--- _id: '1241' abstract: - lang: eng text: 'How likely is it that a population escapes extinction through adaptive evolution? The answer to this question is of great relevance in conservation biology, where we aim at species’ rescue and the maintenance of biodiversity, and in agriculture and medicine, where we seek to hamper the emergence of pesticide or drug resistance. By reshuffling the genome, recombination has two antagonistic effects on the probability of evolutionary rescue: It generates and it breaks up favorable gene combinations. Which of the two effects prevails depends on the fitness effects of mutations and on the impact of stochasticity on the allele frequencies. In this article, we analyze a mathematical model for rescue after a sudden environmental change when adaptation is contingent on mutations at two loci. The analysis reveals a complex nonlinear dependence of population survival on recombination. We moreover find that, counterintuitively, a fast eradication of the wild type can promote rescue in the presence of recombination. The model also shows that two-step rescue is not unlikely to happen and can even be more likely than single-step rescue (where adaptation relies on a single mutation), depending on the circumstances.' acknowledgement: This work was made possible by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with the Austrian Commission for the United Nations Educational, Scientific, and Cultural Organization and the Austrian Academy of Sciences with financial support from the Federal Ministry for Science and Research Austria) and European Research Council grant 250152 (to Nick Barton). author: - first_name: Hildegard full_name: Uecker, Hildegard id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87 last_name: Uecker orcid: 0000-0001-9435-2813 - first_name: Joachim full_name: Hermisson, Joachim last_name: Hermisson citation: ama: Uecker H, Hermisson J. The role of recombination in evolutionary rescue. Genetics. 2016;202(2):721-732. doi:10.1534/genetics.115.180299 apa: Uecker, H., & Hermisson, J. (2016). The role of recombination in evolutionary rescue. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.180299 chicago: Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.180299. ieee: H. Uecker and J. Hermisson, “The role of recombination in evolutionary rescue,” Genetics, vol. 202, no. 2. Genetics Society of America, pp. 721–732, 2016. ista: Uecker H, Hermisson J. 2016. The role of recombination in evolutionary rescue. Genetics. 202(2), 721–732. mla: Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” Genetics, vol. 202, no. 2, Genetics Society of America, 2016, pp. 721–32, doi:10.1534/genetics.115.180299. short: H. Uecker, J. Hermisson, Genetics 202 (2016) 721–732. date_created: 2018-12-11T11:50:54Z date_published: 2016-02-01T00:00:00Z date_updated: 2023-02-21T10:24:19Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.115.180299 ec_funded: 1 intvolume: ' 202' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://biorxiv.org/content/early/2015/07/06/022020.abstract month: '02' oa: 1 oa_version: Preprint page: 721 - 732 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 25B67606-B435-11E9-9278-68D0E5697425 name: L'OREAL Fellowship publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '6091' quality_controlled: '1' scopus_import: 1 status: public title: The role of recombination in evolutionary rescue type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 202 year: '2016' ... --- _id: '1349' abstract: - lang: eng text: Crossing fitness valleys is one of the major obstacles to function optimization. In this paper we investigate how the structure of the fitness valley, namely its depth d and length ℓ, influence the runtime of different strategies for crossing these valleys. We present a runtime comparison between the (1+1) EA and two non-elitist nature-inspired algorithms, Strong Selection Weak Mutation (SSWM) and the Metropolis algorithm. While the (1+1) EA has to jump across the valley to a point of higher fitness because it does not accept decreasing moves, the non-elitist algorithms may cross the valley by accepting worsening moves. We show that while the runtime of the (1+1) EA algorithm depends critically on the length of the valley, the runtimes of the non-elitist algorithms depend crucially only on the depth of the valley. In particular, the expected runtime of both SSWM and Metropolis is polynomial in ℓ and exponential in d while the (1+1) EA is efficient only for valleys of small length. Moreover, we show that both SSWM and Metropolis can also efficiently optimize a rugged function consisting of consecutive valleys. author: - first_name: Pietro full_name: Oliveto, Pietro last_name: Oliveto - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Jorge full_name: Heredia, Jorge last_name: Heredia - first_name: Dirk full_name: Sudholt, Dirk last_name: Sudholt - first_name: Barbora full_name: Trubenova, Barbora id: 42302D54-F248-11E8-B48F-1D18A9856A87 last_name: Trubenova orcid: 0000-0002-6873-2967 citation: ama: 'Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. When non-elitism outperforms elitism for crossing fitness valleys. In: Proceedings of the Genetic and Evolutionary Computation Conference 2016 . ACM; 2016:1163-1170. doi:10.1145/2908812.2908909' apa: 'Oliveto, P., Paixao, T., Heredia, J., Sudholt, D., & Trubenova, B. (2016). When non-elitism outperforms elitism for crossing fitness valleys. In Proceedings of the Genetic and Evolutionary Computation Conference 2016 (pp. 1163–1170). Denver, CO, USA: ACM. https://doi.org/10.1145/2908812.2908909' chicago: Oliveto, Pietro, Tiago Paixao, Jorge Heredia, Dirk Sudholt, and Barbora Trubenova. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” In Proceedings of the Genetic and Evolutionary Computation Conference 2016 , 1163–70. ACM, 2016. https://doi.org/10.1145/2908812.2908909. ieee: P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, and B. Trubenova, “When non-elitism outperforms elitism for crossing fitness valleys,” in Proceedings of the Genetic and Evolutionary Computation Conference 2016 , Denver, CO, USA, 2016, pp. 1163–1170. ista: 'Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. 2016. When non-elitism outperforms elitism for crossing fitness valleys. Proceedings of the Genetic and Evolutionary Computation Conference 2016 . GECCO: Genetic and evolutionary computation conference, 1163–1170.' mla: Oliveto, Pietro, et al. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” Proceedings of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–70, doi:10.1145/2908812.2908909. short: P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, B. Trubenova, in:, Proceedings of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–1170. conference: end_date: 2016-07-24 location: Denver, CO, USA name: 'GECCO: Genetic and evolutionary computation conference' start_date: 2016-07-20 date_created: 2018-12-11T11:51:31Z date_published: 2016-07-20T00:00:00Z date_updated: 2021-01-12T06:50:03Z day: '20' ddc: - '576' department: - _id: NiBa - _id: CaGu doi: 10.1145/2908812.2908909 ec_funded: 1 file: - access_level: open_access checksum: a1896e39e4113f2711e46b435d5f3e69 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:27Z date_updated: 2020-07-14T12:44:45Z file_id: '5214' file_name: IST-2016-650-v1+1_p1163-oliveto.pdf file_size: 979026 relation: main_file file_date_updated: 2020-07-14T12:44:45Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 1163 - 1170 project: - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation publication: 'Proceedings of the Genetic and Evolutionary Computation Conference 2016 ' publication_status: published publisher: ACM publist_id: '5900' pubrep_id: '650' quality_controlled: '1' scopus_import: 1 status: public title: When non-elitism outperforms elitism for crossing