[{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"09","_id":"9710","doi":"10.5061/dryad.s5s7r","publisher":"Dryad","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1199"}]},"title":"Data from: How does epistasis influence the response to selection?","oa":1,"type":"research_data_reference","oa_version":"Published Version","date_published":"2016-09-23T00:00:00Z","department":[{"_id":"NiBa"}],"author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"date_created":"2021-07-23T11:45:47Z","year":"2016","date_updated":"2025-05-28T11:57:03Z","status":"public","abstract":[{"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.","lang":"eng"}],"day":"23","article_processing_charge":"No","citation":{"ama":"Barton NH. Data from: How does epistasis influence the response to selection? 2016. doi:10.5061/dryad.s5s7r","short":"N.H. Barton, (2016).","mla":"Barton, Nicholas H. Data from: How Does Epistasis Influence the Response to Selection? Dryad, 2016, doi: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.","chicago":"Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response to Selection?” Dryad, 2016. https://doi.org/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"},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.s5s7r","open_access":"1"}]},{"article_processing_charge":"No","day":"27","citation":{"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","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.","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.","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).","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"},"date_updated":"2023-02-21T16:21:20Z","year":"2016","date_created":"2021-08-10T08:20:17Z","status":"public","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"oa_version":"Published Version","author":[{"last_name":"Roux","first_name":"Camille","full_name":"Roux, Camille"},{"first_name":"Christelle","full_name":"Fraisse, Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"},{"first_name":"Jonathan","full_name":"Romiguier, Jonathan","last_name":"Romiguier"},{"last_name":"Anciaux","full_name":"Anciaux, Youann","first_name":"Youann"},{"full_name":"Galtier, Nicolas","first_name":"Nicolas","last_name":"Galtier"},{"last_name":"Bierne","full_name":"Bierne, Nicolas","first_name":"Nicolas"}],"publisher":"Public Library of Science","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9862","doi":"10.1371/journal.pbio.2000234.s016","month":"12","type":"research_data_reference","related_material":{"record":[{"id":"1158","relation":"used_in_publication","status":"public"}]},"title":"Simulation study to test the robustness of ABC in face of recent times of divergence"},{"author":[{"last_name":"Roux","first_name":"Camille","full_name":"Roux, Camille"},{"full_name":"Fraisse, Christelle","first_name":"Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Romiguier","full_name":"Romiguier, Jonathan","first_name":"Jonathan"},{"full_name":"Anciaux, Youann","first_name":"Youann","last_name":"Anciaux"},{"last_name":"Galtier","first_name":"Nicolas","full_name":"Galtier, Nicolas"},{"last_name":"Bierne","first_name":"Nicolas","full_name":"Bierne, Nicolas"}],"oa_version":"Published Version","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"related_material":{"record":[{"id":"1158","status":"public","relation":"used_in_publication"}]},"title":"Accessions of surveyed individuals, geographic locations and summary statistics","type":"research_data_reference","_id":"9863","doi":"10.1371/journal.pbio.2000234.s017","month":"12","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","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","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","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.","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.","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.","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","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."},"day":"27","article_processing_charge":"No","status":"public","year":"2016","date_created":"2021-08-10T08:22:52Z","date_updated":"2023-02-21T16:21:20Z"},{"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.4315652.v1","open_access":"1"}],"citation":{"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.","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.","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","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.","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.","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","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016)."},"day":"14","article_processing_charge":"No","status":"public","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."}],"date_created":"2021-08-10T08:29:47Z","year":"2016","date_updated":"2025-05-28T11:57:06Z","author":[{"first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5837-2793"},{"id":"2A181218-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5985-7653","last_name":"de Vladar","first_name":"Harold","full_name":"de Vladar, Harold"},{"full_name":"Włodarski, Tomasz","first_name":"Tomasz","last_name":"Włodarski"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","last_name":"Bollback","first_name":"Jonathan P","full_name":"Bollback, Jonathan P"}],"oa_version":"Published Version","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"date_published":"2016-12-14T00:00:00Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1077"}]},"title":"Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","oa":1,"type":"research_data_reference","month":"12","_id":"9864","doi":"10.6084/m9.figshare.4315652.v1","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"The Royal Society"},{"alternative_title":["ISTA Thesis"],"department":[{"_id":"NiBa"}],"publication_status":"published","related_material":{"record":[{"id":"2023","status":"public","relation":"part_of_dissertation"}]},"oa":1,"title":"Evolutionary proccesses in variable emvironments","_id":"1125","month":"07","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"}],"citation":{"short":"S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of Science and Technology Austria, 2016.","ama":"Novak S. Evolutionary proccesses in variable emvironments. 2016.","ista":"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.","apa":"Novak, S. (2016). Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria.","ieee":"S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of Science and Technology Austria, 2016.","mla":"Novak, Sebastian. Evolutionary Proccesses in Variable Emvironments. Institute of Science and Technology Austria, 2016."},"day":"01","has_accepted_license":"1","status":"public","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."