E4. doi:10.1038/nature09831","ista":"Abbot P et al. 2011. Inclusive fitness theory and eusociality. Nature. 471(7339), E1–E4.","ieee":"P. Abbot et al., “Inclusive fitness theory and eusociality,” Nature, vol. 471, no. 7339. Nature Publishing Group, pp. E1–E4, 2011.","apa":"Abbot, P., Abe, J., Alcock, J., Alizon, S., Alpedrinha, J., Andersson, M., … Zink, A. (2011). Inclusive fitness theory and eusociality. Nature. 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Kazuki","last_name":"Tsuji","first_name":"Kazuki"},{"full_name":"Turillazzi, Stefano","last_name":"Turillazzi","first_name":"Stefano"},{"full_name":"Úbeda, Francisco","last_name":"Úbeda","first_name":"Francisco"},{"full_name":"Vargo, Edward","first_name":"Edward","last_name":"Vargo"},{"last_name":"Voelkl","first_name":"Bernard","full_name":"Voelkl, Bernard"},{"last_name":"Wenseleers","first_name":"Tom","full_name":"Wenseleers, Tom"},{"full_name":"West, Stuart","first_name":"Stuart","last_name":"West"},{"full_name":"West Eberhard, Mary","first_name":"Mary","last_name":"West Eberhard"},{"full_name":"Westneat, David","first_name":"David","last_name":"Westneat"},{"first_name":"Diane","last_name":"Wiernasz","full_name":"Wiernasz, Diane"},{"full_name":"Wild, Geoff","last_name":"Wild","first_name":"Geoff"},{"last_name":"Wrangham","first_name":"Richard","full_name":"Wrangham, Richard"},{"full_name":"Young, Andrew","last_name":"Young","first_name":"Andrew"},{"full_name":"Zeh, David","last_name":"Zeh","first_name":"David"},{"first_name":"Jeanne","last_name":"Zeh","full_name":"Zeh, Jeanne"},{"last_name":"Zink","first_name":"Andrew","full_name":"Zink, Andrew"}],"month":"03","quality_controlled":"1","external_id":{"pmid":["21430721"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836173/"}],"language":[{"iso":"eng"}],"doi":"10.1038/nature09831"},{"page":"227 - 235","publication":"Genetics","citation":{"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.","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.","ista":"Polechova J, Barton NH. 2011. Genetic drift widens the expected cline but narrows the expected cline width. Genetics. 189(1), 227–235.","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","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.","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"},"date_published":"2011-09-01T00:00:00Z","scopus_import":1,"day":"01","status":"public","title":"Genetic drift widens the expected cline but narrows the expected cline width","intvolume":" 189","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3394","oa_version":"Submitted Version","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"1","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176109/","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1534/genetics.111.129817","month":"09","publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"year":"2011","date_created":"2018-12-11T12:03:05Z","date_updated":"2021-01-12T07:43:11Z","volume":189,"author":[{"last_name":"Polechova","first_name":"Jitka","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","full_name":"Polechova, Jitka"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"publist_id":"3213","ec_funded":1},{"title":"The relation between reproductive value and genetic contribution","status":"public","intvolume":" 188","_id":"3390","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","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."}],"issue":"4","page":"953 - 973","publication":"Genetics","citation":{"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.","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.","ista":"Barton NH, Etheridge A. 2011. The relation between reproductive value and genetic contribution. Genetics. 188(4), 953–973.","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","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.","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"},"date_published":"2011-08-01T00:00:00Z","scopus_import":1,"day":"01","publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"year":"2011","date_created":"2018-12-11T12:03:04Z","date_updated":"2021-01-12T07:43:09Z","volume":188,"author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"}],"publist_id":"3217","ec_funded":1,"quality_controlled":"1","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176105/"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1534/genetics.111.127555","month":"08"},{"publist_id":"3216","ec_funded":1,"author":[{"first_name":"Harold","last_name":"de Vladar","id":"2A181218-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5985-7653","full_name":"de Vladar, Harold"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"volume":26,"date_created":"2018-12-11T12:03:04Z","date_updated":"2021-01-12T07:43:10Z","year":"2011","publisher":"Cell Press","department":[{"_id":"NiBa"}],"publication_status":"published","month":"08","doi":"10.1016/j.tree.2011.04.002","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1104.2854"}],"oa":1,"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"quality_controlled":"1","issue":"8","abstract":[{"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","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3391","intvolume":" 26","status":"public","title":"The contribution of statistical physics to evolutionary biology","day":"01","scopus_import":1,"date_published":"2011-08-01T00:00:00Z","citation":{"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.","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","ista":"de Vladar H, Barton NH. 2011. The contribution of statistical physics to evolutionary biology. Trends in Ecology and Evolution. 26(8), 424–432.","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","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.","short":"H. de Vladar, N.H. Barton, Trends in Ecology and Evolution 26 (2011) 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."},"publication":"Trends in Ecology and Evolution","page":"424 - 432"},{"article_processing_charge":"No","day":"01","scopus_import":1,"date_published":"2011-03-01T00:00:00Z","citation":{"short":"F. Palero, G. Guerao, P. Clark, P. Abello, Journal of the Marine Biological Association of the United Kingdom 91 (2011) 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.","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.","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","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.","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","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."},"publication":"Journal of the Marine Biological Association of the United Kingdom","page":"485 - 492","article_type":"original","issue":"2","abstract":[{"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.