fitness valleys tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2016' ... --- _id: '1359' abstract: - lang: eng text: "The role of gene interactions in the evolutionary process has long\r\nbeen controversial. Although some argue that they are not of\r\nimportance, because most variation is additive, others claim that\r\ntheir effect in the long term can be substantial. Here, we focus on\r\nthe long-term effects of genetic interactions under directional\r\nselection assuming no mutation or dominance, and that epistasis is\r\nsymmetrical overall. We ask by how much the mean of a complex\r\ntrait can be increased by selection and analyze two extreme\r\nregimes, in which either drift or selection dominate the dynamics\r\nof allele frequencies. In both scenarios, epistatic interactions affect\r\nthe long-term response to selection by modulating the additive\r\ngenetic variance. When drift dominates, we extend Robertson\r\n’\r\ns\r\n[Robertson A (1960)\r\nProc R Soc Lond B Biol Sci\r\n153(951):234\r\n−\r\n249]\r\nargument to show that, for any form of epistasis, the total response\r\nof a haploid population is proportional to the initial total genotypic\r\nvariance. In contrast, the total response of a diploid population is\r\nincreased by epistasis, for a given initial genotypic variance. When\r\nselection dominates, we show that the total selection response can\r\nonly be increased by epistasis when s\r\nome initially deleterious alleles\r\nbecome favored as the genetic background changes. We find a sim-\r\nple approximation for this effect and show that, in this regime, it is\r\nthe structure of the genotype - phenotype map that matters and not\r\nthe variance components of the population." article_processing_charge: No article_type: original author: - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Paixao T, Barton NH. The effect of gene interactions on the long-term response to selection. PNAS. 2016;113(16):4422-4427. doi:10.1073/pnas.1518830113 apa: Paixao, T., & Barton, N. H. (2016). The effect of gene interactions on the long-term response to selection. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1518830113 chicago: Paixao, Tiago, and Nicholas H Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” PNAS. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1518830113. ieee: T. Paixao and N. H. Barton, “The effect of gene interactions on the long-term response to selection,” PNAS, vol. 113, no. 16. National Academy of Sciences, pp. 4422–4427, 2016. ista: Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term response to selection. PNAS. 113(16), 4422–4427. mla: Paixao, Tiago, and Nicholas H. Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” PNAS, vol. 113, no. 16, National Academy of Sciences, 2016, pp. 4422–27, doi:10.1073/pnas.1518830113. short: T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427. date_created: 2018-12-11T11:51:34Z date_published: 2016-04-19T00:00:00Z date_updated: 2021-01-12T06:50:08Z day: '19' department: - _id: NiBa - _id: CaGu doi: 10.1073/pnas.1518830113 ec_funded: 1 external_id: pmid: - '27044080' intvolume: ' 113' issue: '16' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843425/ month: '04' oa: 1 oa_version: Published Version page: 4422 - 4427 pmid: 1 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5886' quality_controlled: '1' scopus_import: 1 status: public title: The effect of gene interactions on the long-term response to selection type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 113 year: '2016' ... --- _id: '1356' author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Barton NH. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” Genetics. 2016;202(1):3-4. doi:10.1534/genetics.115.184796 apa: Barton, N. H. (2016). Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.184796 chicago: Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.184796. ieee: N. H. Barton, “Sewall Wright on evolution in Mendelian populations and the ‘Shifting Balance,’” Genetics, vol. 202, no. 1. Genetics Society of America, pp. 3–4, 2016. ista: Barton NH. 2016. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”. Genetics. 202(1), 3–4. mla: Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” Genetics, vol. 202, no. 1, Genetics Society of America, 2016, pp. 3–4, doi:10.1534/genetics.115.184796. short: N.H. Barton, Genetics 202 (2016) 3–4. date_created: 2018-12-11T11:51:33Z date_published: 2016-01-05T00:00:00Z date_updated: 2021-01-12T06:50:07Z day: '05' ddc: - '570' department: - _id: NiBa doi: 10.1534/genetics.115.184796 file: - access_level: open_access checksum: 3562b89c821a4be84edf2b6ebd870cf5 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:26Z date_updated: 2020-07-14T12:44:46Z file_id: '4687' file_name: IST-2017-769-v1+1_SewallWright1931.pdf file_size: 112674 relation: main_file file_date_updated: 2020-07-14T12:44:46Z has_accepted_license: '1' intvolume: ' 202' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 3 - 4 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '5889' pubrep_id: '769' quality_controlled: '1' scopus_import: 1 status: public title: Sewall Wright on evolution in Mendelian populations and the “Shifting Balance” type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 202 year: '2016' ... --- _id: '1357' author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Barton NH. Richard Hudson and Norman Kaplan on the coalescent process. Genetics. 2016;202(3):865-866. doi:10.1534/genetics.116.187542 apa: Barton, N. H. (2016). Richard Hudson and Norman Kaplan on the coalescent process. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.187542 chicago: Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.116.187542. ieee: N. H. Barton, “Richard Hudson and Norman Kaplan on the coalescent process,” Genetics, vol. 202, no. 3. Genetics Society of America, pp. 865–866, 2016. ista: Barton NH. 2016. Richard Hudson and Norman Kaplan on the coalescent process. Genetics. 202(3), 865–866. mla: Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” Genetics, vol. 202, no. 3, Genetics Society of America, 2016, pp. 865–66, doi:10.1534/genetics.116.187542. short: N.H. Barton, Genetics 202 (2016) 865–866. date_created: 2018-12-11T11:51:33Z date_published: 2016-03-01T00:00:00Z date_updated: 2021-01-12T06:50:07Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1534/genetics.116.187542 file: - access_level: open_access checksum: b2174bab2de1d1142900062a150f35c9 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:09Z date_updated: 2020-07-14T12:44:46Z file_id: '5127' file_name: IST-2017-768-v1+1_Hudson-Kaplan-1988.pdf file_size: 130779 relation: main_file file_date_updated: 2020-07-14T12:44:46Z has_accepted_license: '1' intvolume: ' 202' issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 865 - 866 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '5888' pubrep_id: '768' quality_controlled: '1' scopus_import: 1 status: public title: Richard Hudson and Norman Kaplan on the coalescent process type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 202 year: '2016' ... --- _id: '1409' author: - first_name: Richard full_name: Abbott, Richard last_name: Abbott - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Jeffrey full_name: Good, Jeffrey last_name: Good citation: ama: Abbott R, Barton NH, Good J. Genomics of hybridization and its evolutionary consequences. Molecular Ecology. 2016;25(11):2325-2332. doi:10.1111/mec.13685 apa: Abbott, R., Barton, N. H., & Good, J. (2016). Genomics of hybridization and its evolutionary consequences. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.13685 chicago: Abbott, Richard, Nicholas H Barton, and Jeffrey Good. “Genomics of Hybridization and Its Evolutionary Consequences.” Molecular Ecology. Wiley-Blackwell, 2016. https://doi.org/10.1111/mec.13685. ieee: R. Abbott, N. H. Barton, and J. Good, “Genomics of hybridization and its evolutionary consequences,” Molecular Ecology, vol. 25, no. 11. Wiley-Blackwell, pp. 2325–2332, 2016. ista: Abbott R, Barton NH, Good J. 2016. Genomics of hybridization and its evolutionary consequences. Molecular Ecology. 