}],"degree_awarded":"PhD","publist_id":"6235","author":[{"full_name":"Novak, Sebastian","first_name":"Sebastian","last_name":"Novak","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87"}],"ddc":["576"],"oa_version":"Published Version","date_published":"2016-07-01T00:00:00Z","language":[{"iso":"eng"}],"type":"dissertation","file_date_updated":"2021-02-22T13:42:47Z","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","file":[{"access_level":"closed","date_updated":"2019-08-13T09:01:00Z","date_created":"2019-08-13T09:01:00Z","file_id":"6811","content_type":"application/pdf","file_name":"Novak_thesis.pdf","creator":"dernst","file_size":3564901,"checksum":"81dcc838dfcf7aa0b1a27ecf4fe2da4e","relation":"main_file"},{"relation":"main_file","checksum":"30808d2f7ca920e09f63a95cdc49bffd","file_size":2814384,"creator":"dernst","file_name":"2016_Novak_Thesis.pdf","file_id":"9186","date_created":"2021-02-22T13:42:47Z","content_type":"application/pdf","success":1,"access_level":"open_access","date_updated":"2021-02-22T13:42:47Z"}],"year":"2016","date_created":"2018-12-11T11:50:17Z","page":"124","date_updated":"2025-05-28T11:57:05Z"},{"title":"Evolution of transcriptional regulatory sequences","oa":1,"related_material":{"record":[{"relation":"research_data","status":"public","id":"5554"},{"status":"public","relation":"part_of_dissertation","id":"1666"}]},"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1131","month":"07","alternative_title":["ISTA Thesis"],"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.","department":[{"_id":"NiBa"}],"abstract":[{"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.","lang":"eng"}],"status":"public","degree_awarded":"PhD","citation":{"chicago":"Tugrul, Murat. “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.","apa":"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.","ieee":"M. Tugrul, “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.","ama":"Tugrul M. Evolution of transcriptional regulatory sequences. 2016."},"supervisor":[{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"has_accepted_license":"1","day":"01","file_date_updated":"2021-02-22T11:45:20Z","type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","ddc":["576"],"author":[{"last_name":"Tugrul","first_name":"Murat","full_name":"Tugrul, Murat","orcid":"0000-0002-8523-0758","id":"37C323C6-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6229","date_published":"2016-07-01T00:00:00Z","oa_version":"Published Version","file":[{"relation":"main_file","checksum":"66cb61a59943e4fb7447c6a86be5ef51","file_size":3695257,"creator":"dernst","file_name":"Tugrul_thesis_w_signature_page.pdf","content_type":"application/pdf","file_id":"6810","date_created":"2019-08-13T08:53:52Z","access_level":"closed","date_updated":"2019-08-13T08:53:52Z"},{"checksum":"293e388d70563760f6b24c3e66283dda","relation":"main_file","creator":"dernst","file_size":3880811,"file_name":"2016_Tugrul_Thesis.pdf","date_updated":"2021-02-22T11:45:20Z","success":1,"access_level":"open_access","date_created":"2021-02-22T11:45:20Z","file_id":"9182","content_type":"application/pdf"}],"date_updated":"2025-05-28T11:57:04Z","page":"89","date_created":"2018-12-11T11:50:19Z","year":"2016","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":1,"year":"2016","date_created":"2018-12-11T11:50:28Z","quality_controlled":"1","date_updated":"2023-02-23T14:11:16Z","file":[{"file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf","date_created":"2018-12-12T10:15:42Z","file_id":"5164","content_type":"application/pdf","date_updated":"2020-07-14T12:44:36Z","access_level":"open_access","relation":"main_file","checksum":"2bab63b068a9840efd532b9ae583f9bb","file_size":2494348,"creator":"system"}],"volume":14,"oa_version":"Published Version","date_published":"2016-12-27T00:00:00Z","publication":"PLoS Biology","publist_id":"6200","issue":"12","author":[{"full_name":"Roux, Camille","first_name":"Camille","last_name":"Roux"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle","last_name":"Fraisse"},{"full_name":"Romiguier, Jonathan","first_name":"Jonathan","last_name":"Romiguier"},{"first_name":"Youann","full_name":"Anciaux, Youann","last_name":"Anciaux"},{"full_name":"Galtier, Nicolas","first_name":"Nicolas","last_name":"Galtier"},{"first_name":"Nicolas","full_name":"Bierne, Nicolas","last_name":"Bierne"}],"ddc":["576"],"doi":"10.1371/journal.pbio.2000234","publisher":"Public Library of Science","language":[{"iso":"eng"}],"type":"journal_article","file_date_updated":"2020-07-14T12:44:36Z","day":"27","has_accepted_license":"1","intvolume":" 14","citation":{"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.","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.","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.","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","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","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS Biology 14 (2016)."},"status":"public","article_number":"e2000234","abstract":[{"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.","lang":"eng"}],"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.","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"pubrep_id":"742","_id":"1158","month":"12","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","oa":1,"related_material":{"record":[{"id":"9862","relation":"research_data","status":"public"},{"relation":"research_data","status":"public","id":"9863"}]}},{"volume":6,"file":[{"file_name":"IST-2017-737-v1+1_srep38840.pdf","date_created":"2018-12-12T10:12:56Z","content_type":"application/pdf","file_id":"4977","access_level":"open_access","date_updated":"2020-07-14T12:44:37Z","relation":"main_file","checksum":"cb378732da885ea4959ec5b845fb6e52","file_size":760967,"creator":"system"}],"date_updated":"2021-01-12T06:48:50Z","quality_controlled":"1","date_created":"2018-12-11T11:50:32Z","year":"2016","scopus_import":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2020-07-14T12:44:37Z","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Nature Publishing Group","doi":"10.1038/srep38840","ddc":["576"],"author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani","first_name":"Himani","last_name":"Sachdeva"},{"first_name":"Mustansir","full_name":"Barma, Mustansir","last_name":"Barma"},{"first_name":"Madan","full_name":"Rao, Madan","last_name":"Rao"}],"publication":"Scientific Reports","publist_id":"6183","date_published":"2016-12-19T00:00:00Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"A central issue in cell biology is the physico-chemical basis of organelle biogenesis in intracellular trafficking pathways, its most impressive manifestation being the biogenesis of Golgi cisternae. At a basic level, such morphologically and chemically distinct compartments should arise from an interplay between the molecular transport and chemical maturation. Here, we formulate analytically tractable, minimalist models, that incorporate this interplay between transport and chemical progression in physical space, and explore the conditions for de novo biogenesis of distinct cisternae. We propose new quantitative measures that can discriminate between the various models of transport in a qualitative manner-this includes measures of the dynamics in steady state and the dynamical response to perturbations of the kind amenable to live-cell imaging."}],"article_number":"38840","status":"public","citation":{"ieee":"H. Sachdeva, M. Barma, and M. Rao, “Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","mla":"Sachdeva, Himani, et al. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” Scientific Reports, vol. 6, 38840, Nature Publishing Group, 2016, doi:10.1038/srep38840.","chicago":"Sachdeva, Himani, Mustansir Barma, and Madan Rao. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep38840.","ista":"Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.","apa":"Sachdeva, H., Barma, M., & Rao, M. (2016). Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep38840","ama":"Sachdeva H, Barma M, Rao M. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 2016;6. doi:10.1038/srep38840","short":"H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016)."},"intvolume":" 6","has_accepted_license":"1","day":"19","title":"Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae","oa":1,"publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"12","_id":"1172","pubrep_id":"737","department":[{"_id":"NiBa"}],"acknowledgement":"H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund Thattai for critical discussions and suggestions."},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"10","_id":"1195","title":"Reconstruction of haplotype-blocks selected during experimental evolution.","oa":1,"publication_status":"published","department":[{"_id":"NiBa"}],"acknowledgement":"The authors thank all members of the Institute of Population\r\nGenetics for discussion and support on the project and par-\r\nticularly N. Barghi for helpful comments on earlier versions of\r\nthe manuscript. This work was supported by the European\r\nResearch Council (ERC) grants “ArchAdapt” and “250152”.","pubrep_id":"770","ec_funded":1,"status":"public","abstract":[{"lang":"eng","text":"The genetic analysis of experimentally evolving populations typically relies on short reads from pooled individuals (Pool-Seq). While this method provides reliable allele frequency estimates, the underlying haplotype structure remains poorly characterized. With small population sizes and adaptive variants that start from low frequencies, the interpretation of selection signatures in most Evolve and Resequencing studies remains challenging. To facilitate the characterization of selection targets, we propose a new approach that reconstructs selected haplotypes from replicated time series, using Pool-Seq data. We identify selected haplotypes through the correlated frequencies of alleles carried by them. Computer simulations indicate that selected haplotype-blocks of several Mb can be reconstructed with high confidence and low error rates, even when allele frequencies change only by 20% across three replicates. Applying this method to real data from D. melanogaster populations adapting to a hot environment, we identify a selected haplotype-block of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations by experimental haplotyping, demonstrating the power and accuracy of our haplotype reconstruction from Pool-Seq data. We propose that the combination of allele frequency estimates with haplotype information will provide the key to understanding the dynamics of adaptive alleles. "}],"day":"03","has_accepted_license":"1","intvolume":" 34","citation":{"ama":"Franssen S, Barton NH, Schlötterer C. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 2016;34(1):174-184. doi:10.1093/molbev/msw210","short":"S. Franssen, N.H. Barton, C. Schlötterer, Molecular Biology and Evolution 34 (2016) 174–184.","mla":"Franssen, Susan, et al. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology and Evolution, vol. 34, no. 1, Oxford University Press, 2016, pp. 174–84, doi:10.1093/molbev/msw210.","ieee":"S. Franssen, N. H. Barton, and C. Schlötterer, “Reconstruction of haplotype-blocks selected during experimental evolution.,” Molecular Biology and Evolution, vol. 34, no. 1. Oxford University Press, pp. 174–184, 2016.","chicago":"Franssen, Susan, Nicholas H Barton, and Christian Schlötterer. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msw210.","apa":"Franssen, S., Barton, N. H., & Schlötterer, C. (2016). Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msw210","ista":"Franssen S, Barton NH, Schlötterer C. 2016. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 34(1), 174–184."},"doi":"10.1093/molbev/msw210","publisher":"Oxford University Press","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:44:38Z","type":"journal_article","oa_version":"Submitted Version","date_published":"2016-10-03T00:00:00Z","publication":"Molecular Biology and Evolution","issue":"1","publist_id":"6155","ddc":["576"],"author":[{"full_name":"Franssen, Susan","first_name":"Susan","last_name":"Franssen"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H"},{"last_name":"Schlötterer","first_name":"Christian","full_name":"Schlötterer, Christian"}],"page":"174 - 184","quality_controlled":"1","date_created":"2018-12-11T11:50:39Z","year":"2016","date_updated":"2021-01-12T06:49:00Z","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7"}],"volume":34,"file":[{"checksum":"1e78d3aaffcb40dc8b02b7b4666019e0","relation":"main_file","creator":"system","file_size":295274,"file_name":"IST-2017-770-v1+1_FranssenEtAl_nofigs-1.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:38Z","date_created":"2018-12-12T10:16:35Z","file_id":"5223","content_type":"application/pdf"},{"date_updated":"2020-07-14T12:44:38Z","access_level":"open_access","date_created":"2018-12-12T10:16:36Z","content_type":"application/pdf","file_id":"5224","file_name":"IST-2017-770-v1+2_Fig1.pdf","creator":"system","file_size":10902625,"checksum":"e13171843283774404c936c581b4543e","relation":"main_file"},{"checksum":"63bc6e6e61f347594d8c00c37f874a0b","relation":"main_file","creator":"system","file_size":21437,"file_name":"IST-2017-770-v1+3_Fig2.pdf","date_updated":"2020-07-14T12:44:38Z","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:16:37Z","file_id":"5225"},{"file_size":1172194,"creator":"system","relation":"main_file","checksum":"da87cc7c78808837f22a3dae1c8397f9","date_created":"2018-12-12T10:16:38Z","file_id":"5226","content_type":"application/pdf","date_updated":"2020-07-14T12:44:38Z","access_level":"open_access","file_name":"IST-2017-770-v1+4_Fig3.pdf"},{"file_name":"IST-2017-770-v1+5_Fig4.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:38Z","content_type":"application/pdf","date_created":"2018-12-12T10:16:38Z","file_id":"5227","checksum":"e47b2a0c32142f423b3100150c0294f8","relation":"main_file","creator":"system","file_size":50045},{"file_size":50705,"creator":"system","relation":"main_file","checksum":"a5a7d6b32e7e17d35d337d7ec2a9f6c9","file_id":"5228","content_type":"application/pdf","date_created":"2018-12-12T10:16:39Z","date_updated":"2020-07-14T12:44:38Z","access_level":"open_access","file_name":"IST-2017-770-v1+6_Fig5.pdf"}],"scopus_import":1},{"department":[{"_id":"NiBa"}],"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).","_id":"1241","month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","das_tickbox":"1","oa":1,"title":"The role of recombination in evolutionary rescue","day":"01","intvolume":" 202","citation":{"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.","ista":"Uecker H, Hermisson J. 2016. The role of recombination in evolutionary rescue. Genetics. 202(2), 721–732.","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","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.","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.","short":"H. Uecker, J. Hermisson, Genetics 202 (2016) 721–732.","ama":"Uecker H, Hermisson J. The role of recombination in evolutionary rescue. Genetics. 2016;202(2):721-732. doi:10.1534/genetics.115.180299"},"ec_funded":1,"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."}],"status":"public","date_published":"2016-02-01T00:00:00Z","oa_version":"Preprint","author":[{"last_name":"Uecker","first_name":"Hildegard","full_name":"Uecker, Hildegard","orcid":"0000-0001-9435-2813","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hermisson","first_name":"Joachim","full_name":"Hermisson, Joachim"}],"ddc":["570"],"issue":"2","publication":"Genetics","publist_id":"6091","publisher":"Genetics Society of America","doi":"10.1534/genetics.115.180299","type":"journal_article","language":[{"iso":"eng"}],"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"http://biorxiv.org/content/early/2015/07/06/022020.abstract"}],"scopus_import":"1","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"_id":"25B67606-B435-11E9-9278-68D0E5697425","name":"L'OREAL Fellowship"}],"date_updated":"2026-06-18T07:59:00Z","year":"2016","date_created":"2018-12-11T11:50:54Z","page":"721 - 732","quality_controlled":"1","volume":202},{"volume":69,"file":[{"file_size":188872,"creator":"system","relation":"main_file","checksum":"fd8d23f476bc194419929b72ca265c02","date_created":"2018-12-12T10:10:34Z","file_id":"4822","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:00Z","file_name":"IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf"},{"file_size":577415,"creator":"system","relation":"main_file","checksum":"b774911e70044641d556e258efcb52ef","content_type":"application/pdf","file_id":"4823","date_created":"2018-12-12T10:10:35Z","date_updated":"2020-07-14T12:45:00Z","access_level":"open_access","file_name":"IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf"}],"date_updated":"2021-01-12T06:51:20Z","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"page":"1101 - 1112","quality_controlled":"1","date_created":"2018-12-11T11:52:29Z","year":"2015","scopus_import":1,"file_date_updated":"2020-07-14T12:45:00Z","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Wiley","doi":"10.1111/evo.12641","ddc":["570"],"author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"},{"last_name":"Servedio","full_name":"Servedio, Maria","first_name":"Maria"}],"publist_id":"5656","issue":"5","publication":"Evolution","date_published":"2015-03-19T00:00:00Z","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Evolutionary biologists have an array of powerful theoretical techniques that can accurately predict changes in the genetic composition of populations. Changes in gene frequencies and genetic associations between loci can be tracked as they respond to a wide variety of evolutionary forces. However, it is often less clear how to decompose these various forces into components that accurately reflect the underlying biology. Here, we present several issues that arise in the definition and interpretation of selection and selection coefficients, focusing on insights gained through the examination of selection coefficients in multilocus notation. Using this notation, we discuss how its flexibility-which allows different biological units to be identified as targets of selection-is reflected in the interpretation of the coefficients that the notation generates. In many situations, it can be difficult to agree on whether loci can be considered to be under "direct" versus "indirect" selection, or to quantify this selection. We present arguments for what the terms direct and indirect selection might best encompass, considering a range of issues, from viability and sexual selection to kin selection. We show how multilocus notation can discriminate between direct and indirect selection, and describe when it can do so."}],"status":"public","ec_funded":1,"citation":{"ama":"Barton NH, Servedio M. The interpretation of selection coefficients. Evolution. 2015;69(5):1101-1112. doi:10.1111/evo.12641","short":"N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112.","mla":"Barton, Nicholas H., and Maria Servedio. “The Interpretation of Selection Coefficients.” Evolution, vol. 69, no. 5, Wiley, 2015, pp. 1101–12, doi:10.1111/evo.12641.","ieee":"N. H. Barton and M. Servedio, “The interpretation of selection coefficients,” Evolution, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015.","apa":"Barton, N. H., & Servedio, M. (2015). The interpretation of selection coefficients. Evolution. Wiley. https://doi.org/10.1111/evo.12641","ista":"Barton NH, Servedio M. 2015. The interpretation of selection coefficients. Evolution. 69(5), 1101–1112.","chicago":"Barton, Nicholas H, and Maria Servedio. “The Interpretation of Selection Coefficients.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12641."},"intvolume":" 69","has_accepted_license":"1","day":"19","title":"The interpretation of selection coefficients","oa":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","_id":"1519","pubrep_id":"560","department":[{"_id":"NiBa"}]},{"title":"Toward a unifying framework for evolutionary processes","oa":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","_id":"1542","pubrep_id":"483","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"status":"public","abstract":[{"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. ","lang":"eng"}],"ec_funded":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.” Journal of Theoretical Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.07.011.","apa":"Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T., … Trubenova, B. (2015). Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.07.011","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.","mla":"Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology, vol. 383, Elsevier, 2015, pp. 28–43, doi:10.1016/j.jtbi.2015.07.011.","ieee":"T. Paixao et al., “Toward a unifying framework for evolutionary processes,” Journal of Theoretical Biology, vol. 383. Elsevier, pp. 28–43, 2015.","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.","ama":"Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 2015;383:28-43. doi:10.1016/j.jtbi.2015.07.011"},"intvolume":" 383","day":"21","has_accepted_license":"1","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:01Z","type":"journal_article","doi":"10.1016/j.jtbi.2015.07.011","publisher":"Elsevier","publist_id":"5629","publication":" Journal of Theoretical Biology","ddc":["570"],"author":[{"first_name":"Tiago","full_name":"Paixao, Tiago","last_name":"Paixao","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Golnaz","full_name":"Badkobeh, Golnaz","last_name":"Badkobeh"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"first_name":"Doğan","full_name":"Çörüş, Doğan","last_name":"Çörüş"},{"full_name":"Dang, Duccuong","first_name":"Duccuong","last_name":"Dang"},{"full_name":"Friedrich, Tobias","first_name":"Tobias","last_name":"Friedrich"},{"full_name":"Lehre, Per","first_name":"Per","last_name":"Lehre"},{"last_name":"Sudholt","full_name":"Sudholt, Dirk","first_name":"Dirk"},{"full_name":"Sutton, Andrew","first_name":"Andrew","last_name":"Sutton"},{"first_name":"Barbora","full_name":"Trubenova, Barbora","last_name":"Trubenova","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","date_published":"2015-10-21T00:00:00Z","volume":383,"file":[{"file_name":"IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:16:53Z","file_id":"5244","date_updated":"2020-07-14T12:45:01Z","access_level":"open_access","relation":"main_file","checksum":"33b60ecfea60764756a9ee9df5eb65ca","file_size":595307,"creator":"system"}],"quality_controlled":"1","page":"28 - 43","year":"2015","date_created":"2018-12-11T11:52:37Z","date_updated":"2021-01-12T06:51:29Z","project":[{"call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"scopus_import":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"}},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":1,"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"date_updated":"2023-09-07T11:53:49Z","year":"2015","date_created":"2018-12-11T11:53:21Z","quality_controlled":"1","file":[{"checksum":"a4e72fca5ccf40ddacf4d08c8e46b554","relation":"main_file","creator":"system","file_size":2580778,"file_name":"IST-2016-463-v1+1_journal.pgen.1005639.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:10Z","file_id":"4657","content_type":"application/pdf","date_created":"2018-12-12T10:07:58Z"}],"volume":11,"date_published":"2015-11-06T00:00:00Z","oa_version":"Published Version","author":[{"last_name":"Tugrul","full_name":"Tugrul, Murat","first_name":"Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8523-0758"},{"last_name":"Paixao","first_name":"Tiago","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","first_name":"Gasper"}],"ddc":["576"],"publist_id":"5483","publication":"PLoS Genetics","issue":"11","publisher":"Public Library of Science","doi":"10.1371/journal.pgen.1005639","type":"journal_article","file_date_updated":"2020-07-14T12:45:10Z","language":[{"iso":"eng"}],"has_accepted_license":"1","day":"06","citation":{"apa":"Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Dynamics of transcription factor binding site evolution. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005639","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11).","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics. Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.","mla":"Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public Library of Science, 2015.","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).","ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639"},"intvolume":" 11","ec_funded":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."}],"status":"public","department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"pubrep_id":"463","month":"11","_id":"1666","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"Dynamics of transcription factor binding site evolution","related_material":{"record":[{"relation":"research_data","status":"public","id":"9712"},{"id":"1131","relation":"dissertation_contains","status":"public"}]},"oa":1},{"month":"09","_id":"1681","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","publication_status":"published","title":"Evolution of decisions in population games with sequentially searching individuals","oa":1,"department":[{"_id":"NiBa"},{"_id":"KrCh"}],"pubrep_id":"448","ec_funded":1,"abstract":[{"lang":"eng","text":"In many social situations, individuals endeavor to find the single best possible partner, but are constrained to evaluate the candidates in sequence. Examples include the search for mates, economic partnerships, or any other long-term ties where the choice to interact involves two parties. Surprisingly, however, previous theoretical work on mutual choice problems focuses on finding equilibrium solutions, while ignoring the evolutionary dynamics of decisions. Empirically, this may be of high importance, as some equilibrium solutions can never be reached unless the population undergoes radical changes and a sufficient number of individuals change their decisions simultaneously. To address this question, we apply a mutual choice sequential search problem in an evolutionary game-theoretical model that allows one to find solutions that are favored by evolution. As an example, we study the influence of sequential search on the evolutionary dynamics of cooperation. For this, we focus on the classic snowdrift game and the prisoner’s dilemma game."}],"status":"public","has_accepted_license":"1","day":"29","intvolume":" 6","citation":{"ista":"Priklopil T, Chatterjee K. 2015. Evolution of decisions in population games with sequentially searching individuals. Games. 6(4), 413–437.","apa":"Priklopil, T., & Chatterjee, K. (2015). Evolution of decisions in population games with sequentially searching individuals. Games. MDPI. https://doi.org/10.3390/g6040413","chicago":"Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in Population Games with Sequentially Searching Individuals.” Games. MDPI, 2015. https://doi.org/10.3390/g6040413.","mla":"Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in Population Games with Sequentially Searching Individuals.” Games, vol. 6, no. 4, MDPI, 2015, pp. 413–37, doi:10.3390/g6040413.","ieee":"T. Priklopil and K. Chatterjee, “Evolution of decisions in population games with sequentially searching individuals,” Games, vol. 6, no. 4. MDPI, pp. 413–437, 2015.","short":"T. Priklopil, K. Chatterjee, Games 6 (2015) 413–437.","ama":"Priklopil T, Chatterjee K. Evolution of decisions in population games with sequentially searching individuals. Games. 2015;6(4):413-437. doi:10.3390/g6040413"},"publisher":"MDPI","doi":"10.3390/g6040413","type":"journal_article","file_date_updated":"2020-07-14T12:45:12Z","language":[{"iso":"eng"}],"date_published":"2015-09-29T00:00:00Z","oa_version":"Published Version","author":[{"id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","last_name":"Priklopil","first_name":"Tadeas","full_name":"Priklopil, Tadeas"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"}],"ddc":["000"],"publication":"Games","publist_id":"5467","issue":"4","project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"date_updated":"2023-10-17T11:42:52Z","year":"2015","date_created":"2018-12-11T11:53:26Z","page":"413 - 437","quality_controlled":"1","file":[{"relation":"main_file","checksum":"912e1acbaf201100f447a43e4d5958bd","file_size":518832,"creator":"system","file_name":"IST-2016-448-v1+1_games-06-00413.pdf","content_type":"application/pdf","file_id":"4959","date_created":"2018-12-12T10:12:41Z","date_updated":"2020-07-14T12:45:12Z","access_level":"open_access"}],"volume":6,"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":"1","publication_identifier":{"eissn":["2073-4336"]}},{"oa_version":"Published Version","date_published":"2015-06-01T00:00:00Z","publication":"Journal of Mathematical Biology","publist_id":"5442","issue":"7","author":[{"full_name":"Uecker, Hildegard","first_name":"Hildegard","last_name":"Uecker","orcid":"0000-0001-9435-2813","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Setter, Derek","first_name":"Derek","last_name":"Setter"},{"first_name":"Joachim","full_name":"Hermisson, Joachim","last_name":"Hermisson"}],"ddc":["576"],"doi":"10.1007/s00285-014-0802-y","publisher":"Springer","language":[{"iso":"eng"}],"type":"journal_article","file_date_updated":"2020-07-14T12:45:12Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":1,"date_created":"2018-12-11T11:53:32Z","year":"2015","quality_controlled":"1","page":"1523 - 1580","project":[{"name":"L'OREAL Fellowship","_id":"25B67606-B435-11E9-9278-68D0E5697425"}],"date_updated":"2023-02-23T10:10:36Z","file":[{"file_size":1321527,"creator":"system","relation":"main_file","checksum":"00e3a67bda05d4cc165b3a48b41ef9ad","file_id":"5079","date_created":"2018-12-12T10:14:27Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:12Z","file_name":"IST-2016-458-v1+1_s00285-014-0802-y.pdf"}],"volume":70,"department":[{"_id":"NiBa"}],"acknowledgement":"This work was made possible with financial support by the Vienna Science and Technology Fund (WWTF), by the Deutsche Forschungsgemeinschaft (DFG), Research Unit 1078 Natural selection in structured populations, by the Austrian Science Fund (FWF) via funding for the Vienna Graduate School for Population Genetics, and by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with the Austrian Commission for UNESCO and the Austrian Academy of Sciences with financial support from the Federal Ministry for Science and Research Austria).","pubrep_id":"458","month":"06","_id":"1699","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"Adaptive gene introgression after secondary contact","oa":1,"day":"01","has_accepted_license":"1","intvolume":" 70","citation":{"apa":"Uecker, H., Setter, D., & Hermisson, J. (2015). Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. Springer. https://doi.org/10.1007/s00285-014-0802-y","ista":"Uecker H, Setter D, Hermisson J. 2015. Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. 70(7), 1523–1580.","chicago":"Uecker, Hildegard, Derek Setter, and Joachim Hermisson. “Adaptive Gene Introgression after Secondary Contact.” Journal of Mathematical Biology. Springer, 2015. https://doi.org/10.1007/s00285-014-0802-y.","ieee":"H. Uecker, D. Setter, and J. Hermisson, “Adaptive gene introgression after secondary contact,” Journal of Mathematical Biology, vol. 70, no. 7. Springer, pp. 1523–1580, 2015.","mla":"Uecker, Hildegard, et al. “Adaptive Gene Introgression after Secondary Contact.” Journal of Mathematical Biology, vol. 70, no. 7, Springer, 2015, pp. 1523–80, doi:10.1007/s00285-014-0802-y.","short":"H. Uecker, D. Setter, J. Hermisson, Journal of Mathematical Biology 70 (2015) 1523–1580.","ama":"Uecker H, Setter D, Hermisson J. Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. 2015;70(7):1523-1580. doi:10.1007/s00285-014-0802-y"},"status":"public","abstract":[{"lang":"eng","text":"By hybridization and backcrossing, alleles can surmount species boundaries and be incorporated into the genome of a related species. This introgression of genes is of particular evolutionary relevance if it involves the transfer of adaptations between populations. However, any beneficial allele will typically be associated with other alien alleles that are often deleterious and hamper the introgression process. In order to describe the introgression of an adaptive allele, we set up a stochastic model with an explicit genetic makeup of linked and unlinked deleterious alleles. Based on the theory of reducible multitype branching processes, we derive a recursive expression for the establishment probability of the beneficial allele after a single hybridization event. We furthermore study the probability that slightly deleterious alleles hitchhike to fixation. The key to the analysis is a split of the process into a stochastic phase in which the advantageous alleles establishes and a deterministic phase in which it sweeps to fixation. We thereafter apply the theory to a set of biologically relevant scenarios such as introgression in the presence of many unlinked or few closely linked deleterious alleles. A comparison to computer simulations shows that the approximations work well over a large parameter range."}]},{"intvolume":" 63","citation":{"ama":"Broadhurst L, Fifield G, Vanzella B, Pickup M. An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. 2015;63(5):455-466. doi:10.1071/BT15023","short":"L. Broadhurst, G. Fifield, B. Vanzella, M. Pickup, Australian Journal of Botany 63 (2015) 455–466.","ieee":"L. Broadhurst, G. Fifield, B. Vanzella, and M. Pickup, “An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas,” Australian Journal of Botany, vol. 63, no. 5. CSIRO, pp. 455–466, 2015.","mla":"Broadhurst, Linda, et al. “An Evaluation of the Genetic Structure of Seed Sources and the Maintenance of Genetic Diversity during Establishment of Two Yellow Box (Eucalyptus Melliodora) Seed-Production Areas.” Australian Journal of Botany, vol. 63, no. 5, CSIRO, 2015, pp. 455–66, doi:10.1071/BT15023.","chicago":"Broadhurst, Linda, Graham Fifield, Bindi Vanzella, and Melinda Pickup. “An Evaluation of the Genetic Structure of Seed Sources and the Maintenance of Genetic Diversity during Establishment of Two Yellow Box (Eucalyptus Melliodora) Seed-Production Areas.” Australian Journal of Botany. CSIRO, 2015. https://doi.org/10.1071/BT15023.","ista":"Broadhurst L, Fifield G, Vanzella B, Pickup M. 2015. An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. 63(5), 455–466.","apa":"Broadhurst, L., Fifield, G., Vanzella, B., & Pickup, M. (2015). An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. CSIRO. https://doi.org/10.1071/BT15023"},"scopus_import":1,"day":"26","status":"public","abstract":[{"text":"Vegetation clearing and land-use change have depleted many natural plant communities to the point where restoration is required. A major impediment to the success of rebuilding complex vegetation communities is having regular access to sufficient quantities of high-quality seed. Seed-production areas (SPAs) can help generate this seed, but these must be underpinned by a broad genetic base to maximise the evolutionary potential of restored populations. However, genetic bottlenecks can occur at the collection, establishment and production stages in SPAs, requiring genetic evaluation. This is especially relevant for species that may take many years before a return on SPA investment is realised. Two recently established yellow box (Eucalyptus melliodora A.Cunn. ex Schauer, Myrtaceae) SPAs were evaluated to determine whether genetic bottlenecks had occurred between seed collection and SPA establishment. No evidence was found to suggest that a significant loss of genetic diversity had occurred at this stage, although there was a significant difference in diversity between the two SPAs. Complex population genetic structure was also observed in the seed used to source the SPAs, with up to eight groups identified. Plant survival in the SPAs was influenced by seed collection location but not by SPA location and was not associated with genetic diversity. There were also no associations between genetic diversity and plant growth. These data highlighted the importance of chance events when establishing SPAs and indicated that the two yellow box SPAs are likely to provide genetically diverse seed sources for future restoration projects, especially by pooling seed from both SPAs.","lang":"eng"}],"volume":63,"year":"2015","date_created":"2018-12-11T11:53:34Z","page":"455 - 466","quality_controlled":"1","date_updated":"2021-01-12T06:52:38Z","publication":"Australian Journal of Botany","issue":"5","publist_id":"5434","author":[{"last_name":"Broadhurst","full_name":"Broadhurst, Linda","first_name":"Linda"},{"full_name":"Fifield, Graham","first_name":"Graham","last_name":"Fifield"},{"last_name":"Vanzella","full_name":"Vanzella, Bindi","first_name":"Bindi"},{"last_name":"Pickup","full_name":"Pickup, Melinda","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541"}],"oa_version":"None","department":[{"_id":"NiBa"}],"date_published":"2015-05-26T00:00:00Z","language":[{"iso":"eng"}],"publication_status":"published","title":"An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas","type":"journal_article","_id":"1703","month":"05","doi":"10.1071/BT15023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"CSIRO"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","_id":"1809","oa":1,"title":"Indirect genetic effects and the dynamics of social interactions","related_material":{"record":[{"relation":"research_data","status":"public","id":"9715"},{"id":"9772","relation":"research_data","status":"public"}]},"publication_status":"published","department":[{"_id":"NiBa"}],"pubrep_id":"453","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"}],"status":"public","has_accepted_license":"1","day":"18","intvolume":" 10","citation":{"ieee":"B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics of social interactions,” PLoS One, vol. 10, no. 5. Public Library of Science, 2015.","mla":"Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.","apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Indirect genetic effects and the dynamics of social interactions. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907","ista":"Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5).","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.","ama":"Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of social interactions. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0126907","short":"B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015)."},"publisher":"Public Library of Science","doi":"10.1371/journal.pone.0126907","file_date_updated":"2020-07-14T12:45:17Z","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2015-05-18T00:00:00Z","oa_version":"Published Version","ddc":["570","576"],"author":[{"last_name":"Trubenova","full_name":"Trubenova, Barbora","first_name":"Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","first_name":"Sebastian","last_name":"Novak"},{"first_name":"Reinmar","full_name":"Hager, Reinmar","last_name":"Hager"}],"publication":"PLoS One","issue":"5","publist_id":"5299","date_updated":"2023-02-23T14:07:48Z","quality_controlled":"1","date_created":"2018-12-11T11:54:07Z","year":"2015","volume":10,"file":[{"relation":"main_file","checksum":"d3a4a58ef4bd3b3e2f32b7fd7af4a743","file_size":2748982,"creator":"system","file_name":"IST-2016-453-v1+1_journal.pone.0126907.pdf","file_id":"4730","date_created":"2018-12-12T10:09:07Z","content_type":"application/pdf","date_updated":"2020-07-14T12:45:17Z","access_level":"open_access"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":1},{"doi":"10.1073/pnas.1421515112","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"type":"journal_article","oa_version":"Submitted Version","external_id":{"pmid":["25941385"]},"date_published":"2015-05-19T00:00:00Z","publication":"PNAS","issue":"20","publist_id":"5288","author":[{"full_name":"Polechova, Jitka","first_name":"Jitka","last_name":"Polechova","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"quality_controlled":"1","page":"6401 - 6406","year":"2015","date_created":"2018-12-11T11:54:11Z","date_updated":"2021-01-12T06:53:24Z","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"volume":112,"scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/"}],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","_id":"1818","oa":1,"title":"Limits to adaptation along environmental gradients","publication_status":"published","department":[{"_id":"NiBa"}],"ec_funded":1,"status":"public","abstract":[{"lang":"eng","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, "swamping" 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."}],"day":"19","citation":{"ieee":"J. Polechova and N. H. Barton, “Limits to adaptation along environmental gradients,” PNAS, 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.” PNAS, vol. 112, no. 20, National Academy of Sciences, 2015, pp. 6401–06, doi:10.1073/pnas.1421515112.","ista":"Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 6401–6406.","apa":"Polechova, J., & Barton, N. H. (2015). Limits to adaptation along environmental gradients. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1421515112","chicago":"Polechova, Jitka, and Nicholas H Barton. “Limits to Adaptation along Environmental Gradients.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1421515112.","ama":"Polechova J, Barton NH. Limits to adaptation along environmental gradients. PNAS. 2015;112(20):6401-6406. doi:10.1073/pnas.1421515112","short":"J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406."},"intvolume":" 112"},{"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.7704"}],"scopus_import":1,"volume":9035,"series_title":"Lecture Notes in Computer Science","date_created":"2018-12-11T11:54:16Z","year":"2015","quality_controlled":"1","page":"469 - 483","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7"},{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"date_updated":"2025-05-28T11:57:04Z","publist_id":"5267","author":[{"full_name":"Giacobbe, Mirco","first_name":"Mirco","last_name":"Giacobbe","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8180-0904"},{"last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"full_name":"Gupta, Ashutosh","first_name":"Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"last_name":"Paixao","first_name":"Tiago","full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953"},{"id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9041-0905","full_name":"Petrov, Tatjana","first_name":"Tatjana","last_name":"Petrov"}],"oa_version":"Preprint","conference":{"end_date":"2015-04-18","location":"London, United Kingdom","start_date":"2015-04-11","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"date_published":"2015-04-01T00:00:00Z","language":[{"iso":"eng"}],"type":"conference","doi":"10.1007/978-3-662-46681-0_47","publisher":"Springer","intvolume":" 9035","citation":{"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. Model Checking Gene Regulatory Networks. Vol. 9035, Springer, 2015, pp. 469–83, doi:10.1007/978-3-662-46681-0_47.","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., & 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. https://doi.org/10.1007/978-3-662-46681-0_47","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. https://doi.org/10.1007/978-3-662-46681-0_47.","ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking gene regulatory networks. 2015;9035:469-483. doi:10.1007/978-3-662-46681-0_47","short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, 9035 (2015) 469–483."},"day":"01","status":"public","abstract":[{"lang":"eng","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."}],"ec_funded":1,"alternative_title":["LNCS"],"department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"acknowledgement":"SNSF Early Postdoc.Mobility Fellowship, the grant number P2EZP2 148797.\r\n","publication_status":"published","title":"Model checking gene regulatory networks","oa":1,"related_material":{"record":[{"status":"public","relation":"later_version","id":"1351"}]},"_id":"1835","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"has_accepted_license":"1","day":"07","intvolume":" 372","citation":{"ieee":"S. Novak and S. Cremer, “Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates,” Journal of Theoretical Biology, vol. 372, no. 5. Elsevier, pp. 54–64, 2015.","mla":"Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect Societies: Optimal Killing Rates and the Ambivalent Effect of High Social Interaction Rates.” Journal of Theoretical Biology, vol. 372, no. 5, Elsevier, 2015, pp. 54–64, doi:10.1016/j.jtbi.2015.02.018.","ista":"Novak S, Cremer S. 2015. Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. 372(5), 54–64.","chicago":"Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect Societies: Optimal Killing Rates and the Ambivalent Effect of High Social Interaction Rates.” Journal of Theoretical Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.02.018.","apa":"Novak, S., & Cremer, S. (2015). Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.02.018","ama":"Novak S, Cremer S. Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. 2015;372(5):54-64. doi:10.1016/j.jtbi.2015.02.018","short":"S. Novak, S. Cremer, Journal of Theoretical Biology 372 (2015) 54–64."},"ec_funded":1,"abstract":[{"lang":"eng","text":"Entomopathogenic fungi are potent biocontrol agents that are widely used against insect pests, many of which are social insects. Nevertheless, theoretical investigations of their particular life history are scarce. We develop a model that takes into account the main distinguishing features between traditionally studied diseases and obligate killing pathogens, like the (biocontrol-relevant) insect-pathogenic fungi Metarhizium and Beauveria. First, obligate killing entomopathogenic fungi produce new infectious particles (conidiospores) only after host death and not yet on the living host. Second, the killing rates of entomopathogenic fungi depend strongly on the initial exposure dosage, thus we explicitly consider the pathogen load of individual hosts. Further, we make the model applicable not only to solitary host species, but also to group living species by incorporating social interactions between hosts, like the collective disease defences of insect societies. Our results identify the optimal killing rate for the pathogen that minimises its invasion threshold. Furthermore, we find that the rate of contact between hosts has an ambivalent effect: dense interaction networks between individuals are considered to facilitate disease outbreaks because of increased pathogen transmission. In social insects, this is compensated by their collective disease defences, i.e., social immunity. For the type of pathogens considered here, we show that even without social immunity, high contact rates between live individuals dilute the pathogen in the host colony and hence can reduce individual pathogen loads below disease-causing levels."}],"status":"public","department":[{"_id":"NiBa"},{"_id":"SyCr"}],"pubrep_id":"329","month":"05","_id":"1850","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates","oa":1,"scopus_import":1,"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7"},{"call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425","grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects"}],"date_updated":"2025-05-28T11:42:49Z","year":"2015","date_created":"2018-12-11T11:54:21Z","quality_controlled":"1","page":"54 - 64","file":[{"file_name":"IST-2015-329-v1+1_manuscript.pdf","date_created":"2018-12-12T10:18:07Z","file_id":"5326","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:19Z","relation":"main_file","checksum":"3c0dcacc900bc45cc65a453dfda4ca43","file_size":1546914,"creator":"system"}],"volume":372,"date_published":"2015-05-07T00:00:00Z","oa_version":"Submitted Version","author":[{"first_name":"Sebastian","full_name":"Novak, Sebastian","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-824X"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer"}],"ddc":["576"],"publist_id":"5251","issue":"5","publication":"Journal of Theoretical Biology","publisher":"Elsevier","doi":"10.1016/j.jtbi.2015.02.018","type":"journal_article","file_date_updated":"2020-07-14T12:45:19Z","language":[{"iso":"eng"}]}]