[{"year":"2015","article_processing_charge":"No","date_published":"2015-11-06T00:00:00Z","title":"Other fitness models for comparison & for interacting TFBSs","date_created":"2021-07-23T12:00:37Z","author":[{"id":"37C323C6-F248-11E8-B48F-1D18A9856A87","full_name":"Tugrul, Murat","first_name":"Murat","last_name":"Tugrul","orcid":"0000-0002-8523-0758"},{"first_name":"Tiago","last_name":"Paixao","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"},{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"date_updated":"2025-09-23T08:31:14Z","month":"11","doi":"10.1371/journal.pgen.1005639.s001","citation":{"ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison &#38; for interacting TFBSs. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">10.1371/journal.pgen.1005639.s001</a>","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for comparison &#38; for interacting TFBSs.” Public Library of Science, 2015.","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015).","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison &#38; for interacting TFBSs, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">10.1371/journal.pgen.1005639.s001</a>.","mla":"Tugrul, Murat, et al. <i>Other Fitness Models for Comparison &#38; for Interacting TFBSs</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">10.1371/journal.pgen.1005639.s001</a>.","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other Fitness Models for Comparison &#38; for Interacting TFBSs.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">https://doi.org/10.1371/journal.pgen.1005639.s001</a>.","apa":"Tugrul, M., Paixao, T., Barton, N. H., &#38; Tkačik, G. (2015). Other fitness models for comparison &#38; for interacting TFBSs. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">https://doi.org/10.1371/journal.pgen.1005639.s001</a>"},"oa_version":"Published Version","_id":"9712","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Public Library of Science","day":"06","related_material":{"record":[{"status":"public","id":"1666","relation":"used_in_publication"}]},"status":"public","type":"research_data_reference"},{"status":"public","type":"research_data_reference","day":"18","related_material":{"record":[{"status":"public","id":"1809","relation":"used_in_publication"}]},"publisher":"Public Library of Science","citation":{"apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Mathematical inference of the results. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">https://doi.org/10.1371/journal.pone.0126907.s001</a>","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Mathematical Inference of the Results.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">https://doi.org/10.1371/journal.pone.0126907.s001</a>.","mla":"Trubenova, Barbora, et al. <i>Mathematical Inference of the Results</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">10.1371/journal.pone.0126907.s001</a>.","ista":"Trubenova B, Novak S, Hager R. 2015. Mathematical inference of the results, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">10.1371/journal.pone.0126907.s001</a>.","short":"B. Trubenova, S. Novak, R. Hager, (2015).","ieee":"B. Trubenova, S. Novak, and R. Hager, “Mathematical inference of the results.” Public Library of Science, 2015.","ama":"Trubenova B, Novak S, Hager R. Mathematical inference of the results. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">10.1371/journal.pone.0126907.s001</a>"},"oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9715","department":[{"_id":"NiBa"}],"doi":"10.1371/journal.pone.0126907.s001","month":"05","author":[{"full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","last_name":"Trubenova","first_name":"Barbora"},{"last_name":"Novak","first_name":"Sebastian","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"full_name":"Hager, Reinmar","first_name":"Reinmar","last_name":"Hager"}],"date_updated":"2025-09-23T09:21:54Z","date_published":"2015-05-18T00:00:00Z","article_processing_charge":"No","title":"Mathematical inference of the results","date_created":"2021-07-23T12:11:30Z","year":"2015"},{"publisher":"Public Library of Science","citation":{"ama":"Trubenova B, Novak S, Hager R. Description of the agent based simulations. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">10.1371/journal.pone.0126907.s003</a>","ieee":"B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.” Public Library of Science, 2015.","short":"B. Trubenova, S. Novak, R. Hager, (2015).","ista":"Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">10.1371/journal.pone.0126907.s003</a>.","mla":"Trubenova, Barbora, et al. <i>Description of the Agent Based Simulations</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">10.1371/journal.pone.0126907.s003</a>.","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of the Agent Based Simulations.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">https://doi.org/10.1371/journal.pone.0126907.s003</a>.","apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Description of the agent based simulations. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">https://doi.org/10.1371/journal.pone.0126907.s003</a>"},"oa_version":"Published Version","_id":"9772","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"NiBa"}],"status":"public","type":"research_data_reference","day":"18","related_material":{"record":[{"relation":"used_in_publication","id":"1809","status":"public"}]},"date_published":"2015-05-18T00:00:00Z","article_processing_charge":"No","title":"Description of the agent based simulations","date_created":"2021-08-05T12:55:20Z","year":"2015","month":"05","doi":"10.1371/journal.pone.0126907.s003","date_updated":"2025-09-23T09:21:54Z","author":[{"orcid":"0000-0002-6873-2967","first_name":"Barbora","last_name":"Trubenova","full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","first_name":"Sebastian","last_name":"Novak","orcid":"0000-0002-2519-824X"},{"last_name":"Hager","first_name":"Reinmar","full_name":"Hager, Reinmar"}]},{"quality_controlled":"1","date_updated":"2025-09-23T09:21:54Z","license":"https://creativecommons.org/licenses/by/4.0/","external_id":{"isi":["000354917300064"]},"month":"05","publist_id":"5299","volume":10,"isi":1,"date_published":"2015-05-18T00:00:00Z","article_processing_charge":"No","title":"Indirect genetic effects and the dynamics of social interactions","related_material":{"record":[{"id":"9715","relation":"research_data","status":"public"},{"relation":"research_data","id":"9772","status":"public"}]},"status":"public","type":"journal_article","oa_version":"Published Version","scopus_import":"1","abstract":[{"text":"Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations.","lang":"eng"}],"citation":{"mla":"Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social Interactions.” <i>PLoS One</i>, vol. 10, no. 5, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907\">10.1371/journal.pone.0126907</a>.","short":"B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015).","ista":"Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5).","apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Indirect genetic effects and the dynamics of social interactions. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907\">https://doi.org/10.1371/journal.pone.0126907</a>","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic Effects and the Dynamics of Social Interactions.” <i>PLoS One</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907\">https://doi.org/10.1371/journal.pone.0126907</a>.","ama":"Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of social interactions. <i>PLoS One</i>. 2015;10(5). doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907\">10.1371/journal.pone.0126907</a>","ieee":"B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics of social interactions,” <i>PLoS One</i>, vol. 10, no. 5. Public Library of Science, 2015."