25(11), 2325–2332. mla: Abbott, Richard, et al. “Genomics of Hybridization and Its Evolutionary Consequences.” Molecular Ecology, vol. 25, no. 11, Wiley-Blackwell, 2016, pp. 2325–32, doi:10.1111/mec.13685. short: R. Abbott, N.H. Barton, J. Good, Molecular Ecology 25 (2016) 2325–2332. date_created: 2018-12-11T11:51:51Z date_published: 2016-06-08T00:00:00Z date_updated: 2021-01-12T06:50:33Z day: '08' ddc: - '576' department: - _id: NiBa doi: 10.1111/mec.13685 file: - access_level: open_access checksum: ede7d0b8a471754f71f17e2b20f3135b content_type: application/pdf creator: system date_created: 2018-12-12T10:10:12Z date_updated: 2020-07-14T12:44:53Z file_id: '4797' file_name: IST-2017-772-v1+1_AbbotEtAl2016-3.pdf file_size: 226137 relation: main_file file_date_updated: 2020-07-14T12:44:53Z has_accepted_license: '1' intvolume: ' 25' issue: '11' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 2325 - 2332 publication: Molecular Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '5798' pubrep_id: '772' quality_controlled: '1' scopus_import: 1 status: public title: Genomics of hybridization and its evolutionary consequences type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2016' ... --- _id: '1420' abstract: - lang: eng text: 'Selection, mutation, and random drift affect the dynamics of allele frequencies and consequently of quantitative traits. While the macroscopic dynamics of quantitative traits can be measured, the underlying allele frequencies are typically unobserved. Can we understand how the macroscopic observables evolve without following these microscopic processes? This problem has been studied previously by analogy with statistical mechanics: the allele frequency distribution at each time point is approximated by the stationary form, which maximizes entropy. We explore the limitations of this method when mutation is small (4Nμ < 1) so that populations are typically close to fixation, and we extend the theory in this regime to account for changes in mutation strength. We consider a single diallelic locus either under directional selection or with overdominance and then generalize to multiple unlinked biallelic loci with unequal effects. We find that the maximum-entropy approximation is remarkably accurate, even when mutation and selection change rapidly. ' article_processing_charge: No author: - first_name: Katarína full_name: Bod'ová, Katarína id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87 last_name: Bod'ová orcid: 0000-0002-7214-0171 - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Bodova K, Tkačik G, Barton NH. A general approximation for the dynamics of quantitative traits. Genetics. 2016;202(4):1523-1548. doi:10.1534/genetics.115.184127 apa: Bodova, K., Tkačik, G., & Barton, N. H. (2016). A general approximation for the dynamics of quantitative traits. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.184127 chicago: Bodova, Katarina, Gašper Tkačik, and Nicholas H Barton. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.184127. ieee: K. Bodova, G. Tkačik, and N. H. Barton, “A general approximation for the dynamics of quantitative traits,” Genetics, vol. 202, no. 4. Genetics Society of America, pp. 1523–1548, 2016. ista: Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548. mla: Bodova, Katarina, et al. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics, vol. 202, no. 4, Genetics Society of America, 2016, pp. 1523–48, doi:10.1534/genetics.115.184127. short: K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548. date_created: 2018-12-11T11:51:55Z date_published: 2016-04-06T00:00:00Z date_updated: 2022-08-01T10:49:55Z day: '06' department: - _id: GaTk - _id: NiBa doi: 10.1534/genetics.115.184127 ec_funded: 1 external_id: arxiv: - '1510.08344' intvolume: ' 202' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1510.08344 month: '04' oa: 1 oa_version: Preprint page: 1523 - 1548 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 255008E4-B435-11E9-9278-68D0E5697425 grant_number: RGP0065/2012 name: Information processing and computation in fish groups publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '5787' quality_controlled: '1' scopus_import: '1' status: public title: A general approximation for the dynamics of quantitative traits type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 202 year: '2016' ... --- _id: '1518' abstract: - lang: eng text: The inference of demographic history from genome data is hindered by a lack of efficient computational approaches. In particular, it has proved difficult to exploit the information contained in the distribution of genealogies across the genome. We have previously shown that the generating function (GF) of genealogies can be used to analytically compute likelihoods of demographic models from configurations of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has a simple, recursive form, the size of such likelihood calculations explodes quickly with the number of individuals and applications of this framework have so far been mainly limited to small samples (pairs and triplets) for which the GF can be written by hand. Here we investigate several strategies for exploiting the inherent symmetries of the coalescent. In particular, we show that the GF of genealogies can be decomposed into a set of equivalence classes that allows likelihood calculations from nontrivial samples. Using this strategy, we automated blockwise likelihood calculations for a general set of demographic scenarios in Mathematica. These histories may involve population size changes, continuous migration, discrete divergence, and admixture between multiple populations. To give a concrete example, we calculate the likelihood for a model of isolation with migration (IM), assuming two diploid samples without phase and outgroup information. We demonstrate the new inference scheme with an analysis of two individual butterfly genomes from the sister species Heliconius melpomene rosina and H. cydno. acknowledgement: "We thank Lynsey Bunnefeld for discussions throughout the project and Joshua Schraiber and one anonymous reviewer\r\nfor constructive comments on an earlier version of this manuscript. This work was supported by funding from the\r\nUnited Kingdom Natural Environment Research Council (to K.L.) (NE/I020288/1) and a grant from the European\r\nResearch Council (250152) (to N.H.B.)." article_processing_charge: No article_type: original author: - first_name: Konrad full_name: Lohse, Konrad last_name: Lohse - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Simon full_name: Martin, Simon last_name: Martin - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Lohse K, Chmelik M, Martin S, Barton NH. Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. 2016;202(2):775-786. doi:10.1534/genetics.115.183814 apa: Lohse, K., Chmelik, M., Martin, S., & Barton, N. H. (2016). Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.183814 chicago: Lohse, Konrad, Martin Chmelik, Simon Martin, and Nicholas H Barton. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.183814. ieee: K. Lohse, M. Chmelik, S. Martin, and N. H. Barton, “Efficient strategies for calculating blockwise likelihoods under the coalescent,” Genetics, vol. 202, no. 2. Genetics Society of America, pp. 775–786, 2016. ista: Lohse K, Chmelik M, Martin S, Barton NH. 2016. Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. 202(2), 775–786. mla: Lohse, Konrad, et al. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” Genetics, vol. 202, no. 2, Genetics Society of America, 2016, pp. 775–86, doi:10.1534/genetics.115.183814. short: K. Lohse, M. Chmelik, S. Martin, N.H. Barton, Genetics 202 (2016) 775–786. date_created: 2018-12-11T11:52:29Z date_published: 2016-02-01T00:00:00Z date_updated: 2022-05-24T09:16:22Z day: '01' ddc: - '570' department: - _id: KrCh - _id: NiBa doi: 10.1534/genetics.115.183814 ec_funded: 1 external_id: pmid: - '26715666' file: - access_level: open_access checksum: 41c9b5d72e7fe4624dd22dfe622337d5 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:51Z date_updated: 2020-07-14T12:45:00Z file_id: '5241' file_name: IST-2016-561-v1+1_Lohse_et_al_Genetics_2015.pdf file_size: 957466 relation: main_file file_date_updated: 2020-07-14T12:45:00Z has_accepted_license: '1' intvolume: ' 202' issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Preprint page: 775 - 786 pmid: 1 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '5658' pubrep_id: '561' quality_controlled: '1' scopus_import: '1' status: public title: Efficient strategies for calculating blockwise likelihoods under the coalescent type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 202 year: '2016' ... --- _id: '1631' abstract: - lang: eng text: 'Ancestral processes are fundamental to modern population genetics and spatial structure has been the subject of intense interest for many years. Despite this interest, almost nothing is known about the distribution of the locations of pedigree or genetic ancestors. Using both spatially continuous and stepping-stone models, we show that the distribution of pedigree ancestors approaches a travelling wave, for which we develop two alternative approximations. The speed and width of the wave are sensitive to the local details of the model. After a short time, genetic ancestors spread far more slowly than pedigree ancestors, ultimately diffusing out with radius ## rather than spreading at constant speed. In contrast to the wave of pedigree ancestors, the spread of genetic ancestry is insensitive to the local details of the models.' author: - first_name: Jerome full_name: Kelleher, Jerome last_name: Kelleher - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge - first_name: Amandine full_name: Véber, Amandine last_name: Véber - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Kelleher J, Etheridge A, Véber A, Barton NH. Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. 2016;108:1-12. doi:10.1016/j.tpb.2015.10.008 apa: Kelleher, J., Etheridge, A., Véber, A., & Barton, N. H. (2016). Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2015.10.008 chicago: Kelleher, Jerome, Alison Etheridge, Amandine Véber, and Nicholas H Barton. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” Theoretical Population Biology. Academic Press, 2016. https://doi.org/10.1016/j.tpb.2015.10.008. ieee: J. Kelleher, A. Etheridge, A. Véber, and N. H. Barton, “Spread of pedigree versus genetic ancestry in spatially distributed populations,” Theoretical Population Biology, vol. 108. Academic Press, pp. 1–12, 2016. ista: Kelleher J, Etheridge A, Véber A, Barton NH. 2016. Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. 108, 1–12. mla: Kelleher, Jerome, et al. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” Theoretical Population Biology, vol. 108, Academic Press, 2016, pp. 1–12, doi:10.1016/j.tpb.2015.10.008. short: J. Kelleher, A. Etheridge, A. Véber, N.H. Barton, Theoretical Population Biology 108 (2016) 1–12. date_created: 2018-12-11T11:53:08Z date_published: 2016-04-01T00:00:00Z date_updated: 2021-01-12T06:52:07Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1016/j.tpb.2015.10.008 ec_funded: 1 file: - access_level: open_access checksum: 6a65ba187994d4ad86c1c509e0ff482a content_type: application/pdf creator: system date_created: 2018-12-12T10:11:12Z date_updated: 2020-07-14T12:45:07Z file_id: '4865' file_name: IST-2016-465-v1+1_1-s2.0-S0040580915001094-main.pdf file_size: 1684043 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 108' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1 - 12 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Theoretical Population Biology publication_status: published publisher: Academic Press publist_id: '5524' pubrep_id: '465' quality_controlled: '1' scopus_import: 1 status: public title: Spread of pedigree versus genetic ancestry in spatially distributed populations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 108 year: '2016' ... --- _id: '1158' abstract: - lang: eng text: Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids—the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate "grey zone" of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation. acknowledgement: "European Research Council (ERC) https://erc.europa.eu/ (grant number ERC grant 232971). PopPhyl project. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/ (grant number ANR-12-BSV7- 0011). HYSEA project.\r\nWe thank Aude Darracq, Vincent Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch) Center for high-performance computing of the SIB Swiss Institute of Bioinformatics and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité." article_number: e2000234 author: - first_name: Camille full_name: Roux, Camille last_name: Roux - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Jonathan full_name: Romiguier, Jonathan last_name: Romiguier - first_name: Youann full_name: Anciaux, Youann last_name: Anciaux - first_name: Nicolas full_name: Galtier, Nicolas last_name: Galtier - first_name: Nicolas full_name: Bierne, Nicolas last_name: Bierne citation: ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 2016;14(12). doi:10.1371/journal.pbio.2000234 apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne, N. (2016). Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234 chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” PLoS Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234. ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Shedding light on the grey zone of speciation along a continuum of genomic divergence,” PLoS Biology, vol. 14, no. 12. Public Library of Science, 2016. ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 14(12), e2000234. mla: Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” PLoS Biology, vol. 14, no. 12, e2000234, Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234. short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS Biology 14 (2016). date_created: 2018-12-11T11:50:28Z date_published: 2016-12-27T00:00:00Z date_updated: 2023-02-23T14:11:16Z day: '27' ddc: - '576' department: - _id: BeVi - _id: NiBa doi: 10.1371/journal.pbio.2000234 file: - access_level: open_access checksum: 2bab63b068a9840efd532b9ae583f9bb content_type: application/pdf creator: system date_created: 2018-12-12T10:15:42Z date_updated: 2020-07-14T12:44:36Z file_id: '5164' file_name: IST-2017-742-v1+1_journal.pbio.2000234.pdf file_size: 2494348 relation: main_file file_date_updated: 2020-07-14T12:44:36Z has_accepted_license: '1' intvolume: ' 14' issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: PLoS Biology publication_status: published publisher: Public Library of Science publist_id: '6200' pubrep_id: '742' quality_controlled: '1' related_material: record: - id: '9862' relation: research_data status: public - id: '9863' relation: research_data status: public scopus_import: 1 status: public title: Shedding light on the grey zone of speciation along a continuum of genomic divergence tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2016' ... --- _id: '9862' article_processing_charge: No author: - first_name: Camille full_name: Roux, Camille last_name: Roux - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Jonathan full_name: Romiguier, Jonathan last_name: Romiguier - first_name: Youann full_name: Anciaux, Youann last_name: Anciaux - first_name: Nicolas full_name: Galtier, Nicolas last_name: Galtier - first_name: Nicolas full_name: Bierne, Nicolas last_name: Bierne citation: ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Simulation study to test the robustness of ABC in face of recent times of divergence. 