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3784","intvolume":" 91","status":"public","title":"Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description","month":"03","doi":"10.1017/S0025315410000287","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://digital.csic.es/bitstream/10261/32783/3/Palero_et_al_2011.pdf"}],"quality_controlled":"1","publist_id":"2443","author":[{"id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0343-8329","first_name":"Ferran","last_name":"Palero","full_name":"Palero, Ferran"},{"first_name":"Guillermo","last_name":"Guerao","full_name":"Guerao, Guillermo"},{"first_name":"Paul","last_name":"Clark","full_name":"Clark, Paul"},{"full_name":"Abello, Pere","first_name":"Pere","last_name":"Abello"}],"volume":91,"date_updated":"2021-01-12T07:52:10Z","date_created":"2018-12-11T12:05:09Z","year":"2011","department":[{"_id":"NiBa"}],"publisher":"Cambridge University Press","publication_status":"published"},{"month":"11","doi":"10.1534/genetics.111.129569","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213358/","open_access":"1"}],"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"quality_controlled":"1","publist_id":"3355","ec_funded":1,"author":[{"first_name":"Konrad","last_name":"Lohse","full_name":"Lohse, Konrad"},{"last_name":"Harrison","first_name":"Richard","full_name":"Harrison, Richard"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"volume":189,"date_updated":"2021-01-12T07:42:26Z","date_created":"2018-12-11T12:02:29Z","year":"2011","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","publication_status":"published","day":"01","scopus_import":1,"date_published":"2011-11-01T00:00:00Z","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","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.","short":"K. Lohse, R. Harrison, N.H. Barton, Genetics 189 (2011) 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.","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."},"publication":"Genetics","page":"977 - 987","issue":"3","abstract":[{"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.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3290","intvolume":" 189","title":"A general method for calculating likelihoods under the coalescent process","status":"public"},{"year":"2011","publication_status":"published","publisher":"Cambridge University Press","department":[{"_id":"NiBa"}],"author":[{"full_name":"Logeswaran, Sayanthan","first_name":"Sayanthan","last_name":"Logeswaran"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"date_updated":"2021-01-12T07:43:05Z","date_created":"2018-12-11T12:03:00Z","volume":93,"publist_id":"3227","main_file_link":[{"open_access":"1","url":"https://www.pure.ed.ac.uk/ws/files/8144621/GR_2011_Barton.pdf"}],"oa":1,"quality_controlled":"1","doi":"10.1017/S0016672311000115","language":[{"iso":"eng"}],"month":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3380","status":"public","title":"Mapping Mendelian traits in asexual progeny using changes in marker allele frequency","intvolume":" 93","oa_version":"Published Version","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"3","publication":"Genetical Research","citation":{"ista":"Logeswaran S, Barton NH. 2011. Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. Genetical Research. 93(3), 221–232.","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.","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","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","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.","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."},"article_type":"original","page":"221 - 232","date_published":"2011-05-18T00:00:00Z","scopus_import":1,"day":"18","article_processing_charge":"No"},{"scopus_import":1,"day":"01","month":"02","page":"205 - 206","publication":"Heredity","external_id":{"pmid":["20502479"]},"citation":{"ama":"Barton NH. Estimating linkage disequilibria. Heredity. 2011;106(2):205-206. doi:10.1038/hdy.2010.67","ieee":"N. H. Barton, “Estimating linkage disequilibria,” Heredity, vol. 106, no. 2. Nature Publishing Group, pp. 205–206, 2011.","apa":"Barton, N. H. (2011). Estimating linkage disequilibria. Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2010.67","ista":"Barton NH. 2011. Estimating linkage disequilibria. Heredity. 106(2), 205–206.","short":"N.H. Barton, Heredity 106 (2011) 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.","chicago":"Barton, Nicholas H. “Estimating Linkage Disequilibria.” Heredity. Nature Publishing Group, 2011. https://doi.org/10.1038/hdy.2010.67."},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3183869/","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/hdy.2010.67","date_published":"2011-02-01T00:00:00Z","type":"journal_article","issue":"2","publist_id":"2449","publication_status":"published","status":"public","title":"Estimating linkage disequilibria","intvolume":" 106","department":[{"_id":"NiBa"}],"publisher":"Nature Publishing Group","_id":"3778","year":"2011","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","pmid":1,"date_updated":"2021-01-12T07:52:08Z","date_created":"2018-12-11T12:05:07Z","oa_version":"Submitted Version","volume":106,"author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}]},{"title":"Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas","status":"public","intvolume":" 104","_id":"3395","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"None","type":"journal_article","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."}],"issue":"2","page":"407 - 418","publication":"Biological Journal of the Linnean Society","citation":{"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.","short":"F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, Biological Journal of the Linnean Society 104 (2011) 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.","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.","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","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.","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"},"date_published":"2011-09-14T00:00:00Z","scopus_import":"1","day":"14","article_processing_charge":"No","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley-Blackwell","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).","year":"2011","date_updated":"2023-02-23T14:07:31Z","date_created":"2018-12-11T12:03:06Z","volume":104,"author":[{"last_name":"Palero","first_name":"Ferran","orcid":"0000-0002-0343-8329","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","full_name":"Palero, Ferran"},{"full_name":"Abello, Pere","first_name":"Pere","last_name":"Abello"},{"first_name":"Enrique","last_name":"Macpherson","full_name":"Macpherson, Enrique"},{"full_name":"Beaumont, Mark","last_name":"Beaumont","first_name":"Mark"},{"last_name":"Pascual","first_name":"Marta","full_name":"Pascual, Marta"}],"related_material":{"record":[{"id":"9762","status":"public","relation":"research_data"}]},"publist_id":"3212","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1111/j.1095-8312.2011.01728.x","month":"09"},{"author":[{"full_name":"Palero, Ferran","last_name":"Palero","first_name":"Ferran","orcid":"0000-0002-0343-8329","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Abello, Pere","first_name":"Pere","last_name":"Abello"},{"first_name":"Enrique","last_name":"Macpherson","full_name":"Macpherson, Enrique"},{"last_name":"Beaumont","first_name":"Mark","full_name":"Beaumont, Mark"},{"last_name":"Pascual","first_name":"Marta","full_name":"Pascual, Marta"}],"related_material":{"record":[{"id":"3395","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-02T07:11:19Z","date_updated":"2023-02-23T11:25:25Z","oa_version":"Published Version","_id":"9762","year":"2011","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas)","department":[{"_id":"NiBa"}],"publisher":"IST Austria","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."}],"type":"research_data_reference","doi":"10.5061/dryad.299h8","date_published":"2011-05-12T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.5061/dryad.299h8","open_access":"1"}],"oa":1,"citation":{"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.","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).","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.","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.","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","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"},"day":"12","month":"05","article_processing_charge":"No"},{"article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2011-05-01T00:00:00Z","page":"720 - 739","article_type":"original","citation":{"short":"H. de Vladar, N.H. Barton, Journal of the Royal Society Interface 8 (2011) 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.","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.","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","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."},"publication":"Journal of the Royal Society Interface","issue":"58","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."}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 8","title":"The statistical mechanics of a polygenic character under stabilizing selection mutation and drift","status":"public","_id":"3375","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","language":[{"iso":"eng"}],"doi":"10.1098/rsif.2010.0438","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","external_id":{"pmid":["21084341"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061091/"}],"ec_funded":1,"publist_id":"3232","volume":8,"date_created":"2018-12-11T12:02:58Z","date_updated":"2023-10-18T06:39:05Z","author":[{"full_name":"de Vladar, Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5985-7653","first_name":"Harold","last_name":"de Vladar"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"publisher":"The Royal Society","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2011"},{"type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"3","_id":"3393","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects","ddc":["570"],"intvolume":" 178","pubrep_id":"554","file":[{"file_id":"4692","relation":"main_file","date_updated":"2020-07-14T12:46:11Z","date_created":"2018-12-12T10:08:31Z","checksum":"7fd22a2ef3321a6fca6a439b3be5d8f4","file_name":"IST-2016-554-v1+1_BartonTurelli2011_copy.pdf","access_level":"open_access","creator":"system","file_size":629130,"content_type":"application/pdf"}],"oa_version":"Submitted Version","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication":"American Naturalist","citation":{"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.","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.","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.","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.","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","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"},"article_type":"original","page":"E48 - E75","date_published":"2011-09-01T00:00:00Z","file_date_updated":"2020-07-14T12:46:11Z","publist_id":"3214","year":"2011","publication_status":"published","publisher":"The University of Chicago Press","department":[{"_id":"NiBa"}],"author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"full_name":"Turelli, Michael","first_name":"Michael","last_name":"Turelli"}],"date_updated":"2023-10-18T08:01:43Z","date_created":"2018-12-11T12:03:05Z","volume":178,"month":"09","publication_identifier":{"eissn":["1537-5323"],"issn":["0003-0147"]},"oa":1,"quality_controlled":"1","doi":"10.1086/661246","language":[{"iso":"eng"}]},{"intvolume":" 186","status":"public","title":"The rate of fitness-valley crossing in sexual populations","_id":"3303","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","issue":"4","abstract":[{"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. ","lang":"eng"}],"page":"1389 - 1410","citation":{"short":"D. Weissman, M. Feldman, D. Fisher, Genetics 186 (2010) 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.","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.","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","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.","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","ista":"Weissman D, Feldman M, Fisher D. 2010. The rate of fitness-valley crossing in sexual populations. Genetics. 186(4), 1389–1410."},"publication":"Genetics","date_published":"2010-12-01T00:00:00Z","scopus_import":1,"day":"01","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","publication_status":"published","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. ","year":"2010","volume":186,"date_updated":"2021-01-12T07:42:31Z","date_created":"2018-12-11T12:02:33Z","author":[{"last_name":"Weissman","first_name":"Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","full_name":"Weissman, Daniel"},{"full_name":"Feldman, Marcus","last_name":"Feldman","first_name":"Marcus"},{"first_name":"Daniel","last_name":"Fisher","full_name":"Fisher, Daniel"}],"ec_funded":1,"publist_id":"3337","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998319/","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1534/genetics.110.123240","month":"12"},{"language":[{"iso":"eng"}],"date_published":"2010-03-01T00:00:00Z","doi":"10.1111/j.1365-294X.2009.04497.x","quality_controlled":"1","page":"910 - 924","publication":"Molecular Ecology","citation":{"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.","short":"H. Senn, S. Goodman, G. Swanson, N.H. Barton, J. Pemberton, Molecular Ecology 19 (2010) 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.","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.","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","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.","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"},"month":"03","day":"01","scopus_import":1,"date_updated":"2021-01-12T07:44:36Z","date_created":"2018-12-11T12:04:12Z","oa_version":"None","volume":19,"author":[{"full_name":"Senn, Helen","last_name":"Senn","first_name":"Helen"},{"full_name":"Goodman, Simon","first_name":"Simon","last_name":"Goodman"},{"full_name":"Swanson, Graeme","last_name":"Swanson","first_name":"Graeme"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"full_name":"Pemberton, Josephine","last_name":"Pemberton","first_name":"Josephine"}],"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","publication_status":"published","intvolume":" 19","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"_id":"3604","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2010","abstract":[{"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.","lang":"eng"}],"issue":"5","publist_id":"2779","type":"journal_article"},{"author":[{"full_name":"Palero, Ferran","first_name":"Ferran","last_name":"Palero","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0343-8329"},{"full_name":"González Candelas, Fernando","last_name":"González Candelas","first_name":"Fernando"},{"first_name":"Marta","last_name":"Pascual","full_name":"Pascual, Marta"}],"date_created":"2018-12-11T12:05:09Z","date_updated":"2021-01-12T07:52:10Z","oa_version":"None","volume":102,"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.","_id":"3783","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2010","publication_status":"published","title":"Microsatelight – Pipeline to expedite microsatellite analysis","status":"public","department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","intvolume":" 102","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/."}],"publist_id":"2444","issue":"2","type":"journal_article","date_published":"2010-12-02T00:00:00Z","doi":"10.1093/jhered/esq111","language":[{"iso":"eng"}],"publication":"Journal of Heredity","citation":{"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","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.","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","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.","short":"F. Palero, F. González Candelas, M. Pascual, Journal of Heredity 102 (2010) 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."},"quality_controlled":"1","page":"247 - 249","month":"12","day":"02","scopus_import":1},{"intvolume":" 13","status":"public","title":"Why is adaptation prevented at ecological margins? New insights from individual-based simulations","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"4134","oa_version":"None","type":"journal_article","issue":"4","abstract":[{"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. ","lang":"eng"}],"page":"485 - 494","citation":{"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.","short":"J. Bridle, J. Polechova, M. Kawata, R. Butlin, Ecology Letters 13 (2010) 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.","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","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.","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"},"publication":"Ecology Letters","date_published":"2010-03-15T00:00:00Z","scopus_import":1,"day":"15","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2010","acknowledgement":"We are very grateful to Nick Barton.","volume":13,"date_created":"2018-12-11T12:07:08Z","date_updated":"2021-01-12T07:54:45Z","author":[{"full_name":"Bridle, Jon","first_name":"Jon","last_name":"Bridle"},{"full_name":"Polechova, Jitka","first_name":"Jitka","last_name":"Polechova","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112"},{"last_name":"Kawata","first_name":"Masakado","full_name":"Kawata, Masakado"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"}],"publist_id":"1987","ec_funded":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1111/j.1461-0248.2010.01442.x","month":"03"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1214/EJP.v15-741","language":[{"iso":"eng"}],"month":"02","year":"2010","department":[{"_id":"NiBa"}],"publisher":"Institute of Mathematical Statistics","publication_status":"published","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"},{"first_name":"Amandine","last_name":"Véber","full_name":"Véber, Amandine"}],"volume":15,"date_updated":"2021-01-12T07:55:34Z","date_created":"2018-12-11T12:07:48Z","publist_id":"1863","file_date_updated":"2020-07-14T12:46:26Z","citation":{"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.","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","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.","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","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.","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."},"publication":"Electronic Journal of Probability","page":"162 - 216","date_published":"2010-02-03T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"03","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"4243","intvolume":" 15","ddc":["576"],"status":"public","title":"A new model for evolution in a spatial continuum","pubrep_id":"369","oa_version":"Published Version","file":[{"checksum":"bab577546dd4e8f882e9a9dd645cd01e","date_created":"2018-12-12T10:15:21Z","date_updated":"2020-07-14T12:46:26Z","file_id":"5140","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":450171,"access_level":"open_access","file_name":"IST-2015-369-v1+1_741-2535-1-PB.pdf"}],"type":"journal_article","issue":"7","abstract":[{"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).","lang":"eng"}]},{"month":"08","language":[{"iso":"eng"}],"doi":"10.1098/rstb.2010.0106","quality_controlled":"1","oa":1,"publist_id":"2450","file_date_updated":"2020-07-14T12:46:15Z","volume":365,"date_updated":"2021-01-12T07:52:07Z","date_created":"2018-12-11T12:05:06Z","author":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"department":[{"_id":"NiBa"}],"publisher":"Royal Society","publication_status":"published","acknowledgement":"Royal Society and Wolfson Foundation for their support\r\nWe would like to thank Brian Charlesworth and Sally Otto for their helpful comments.","year":"2010","has_accepted_license":"1","day":"27","scopus_import":1,"date_published":"2010-08-27T00:00:00Z","page":"2559 - 2569","citation":{"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","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.","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","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.","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 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."},"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","issue":"1552","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."}],"type":"journal_article","file":[{"creator":"system","file_size":250255,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-555-v1+1_RS2009_revised.pdf","checksum":"4d8aade10db030124ab158b622e337e0","date_updated":"2020-07-14T12:46:15Z","date_created":"2018-12-12T10:14:40Z","file_id":"5093","relation":"main_file"}],"oa_version":"Submitted Version","pubrep_id":"555","intvolume":" 365","title":"Genetic linkage and natural selection","ddc":["570"],"status":"public","_id":"3776","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"type":"journal_article","issue":"1547","abstract":[{"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.","lang":"eng"}],"_id":"3773","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 365","status":"public","title":"What role does natural selection play in speciation?","oa_version":"Submitted Version","scopus_import":1,"day":"12","citation":{"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.","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 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.","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","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.","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"},"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","page":"1825 - 1840","date_published":"2010-06-12T00:00:00Z","publist_id":"2455","pmid":1,"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","year":"2010","publisher":"Royal Society","department":[{"_id":"NiBa"}],"publication_status":"published","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"volume":365,"date_updated":"2021-01-12T07:52:06Z","date_created":"2018-12-11T12:05:05Z","month":"06","oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pubmed/20439284"}],"external_id":{"pmid":["20439284"]},"quality_controlled":"1","doi":"10.1098/rstb.2010.0001","language":[{"iso":"eng"}]},{"oa_version":"Submitted Version","intvolume":" 365","title":"Mutation and the evolution of recombination","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3777","issue":"1544","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."}],"type":"journal_article","date_published":"2010-04-27T00:00:00Z","page":"1281 - 1294","citation":{"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.","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.","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","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.","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.","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"},"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","day":"27","scopus_import":1,"volume":365,"date_updated":"2021-01-12T07:52:07Z","date_created":"2018-12-11T12:05:07Z","author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"department":[{"_id":"NiBa"}],"publisher":"Royal Society","publication_status":"published","pmid":1,"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.","year":"2010","publist_id":"2451","language":[{"iso":"eng"}],"doi":"10.1098/rstb.2009.0320","quality_controlled":"1","oa":1,"external_id":{"pmid":["20308104"]},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pubmed/20308104"}],"month":"04"},{"scopus_import":1,"day":"01","page":"414 - 425","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","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.","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","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.","short":"H. Senn, G. Swanson, S. Goodman, N.H. Barton, J. Pemberton, Journal of Animal Ecology 79 (2010) 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.","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."},"publication":"Journal of Animal Ecology","date_published":"2010-03-01T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"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.","lang":"eng"}],"intvolume":" 79","title":"Phenotypic correlates of hybridisation between red and sika deer (genus Cervus)","status":"public","_id":"3774","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"None","month":"03","quality_controlled":"1","external_id":{"pmid":["20002231"]},"language":[{"iso":"eng"}],"doi":"10.1111/j.1365-2656.2009.01633.x","publist_id":"2453","department":[{"_id":"NiBa"}],"publisher":"Wiley-Blackwell","publication_status":"published","pmid":1,"year":"2010","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.","volume":79,"date_created":"2018-12-11T12:05:06Z","date_updated":"2021-01-12T07:52:06Z","author":[{"full_name":"Senn, Helen","last_name":"Senn","first_name":"Helen"},{"full_name":"Swanson, Graeme","first_name":"Graeme","last_name":"Swanson"},{"full_name":"Goodman, Simon","first_name":"Simon","last_name":"Goodman"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"last_name":"Pemberton","first_name":"Josephine","full_name":"Pemberton, Josephine"}]},{"date_published":"2010-06-17T00:00:00Z","citation":{"apa":"Barton, N. H. (2010). Understanding adaptation in large populations. PLoS Genetics. Public Library of Science. 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.","ama":"Barton NH. Understanding adaptation in large populations. PLoS Genetics. 2010;6(6). doi: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.","short":"N.H. Barton, PLoS Genetics 6 (2010).","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."},"publication":"PLoS Genetics","has_accepted_license":"1","day":"17","scopus_import":1,"file":[{"content_type":"application/pdf","file_size":349965,"creator":"system","access_level":"open_access","file_name":"IST-2016-524-v1+1_journal.pgen.1000987.PDF","checksum":"5c14de2680ab483cb835096c99ee734d","date_updated":"2020-07-14T12:46:15Z","date_created":"2018-12-12T10:14:24Z","relation":"main_file","file_id":"5075"}],"oa_version":"Published Version","pubrep_id":"524","intvolume":" 6","ddc":["570","576"],"title":"Understanding adaptation in large populations","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3772","issue":"6","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1000987","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"06","volume":6,"date_updated":"2021-01-12T07:52:05Z","date_created":"2018-12-11T12:05:05Z","author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2010","publist_id":"2454","file_date_updated":"2020-07-14T12:46:15Z","article_number":"e1000987"},{"month":"09","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://eprints.soton.ac.uk/68731/","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.3989/scimar.2010.74n3465","publist_id":"2440","publisher":"Consejo Superior de Investigaciones Científicas","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2010","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","volume":74,"date_updated":"2021-01-12T07:52:11Z","date_created":"2018-12-11T12:05:10Z","author":[{"full_name":"Palero, Ferran","orcid":"0000-0002-0343-8329","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","last_name":"Palero","first_name":"Ferran"},{"last_name":"Hall","first_name":"Sally","full_name":"Hall, Sally"},{"full_name":"Clark, Paul","first_name":"Paul","last_name":"Clark"},{"last_name":"Johnston","first_name":"David","full_name":"Johnston, David"},{"full_name":"Mackenzie Dodds, Jackie","last_name":"Mackenzie Dodds","first_name":"Jackie"},{"last_name":"Thatje","first_name":"Sven","full_name":"Thatje, Sven"}],"scopus_import":1,"day":"01","page":"465 - 470","citation":{"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","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.","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","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.","short":"F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, S. Thatje, Scientia Marina 74 (2010) 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."},"publication":"Scientia Marina","date_published":"2010-09-01T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"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.","lang":"eng"}],"intvolume":" 74","status":"public","title":"DNA extraction from formalin-fixed tissue: new light from the deep sea","_id":"3787","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version"},{"oa_version":"None","volume":2403,"date_created":"2018-12-11T12:05:10Z","date_updated":"2022-03-21T08:22:58Z","author":[{"last_name":"Palero","first_name":"Ferran","orcid":"0000-0002-0343-8329","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","full_name":"Palero, Ferran"},{"full_name":"Guerao, Guillermo","last_name":"Guerao","first_name":"Guillermo"},{"last_name":"Clark","first_name":"Paul","full_name":"Clark, Paul"},{"last_name":"Abello","first_name":"Pere","full_name":"Abello, Pere"}],"intvolume":" 2403","department":[{"_id":"NiBa"}],"publisher":"Magnolia Press","title":"Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description","publication_status":"published","status":"public","year":"2010","_id":"3786","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"2441","issue":"1","abstract":[{"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.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.11646/zootaxa.2403.1.4","date_published":"2010-03-19T00:00:00Z","page":"42 - 58","quality_controlled":"1","article_type":"original","citation":{"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.","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","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.","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","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.","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."},"publication":"Zootaxa","article_processing_charge":"No","day":"19","month":"03","scopus_import":"1"},{"type":"journal_article","abstract":[{"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.","lang":"eng"}],"publist_id":"2780","issue":"9","year":"2010","_id":"474","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","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.","publication_status":"published","title":"A new model for extinction and recolonization in two dimensions: Quantifying phylogeography","status":"public","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"intvolume":" 64","author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"last_name":"Kelleher","first_name":"Jerome","full_name":"Kelleher, Jerome"},{"first_name":"Alison","last_name":"Etheridge","full_name":"Etheridge, Alison"}],"date_created":"2018-12-11T11:46:40Z","date_updated":"2021-01-12T08:00:52Z","oa_version":"None","volume":64,"scopus_import":1,"month":"09","day":"01","publication":"Evolution","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","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.","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.","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","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.","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."},"quality_controlled":"1","page":"2701 - 2715","doi":"10.1111/j.1558-5646.2010.01019.x","date_published":"2010-09-01T00:00:00Z","language":[{"iso":"eng"}]},{"day":"20","has_accepted_license":"1","scopus_import":1,"date_published":"2010-07-20T00:00:00Z","publication":"PLoS Biology","citation":{"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","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.","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","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.","short":"U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, PLoS Biology 8 (2010).","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."},"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."}],"issue":"7","type":"journal_article","pubrep_id":"366","oa_version":"Published Version","file":[{"file_size":1089530,"content_type":"application/pdf","creator":"system","file_name":"IST-2015-366-v1+1_journal.pbio.1000429.pdf","access_level":"open_access","date_created":"2018-12-12T10:14:11Z","date_updated":"2020-07-14T12:46:15Z","checksum":"ee1ce2fb283a6b4127544ae532d0b4a1","relation":"main_file","file_id":"5060"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3779","ddc":["576"],"status":"public","title":"Cryptic variation between species and the basis of hybrid performance","intvolume":" 8","month":"07","doi":"10.1371/journal.pbio.1000429","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","file_date_updated":"2020-07-14T12:46:15Z","publist_id":"2448","article_number":"e1000429","author":[{"last_name":"Rosas","first_name":"Ulises","full_name":"Rosas, Ulises"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Copsey, Lucy","first_name":"Lucy","last_name":"Copsey"},{"last_name":"Barbier De Reuille","first_name":"Pierre","full_name":"Barbier De Reuille, Pierre"},{"full_name":"Coen, Enrico","last_name":"Coen","first_name":"Enrico"}],"related_material":{"record":[{"id":"9764","relation":"research_data","status":"public"}]},"date_created":"2018-12-11T12:05:07Z","date_updated":"2023-02-23T14:07:34Z","volume":8,"year":"2010","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","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science"},{"type":"research_data_reference","author":[{"full_name":"Rosas, Ulises","last_name":"Rosas","first_name":"Ulises"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Copsey, Lucy","first_name":"Lucy","last_name":"Copsey"},{"first_name":"Pierre","last_name":"Barbier De Reuille","full_name":"Barbier De Reuille, Pierre"},{"first_name":"Enrico","last_name":"Coen","full_name":"Coen, Enrico"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"3779"}]},"date_updated":"2023-02-23T11:42:17Z","date_created":"2021-08-02T09:45:39Z","oa_version":"Published Version","_id":"9764","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2010","status":"public","title":"Heterosis and the drift load","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","day":"20","month":"07","article_processing_charge":"No","doi":"10.1371/journal.pbio.1000429.s003","date_published":"2010-07-20T00:00:00Z","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","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.","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","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.","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).","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."}},{"publist_id":"2442","issue":"4","abstract":[{"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.","lang":"eng"}],"type":"journal_article","volume":30,"oa_version":"None","date_created":"2018-12-11T12:05:09Z","date_updated":"2023-10-16T09:51:05Z","author":[{"full_name":"Palero, Ferran","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0343-8329","first_name":"Ferran","last_name":"Palero"},{"full_name":"Abello, Pere","last_name":"Abello","first_name":"Pere"},{"full_name":"Macpherson, E.","last_name":"Macpherson","first_name":"E."},{"full_name":"Matthee, C.","last_name":"Matthee","first_name":"C."},{"full_name":"Pascual, Marta","first_name":"Marta","last_name":"Pascual"}],"department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","intvolume":" 30","status":"public","publication_status":"published","title":"Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3785","year":"2010","publication_identifier":{"issn":["0278-0372"],"eissn":["1937-240X"]},"article_processing_charge":"No","day":"01","month":"10","scopus_import":"1","language":[{"iso":"eng"}],"date_published":"2010-10-01T00:00:00Z","doi":"10.1651/09-3192.1","page":"658 - 663","quality_controlled":"1","citation":{"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.","short":"F. Palero, P. Abello, E. Macpherson, C. Matthee, M. Pascual, Journal of Crustacean Biology 30 (2010) 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.","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.","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","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.","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"},"publication":"Journal of Crustacean Biology"},{"type":"journal_article","issue":"8","abstract":[{"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.","lang":"eng"}],"intvolume":" 22","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","status":"public","ddc":["570"],"_id":"3780","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"f70c15c6ab9306121d4153a3be0d2346","date_created":"2019-02-22T09:21:44Z","date_updated":"2020-07-14T12:46:15Z","file_id":"6044","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":2583812,"access_level":"open_access","file_name":"Davison_JEB_v31_2009.pdf"}],"oa_version":"Submitted Version","pubrep_id":"553","scopus_import":1,"has_accepted_license":"1","day":"01","page":"1624 - 1635","citation":{"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.","short":"A. Davison, N.H. Barton, B. Clarke, Journal of Evolutionary Biology 22 (2009) 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.","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","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.","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"},"publication":"Journal of Evolutionary Biology","date_published":"2009-08-01T00:00:00Z","publist_id":"2447","file_date_updated":"2020-07-14T12:46:15Z","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","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.","year":"2009","volume":22,"date_updated":"2021-01-12T07:52:09Z","date_created":"2018-12-11T12:05:08Z","author":[{"last_name":"Davison","first_name":"Angus","full_name":"Davison, Angus"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"full_name":"Clarke, Bryan","last_name":"Clarke","first_name":"Bryan"}],"month":"08","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/j.1420-9101.2009.01770.x"},{"oa_version":"Published Version","pubrep_id":"552","intvolume":" 174","ddc":["570"],"title":"Species' range: Adaptation in space and time","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"4136","issue":"5","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."}],"type":"journal_article","date_published":"2009-11-05T00:00:00Z","page":"E186 - E204","article_type":"original","citation":{"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.","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.","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","ista":"Polechova J, Barton NH, Marion G. 2009. Species’ range: Adaptation in space and time. American Naturalist. 174(5), E186–E204.","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.","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"},"publication":"American Naturalist","article_processing_charge":"No","day":"05","scopus_import":1,"volume":174,"date_created":"2018-12-11T12:07:09Z","date_updated":"2021-01-12T07:54:46Z","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1086/659642"}]},"author":[{"full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","first_name":"Jitka"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"},{"last_name":"Marion","first_name":"Glenn","full_name":"Marion, Glenn"}],"department":[{"_id":"NiBa"}],"publisher":"University of Chicago Press","publication_status":"published","pmid":1,"year":"2009","publist_id":"1986","language":[{"iso":"eng"}],"doi":"10.1086/605958","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.1086/605958"}],"oa":1,"external_id":{"pmid":[" 19788353"]},"month":"11"},{"publist_id":"1866","file_date_updated":"2020-07-14T12:46:25Z","author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"De Cara, Maria","last_name":"De Cara","first_name":"Maria"}],"volume":63,"date_updated":"2021-01-12T07:55:33Z","date_created":"2018-12-11T12:07:48Z","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.","year":"2009","publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","month":"05","doi":"10.1111/j.1558-5646.2009.00622.x","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","issue":"5","abstract":[{"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.","lang":"eng"}],"type":"journal_article","pubrep_id":"551","oa_version":"Submitted Version","file":[{"file_name":"IST-2016-551-v1+1_BartonDeCaraRevNew.pdf","access_level":"open_access","file_size":720913,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4903","date_created":"2018-12-12T10:11:46Z","date_updated":"2020-07-14T12:46:25Z","checksum":"1920d2e25ef335833764256c1a47bbfb"},{"creator":"system","file_size":290160,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-551-v1+2_BartonDeCaraRevNewSI.pdf","checksum":"c1c51bbc10d4f328fc96fc5b0e5dc25d","date_created":"2018-12-12T10:11:47Z","date_updated":"2020-07-14T12:46:25Z","file_id":"4904","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"4242","intvolume":" 63","title":"The evolution of strong reproductive isolation","status":"public","ddc":["570"],"has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2009-05-01T00:00:00Z","citation":{"short":"N.H. Barton, M. De Cara, Evolution; International Journal of Organic Evolution 63 (2009) 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.","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.","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","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."},"publication":"Evolution; International Journal of Organic Evolution","page":"1171 - 1190"},{"publication_status":"published","status":"public","title":"Why sex and recombination? ","intvolume":" 74","department":[{"_id":"NiBa"}],"publisher":"Cold Spring Harbor Laboratory Press","year":"2009","_id":"3675","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Royal Society and the Engineering and Physical Sciences for support (GR/ T11753/01)","date_updated":"2021-01-12T07:45:04Z","date_created":"2018-12-11T12:04:33Z","oa_version":"None","volume":74,"author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"type":"book_chapter","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."}],"publist_id":"2708","quality_controlled":"1","page":"187 - 195","publication":"Cold Spring Harbor Symposia on Quantitative Biology","citation":{"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.","short":"N.H. Barton, in:, Cold Spring Harbor Symposia on Quantitative Biology, Cold Spring Harbor Laboratory Press, 2009, pp. 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.","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","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.","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"},"language":[{"iso":"eng"}],"doi":"10.1101/sqb.2009.74.030","date_published":"2009-11-10T00:00:00Z","scopus_import":1,"day":"10","month":"11"},{"publist_id":"2452","year":"2009","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.","publication_status":"published","publisher":"Elsevier","department":[{"_id":"NiBa"}],"author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Coe, Jason","last_name":"Coe","first_name":"Jason"}],"date_created":"2018-12-11T12:05:06Z","date_updated":"2021-01-12T07:52:06Z","volume":259,"month":"07","oa":1,"main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-00554594/document","open_access":"1"}],"quality_controlled":"1","doi":"10.1016/j.jtbi.2009.03.019","language":[{"iso":"eng"}],"type":"journal_article","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."}],"issue":"2","_id":"3775","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"On the application of statistical physics to evolutionary biology","intvolume":" 259","oa_version":"Submitted Version","scopus_import":1,"day":"21","publication":"Journal of Theoretical Biology","citation":{"ista":"Barton NH, Coe J. 2009. On the application of statistical physics to evolutionary biology. Journal of Theoretical Biology. 259(2), 317–324.","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","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.","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","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.","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."},"page":"317 - 324","date_published":"2009-07-21T00:00:00Z"},{"month":"03","day":"01","scopus_import":1,"date_published":"2009-03-01T00:00:00Z","doi":"10.1534/genetics.108.099309","language":[{"iso":"eng"}],"publication":"Genetics","citation":{"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.","short":"N.H. Barton, H. De Vladar, Genetics 181 (2009) 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.","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","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.","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"},"quality_controlled":"1","page":"997 - 1011","abstract":[{"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.","lang":"eng"}],"issue":"3","publist_id":"1882","type":"journal_article","author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"De Vladar","first_name":"Harold","full_name":"De Vladar, Harold"}],"date_updated":"2021-01-12T07:55:29Z","date_created":"2018-12-11T12:07:44Z","oa_version":"None","volume":181,"_id":"4231","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.” ","year":"2009","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Statistical mechanics and the evolution of polygenic quantitative traits","intvolume":" 181","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America"},{"article_processing_charge":"No","month":"10","day":"29","scopus_import":"1","language":[{"iso":"eng"}],"doi":"10.1017/S0016672308009683","date_published":"2008-10-29T00:00:00Z","page":"475 - 477","quality_controlled":"1","citation":{"short":"N.H. Barton, Genetics Research 89 (2008) 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.","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.","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","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.","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","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."},"publication":"Genetics Research","issue":"5-6","publist_id":"7302","type":"journal_article","oa_version":"None","volume":89,"date_created":"2018-12-11T11:46:55Z","date_updated":"2024-02-14T09:51:09Z","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"publisher":"Cambridge University Press","department":[{"_id":"NiBa"}],"intvolume":" 89","publication_status":"published","status":"public","title":"Identity and coalescence in structured populations: A commentary on 'Inbreeding coefficients and coalescence times' by Montgomery Slatkin","_id":"517","year":"2008","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"}]