},"publisher":"Public Library of Science","author":[{"full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","last_name":"Trubenova","first_name":"Barbora"},{"first_name":"Sebastian","last_name":"Novak","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"first_name":"Reinmar","last_name":"Hager","full_name":"Hager, Reinmar"}],"language":[{"iso":"eng"}],"ddc":["570","576"],"pubrep_id":"453","file_date_updated":"2020-07-14T12:45:17Z","intvolume":"        10","doi":"10.1371/journal.pone.0126907","file":[{"file_name":"IST-2016-453-v1+1_journal.pone.0126907.pdf","access_level":"open_access","creator":"system","checksum":"d3a4a58ef4bd3b3e2f32b7fd7af4a743","file_id":"4730","date_created":"2018-12-12T10:09:07Z","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:45:17Z","file_size":2748982}],"publication_status":"published","oa":1,"year":"2015","date_created":"2018-12-11T11:54:07Z","day":"18","publication":"PLoS One","corr_author":"1","department":[{"_id":"NiBa"}],"issue":"5","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1809","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"language":[{"iso":"eng"}],"author":[{"full_name":"Polechova, Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112","last_name":"Polechova","first_name":"Jitka"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"       112","oa":1,"publication_status":"published","doi":"10.1073/pnas.1421515112","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"year":"2015","date_created":"2018-12-11T11:54:11Z","day":"19","publication":"PNAS","corr_author":"1","pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1818","ec_funded":1,"department":[{"_id":"NiBa"}],"issue":"20","page":"6401 - 6406","date_updated":"2025-09-23T09:27:16Z","quality_controlled":"1","external_id":{"pmid":["25941385"],"isi":["000354729500058"]},"month":"05","publist_id":"5288","volume":112,"article_processing_charge":"No","date_published":"2015-05-19T00:00:00Z","isi":1,"title":"Limits to adaptation along environmental gradients","status":"public","type":"journal_article","abstract":[{"text":"Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, &quot;swamping&quot; by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible.","lang":"eng"}],"citation":{"ama":"Polechova J, Barton NH. Limits to adaptation along environmental gradients. <i>PNAS</i>. 2015;112(20):6401-6406. doi:<a href=\"https://doi.org/10.1073/pnas.1421515112\">10.1073/pnas.1421515112</a>","ieee":"J. Polechova and N. H. Barton, “Limits to adaptation along environmental gradients,” <i>PNAS</i>, vol. 112, no. 20. National Academy of Sciences, pp. 6401–6406, 2015.","mla":"Polechova, Jitka, and Nicholas H. Barton. “Limits to Adaptation along Environmental Gradients.” <i>PNAS</i>, vol. 112, no. 20, National Academy of Sciences, 2015, pp. 6401–06, doi:<a href=\"https://doi.org/10.1073/pnas.1421515112\">10.1073/pnas.1421515112</a>.","ista":"Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 6401–6406.","short":"J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.","apa":"Polechova, J., &#38; Barton, N. H. (2015). Limits to adaptation along environmental gradients. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1421515112\">https://doi.org/10.1073/pnas.1421515112</a>","chicago":"Polechova, Jitka, and Nicholas H Barton. “Limits to Adaptation along Environmental Gradients.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1421515112\">https://doi.org/10.1073/pnas.1421515112</a>."},"scopus_import":"1","oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/","open_access":"1"}],"publisher":"National Academy of Sciences"},{"alternative_title":["LNCS"],"date_created":"2018-12-11T11:54:16Z","year":"2015","intvolume":"      9035","doi":"10.1007/978-3-662-46681-0_47","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"publication_status":"published","series_title":"Lecture Notes in Computer Science","oa":1,"author":[{"orcid":"0000-0001-8180-0904","last_name":"Giacobbe","first_name":"Mirco","full_name":"Giacobbe, Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"},{"full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh","last_name":"Gupta"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"},{"last_name":"Petrov","first_name":"Tatjana","orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrov, Tatjana"}],"language":[{"iso":"eng"}],"page":"469 - 483","ec_funded":1,"conference":{"location":"London, United Kingdom","start_date":"2015-04-11","end_date":"2015-04-18","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1835","day":"01","acknowledgement":"SNSF Early Postdoc.Mobility Fellowship, the grant number P2EZP2 148797.\r\n","article_processing_charge":"No","arxiv":1,"date_published":"2015-04-01T00:00:00Z","title":"Model checking gene regulatory networks","publist_id":"5267","volume":9035,"month":"04","quality_controlled":"1","date_updated":"2025-07-10T11:50:42Z","external_id":{"arxiv":["1410.7704"]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.7704"}],"publisher":"Springer","oa_version":"Preprint","abstract":[{"text":"The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs –an important problem of interest in evolutionary biology– more efficiently than the classical simulation method. We specify the property in linear temporal logics. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights.","lang":"eng"}],"citation":{"ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking gene regulatory networks. 2015;9035:469-483. doi:<a href=\"https://doi.org/10.1007/978-3-662-46681-0_47\">10.1007/978-3-662-46681-0_47</a>","ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking gene regulatory networks,” vol. 9035. Springer, pp. 469–483, 2015.","mla":"Giacobbe, Mirco, et al. <i>Model Checking Gene Regulatory Networks</i>. Vol. 9035, Springer, 2015, pp. 469–83, doi:<a href=\"https://doi.org/10.1007/978-3-662-46681-0_47\">10.1007/978-3-662-46681-0_47</a>.","short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, 9035 (2015) 469–483.","ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2015. Model checking gene regulatory networks. 9035, 469–483.","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., &#38; Petrov, T. (2015). Model checking gene regulatory networks. Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-662-46681-0_47\">https://doi.org/10.1007/978-3-662-46681-0_47</a>","chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking Gene Regulatory Networks.” Lecture Notes in Computer Science. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-662-46681-0_47\">https://doi.org/10.1007/978-3-662-46681-0_47</a>."},"scopus_import":"1","status":"public","type":"conference","related_material":{"record":[{"relation":"later_version","id":"1351","status":"public"}]}},{"page":"28 - 43","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1542","ec_funded":1,"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"corr_author":"1","publication":"Journal of Theoretical Biology","day":"21","date_created":"2018-12-11T11:52:37Z","year":"2015","publication_status":"published","oa":1,"doi":"10.1016/j.jtbi.2015.07.011","file":[{"date_updated":"2020-07-14T12:45:01Z","content_type":"application/pdf","relation":"main_file","file_size":595307,"file_id":"5244","date_created":"2018-12-12T10:16:53Z","access_level":"open_access","file_name":"IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf","checksum":"33b60ecfea60764756a9ee9df5eb65ca","creator":"system"}],"project":[{"grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"},{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"intvolume":"       383","file_date_updated":"2020-07-14T12:45:01Z","pubrep_id":"483","language":[{"iso":"eng"}],"ddc":["570"],"author":[{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","first_name":"Tiago","last_name":"Paixao","orcid":"0000-0003-2361-3953"},{"last_name":"Badkobeh","first_name":"Golnaz","full_name":"Badkobeh, Golnaz"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"},{"full_name":"Çörüş, Doğan","first_name":"Doğan","last_name":"Çörüş"},{"full_name":"Dang, Duccuong","last_name":"Dang","first_name":"Duccuong"},{"first_name":"Tobias","last_name":"Friedrich","full_name":"Friedrich, Tobias"},{"last_name":"Lehre","first_name":"Per","full_name":"Lehre, Per"},{"first_name":"Dirk","last_name":"Sudholt","full_name":"Sudholt, Dirk"},{"full_name":"Sutton, Andrew","last_name":"Sutton","first_name":"Andrew"},{"orcid":"0000-0002-6873-2967","first_name":"Barbora","last_name":"Trubenova","full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Elsevier","das_tickbox":"1","abstract":[{"lang":"eng","text":"The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. "}],"scopus_import":"1","citation":{"chicago":"Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova. “Toward a Unifying Framework for Evolutionary Processes.” <i>Journal of Theoretical Biology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">https://doi.org/10.1016/j.jtbi.2015.07.011</a>.","apa":"Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T., … Trubenova, B. (2015). Toward a unifying framework for evolutionary processes. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">https://doi.org/10.1016/j.jtbi.2015.07.011</a>","ista":"Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 383, 28–43.","short":"T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P. Lehre, D. Sudholt, A. Sutton, B. Trubenova, Journal of Theoretical Biology 383 (2015) 28–43.","mla":"Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.” <i>Journal of Theoretical Biology</i>, vol. 383, Elsevier, 2015, pp. 28–43, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">10.1016/j.jtbi.2015.07.011</a>.","ieee":"T. Paixao <i>et al.</i>, “Toward a unifying framework for evolutionary processes,” <i>Journal of Theoretical Biology</i>, vol. 383. Elsevier, pp. 28–43, 2015.","ama":"Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. <i>Journal of Theoretical Biology</i>. 2015;383:28-43. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">10.1016/j.jtbi.2015.07.011</a>"},"oa_version":"Published Version","type":"journal_article","status":"public","title":"Toward a unifying framework for evolutionary processes","article_processing_charge":"No","date_published":"2015-10-21T00:00:00Z","isi":1,"volume":383,"publist_id":"5629","month":"10","external_id":{"isi":["000362056300005"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_updated":"2026-07-07T13:12:13Z","quality_controlled":"1"},{"related_material":{"record":[{"status":"public","id":"9712","relation":"research_data"},{"status":"public","id":"1131","relation":"dissertation_contains"}]},"status":"public","type":"journal_article","oa_version":"Published Version","citation":{"chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics of Transcription Factor Binding Site Evolution.” <i>PLoS Genetics</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pgen.1005639\">https://doi.org/10.1371/journal.pgen.1005639</a>.","apa":"Tugrul, M., Paixao, T., Barton, N. H., &#38; Tkačik, G. (2015). Dynamics of transcription factor binding site evolution. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1005639\">https://doi.org/10.1371/journal.pgen.1005639</a>","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11).","mla":"Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” <i>PLoS Genetics</i>, vol. 11, no. 11, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639\">10.1371/journal.pgen.1005639</a>.","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” <i>PLoS Genetics</i>, vol. 11, no. 11. Public Library of Science, 2015.","ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. <i>PLoS Genetics</i>. 2015;11(11). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639\">10.1371/journal.pgen.1005639</a>"},"scopus_import":"1","abstract":[{"lang":"eng","text":"Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics."}],"publisher":"Public Library of Science","date_updated":"2026-07-29T11:31:13Z","quality_controlled":"1","external_id":{"isi":["000366179000022"]},"month":"11","publist_id":"5483","volume":11,"isi":1,"article_processing_charge":"No","date_published":"2015-11-06T00:00:00Z","title":"Dynamics of transcription factor binding site evolution","day":"06","publication":"PLoS Genetics","issue":"11","ec_funded":1,"department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"_id":"1666","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"id":"37C323C6-F248-11E8-B48F-1D18A9856A87","full_name":"Tugrul, Murat","last_name":"Tugrul","first_name":"Murat","orcid":"0000-0002-8523-0758"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"},{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"ddc":["576"],"pubrep_id":"463","file_date_updated":"2020-07-14T12:45:10Z","intvolume":"        11","doi":"10.1371/journal.pgen.1005639","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"file":[{"file_name":"IST-2016-463-v1+1_journal.pgen.1005639.pdf","access_level":"open_access","checksum":"a4e72fca5ccf40ddacf4d08c8e46b554","creator":"system","file_id":"4657","date_created":"2018-12-12T10:07:58Z","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:45:10Z","file_size":2580778}],"publication_status":"published","oa":1,"year":"2015","date_created":"2018-12-11T11:53:21Z"},{"year":"2014","date_created":"2018-12-11T11:56:35Z","author":[{"last_name":"Phadke","first_name":"Sujal","full_name":"Phadke, Sujal"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","first_name":"Tiago","last_name":"Paixao","orcid":"0000-0003-2361-3953"},{"last_name":"Pham","first_name":"Tuan","full_name":"Pham, Tuan"},{"full_name":"Pham, Stephanie","first_name":"Stephanie","last_name":"Pham"},{"last_name":"Zufall","first_name":"Rebecca","full_name":"Zufall, Rebecca"}],"language":[{"iso":"eng"}],"intvolume":"       105","doi":"10.1093/jhered/est063","publication_status":"published","department":[{"_id":"NiBa"}],"issue":"1","_id":"2252","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"130 - 135","day":"01","publication":"Journal of Heredity","corr_author":"1","publist_id":"4695","volume":105,"isi":1,"date_published":"2014-01-01T00:00:00Z","article_processing_charge":"No","title":"Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila","date_updated":"2025-09-29T11:16:03Z","quality_controlled":"1","external_id":{"isi":["000328427800013"]},"month":"01","oa_version":"None","citation":{"ieee":"S. Phadke, T. Paixao, T. Pham, S. Pham, and R. Zufall, “Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila,” <i>Journal of Heredity</i>, vol. 105, no. 1. Oxford University Press, pp. 130–135, 2014.","ama":"Phadke S, Paixao T, Pham T, Pham S, Zufall R. Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. <i>Journal of Heredity</i>. 2014;105(1):130-135. doi:<a href=\"https://doi.org/10.1093/jhered/est063\">10.1093/jhered/est063</a>","apa":"Phadke, S., Paixao, T., Pham, T., Pham, S., &#38; Zufall, R. (2014). Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. <i>Journal of Heredity</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jhered/est063\">https://doi.org/10.1093/jhered/est063</a>","chicago":"Phadke, Sujal, Tiago Paixao, Tuan Pham, Stephanie Pham, and Rebecca Zufall. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” <i>Journal of Heredity</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/jhered/est063\">https://doi.org/10.1093/jhered/est063</a>.","mla":"Phadke, Sujal, et al. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” <i>Journal of Heredity</i>, vol. 105, no. 1, Oxford University Press, 2014, pp. 130–35, doi:<a href=\"https://doi.org/10.1093/jhered/est063\">10.1093/jhered/est063</a>.","ista":"Phadke S, Paixao T, Pham T, Pham S, Zufall R. 2014. Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal of Heredity. 105(1), 130–135.","short":"S. Phadke, T. Paixao, T. Pham, S. Pham, R. Zufall, Journal of Heredity 105 (2014) 130–135."},"scopus_import":"1","abstract":[{"text":"The pattern of inheritance and mechanism of sex determination can have important evolutionary consequences. We studied probabilistic sex determination in the ciliate Tetrahymena thermophila, which was previously shown to cause evolution of skewed sex ratios. We find that the genetic background alters the sex determination patterns of mat alleles in heterozygotes and that allelic interaction can differentially influence the expression probability of the 7 sexes. We quantify the dominance relationships between several mat alleles and find that A-type alleles, which specify sex I, are indeed recessive to B-type alleles, which are unable to specify that sex. Our results provide additional support for the presence of modifier loci and raise implications for the dynamics of sex ratios in populations of T. thermophila.","lang":"eng"}],"publisher":"Oxford University Press","status":"public","publication_identifier":{"issn":["0022-1503"]},"type":"journal_article"},{"title":"Coalescent simulation in continuous space: Algorithms for large neighbourhood size","isi":1,"article_processing_charge":"No","date_published":"2014-08-01T00:00:00Z","volume":95,"publist_id":"4816","month":"08","external_id":{"isi":["000339460300002"]},"date_updated":"2025-09-29T11:39:51Z","quality_controlled":"1","publisher":"Academic Press","oa_version":"Published Version","scopus_import":"1","abstract":[{"text":"Many species have an essentially continuous distribution in space, in which there are no natural divisions between randomly mating subpopulations. Yet, the standard approach to modelling these populations is to impose an arbitrary grid of demes, adjusting deme sizes and migration rates in an attempt to capture the important features of the population. Such indirect methods are required because of the failure of the classical models of isolation by distance, which have been shown to have major technical flaws. A recently introduced model of extinction and recolonisation in two dimensions solves these technical problems, and provides a rigorous technical foundation for the study of populations evolving in a spatial continuum. The coalescent process for this model is simply stated, but direct simulation is very inefficient for large neighbourhood sizes. We present efficient and exact algorithms to simulate this coalescent process for arbitrary sample sizes and numbers of loci, and analyse these algorithms in detail.","lang":"eng"}],"citation":{"chicago":"Kelleher, Jerome, Alison Etheridge, and Nicholas H Barton. “Coalescent Simulation in Continuous Space: Algorithms for Large Neighbourhood Size.” <i>Theoretical Population Biology</i>. Academic Press, 2014. <a href=\"https://doi.org/10.1016/j.tpb.2014.05.001\">https://doi.org/10.1016/j.tpb.2014.05.001</a>.","apa":"Kelleher, J., Etheridge, A., &#38; Barton, N. H. (2014). Coalescent simulation in continuous space: Algorithms for large neighbourhood size. <i>Theoretical Population Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.tpb.2014.05.001\">https://doi.org/10.1016/j.tpb.2014.05.001</a>","ista":"Kelleher J, Etheridge A, Barton NH. 2014. Coalescent simulation in continuous space: Algorithms for large neighbourhood size. Theoretical Population Biology. 95, 13–23.","short":"J. Kelleher, A. Etheridge, N.H. Barton, Theoretical Population Biology 95 (2014) 13–23.","mla":"Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space: Algorithms for Large Neighbourhood Size.” <i>Theoretical Population Biology</i>, vol. 95, Academic Press, 2014, pp. 13–23, doi:<a href=\"https://doi.org/10.1016/j.tpb.2014.05.001\">10.1016/j.tpb.2014.05.001</a>.","ieee":"J. Kelleher, A. Etheridge, and N. H. Barton, “Coalescent simulation in continuous space: Algorithms for large neighbourhood size,” <i>Theoretical Population Biology</i>, vol. 95. Academic Press, pp. 13–23, 2014.","ama":"Kelleher J, Etheridge A, Barton NH. Coalescent simulation in continuous space: Algorithms for large neighbourhood size. <i>Theoretical Population Biology</i>. 2014;95:13-23. doi:<a href=\"https://doi.org/10.1016/j.tpb.2014.05.001\">10.1016/j.tpb.2014.05.001</a>"},"type":"journal_article","status":"public","date_created":"2018-12-11T11:56:06Z","year":"2014","doi":"10.1016/j.tpb.2014.05.001","file":[{"file_id":"4839","date_created":"2018-12-12T10:10:49Z","file_name":"IST-2015-391-v1+1_1-s2.0-S0040580914000355-main.pdf","access_level":"open_access","creator":"system","checksum":"979d7a8034e9df198f068f0d251f31bd","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:45:31Z","file_size":569005}],"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"publication_status":"published","oa":1,"intvolume":"        95","pubrep_id":"391","file_date_updated":"2020-07-14T12:45:31Z","author":[{"last_name":"Kelleher","first_name":"Jerome","full_name":"Kelleher, Jerome"},{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"ddc":["570"],"language":[{"iso":"eng"}],"page":"13 - 23","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"NiBa"}],"ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2168","publication":"Theoretical Population Biology","day":"01"},{"day":"22","publication":"PNAS","corr_author":"1","issue":"29","department":[{"_id":"NiBa"}],"_id":"2169","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"10398 - 10399","author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"},{"orcid":"0000-0002-2519-824X","last_name":"Novak","first_name":"Sebastian","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","last_name":"Paixao","first_name":"Tiago"}],"language":[{"iso":"eng"}],"intvolume":"       111","doi":"10.1073/pnas.1410107111","publication_status":"published","oa":1,"year":"2014","date_created":"2018-12-11T11:56:07Z","status":"public","type":"journal_article","oa_version":"Submitted Version","scopus_import":"1","citation":{"apa":"Barton, N. H., Novak, S., &#38; Paixao, T. (2014). Diverse forms of selection in evolution and computer science. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1410107111\">https://doi.org/10.1073/pnas.1410107111</a>","chicago":"Barton, Nicholas H, Sebastian Novak, and Tiago Paixao. “Diverse Forms of Selection in Evolution and Computer Science.” <i>PNAS</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1410107111\">https://doi.org/10.1073/pnas.1410107111</a>.","mla":"Barton, Nicholas H., et al. “Diverse Forms of Selection in Evolution and Computer Science.” <i>PNAS</i>, vol. 111, no. 29, National Academy of Sciences, 2014, pp. 10398–99, doi:<a href=\"https://doi.org/10.1073/pnas.1410107111\">10.1073/pnas.1410107111</a>.","short":"N.H. Barton, S. Novak, T. Paixao, PNAS 111 (2014) 10398–10399.","ista":"Barton NH, Novak S, Paixao T. 2014. Diverse forms of selection in evolution and computer science. PNAS. 111(29), 10398–10399.","ieee":"N. H. Barton, S. Novak, and T. Paixao, “Diverse forms of selection in evolution and computer science,” <i>PNAS</i>, vol. 111, no. 29. National Academy of Sciences, pp. 10398–10399, 2014.","ama":"Barton NH, Novak S, Paixao T. Diverse forms of selection in evolution and computer science. <i>PNAS</i>. 2014;111(29):10398-10399. doi:<a href=\"https://doi.org/10.1073/pnas.1410107111\">10.1073/pnas.1410107111</a>"},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4115508/"}],"publisher":"National Academy of Sciences","quality_controlled":"1","date_updated":"2025-09-29T11:39:19Z","external_id":{"isi":["000339310700017"]},"month":"07","publist_id":"4815","volume":111,"isi":1,"date_published":"2014-07-22T00:00:00Z","article_processing_charge":"No","title":"Diverse forms of selection in evolution and computer science"},{"publication":"Molecular Ecology","day":"01","has_accepted_license":"1","page":"198 - 211","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2170","issue":"1","department":[{"_id":"NiBa"}],"intvolume":"        23","publication_status":"published","oa":1,"doi":"10.1111/mec.12578","file":[{"content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:45:31Z","file_size":807444,"access_level":"open_access","file_name":"IST-2016-559-v1+1_Hearn_et_al.pdf","creator":"system","checksum":"4de1ab255976a8ae77eb0e55ad62ecc9","file_id":"4651","date_created":"2018-12-12T10:07:52Z"},{"creator":"system","checksum":"01a8073e071c088500425f910b0f1f71","file_name":"IST-2016-559-v1+2_Hearn_et_al_Suppl.pdf","access_level":"open_access","date_created":"2018-12-12T10:07:53Z","file_id":"4652","file_size":1518088,"date_updated":"2020-07-14T12:45:31Z","relation":"main_file","content_type":"application/pdf"}],"ddc":["570"],"language":[{"iso":"eng"}],"author":[{"full_name":"Hearn, Jack","first_name":"Jack","last_name":"Hearn"},{"last_name":"Stone","first_name":"Graham","full_name":"Stone, Graham"},{"first_name":"Lynsey","last_name":"Bunnefeld","full_name":"Bunnefeld, Lynsey"},{"full_name":"Nicholls, James","first_name":"James","last_name":"Nicholls"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"},{"last_name":"Lohse","first_name":"Konrad","full_name":"Lohse, Konrad"}],"file_date_updated":"2020-07-14T12:45:31Z","pubrep_id":"559","date_created":"2018-12-11T11:56:07Z","year":"2014","status":"public","type":"journal_article","related_material":{"record":[{"status":"public","id":"9754","relation":"research_data"}]},"publisher":"Wiley-Blackwell","citation":{"chicago":"Hearn, Jack, Graham Stone, Lynsey Bunnefeld, James Nicholls, Nicholas H Barton, and Konrad Lohse. “Likelihood-Based Inference of Population History from Low-Coverage de Novo Genome Assemblies.” <i>Molecular Ecology</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1111/mec.12578\">https://doi.org/10.1111/mec.12578</a>.","apa":"Hearn, J., Stone, G., Bunnefeld, L., Nicholls, J., Barton, N. H., &#38; Lohse, K. (2014). Likelihood-based inference of population history from low-coverage de novo genome assemblies. <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/mec.12578\">https://doi.org/10.1111/mec.12578</a>","ista":"Hearn J, Stone G, Bunnefeld L, Nicholls J, Barton NH, Lohse K. 2014. Likelihood-based inference of population history from low-coverage de novo genome assemblies. Molecular Ecology. 23(1), 198–211.","short":"J. Hearn, G. Stone, L. Bunnefeld, J. Nicholls, N.H. Barton, K. Lohse, Molecular Ecology 23 (2014) 198–211.","mla":"Hearn, Jack, et al. “Likelihood-Based Inference of Population History from Low-Coverage de Novo Genome Assemblies.” <i>Molecular Ecology</i>, vol. 23, no. 1, Wiley-Blackwell, 2014, pp. 198–211, doi:<a href=\"https://doi.org/10.1111/mec.12578\">10.1111/mec.12578</a>.","ieee":"J. Hearn, G. Stone, L. Bunnefeld, J. Nicholls, N. H. Barton, and K. Lohse, “Likelihood-based inference of population history from low-coverage de novo genome assemblies,” <i>Molecular Ecology</i>, vol. 23, no. 1. Wiley-Blackwell, pp. 198–211, 2014.","ama":"Hearn J, Stone G, Bunnefeld L, Nicholls J, Barton NH, Lohse K. Likelihood-based inference of population history from low-coverage de novo genome assemblies. <i>Molecular Ecology</i>. 2014;23(1):198-211. doi:<a href=\"https://doi.org/10.1111/mec.12578\">10.1111/mec.12578</a>"},"abstract":[{"text":" Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate between recent, nonequilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida), which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning the Western Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources.","lang":"eng"}],"scopus_import":"1","oa_version":"Submitted Version","month":"01","date_updated":"2025-09-29T11:38:51Z","quality_controlled":"1","external_id":{"isi":["000330950900017"]},"date_published":"2014-01-01T00:00:00Z","article_processing_charge":"No","acknowledgement":"This work was funded by NERC grants to G Stone, J Nicholls, K Lohse and N Barton (NE/J010499, NBAF375, NE/E014453/1 and NER/B/S2003/00856).","isi":1,"title":"Likelihood-based inference of population history from low-coverage de novo genome assemblies","publist_id":"4814","volume":23},{"type":"journal_article","status":"public","publisher":"Genetics Society of America","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.1017"}],"oa_version":"Submitted Version","citation":{"ama":"De Vladar H, Barton NH. Stability and response of polygenic traits to stabilizing selection and mutation. <i>Genetics</i>. 2014;197(2):749-767. doi:<a href=\"https://doi.org/10.1534/genetics.113.159111\">10.1534/genetics.113.159111</a>","ieee":"H. De Vladar and N. H. Barton, “Stability and response of polygenic traits to stabilizing selection and mutation,” <i>Genetics</i>, vol. 197, no. 2. Genetics Society of America, pp. 749–767, 2014.","mla":"De Vladar, Harold, and Nicholas H. Barton. “Stability and Response of Polygenic Traits to Stabilizing Selection and Mutation.” <i>Genetics</i>, vol. 197, no. 2, Genetics Society of America, 2014, pp. 749–67, doi:<a href=\"https://doi.org/10.1534/genetics.113.159111\">10.1534/genetics.113.159111</a>.","short":"H. De Vladar, N.H. Barton, Genetics 197 (2014) 749–767.","ista":"De Vladar H, Barton NH. 2014. Stability and response of polygenic traits to stabilizing selection and mutation. Genetics. 197(2), 749–767.","apa":"De Vladar, H., &#38; Barton, N. H. (2014). Stability and response of polygenic traits to stabilizing selection and mutation. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.113.159111\">https://doi.org/10.1534/genetics.113.159111</a>","chicago":"De Vladar, Harold, and Nicholas H Barton. “Stability and Response of Polygenic Traits to Stabilizing Selection and Mutation.” <i>Genetics</i>. Genetics Society of America, 2014. <a href=\"https://doi.org/10.1534/genetics.113.159111\">https://doi.org/10.1534/genetics.113.159111</a>."},"scopus_import":"1","abstract":[{"text":"When polygenic traits are under stabilizing selection, many different combinations of alleles allow close adaptation to the optimum. If alleles have equal effects, all combinations that result in the same deviation from the optimum are equivalent. Furthermore, the genetic variance that is maintained by mutation-selection balance is 2μ/S per locus, where μ is the mutation rate and S the strength of stabilizing selection. In reality, alleles vary in their effects, making the fitness landscape asymmetric and complicating analysis of the equilibria. We show that that the resulting genetic variance depends on the fraction of alleles near fixation, which contribute by 2μ/S, and on the total mutational effects of alleles that are at intermediate frequency. The inpplayfi between stabilizing selection and mutation leads to a sharp transition: alleles with effects smaller than a threshold value of 2 remain polymorphic, whereas those with larger effects are fixed. The genetic load in equilibrium is less than for traits of equal effects, and the fitness equilibria are more similar. We find p the optimum is displaced, alleles with effects close to the threshold value sweep first, and their rate of increase is bounded by Long-term response leads in general to well-adapted traits, unlike the case of equal effects that often end up at a suboptimal fitness peak. However, the particular peaks to which the populations converge are extremely sensitive to the initial states and to the speed of the shift of the optimum trait value.","lang":"eng"}],"month":"06","external_id":{"arxiv":["1404.1017"],"isi":["000338697000027"]},"quality_controlled":"1","date_updated":"2025-09-29T11:37:14Z","title":"Stability and response of polygenic traits to stabilizing selection and mutation","isi":1,"date_published":"2014-06-01T00:00:00Z","arxiv":1,"article_processing_charge":"No","volume":197,"publist_id":"4809","corr_author":"1","publication":"Genetics","day":"01","page":"749 - 767","ec_funded":1,"issue":"2","department":[{"_id":"NiBa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2174","doi":"10.1534/genetics.113.159111","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"oa":1,"publication_status":"published","intvolume":"       197","author":[{"last_name":"De Vladar","first_name":"Harold","full_name":"De Vladar, Harold"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:56:08Z","year":"2014"},{"author":[{"last_name":"Kollár","first_name":"Richard","full_name":"Kollár, Richard"},{"orcid":"0000-0002-7214-0171","last_name":"Bod'ová","first_name":"Katarína","full_name":"Bod'ová, Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nosek, Jozef","first_name":"Jozef","last_name":"Nosek"},{"full_name":"Tomáška, Ľubomír","first_name":"Ľubomír","last_name":"Tomáška"}],"language":[{"iso":"eng"}],"intvolume":"        89","doi":"10.1103/PhysRevE.89.032701","publication_status":"published","oa":1,"year":"2014","date_created":"2018-12-11T11:54:35Z","day":"04","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"issue":"3","_id":"1896","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-29T13:03:34Z","external_id":{"isi":["000332274100002"],"arxiv":["1402.0430"]},"month":"03","publist_id":"5198","volume":89,"acknowledgement":"The work was supported by the VEGA Grant No. 1/0459/13 (R.K. and K.B.).","isi":1,"article_processing_charge":"No","arxiv":1,"date_published":"2014-03-04T00:00:00Z","title":"Mathematical model of alternative mechanism of telomere length maintenance","status":"public","type":"journal_article","oa_version":"Submitted Version","citation":{"ama":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism of telomere length maintenance. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2014;89(3). doi:<a href=\"https://doi.org/10.1103/PhysRevE.89.032701\">10.1103/PhysRevE.89.032701</a>","ieee":"R. Kollár, K. Bodova, J. Nosek, and Ľ. Tomáška, “Mathematical model of alternative mechanism of telomere length maintenance,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 89, no. 3. American Institute of Physics, 2014.","mla":"Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 89, no. 3, 032701, American Institute of Physics, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevE.89.032701\">10.1103/PhysRevE.89.032701</a>.","short":"R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).","ista":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. 2014. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(3), 032701.","apa":"Kollár, R., Bodova, K., Nosek, J., &#38; Tomáška, Ľ. (2014). Mathematical model of alternative mechanism of telomere length maintenance. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.89.032701\">https://doi.org/10.1103/PhysRevE.89.032701</a>","chicago":"Kollár, Richard, Katarina Bodova, Jozef Nosek, and Ľubomír Tomáška. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2014. <a href=\"https://doi.org/10.1103/PhysRevE.89.032701\">https://doi.org/10.1103/PhysRevE.89.032701</a>."},"article_number":"032701","abstract":[{"text":"Biopolymer length regulation is a complex process that involves a large number of biological, chemical, and physical subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length regulation of telomeres - nucleoprotein structures at the ends of linear chromosomes consisting of tandemly repeated DNA sequences and a specialized set of proteins. Maintenance of telomeres is often facilitated by the enzyme telomerase but, particularly in telomerase-free systems, the maintenance of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms mediated by recombination. Various linear and circular DNA structures were identified to participate in ALT, however, dynamics of the whole process is still poorly understood. We propose a chemical kinetics model of ALT with kinetic rates systematically derived from the biophysics of DNA diffusion and looping. The reaction system is reduced to a coagulation-fragmentation system by quasi-steady-state approximation. The detailed treatment of kinetic rates yields explicit formulas for expected size distributions of telomeres that demonstrate the key role played by the J factor, a quantitative measure of bending of polymers. The results are in agreement with experimental data and point out interesting phenomena: an appearance of very long telomeric circles if the total telomere density exceeds a critical value (excess mass) and a nonlinear response of the telomere size distributions to the amount of telomeric DNA in the system. The results can be of general importance for understanding dynamics of telomeres in telomerase-independent systems as this mode of telomere maintenance is similar to the situation in tumor cells lacking telomerase activity. Furthermore, due to its universality, the model may also serve as a prototype of an interaction between linear and circular DNA structures in various settings.","lang":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1402.0430"}],"publisher":"American Institute of Physics"},{"page":"1167 - 1183","_id":"1908","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"department":[{"_id":"NiBa"}],"issue":"4","corr_author":"1","publication":"Genetics","day":"01","date_created":"2018-12-11T11:54:39Z","year":"2014","oa":1,"publication_status":"published","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"doi":"10.1534/genetics.113.160705","intvolume":"       196","language":[{"iso":"eng"}],"author":[{"first_name":"Daniel","last_name":"Weissman","full_name":"Weissman, Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hallatschek, Oskar","last_name":"Hallatschek","first_name":"Oskar"}],"publisher":"Genetics Society of America","main_file_link":[{"url":"http://arxiv.org/abs/1307.0737","open_access":"1"}],"abstract":[{"text":"In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can bring together beneficial alleles from different backgrounds, but tightly linked alleles may still greatly interfere with each other. We show for well-mixed populations that when this interference is strong, the genome can be seen as consisting of many effectively asexual stretches linked together. The rate at which beneficial alleles fix is thus roughly proportional to the rate of recombination and depends only logarithmically on the mutation supply and the strength of selection. Our scaling arguments also allow us to predict, with reasonable accuracy, the fitness distribution of fixed mutations when the mutational effect sizes are broad. We focus on the regime in which crossovers occur more frequently than beneficial mutations, as is likely to be the case for many natural populations.","lang":"eng"}],"scopus_import":"1","citation":{"ieee":"D. Weissman and O. Hallatschek, “The rate of adaptation in large sexual populations with linear chromosomes,” <i>Genetics</i>, vol. 196, no. 4. Genetics Society of America, pp. 1167–1183, 2014.","ama":"Weissman D, Hallatschek O. The rate of adaptation in large sexual populations with linear chromosomes. <i>Genetics</i>. 2014;196(4):1167-1183. doi:<a href=\"https://doi.org/10.1534/genetics.113.160705\">10.1534/genetics.113.160705</a>","apa":"Weissman, D., &#38; Hallatschek, O. (2014). The rate of adaptation in large sexual populations with linear chromosomes. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.113.160705\">https://doi.org/10.1534/genetics.113.160705</a>","chicago":"Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” <i>Genetics</i>. Genetics Society of America, 2014. <a href=\"https://doi.org/10.1534/genetics.113.160705\">https://doi.org/10.1534/genetics.113.160705</a>.","mla":"Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” <i>Genetics</i>, vol. 196, no. 4, Genetics Society of America, 2014, pp. 1167–83, doi:<a href=\"https://doi.org/10.1534/genetics.113.160705\">10.1534/genetics.113.160705</a>.","short":"D. Weissman, O. Hallatschek, Genetics 196 (2014) 1167–1183.","ista":"Weissman D, Hallatschek O. 2014. The rate of adaptation in large sexual populations with linear chromosomes. Genetics. 196(4), 1167–1183."},"oa_version":"Submitted Version","type":"journal_article","status":"public","title":"The rate of adaptation in large sexual populations with linear chromosomes","arxiv":1,"date_published":"2014-04-01T00:00:00Z","article_processing_charge":"No","isi":1,"volume":196,"publist_id":"5187","month":"04","external_id":{"isi":["000334179300022"],"arxiv":["1307.0737"]},"quality_controlled":"1","date_updated":"2025-09-29T12:27:03Z"},{"abstract":[{"lang":"eng","text":"Summary: Phenotypes are often environmentally dependent, which requires organisms to track environmental change. The challenge for organisms is to construct phenotypes using the most accurate environmental cue. Here, we use a quantitative genetic model of adaptation by additive genetic variance, within- and transgenerational plasticity via linear reaction norms and indirect genetic effects respectively. We show how the relative influence on the eventual phenotype of these components depends on the predictability of environmental change (fast or slow, sinusoidal or stochastic) and the developmental lag τ between when the environment is perceived and when selection acts. We then decompose expected mean fitness into three components (variance load, adaptation and fluctuation load) to study the fitness costs of within- and transgenerational plasticity. A strongly negative maternal effect coefficient m minimizes the variance load, but a strongly positive m minimises the fluctuation load. The adaptation term is maximized closer to zero, with positive or negative m preferred under different environmental scenarios. Phenotypic plasticity is higher when τ is shorter and when the environment changes frequently between seasonal extremes. Expected mean population fitness is highest away from highest observed levels of phenotypic plasticity. Within- and transgenerational plasticity act in concert to deliver well-adapted phenotypes, which emphasizes the need to study both simultaneously when investigating phenotypic evolution."}],"citation":{"ama":"Ezard T, Prizak R, Hoyle R. The fitness costs of adaptation via phenotypic plasticity and maternal effects. <i>Functional Ecology</i>. 2014;28(3):693-701. doi:<a href=\"https://doi.org/10.1111/1365-2435.12207\">10.1111/1365-2435.12207</a>","ieee":"T. Ezard, R. Prizak, and R. Hoyle, “The fitness costs of adaptation via phenotypic plasticity and maternal effects,” <i>Functional Ecology</i>, vol. 28, no. 3. Wiley-Blackwell, pp. 693–701, 2014.","short":"T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701.","ista":"Ezard T, Prizak R, Hoyle R. 2014. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 28(3), 693–701.","mla":"Ezard, Thomas, et al. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” <i>Functional Ecology</i>, vol. 28, no. 3, Wiley-Blackwell, 2014, pp. 693–701, doi:<a href=\"https://doi.org/10.1111/1365-2435.12207\">10.1111/1365-2435.12207</a>.","chicago":"Ezard, Thomas, Roshan Prizak, and Rebecca Hoyle. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” <i>Functional Ecology</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1111/1365-2435.12207\">https://doi.org/10.1111/1365-2435.12207</a>.","apa":"Ezard, T., Prizak, R., &#38; Hoyle, R. (2014). The fitness costs of adaptation via phenotypic plasticity and maternal effects. <i>Functional Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/1365-2435.12207\">https://doi.org/10.1111/1365-2435.12207</a>"},"scopus_import":"1","oa_version":"Published Version","publisher":"Wiley-Blackwell","type":"journal_article","status":"public","volume":28,"publist_id":"5186","title":"The fitness costs of adaptation via phenotypic plasticity and maternal effects","article_processing_charge":"No","date_published":"2014-06-01T00:00:00Z","acknowledgement":"Engineering and Physical Sciences Research Council. Grant Number: EP/H031928/1","isi":1,"external_id":{"isi":["000335954900016"]},"date_updated":"2025-09-29T12:26:34Z","month":"06","_id":"1909","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"issue":"3","page":"693 - 701","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","day":"01","publication":"Functional Ecology","year":"2014","date_created":"2018-12-11T11:54:40Z","file_date_updated":"2020-07-14T12:45:20Z","pubrep_id":"419","language":[{"iso":"eng"}],"ddc":["570"],"author":[{"full_name":"Ezard, Thomas","first_name":"Thomas","last_name":"Ezard"},{"first_name":"Roshan","last_name":"Prizak","id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan"},{"first_name":"Rebecca","last_name":"Hoyle","full_name":"Hoyle, Rebecca"}],"publication_status":"published","oa":1,"file":[{"file_size":536154,"content_type":"application/pdf","date_updated":"2020-07-14T12:45:20Z","relation":"main_file","creator":"system","checksum":"3cbe8623174709a8ceec2103246f8fe0","access_level":"open_access","file_name":"IST-2016-419-v1+1_Ezard_et_al-2014-Functional_Ecology.pdf","date_created":"2018-12-12T10:15:45Z","file_id":"5167"}],"doi":"10.1111/1365-2435.12207","intvolume":"        28"},{"date_created":"2018-12-11T11:54:47Z","year":"2014","intvolume":"        68","oa":1,"publication_status":"published","doi":"10.1111/evo.12517","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"author":[{"last_name":"Trotter","first_name":"Meredith","full_name":"Trotter, Meredith"},{"first_name":"Daniel","last_name":"Weissman","full_name":"Weissman, Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Peterson, Grant","first_name":"Grant","last_name":"Peterson"},{"full_name":"Peck, Kayla","first_name":"Kayla","last_name":"Peck"},{"last_name":"Masel","first_name":"Joanna","full_name":"Masel, Joanna"}],"page":"3357 - 3367","_id":"1932","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"department":[{"_id":"NiBa"}],"issue":"12","publication":"Evolution","day":"01","arxiv":1,"article_processing_charge":"No","date_published":"2014-12-01T00:00:00Z","acknowledgement":"Funded by National Institutes of Health. Grant Numbers: R01GM076041, R01GM104040         \r\n\r\nSimons Foundation\r\n\r\n","isi":1,"title":"Cryptic genetic variation can make &quot;irreducible complexity&quot; a common mode of adaptation in sexual populations","publist_id":"5162","volume":68,"month":"12","date_updated":"2025-09-29T12:10:43Z","quality_controlled":"1","external_id":{"arxiv":["1310.6077"],"isi":["000346075600001"]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1310.6077"}],"publisher":"Wiley-Blackwell","abstract":[{"text":"The existence of complex (multiple-step) genetic adaptations that are &quot;irreducible&quot; (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard genetics parlance, these adaptations require the crossing of a wide adaptive valley of deleterious intermediate stages. Here, we demonstrate, using a simple model, that evolution can cross wide valleys to produce &quot;irreducibly complex&quot; adaptations by making use of previously cryptic mutations. When revealed by an evolutionary capacitor, previously cryptic mutants have higher initial frequencies than do new mutations, bringing them closer to a valley-crossing saddle in allele frequency space. Moreover, simple combinatorics implies an enormous number of candidate combinations exist within available cryptic genetic variation. We model the dynamics of crossing of a wide adaptive valley after a capacitance event using both numerical simulations and analytical approximations. Although individual valley crossing events become less likely as valleys widen, by taking the combinatorics of genotype space into account, we see that revealing cryptic variation can cause the frequent evolution of complex adaptations.","lang":"eng"}],"citation":{"apa":"Trotter, M., Weissman, D., Peterson, G., Peck, K., &#38; Masel, J. (2014). Cryptic genetic variation can make &#38;quot;irreducible complexity&#38;quot; a common mode of adaptation in sexual populations. <i>Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/evo.12517\">https://doi.org/10.1111/evo.12517</a>","chicago":"Trotter, Meredith, Daniel Weissman, Grant Peterson, Kayla Peck, and Joanna Masel. “Cryptic Genetic Variation Can Make &#38;quot;Irreducible Complexity&#38;quot; a Common Mode of Adaptation in Sexual Populations.” <i>Evolution</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1111/evo.12517\">https://doi.org/10.1111/evo.12517</a>.","mla":"Trotter, Meredith, et al. “Cryptic Genetic Variation Can Make &#38;quot;Irreducible Complexity&#38;quot; a Common Mode of Adaptation in Sexual Populations.” <i>Evolution</i>, vol. 68, no. 12, Wiley-Blackwell, 2014, pp. 3357–67, doi:<a href=\"https://doi.org/10.1111/evo.12517\">10.1111/evo.12517</a>.","short":"M. Trotter, D. Weissman, G. Peterson, K. Peck, J. Masel, Evolution 68 (2014) 3357–3367.","ista":"Trotter M, Weissman D, Peterson G, Peck K, Masel J. 2014. Cryptic genetic variation can make &#38;quot;irreducible complexity&#38;quot; a common mode of adaptation in sexual populations. Evolution. 68(12), 3357–3367.","ieee":"M. Trotter, D. Weissman, G. Peterson, K. Peck, and J. Masel, “Cryptic genetic variation can make &#38;quot;irreducible complexity&#38;quot; a common mode of adaptation in sexual populations,” <i>Evolution</i>, vol. 68, no. 12. Wiley-Blackwell, pp. 3357–3367, 2014.","ama":"Trotter M, Weissman D, Peterson G, Peck K, Masel J. Cryptic genetic variation can make &#38;quot;irreducible complexity&#38;quot; a common mode of adaptation in sexual populations. <i>Evolution</i>. 2014;68(12):3357-3367. doi:<a href=\"https://doi.org/10.1111/evo.12517\">10.1111/evo.12517</a>"},"scopus_import":"1","oa_version":"Submitted Version","status":"public","type":"journal_article"},{"type":"journal_article","status":"public","oa_version":"Submitted Version","scopus_import":"1","citation":{"ama":"Arbilly M, Weissman D, Feldman M, Grodzinski U. An arms race between producers and scroungers can drive the evolution of social cognition. <i>Behavioral Ecology</i>. 2014;25(3):487-495. doi:<a href=\"https://doi.org/10.1093/beheco/aru002\">10.1093/beheco/aru002</a>","ieee":"M. Arbilly, D. Weissman, M. Feldman, and U. Grodzinski, “An arms race between producers and scroungers can drive the evolution of social cognition,” <i>Behavioral Ecology</i>, vol. 25, no. 3. Oxford University Press, pp. 487–495, 2014.","mla":"Arbilly, Michal, et al. “An Arms Race between Producers and Scroungers Can Drive the Evolution of Social Cognition.” <i>Behavioral Ecology</i>, vol. 25, no. 3, Oxford University Press, 2014, pp. 487–95, doi:<a href=\"https://doi.org/10.1093/beheco/aru002\">10.1093/beheco/aru002</a>.","ista":"Arbilly M, Weissman D, Feldman M, Grodzinski U. 2014. An arms race between producers and scroungers can drive the evolution of social cognition. Behavioral Ecology. 25(3), 487–495.","short":"M. Arbilly, D. Weissman, M. Feldman, U. Grodzinski, Behavioral Ecology 25 (2014) 487–495.","apa":"Arbilly, M., Weissman, D., Feldman, M., &#38; Grodzinski, U. (2014). An arms race between producers and scroungers can drive the evolution of social cognition. <i>Behavioral Ecology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/beheco/aru002\">https://doi.org/10.1093/beheco/aru002</a>","chicago":"Arbilly, Michal, Daniel Weissman, Marcus Feldman, and Uri Grodzinski. “An Arms Race between Producers and Scroungers Can Drive the Evolution of Social Cognition.” <i>Behavioral Ecology</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/beheco/aru002\">https://doi.org/10.1093/beheco/aru002</a>."},"abstract":[{"text":"The social intelligence hypothesis states that the need to cope with complexities of social life has driven the evolution of advanced cognitive abilities. It is usually invoked in the context of challenges arising from complex intragroup structures, hierarchies, and alliances. However, a fundamental aspect of group living remains largely unexplored as a driving force in cognitive evolution: the competition between individuals searching for resources (producers) and conspecifics that parasitize their findings (scroungers). In populations of social foragers, abilities that enable scroungers to steal by outsmarting producers, and those allowing producers to prevent theft by outsmarting scroungers, are likely to be beneficial and may fuel a cognitive arms race. Using analytical theory and agent-based simulations, we present a general model for such a race that is driven by the producer-scrounger game and show that the race's plausibility is dramatically affected by the nature of the evolving abilities. If scrounging and scrounging avoidance rely on separate, strategy-specific cognitive abilities, arms races are short-lived and have a limited effect on cognition. However, general cognitive abilities that facilitate both scrounging and scrounging avoidance undergo stable, long-lasting arms races. Thus, ubiquitous foraging interactions may lead to the evolution of general cognitive abilities in social animals, without the requirement of complex intragroup structures.","lang":"eng"}],"publisher":"Oxford University Press","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014306/"}],"external_id":{"isi":["000336486100012"]},"date_updated":"2025-09-29T12:07:50Z","quality_controlled":"1","month":"02","volume":25,"publist_id":"5157","title":"An arms race between producers and scroungers can drive the evolution of social cognition","isi":1,"article_processing_charge":"No","date_published":"2014-02-13T00:00:00Z","day":"13","publication":"Behavioral Ecology","ec_funded":1,"issue":"3","department":[{"_id":"NiBa"}],"_id":"1936","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"487 - 495","author":[{"last_name":"Arbilly","first_name":"Michal","full_name":"Arbilly, Michal"},{"id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","full_name":"Weissman, Daniel","first_name":"Daniel","last_name":"Weissman"},{"full_name":"Feldman, Marcus","last_name":"Feldman","first_name":"Marcus"},{"full_name":"Grodzinski, Uri","first_name":"Uri","last_name":"Grodzinski"}],"language":[{"iso":"eng"}],"doi":"10.1093/beheco/aru002","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"oa":1,"publication_status":"published","intvolume":"        25","year":"2014","date_created":"2018-12-11T11:54:48Z"},{"date_updated":"2025-09-29T13:17:53Z","external_id":{"isi":["000340575000015"]},"month":"07","publist_id":"7280","volume":4,"article_processing_charge":"No","date_published":"2014-07-19T00:00:00Z","isi":1,"title":"Fitness consequences of maternal and grandmaternal effects","status":"public","type":"journal_article","citation":{"ieee":"R. Prizak, T. Ezard, and R. Hoyle, “Fitness consequences of maternal and grandmaternal effects,” <i>Ecology and Evolution</i>, vol. 4, no. 15. Wiley-Blackwell, pp. 3139–3145, 2014.","ama":"Prizak R, Ezard T, Hoyle R. Fitness consequences of maternal and grandmaternal effects. <i>Ecology and Evolution</i>. 2014;4(15):3139-3145. doi:<a href=\"https://doi.org/10.1002/ece3.1150\">10.1002/ece3.1150</a>","chicago":"Prizak, Roshan, Thomas Ezard, and Rebecca Hoyle. “Fitness Consequences of Maternal and Grandmaternal Effects.” <i>Ecology and Evolution</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/ece3.1150\">https://doi.org/10.1002/ece3.1150</a>.","apa":"Prizak, R., Ezard, T., &#38; Hoyle, R. (2014). Fitness consequences of maternal and grandmaternal effects. <i>Ecology and Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/ece3.1150\">https://doi.org/10.1002/ece3.1150</a>","ista":"Prizak R, Ezard T, Hoyle R. 2014. Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. 4(15), 3139–3145.","short":"R. Prizak, T. Ezard, R. Hoyle, Ecology and Evolution 4 (2014) 3139–3145.","mla":"Prizak, Roshan, et al. “Fitness Consequences of Maternal and Grandmaternal Effects.” <i>Ecology and Evolution</i>, vol. 4, no. 15, Wiley-Blackwell, 2014, pp. 3139–45, doi:<a href=\"https://doi.org/10.1002/ece3.1150\">10.1002/ece3.1150</a>."},"abstract":[{"text":"Transgenerational effects are broader than only parental relationships. Despite mounting evidence that multigenerational effects alter phenotypic and life-history traits, our understanding of how they combine to determine fitness is not well developed because of the added complexity necessary to study them. Here, we derive a quantitative genetic model of adaptation to an extraordinary new environment by an additive genetic component, phenotypic plasticity, maternal and grandmaternal effects. We show how, at equilibrium, negative maternal and negative grandmaternal effects maximize expected population mean fitness. We define negative transgenerational effects as those that have a negative effect on trait expression in the subsequent generation, that is, they slow, or potentially reverse, the expected evolutionary dynamic. When maternal effects are positive, negative grandmaternal effects are preferred. As expected under Mendelian inheritance, the grandmaternal effects have a lower impact on fitness than the maternal effects, but this dual inheritance model predicts a more complex relationship between maternal and grandmaternal effects to constrain phenotypic variance and so maximize expected population mean fitness in the offspring.","lang":"eng"}],"scopus_import":"1","oa_version":"Published Version","publisher":"Wiley-Blackwell","language":[{"iso":"eng"}],"ddc":["530","571"],"author":[{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan","first_name":"Roshan","last_name":"Prizak"},{"first_name":"Thomas","last_name":"Ezard","full_name":"Ezard, Thomas"},{"full_name":"Hoyle, Rebecca","first_name":"Rebecca","last_name":"Hoyle"}],"file_date_updated":"2020-07-14T12:46:38Z","pubrep_id":"934","intvolume":"         4","publication_status":"published","oa":1,"file":[{"checksum":"e32abf75a248e7a11811fd7f60858769","creator":"system","file_name":"IST-2018-934-v1+1_Prizak_et_al-2014-Ecology_and_Evolution.pdf","access_level":"open_access","date_created":"2018-12-12T10:11:31Z","file_id":"4886","file_size":621582,"date_updated":"2020-07-14T12:46:38Z","content_type":"application/pdf","relation":"main_file"}],"doi":"10.1002/ece3.1150","year":"2014","date_created":"2018-12-11T11:47:02Z","day":"19","publication":"Ecology and Evolution","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"537","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"issue":"15","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","page":"3139 - 3145"},{"status":"public","type":"journal_article","related_material":{"record":[{"relation":"dissertation_contains","id":"1125","status":"public"}]},"publisher":"Wiley-Blackwell","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Understanding the evolution of dispersal is essential for understanding and predicting the dynamics of natural populations. Two main factors are known to influence dispersal evolution: spatio-temporal variation in the environment and relatedness between individuals. However, the relation between these factors is still poorly understood, and they are usually treated separately. In this article, I present a theoretical framework that contains and connects effects of both environmental variation and relatedness, and reproduces and extends their known features. Spatial habitat variation selects for balanced dispersal strategies, whereby the population is kept at an ideal free distribution. Within this class of dispersal strategies, I explain how increased dispersal is promoted by perturbations to the dispersal type frequencies. An explicit formula shows the magnitude of the selective advantage of increased dispersal in terms of the spatial variability in the frequencies of the different dispersal strategies present. These variances are capable of capturing various sources of stochasticity and hence establish a common scale for their effects on the evolution of dispersal. The results furthermore indicate an alternative approach to identifying effects of relatedness on dispersal evolution."}],"scopus_import":"1","citation":{"ama":"Novak S. Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. <i>Ecology and Evolution</i>. 2014;4(24):4589-4597. doi:<a href=\"https://doi.org/10.1002/ece3.1289\">10.1002/ece3.1289</a>","ieee":"S. Novak, “Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution,” <i>Ecology and Evolution</i>, vol. 4, no. 24. Wiley-Blackwell, pp. 4589–4597, 2014.","mla":"Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances as Driving Forces of Dispersal Evolution.” <i>Ecology and Evolution</i>, vol. 4, no. 24, Wiley-Blackwell, 2014, pp. 4589–97, doi:<a href=\"https://doi.org/10.1002/ece3.1289\">10.1002/ece3.1289</a>.","short":"S. Novak, Ecology and Evolution 4 (2014) 4589–4597.","ista":"Novak S. 2014. Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. Ecology and Evolution. 4(24), 4589–4597.","apa":"Novak, S. (2014). Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. <i>Ecology and Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/ece3.1289\">https://doi.org/10.1002/ece3.1289</a>","chicago":"Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances as Driving Forces of Dispersal Evolution.” <i>Ecology and Evolution</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/ece3.1289\">https://doi.org/10.1002/ece3.1289</a>."},"month":"11","date_updated":"2026-07-29T11:27:43Z","quality_controlled":"1","external_id":{"isi":["000346736200003"]},"isi":1,"date_published":"2014-11-27T00:00:00Z","article_processing_charge":"No","title":"Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution","publist_id":"5049","volume":4,"publication":"Ecology and Evolution","corr_author":"1","day":"27","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"page":"4589 - 4597","ec_funded":1,"issue":"24","department":[{"_id":"NiBa"}],"_id":"2023","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"         4","doi":"10.1002/ece3.1289","file":[{"date_created":"2018-12-12T10:12:28Z","file_id":"4946","checksum":"9ab43db1b0fede7bfe560ed77e177b76","creator":"system","access_level":"open_access","file_name":"IST-2016-462-v1+1_Novak-2014-Ecology_and_Evolution.pdf","file_size":118813,"content_type":"application/pdf","date_updated":"2020-07-14T12:45:25Z","relation":"main_file"}],"project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"publication_status":"published","oa":1,"author":[{"last_name":"Novak","first_name":"Sebastian","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"}],"language":[{"iso":"eng"}],"ddc":["570"],"pubrep_id":"462","file_date_updated":"2020-07-14T12:45:25Z","date_created":"2018-12-11T11:55:16Z","year":"2014"}]