2016. doi:10.1371/journal.pbio.2000234.s016 apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne, N. (2016). Simulation study to test the robustness of ABC in face of recent times of divergence. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s016 chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.s016. ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Simulation study to test the robustness of ABC in face of recent times of divergence.” Public Library of Science, 2016. ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Simulation study to test the robustness of ABC in face of recent times of divergence, Public Library of Science, 10.1371/journal.pbio.2000234.s016. mla: Roux, Camille, et al. Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s016. short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016). date_created: 2021-08-10T08:20:17Z date_updated: 2023-02-21T16:21:20Z day: '27' department: - _id: BeVi - _id: NiBa doi: 10.1371/journal.pbio.2000234.s016 month: '12' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1158' relation: used_in_publication status: public status: public title: Simulation study to test the robustness of ABC in face of recent times of divergence type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2016' ... --- _id: '9863' article_processing_charge: No author: - first_name: Camille full_name: Roux, Camille last_name: Roux - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Jonathan full_name: Romiguier, Jonathan last_name: Romiguier - first_name: Youann full_name: Anciaux, Youann last_name: Anciaux - first_name: Nicolas full_name: Galtier, Nicolas last_name: Galtier - first_name: Nicolas full_name: Bierne, Nicolas last_name: Bierne citation: ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions of surveyed individuals, geographic locations and summary statistics. 2016. doi:10.1371/journal.pbio.2000234.s017 apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne, N. (2016). Accessions of surveyed individuals, geographic locations and summary statistics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s017 chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.s017. ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Accessions of surveyed individuals, geographic locations and summary statistics.” Public Library of Science, 2016. ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Accessions of surveyed individuals, geographic locations and summary statistics, Public Library of Science, 10.1371/journal.pbio.2000234.s017. mla: Roux, Camille, et al. Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s017. short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016). date_created: 2021-08-10T08:22:52Z date_updated: 2023-02-21T16:21:20Z day: '27' department: - _id: BeVi - _id: NiBa doi: 10.1371/journal.pbio.2000234.s017 month: '12' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1158' relation: used_in_publication status: public status: public title: Accessions of surveyed individuals, geographic locations and summary statistics type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2016' ... --- _id: '1125' abstract: - lang: eng text: "Natural environments are never constant but subject to spatial and temporal change on\r\nall scales, increasingly so due to human activity. Hence, it is crucial to understand the\r\nimpact of environmental variation on evolutionary processes. In this thesis, I present\r\nthree topics that share the common theme of environmental variation, yet illustrate its\r\neffect from different perspectives.\r\nFirst, I show how a temporally fluctuating environment gives rise to second-order\r\nselection on a modifier for stress-induced mutagenesis. Without fluctuations, when\r\npopulations are adapted to their environment, mutation rates are minimized. I argue\r\nthat a stress-induced mutator mechanism may only be maintained if the population is\r\nrepeatedly subjected to diverse environmental challenges, and I outline implications of\r\nthe presented results to antibiotic treatment strategies.\r\nSecond, I discuss my work on the evolution of dispersal. Besides reproducing\r\nknown results about the effect of heterogeneous habitats on dispersal, it identifies\r\nspatial changes in dispersal type frequencies as a source for selection for increased\r\npropensities to disperse. This concept contains effects of relatedness that are known\r\nto promote dispersal, and I explain how it identifies other forces selecting for dispersal\r\nand puts them on a common scale.\r\nThird, I analyse genetic variances of phenotypic traits under multivariate stabilizing\r\nselection. For the case of constant environments, I generalize known formulae of\r\nequilibrium variances to multiple traits and discuss how the genetic variance of a focal\r\ntrait is influenced by selection on background traits. I conclude by presenting ideas and\r\npreliminary work aiming at including environmental fluctuations in the form of moving\r\ntrait optima into the model." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak orcid: 0000-0002-2519-824X citation: ama: Novak S. Evolutionary proccesses in variable emvironments. 2016. apa: Novak, S. (2016). Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria. chicago: Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute of Science and Technology Austria, 2016. ieee: S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of Science and Technology Austria, 2016. ista: Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria. mla: Novak, Sebastian. Evolutionary Proccesses in Variable Emvironments. Institute of Science and Technology Austria, 2016. short: S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of Science and Technology Austria, 2016. date_created: 2018-12-11T11:50:17Z date_published: 2016-07-01T00:00:00Z date_updated: 2023-09-07T11:55:53Z day: '01' ddc: - '576' degree_awarded: PhD department: - _id: NiBa file: - access_level: closed checksum: 81dcc838dfcf7aa0b1a27ecf4fe2da4e content_type: application/pdf creator: dernst date_created: 2019-08-13T09:01:00Z date_updated: 2019-08-13T09:01:00Z file_id: '6811' file_name: Novak_thesis.pdf file_size: 3564901 relation: main_file - access_level: open_access checksum: 30808d2f7ca920e09f63a95cdc49bffd content_type: application/pdf creator: dernst date_created: 2021-02-22T13:42:47Z date_updated: 2021-02-22T13:42:47Z file_id: '9186' file_name: 2016_Novak_Thesis.pdf file_size: 2814384 relation: main_file success: 1 file_date_updated: 2021-02-22T13:42:47Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '124' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6235' related_material: record: - id: '2023' relation: part_of_dissertation status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: Evolutionary proccesses in variable emvironments type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2016' ... --- _id: '1358' abstract: - lang: eng text: 'Gene regulation relies on the specificity of transcription factor (TF)–DNA interactions. Limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF–DNA interactions or remains erroneously inactive. As each TF can have numerous interactions with noncognate cis-regulatory elements, crosstalk is inherently a global problem, yet has previously not been studied as such. We construct a theoretical framework to analyse the effects of global crosstalk on gene regulation. We find that crosstalk presents a significant challenge for organisms with low-specificity TFs, such as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting at equilibrium, including variants of cooperativity and combinatorial regulation. Our results suggest that crosstalk imposes a previously unexplored global constraint on the functioning and evolution of regulatory networks, which is qualitatively distinct from the known constraints that act at the level of individual gene regulatory elements.' article_number: '12307' author: - first_name: Tamar full_name: Friedlander, Tamar id: 36A5845C-F248-11E8-B48F-1D18A9856A87 last_name: Friedlander - first_name: Roshan full_name: Prizak, Roshan id: 4456104E-F248-11E8-B48F-1D18A9856A87 last_name: Prizak - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 2016;7. doi:10.1038/ncomms12307 apa: Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., & Tkačik, G. (2016). Intrinsic limits to gene regulation by global crosstalk. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms12307 chicago: Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms12307. ieee: T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” Nature Communications, vol. 7. Nature Publishing Group, 2016. ista: Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307. mla: Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications, vol. 7, 12307, Nature Publishing Group, 2016, doi:10.1038/ncomms12307. short: T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016). date_created: 2018-12-11T11:51:34Z date_published: 2016-08-04T00:00:00Z date_updated: 2023-09-07T12:53:49Z day: '04' ddc: - '576' department: - _id: GaTk - _id: NiBa - _id: CaGu doi: 10.1038/ncomms12307 ec_funded: 1 file: - access_level: open_access checksum: fe3f3a1526d180b29fe691ab11435b78 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:01Z date_updated: 2020-07-14T12:44:46Z file_id: '4919' file_name: IST-2016-627-v1+1_ncomms12307.pdf file_size: 861805 relation: main_file - access_level: open_access checksum: 164864a1a675f3ad80e9917c27aba07f content_type: application/pdf creator: system date_created: 2018-12-12T10:12:02Z date_updated: 2020-07-14T12:44:46Z file_id: '4920' file_name: IST-2016-627-v1+2_ncomms12307-s1.pdf file_size: 1084703 relation: main_file file_date_updated: 2020-07-14T12:44:46Z has_accepted_license: '1' intvolume: ' 7' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5887' pubrep_id: '627' quality_controlled: '1' related_material: record: - id: '6071' relation: dissertation_contains status: public scopus_import: 1 status: public title: Intrinsic limits to gene regulation by global crosstalk tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2016' ... --- _id: '9710' abstract: - lang: eng text: Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects. article_processing_charge: No author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Barton NH. Data from: How does epistasis influence the response to selection? 2016. doi:10.5061/dryad.s5s7r' apa: 'Barton, N. H. (2016). Data from: How does epistasis influence the response to selection? Dryad. https://doi.org/10.5061/dryad.s5s7r' chicago: 'Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response to Selection?” Dryad, 2016. https://doi.org/10.5061/dryad.s5s7r.' ieee: 'N. H. Barton, “Data from: How does epistasis influence the response to selection?” Dryad, 2016.' ista: 'Barton NH. 2016. Data from: How does epistasis influence the response to selection?, Dryad, 10.5061/dryad.s5s7r.' mla: 'Barton, Nicholas H. Data from: How Does Epistasis Influence the Response to Selection? Dryad, 2016, doi:10.5061/dryad.s5s7r.' short: N.H. Barton, (2016). date_created: 2021-07-23T11:45:47Z date_published: 2016-09-23T00:00:00Z date_updated: 2023-09-20T11:17:47Z day: '23' department: - _id: NiBa doi: 10.5061/dryad.s5s7r main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.s5s7r month: '09' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '1199' relation: used_in_publication status: public status: public title: 'Data from: How does epistasis influence the response to selection?' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2016' ... --- _id: '9864' abstract: - lang: eng text: Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima. article_processing_charge: No author: - first_name: Rodrigo A full_name: Fernandes Redondo, Rodrigo A id: 409D5C96-F248-11E8-B48F-1D18A9856A87 last_name: Fernandes Redondo orcid: 0000-0002-5837-2793 - first_name: Harold full_name: de Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: de Vladar orcid: 0000-0002-5985-7653 - first_name: Tomasz full_name: Włodarski, Tomasz last_name: Włodarski - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. 2016. doi:10.6084/m9.figshare.4315652.v1 apa: Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J. P. (2016). Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. The Royal Society. https://doi.org/10.6084/m9.figshare.4315652.v1 chicago: Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. https://doi.org/10.6084/m9.figshare.4315652.v1. ieee: R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family.” The Royal Society, 2016. ista: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family, The Royal Society, 10.6084/m9.figshare.4315652.v1. mla: Fernandes Redondo, Rodrigo A., et al. Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family. The Royal Society, 2016, doi:10.6084/m9.figshare.4315652.v1. short: R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016). date_created: 2021-08-10T08:29:47Z date_published: 2016-12-14T00:00:00Z date_updated: 2023-09-20T11:56:33Z day: '14' department: - _id: NiBa - _id: JoBo doi: 10.6084/m9.figshare.4315652.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.4315652.v1 month: '12' oa: 1 oa_version: Published Version publisher: The Royal Society related_material: record: - id: '1077' relation: used_in_publication status: public status: public title: Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2016' ... --- _id: '1382' abstract: - lang: eng text: Background and aims Angiosperms display remarkable diversity in flower colour, implying that transitions between pigmentation phenotypes must have been common. Despite progress in understanding transitions between anthocyanin (blue, purple, pink or red) and unpigmented (white) flowers, little is known about the evolutionary patterns of flower-colour transitions in lineages with both yellow and anthocyanin-pigmented flowers. This study investigates the relative rates of evolutionary transitions between different combinations of yellow- and anthocyanin-pigmentation phenotypes in the tribe Antirrhineae. Methods We surveyed taxonomic literature for data on anthocyanin and yellow floral pigmentation for 369 species across the tribe. We then reconstructed the phylogeny of 169 taxa and used phylogenetic comparative methods to estimate transition rates among pigmentation phenotypes across the phylogeny. Key Results In contrast to previous studies we found a bias towards transitions involving a gain in pigmentation, although transitions to phenotypes with both anthocyanin and yellow taxa are nevertheless extremely rare. Despite the dominance of yellow and anthocyanin-pigmented taxa, transitions between these phenotypes are constrained to move through a white intermediate stage, whereas transitions to double-pigmentation are very rare. The most abundant transitions are between anthocyanin-pigmented and unpigmented flowers, and similarly the most abundant polymorphic taxa were those with anthocyanin-pigmented and unpigmented flowers. Conclusions Our findings show that pigment evolution is limited by the presence of other floral pigments. This interaction between anthocyanin and yellow pigments constrains the breadth of potential floral diversity observed in nature. In particular, they suggest that selection has repeatedly acted to promote the spread of single-pigmented phenotypes across the Antirrhineae phylogeny. Furthermore, the correlation between transition rates and polymorphism suggests that the forces causing and maintaining variance in the short term reflect evolutionary processes on longer time scales. acknowledgement: We thank Melinda Pickup, Spencer Barrett, Nick Barton and four anonymous reviewers for helpful discussions on previous versions of this manuscript. We also thank Jana Porsche for her efforts in tracking down the more obscure references. author: - first_name: Thomas full_name: Ellis, Thomas id: 3153D6D4-F248-11E8-B48F-1D18A9856A87 last_name: Ellis orcid: 0000-0002-8511-0254 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 citation: ama: Ellis T, Field D. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. 2016;117(7):1133-1140. doi:10.1093/aob/mcw043 apa: Ellis, T., & Field, D. (2016). Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. Oxford University Press. https://doi.org/10.1093/aob/mcw043 chicago: Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” Annals of Botany. Oxford University Press, 2016. https://doi.org/10.1093/aob/mcw043. ieee: T. Ellis and D. Field, “Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae,” Annals of Botany, vol. 117, no. 7. Oxford University Press, pp. 1133–1140, 2016. ista: Ellis T, Field D. 2016. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. 117(7), 1133–1140. mla: Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” Annals of Botany, vol. 117, no. 7, Oxford University Press, 2016, pp. 1133–40, doi:10.1093/aob/mcw043. short: T. Ellis, D. Field, Annals of Botany 117 (2016) 1133–1140. date_created: 2018-12-11T11:51:42Z date_published: 2016-06-01T00:00:00Z date_updated: 2024-02-21T13:49:53Z day: '1' department: - _id: NiBa doi: 10.1093/aob/mcw043 intvolume: ' 117' issue: '7' language: - iso: eng month: '06' oa_version: None page: 1133 - 1140 publication: Annals of Botany publication_status: published publisher: Oxford University Press publist_id: '5828' quality_controlled: '1' related_material: record: - id: '5550' relation: popular_science status: public scopus_import: 1 status: public title: Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 117 year: '2016' ... --- _id: '1398' abstract: - lang: eng text: Hybrid zones represent evolutionary laboratories, where recombination brings together alleles in combinations which have not previously been tested by selection. This provides an excellent opportunity to test the effect of molecular variation on fitness, and how this variation is able to spread through populations in a natural context. The snapdragon Antirrhinum majus is polymorphic in the wild for two loci controlling the distribution of yellow and magenta floral pigments. Where the yellow A. m. striatum and the magenta A. m. pseudomajus meet along a valley in the Spanish Pyrenees they form a stable hybrid zone Alleles at these loci recombine to give striking transgressive variation for flower colour. The sharp transition in phenotype over ~1km implies strong selection maintaining the hybrid zone. An indirect assay of pollinator visitation in the field found that pollinators forage in a positive-frequency dependent manner on Antirrhinum, matching previous data on fruit set. Experimental arrays and paternity analysis of wild-pollinated seeds demonstrated assortative mating for pigmentation alleles, and that pollinator behaviour alone is sufficient to explain this pattern. Selection by pollinators should be sufficiently strong to maintain the hybrid zone, although other mechanisms may be at work. At a broader scale I examined evolutionary transitions between yellow and anthocyanin pigmentation in the tribe Antirrhinae, and found that selection has acted strate that pollinators are a major determinant of reproductive success and mating patterns in wild Antirrhinum. acknowledgement: "I am indebted to many people for their support during my PhD, but I particularly wish to thank Nick Barton for his guidance and intuition, and for encouraging me to take the time to look beyond the immediate topic of my PhD to understand the broader context. I am also especially grateful to David Field his bottomless patience, invaluable advice on experimental design, analysis and scientific writing, and for tireless work on the population surveys and genomic work without most of my thesis could not have happened. \r\n\r\nIt has been a pleasure to work with the combined strengths of the groups at The John Innes Centre, University of Toulouse and IST Austria. Thanks to Enrico Coen and his group for hosting me in Norwich in 2011 and especially for setting up the tag experiment. \r\n\r\nI thank David Field, Desmond Bradley and Maria Clara Melo-Hurtado for organising field collections, as well as Monique Burrus and Christophe Andalo and a large number of volunteers for their e ff orts helping with the field work. Furthermore I thank Coline Jaworski for providing seeds and for her input into the design of the experimental arrays, and Matthew Couchman for maintaining the database of. \r\n\r\nIn addition to those mentioned above, I am grateful to Melinda Pickup, Spencer Barrett, and four anonymous reviewers for their insightful comments on sections of this manuscript. I also thank Jana Porsche for her e ff orts in tracking down the more obscure references for chapter 5, and Jon Bollback for his advice about the analysis. \r\n\r\nI am indebted to Jon Ågren for his patience whilst I finished this thesis, and to Sylvia Cremer and Magnus Nordborg for taking the time to read and evaluate the thesis given a shorter deadline than was fair. \r\n\r\nA very positive aspect of my PhD has been the supportive atmosphere of IST. In particular, I have come to appreciate the enormous support from our group assistants Nicole Hotzy, Julia Asimakis, Christine Ostermann and Jerneja Beslagic. I also thank Christian Chaloupka and Stefan Hipfinger for their enthusiasm and readiness to help where possible in setting up our greenhouse and experiments. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Thomas full_name: Ellis, Thomas id: 3153D6D4-F248-11E8-B48F-1D18A9856A87 last_name: Ellis orcid: 0000-0002-8511-0254 citation: ama: Ellis T. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. 2016. doi:10.15479/AT:ISTA:TH_526 apa: Ellis, T. (2016). The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_526 chicago: Ellis, Thomas. “The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:TH_526 . ieee: T. Ellis, “The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone,” Institute of Science and Technology Austria, 2016. ista: Ellis T. 2016. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute of Science and Technology Austria. mla: Ellis, Thomas. The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:TH_526 . short: T. Ellis, The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone, Institute of Science and Technology Austria, 2016. date_created: 2018-12-11T11:51:47Z date_published: 2016-02-18T00:00:00Z date_updated: 2024-02-21T13:51:39Z day: '18' ddc: - '576' degree_awarded: PhD department: - _id: NiBa doi: '10.15479/AT:ISTA:TH_526 ' file: - access_level: open_access checksum: a89b17ff27cf92c9a15f6b3d46bd7e53 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:51Z date_updated: 2020-07-14T12:44:48Z file_id: '5106' file_name: IST-2016-526-v1+1_Ellis_signed_thesis.pdf file_size: 11928241 relation: main_file file_date_updated: 2020-07-14T12:44:48Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '130' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '5809' pubrep_id: '526' related_material: record: - id: '5553' relation: popular_science status: public - id: '5551' relation: popular_science status: public - id: '5552' relation: popular_science status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2016' ... --- _id: '1131' abstract: - lang: eng text: "Evolution of gene regulation is important for phenotypic evolution and diversity. Sequence-specific binding of regulatory proteins is one of the key regulatory mechanisms determining gene expression. Although there has been intense interest in evolution of regulatory binding sites in the last decades, a theoretical understanding is far from being complete. In this thesis, I aim at a better understanding of the evolution of transcriptional regulatory binding sequences by using biophysical and population genetic models.\r\nIn the first part of the thesis, I discuss how to formulate the evolutionary dynamics of binding se- quences in a single isolated binding site and in promoter/enhancer regions. I develop a theoretical framework bridging between a thermodynamical model for transcription and a mutation-selection-drift model for monomorphic populations. I mainly address the typical evolutionary rates, and how they de- pend on biophysical parameters (e.g. binding length and specificity) and population genetic parameters (e.g. population size and selection strength).\r\nIn the second part of the thesis, I analyse empirical data for a better evolutionary and biophysical understanding of sequence-specific binding of bacterial RNA polymerase. First, I infer selection on regulatory and non-regulatory binding sites of RNA polymerase in the E. coli K12 genome. Second, I infer the chemical potential of RNA polymerase, an important but unknown physical parameter defining the threshold energy for strong binding. Furthermore, I try to understand the relation between the lac promoter sequence diversity and the LacZ activity variation among 20 bacterial isolates by constructing a simple but biophysically motivated gene expression model. Lastly, I lay out a statistical framework to predict adaptive point mutations in de novo promoter evolution in a selection experiment." acknowledgement: This PhD thesis may not have been completed without the help and care I received from some peo- ple during my PhD life. I am especially grateful to Tiago Paixao, Gasper Tkacik, Nick Barton, not only for their scientific advices but also for their patience and support. I thank Calin Guet and Jonathan Bollback for allowing me to “play around” in their labs and get some experience on experimental evolution. I thank Magdalena Steinrueck and Fabienne Jesse for collaborating and sharing their experimental data with me. I thank Johannes Jaeger for reviewing my thesis. I thank all members of Barton group (aka bartonians) for their feedback, and all workers of IST Austria for making the best working conditions. Lastly, I thank two special women, Nejla Sag ̆lam and Setenay Dog ̆an, for their continuous support and encouragement. I truly had a great chance of having right people around me. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Murat full_name: Tugrul, Murat id: 37C323C6-F248-11E8-B48F-1D18A9856A87 last_name: Tugrul orcid: 0000-0002-8523-0758 citation: ama: Tugrul M. Evolution of transcriptional regulatory sequences. 2016. apa: Tugrul, M. (2016). Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria. chicago: Tugrul, Murat. “Evolution of Transcriptional Regulatory Sequences.” Institute of Science and Technology Austria, 2016. ieee: M. Tugrul, “Evolution of transcriptional regulatory sequences,” Institute of Science and Technology Austria, 2016. ista: Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria. mla: Tugrul, Murat. Evolution of Transcriptional Regulatory Sequences. Institute of Science and Technology Austria, 2016. short: M. Tugrul, Evolution of Transcriptional Regulatory Sequences, Institute of Science and Technology Austria, 2016. date_created: 2018-12-11T11:50:19Z date_published: 2016-07-01T00:00:00Z date_updated: 2024-02-21T13:50:34Z day: '01' ddc: - '576' degree_awarded: PhD department: - _id: NiBa file: - access_level: closed checksum: 66cb61a59943e4fb7447c6a86be5ef51 content_type: application/pdf creator: dernst date_created: 2019-08-13T08:53:52Z date_updated: 2019-08-13T08:53:52Z file_id: '6810' file_name: Tugrul_thesis_w_signature_page.pdf file_size: 3695257 relation: main_file - access_level: open_access checksum: 293e388d70563760f6b24c3e66283dda content_type: application/pdf creator: dernst date_created: 2021-02-22T11:45:20Z date_updated: 2021-02-22T11:45:20Z file_id: '9182' file_name: 2016_Tugrul_Thesis.pdf file_size: 3880811 relation: main_file success: 1 file_date_updated: 2021-02-22T11:45:20Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '89' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6229' related_material: record: - id: '1666' relation: part_of_dissertation status: public - id: '5554' relation: research_data status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: Evolution of transcriptional regulatory sequences type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2016' ... --- _id: '1430' abstract: - lang: eng text: Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse their runtime on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrence of new mutations is much longer than the time it takes for a new beneficial mutation to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a (1+1)-type process where the probability of accepting a new genotype (improvements or worsenings) depends on the change in fitness. We present an initial runtime analysis of SSWM, quantifying its performance for various parameters and investigating differences to the (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient. author: - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Dirk full_name: Sudholt, Dirk last_name: Sudholt - first_name: Jorge full_name: Heredia, Jorge last_name: Heredia - first_name: Barbora full_name: Trubenova, Barbora id: 42302D54-F248-11E8-B48F-1D18A9856A87 last_name: Trubenova orcid: 0000-0002-6873-2967 citation: ama: 'Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime comparison of natural and artificial evolution. In: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. ACM; 2015:1455-1462. doi:10.1145/2739480.2754758' apa: 'Paixao, T., Sudholt, D., Heredia, J., & Trubenova, B. (2015). First steps towards a runtime comparison of natural and artificial evolution. In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation (pp. 1455–1462). Madrid, Spain: ACM. https://doi.org/10.1145/2739480.2754758' chicago: Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, 1455–62. ACM, 2015. https://doi.org/10.1145/2739480.2754758. ieee: T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards a runtime comparison of natural and artificial evolution,” in Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, Madrid, Spain, 2015, pp. 1455–1462. ista: 'Paixao T, Sudholt D, Heredia J, Trubenova B. 2015. First steps towards a runtime comparison of natural and artificial evolution. Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and evolutionary computation conference, 1455–1462.' mla: Paixao, Tiago, et al. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–62, doi:10.1145/2739480.2754758. short: T. Paixao, D. Sudholt, J. Heredia, B. Trubenova, in:, Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–1462. conference: end_date: 2015-07-15 location: Madrid, Spain name: 'GECCO: Genetic and evolutionary computation conference' start_date: 2015-07-11 date_created: 2018-12-11T11:51:58Z date_published: 2015-07-11T00:00:00Z date_updated: 2021-01-12T06:50:41Z day: '11' department: - _id: NiBa - _id: CaGu doi: 10.1145/2739480.2754758 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1504.06260 month: '07' oa: 1 oa_version: Preprint page: 1455 - 1462 project: - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation publication: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation publication_status: published publisher: ACM publist_id: '5768' quality_controlled: '1' scopus_import: 1 status: public title: First steps towards a runtime comparison of natural and artificial evolution type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ...