[{"keyword":["Insect Science","Molecular Biology","Animal Science and Zoology","Aquatic Science","Physiology","Ecology","Evolution","Behavior and Systematics"],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"10","citation":{"chicago":"Pal, Arka, Mihir Joshi, and Maria Thaker. “Too Much Information? Males Convey Parasite Levels Using More Signal Modalities than Females Utilise.” Journal of Experimental Biology. The Company of Biologists, 2024. https://doi.org/10.1242/jeb.246217.","short":"A. Pal, M. Joshi, M. Thaker, Journal of Experimental Biology 227 (2024).","mla":"Pal, Arka, et al. “Too Much Information? Males Convey Parasite Levels Using More Signal Modalities than Females Utilise.” Journal of Experimental Biology, vol. 227, no. 1, jeb246217, The Company of Biologists, 2024, doi:10.1242/jeb.246217.","apa":"Pal, A., Joshi, M., & Thaker, M. (2024). Too much information? Males convey parasite levels using more signal modalities than females utilise. Journal of Experimental Biology. The Company of Biologists. https://doi.org/10.1242/jeb.246217","ieee":"A. Pal, M. Joshi, and M. Thaker, “Too much information? Males convey parasite levels using more signal modalities than females utilise,” Journal of Experimental Biology, vol. 227, no. 1. The Company of Biologists, 2024.","ista":"Pal A, Joshi M, Thaker M. 2024. Too much information? Males convey parasite levels using more signal modalities than females utilise. Journal of Experimental Biology. 227(1), jeb246217.","ama":"Pal A, Joshi M, Thaker M. Too much information? Males convey parasite levels using more signal modalities than females utilise. Journal of Experimental Biology. 2024;227(1). doi:10.1242/jeb.246217"},"publication":"Journal of Experimental Biology","article_type":"original","date_published":"2024-01-10T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Elaborate sexual signals are thought to have evolved and be maintained to serve as honest indicators of signaller quality. One measure of quality is health, which can be affected by parasite infection. Cnemaspis mysoriensis is a diurnal gecko that is often infested with ectoparasites in the wild, and males of this species express visual (coloured gular patches) and chemical (femoral gland secretions) traits that receivers could assess during social interactions. In this paper, we tested whether ectoparasites affect individual health, and whether signal quality is an indicator of ectoparasite levels. In wild lizards, we found that ectoparasite level was negatively correlated with body condition in both sexes. Moreover, some characteristics of both visual and chemical traits in males were strongly associated with ectoparasite levels. Specifically, males with higher ectoparasite levels had yellow gular patches with lower brightness and chroma, and chemical secretions with a lower proportion of aromatic compounds. We then determined whether ectoparasite levels in males influence female behaviour. Using sequential choice trials, wherein females were provided with either the visual or the chemical signals of wild-caught males that varied in ectoparasite level, we found that only chemical secretions evoked an elevated female response towards less parasitised males. Simultaneous choice trials in which females were exposed to the chemical secretions from males that varied in parasite level further confirmed a preference for males with lower parasites loads. Overall, we find that although health (body condition) or ectoparasite load can be honestly advertised through multiple modalities, the parasite-mediated female response is exclusively driven by chemical signals."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14850","intvolume":" 227","title":"Too much information? Males convey parasite levels using more signal modalities than females utilise","ddc":["570"],"status":"public","file":[{"creator":"dernst","content_type":"application/pdf","file_size":594128,"file_name":"2024_JourExperimBiology_Pal.pdf","access_level":"open_access","date_updated":"2024-01-23T12:08:24Z","date_created":"2024-01-23T12:08:24Z","success":1,"checksum":"136325372f6f45abaa62a71e2d23bfb6","file_id":"14877","relation":"main_file"}],"oa_version":"Published Version","publication_identifier":{"issn":["1477-9145"],"eissn":["0022-0949"]},"month":"01","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["38054353"]},"quality_controlled":"1","doi":"10.1242/jeb.246217","language":[{"iso":"eng"}],"article_number":"jeb246217","file_date_updated":"2024-01-23T12:08:24Z","license":"https://creativecommons.org/licenses/by/4.0/","pmid":1,"year":"2024","acknowledgement":"We thank Anuradha Batabyal and Shakilur Kabir for scientific discussions, and help with sampling and colour analyses. We thank Muralidhar and the central LCMS facility of the IISc for their technical support with the GCMS.\r\nResearch funding was provided by the Department of Science and Technology Fund for Improvement of S&T Infrastructure (DST-FIST), the Department of Biotechnology-Indian Institute of Science (DBT-IISc) partnership program and a Science and Engineering Research Board (SERB) grant to M.T. (EMR/2017/002228). Open Access funding provided by Indian Institute of Science. Deposited in PMC for immediate release.","publisher":"The Company of Biologists","department":[{"_id":"NiBa"}],"publication_status":"published","related_material":{"link":[{"url":"https://github.com/arka-pal/Cnemaspis-SexualSignaling","relation":"software"}]},"author":[{"full_name":"Pal, Arka","first_name":"Arka","last_name":"Pal","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","orcid":"0000-0002-4530-8469"},{"full_name":"Joshi, Mihir","last_name":"Joshi","first_name":"Mihir"},{"first_name":"Maria","last_name":"Thaker","full_name":"Thaker, Maria"}],"volume":227,"date_updated":"2024-01-23T12:13:08Z","date_created":"2024-01-22T08:14:49Z"},{"publication_identifier":{"issn":["2663 - 337X"]},"month":"01","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Causes and consequences of population fragmentation","grant_number":"P32896","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"},{"name":"Polygenic Adaptation in a Metapopulation","grant_number":"26380","_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"first_name":"Jitka","last_name":"Polechova","full_name":"Polechova, Jitka"},{"first_name":"Himani","last_name":"Sachdeva","full_name":"Sachdeva, Himani"}],"acknowledged_ssus":[{"_id":"SSU"}],"doi":"10.15479/at:ista:14711","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ec_funded":1,"file_date_updated":"2024-01-03T18:31:34Z","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2024","date_created":"2023-12-26T22:49:53Z","date_updated":"2024-01-26T12:00:54Z","related_material":{"record":[{"id":"10658","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10787"},{"id":"14732","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Olusanya, Oluwafunmilola O","last_name":"Olusanya","first_name":"Oluwafunmilola O","orcid":"0000-0003-1971-8314","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","has_accepted_license":"1","day":"19","page":"183","citation":{"ama":"Olusanya OO. Local adaptation, genetic load and extinction in metapopulations. 2024. doi:10.15479/at:ista:14711","ista":"Olusanya OO. 2024. Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria.","ieee":"O. O. Olusanya, “Local adaptation, genetic load and extinction in metapopulations,” Institute of Science and Technology Austria, 2024.","apa":"Olusanya, O. O. (2024). Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14711","mla":"Olusanya, Oluwafunmilola O. Local Adaptation, Genetic Load and Extinction in Metapopulations. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:14711.","short":"O.O. Olusanya, Local Adaptation, Genetic Load and Extinction in Metapopulations, Institute of Science and Technology Austria, 2024.","chicago":"Olusanya, Oluwafunmilola O. “Local Adaptation, Genetic Load and Extinction in Metapopulations.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:14711."},"date_published":"2024-01-19T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"In nature, different species find their niche in a range of environments, each with its unique characteristics. While some thrive in uniform (homogeneous) landscapes where environmental conditions stay relatively consistent across space, others traverse the complexities of spatially heterogeneous terrains. Comprehending how species are distributed and how they interact within these landscapes holds the key to gaining insights into their evolutionary dynamics while also informing conservation and management strategies.\r\n\r\nFor species inhabiting heterogeneous landscapes, when the rate of dispersal is low compared to spatial fluctuations in selection pressure, localized adaptations may emerge. Such adaptation in response to varying selection strengths plays an important role in the persistence of populations in our rapidly changing world. Hence, species in nature are continuously in a struggle to adapt to local environmental conditions, to ensure their continued survival. Natural populations can often adapt in time scales short enough for evolutionary changes to influence ecological dynamics and vice versa, thereby creating a feedback between evolution and demography. The analysis of this feedback and the relative contributions of gene flow, demography, drift, and natural selection to genetic variation and differentiation has remained a recurring theme in evolutionary biology. Nevertheless, the effective role of these forces in maintaining variation and shaping patterns of diversity is not fully understood. Even in homogeneous environments devoid of local adaptations, such understanding remains elusive. Understanding this feedback is crucial, for example in determining the conditions under which extinction risk can be mitigated in peripheral populations subject to deleterious mutation accumulation at the edges of species’ ranges\r\nas well as in highly fragmented populations.\r\n\r\nIn this thesis we explore both uniform and spatially heterogeneous metapopulations, investigating and providing theoretical insights into the dynamics of local adaptation in the latter and examining the dynamics of load and extinction as well as the impact of joint ecological and evolutionary (eco-evolutionary) dynamics in the former. The thesis is divided into 5 chapters.\r\n\r\nChapter 1 provides a general introduction into the subject matter, clarifying concepts and ideas used throughout the thesis. In chapter 2, we explore how fast a species distributed across a heterogeneous landscape adapts to changing conditions marked by alterations in carrying capacity, selection pressure, and migration rate.\r\n\r\nIn chapter 3, we investigate how migration selection and drift influences adaptation and the maintenance of variation in a metapopulation with three habitats, an extension of previous models of adaptation in two habitats. We further develop analytical approximations for the critical threshold required for polymorphism to persist.\r\n\r\nThe focus of chapter 4 of the thesis is on understanding the interplay between ecology and evolution as coupled processes. We investigate how eco-evolutionary feedback between migration, selection, drift, and demography influences eco-evolutionary outcomes in marginal populations subject to deleterious mutation accumulation. Using simulations as well as theoretical approximations of the coupled dynamics of population size and allele frequency, we analyze how gene flow from a large mainland source influences genetic load and population size on an island (i.e., in a marginal population) under genetically realistic assumptions. Analyses of this sort are important because small isolated populations, are repeatedly affected by complex interactions between ecological and evolutionary processes, which can lead to their death. Understanding these interactions can therefore provide an insight into the conditions under which extinction risk can be mitigated in peripheral populations thus, contributing to conservation and restoration efforts.\r\n\r\nChapter 5 extends the analysis in chapter 4 to consider the dynamics of load (due to deleterious mutation accumulation) and extinction risk in a metapopulation. We explore the role of gene flow, selection, and dominance on load and extinction risk and further pinpoint critical thresholds required for metapopulation persistence.\r\n\r\nOverall this research contributes to our understanding of ecological and evolutionary mechanisms that shape species’ persistence in fragmented landscapes, a crucial foundation for successful conservation efforts and biodiversity management.","lang":"eng"}],"title":"Local adaptation, genetic load and extinction in metapopulations","status":"public","ddc":["576"],"_id":"14711","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","file":[{"creator":"oolusany","content_type":"application/zip","file_size":16986244,"access_level":"closed","file_name":"FinalSubmission_Thesis_OLUSANYA.zip","checksum":"de179b1c6758f182ff0c70d8b38c1501","date_created":"2024-01-03T18:30:13Z","date_updated":"2024-01-03T18:30:13Z","file_id":"14730","relation":"source_file"},{"access_level":"open_access","file_name":"FinalSubmission2_Thesis_OLUSANYA.pdf","file_size":6460403,"content_type":"application/pdf","creator":"oolusany","relation":"main_file","file_id":"14731","checksum":"0e331585e3cd4823320aab4e69e64ccf","success":1,"date_created":"2024-01-03T18:31:34Z","date_updated":"2024-01-03T18:31:34Z"}]},{"quality_controlled":"1","external_id":{"pmid":["38175895"]},"language":[{"iso":"eng"}],"doi":"10.1126/science.adi2982","month":"01","publication_identifier":{"eissn":["1095-9203"]},"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"publisher":"American Association for the Advancement of Science","year":"2024","acknowledgement":"We thank J. Galindo, M. Montaño-Rendón, N. Mikhailova, A. Blakeslee, E. Arnason, and P. Kemppainen for providing samples; R. Turney, G. Sotelo, J. Larsson, T. Broquet, and S. Loisel for help collecting samples; Science Animated for providing the snail cartoons shown in Fig. 1; M. Dunning for help in developing bioinformatic pipelines; R. Faria, H. Morales, and V. Sousa for advice; and M. Hahn, J. Slate, M. Ravinet, J. Raeymaekers, A. Comeault, and N. Barton for feedback on a draft manuscript.\r\nThis work was supported by the Natural Environment Research Council (grant NE/P001610/1 to R.K.B.), the European Research Council (grant ERC-2015-AdG693030-BARRIERS to R.K.B.), the Norwegian Research Council (RCN Project 315287 to A.M.W.), and the Swedish Research Council (grant 2020-05385 to E.L.).","pmid":1,"date_updated":"2024-03-05T09:35:25Z","date_created":"2024-01-14T23:00:56Z","volume":383,"author":[{"last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"full_name":"Zagrodzka, Zuzanna B.","first_name":"Zuzanna B.","last_name":"Zagrodzka"},{"first_name":"Martin D.","last_name":"Garlovsky","full_name":"Garlovsky, Martin D."},{"first_name":"Arka","last_name":"Pal","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","orcid":"0000-0002-4530-8469","full_name":"Pal, Arka"},{"full_name":"Shipilina, Daria","orcid":"0000-0002-1145-9226","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","last_name":"Shipilina","first_name":"Daria"},{"full_name":"Garcia Castillo, Diego Fernando","last_name":"Garcia Castillo","first_name":"Diego Fernando","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701"},{"first_name":"Hila","last_name":"Lifchitz","id":"d6ab5470-2fb3-11ed-8633-986a9b84edac","full_name":"Lifchitz, Hila"},{"first_name":"Alan","last_name":"Le Moan","full_name":"Le Moan, Alan"},{"last_name":"Leder","first_name":"Erica","full_name":"Leder, Erica"},{"first_name":"James","last_name":"Reeve","full_name":"Reeve, James"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"14812"}],"link":[{"url":"https://ista.ac.at/en/news/the-snail-or-the-egg/","description":"News on ISTA Website","relation":"press_release"}]},"article_type":"original","page":"114-119","publication":"Science","citation":{"apa":"Stankowski, S., Zagrodzka, Z. B., Garlovsky, M. D., Pal, A., Shipilina, D., Garcia Castillo, D. F., … Butlin, R. K. (2024). The genetic basis of a recent transition to live-bearing in marine snails. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adi2982","ieee":"S. Stankowski et al., “The genetic basis of a recent transition to live-bearing in marine snails,” Science, vol. 383, no. 6678. American Association for the Advancement of Science, pp. 114–119, 2024.","ista":"Stankowski S, Zagrodzka ZB, Garlovsky MD, Pal A, Shipilina D, Garcia Castillo DF, Lifchitz H, Le Moan A, Leder E, Reeve J, Johannesson K, Westram AM, Butlin RK. 2024. The genetic basis of a recent transition to live-bearing in marine snails. Science. 383(6678), 114–119.","ama":"Stankowski S, Zagrodzka ZB, Garlovsky MD, et al. The genetic basis of a recent transition to live-bearing in marine snails. Science. 2024;383(6678):114-119. doi:10.1126/science.adi2982","chicago":"Stankowski, Sean, Zuzanna B. Zagrodzka, Martin D. Garlovsky, Arka Pal, Daria Shipilina, Diego Fernando Garcia Castillo, Hila Lifchitz, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/science.adi2982.","short":"S. Stankowski, Z.B. Zagrodzka, M.D. Garlovsky, A. Pal, D. Shipilina, D.F. Garcia Castillo, H. Lifchitz, A. Le Moan, E. Leder, J. Reeve, K. Johannesson, A.M. Westram, R.K. Butlin, Science 383 (2024) 114–119.","mla":"Stankowski, Sean, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science, vol. 383, no. 6678, American Association for the Advancement of Science, 2024, pp. 114–19, doi:10.1126/science.adi2982."},"date_published":"2024-01-05T00:00:00Z","scopus_import":"1","day":"05","article_processing_charge":"No","title":"The genetic basis of a recent transition to live-bearing in marine snails","status":"public","intvolume":" 383","_id":"14796","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step."}],"issue":"6678"},{"month":"02","publication_identifier":{"issn":["2663 - 337X"]},"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"}],"oa":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"supervisor":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:15020","file_date_updated":"2024-02-23T14:20:16Z","ec_funded":1,"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"year":"2024","date_updated":"2024-03-06T14:22:52Z","date_created":"2024-02-23T14:02:04Z","author":[{"last_name":"Hledik","first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal"}],"related_material":{"record":[{"id":"7553","relation":"part_of_dissertation","status":"public"},{"id":"12081","relation":"part_of_dissertation","status":"public"},{"id":"7606","relation":"part_of_dissertation","status":"public"}]},"keyword":["Theoretical biology","Optimality","Evolution","Information"],"day":"23","article_processing_charge":"No","has_accepted_license":"1","page":"158","citation":{"ama":"Hledik M. Genetic information and biological optimization. 2024. doi:10.15479/at:ista:15020","apa":"Hledik, M. (2024). Genetic information and biological optimization. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15020","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria.","short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.","mla":"Hledik, Michal. Genetic Information and Biological Optimization. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15020.","chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15020."},"date_published":"2024-02-23T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.\r\nChapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?\r\nChapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal.","lang":"eng"}],"ddc":["576","519"],"title":"Genetic information and biological optimization","status":"public","_id":"15020","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","file":[{"file_size":7102089,"content_type":"application/pdf","creator":"mhledik","file_name":"hledik thesis pdfa 2b.pdf","access_level":"open_access","date_updated":"2024-02-23T13:50:53Z","date_created":"2024-02-23T13:50:53Z","checksum":"b2d3da47c98d481577a4baf68944fe41","success":1,"relation":"main_file","file_id":"15021"},{"creator":"mhledik","file_size":14014790,"content_type":"application/zip","access_level":"closed","file_name":"hledik thesis source.zip","checksum":"eda9b9430da2610fee7ce1c1419a479a","date_created":"2024-02-23T13:50:54Z","date_updated":"2024-02-23T14:20:16Z","file_id":"15022","relation":"source_file"}]},{"publication_identifier":{"eissn":["1362-4555"],"issn":["0168-9525"]},"month":"02","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["38395682"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.tig.2024.01.002","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.tig.2024.01.002","publisher":"Cell Press","department":[{"_id":"NiBa"}],"publication_status":"epub_ahead","pmid":1,"acknowledgement":"KJ, MR, and RKB were supported by grants from the Swedish Research Council (2021-0419, 2021-05243, and 2018-03695, respectively). RKB was also supported by the Leverhulme Trust (RPG-2021-141), RF by FCT- Portuguese Science Foundation (PTDC/BIA-EVL/1614/2021 and 2020.00275.CEECIND), and AMW by Norwegian Research Council RCN (Project number 315287). We thank the members of the Integration of Speciation Research network for stimulating discussions, the Littorina research community for important contributions of data and analyses, and Cynthia Riginos for useful comments on an earlier draft.","year":"2024","date_created":"2024-03-10T23:00:54Z","date_updated":"2024-03-13T12:08:57Z","author":[{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"full_name":"Le Moan, Alan","first_name":"Alan","last_name":"Le Moan"},{"full_name":"Rafajlović, Marina","first_name":"Marina","last_name":"Rafajlović"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean","full_name":"Stankowski, Sean"}],"scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"22","article_type":"review","citation":{"ama":"Johannesson K, Faria R, Le Moan A, et al. Diverse pathways to speciation revealed by marine snails. Trends in Genetics. 2024. doi:10.1016/j.tig.2024.01.002","ista":"Johannesson K, Faria R, Le Moan A, Rafajlović M, Westram AM, Butlin RK, Stankowski S. 2024. Diverse pathways to speciation revealed by marine snails. Trends in Genetics.","apa":"Johannesson, K., Faria, R., Le Moan, A., Rafajlović, M., Westram, A. M., Butlin, R. K., & Stankowski, S. (2024). Diverse pathways to speciation revealed by marine snails. Trends in Genetics. Cell Press. https://doi.org/10.1016/j.tig.2024.01.002","ieee":"K. Johannesson et al., “Diverse pathways to speciation revealed by marine snails,” Trends in Genetics. Cell Press, 2024.","mla":"Johannesson, Kerstin, et al. “Diverse Pathways to Speciation Revealed by Marine Snails.” Trends in Genetics, Cell Press, 2024, doi:10.1016/j.tig.2024.01.002.","short":"K. Johannesson, R. Faria, A. Le Moan, M. Rafajlović, A.M. Westram, R.K. Butlin, S. Stankowski, Trends in Genetics (2024).","chicago":"Johannesson, Kerstin, Rui Faria, Alan Le Moan, Marina Rafajlović, Anja M Westram, Roger K. Butlin, and Sean Stankowski. “Diverse Pathways to Speciation Revealed by Marine Snails.” Trends in Genetics. Cell Press, 2024. https://doi.org/10.1016/j.tig.2024.01.002."},"publication":"Trends in Genetics","date_published":"2024-02-22T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems."}],"status":"public","ddc":["570"],"title":"Diverse pathways to speciation revealed by marine snails","_id":"15099","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version"},{"file_date_updated":"2023-02-27T07:10:17Z","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"publisher":"Wiley","publication_status":"published","acknowledgement":"We greatly thank all the corresponding authors of the studies that were included in our synthesis for the sharing of additional data: Thomas Broquet, Dmitry Filatov, Quentin Rougemont, Paolo Momigliano, Pierre-Alexandre Gagnaire, Carlos Prada, Ahmed Souissi, Michael Møller Hansen, Sylvie Lapègue, Joseph Di Battista, Michael Hellberg and Carlos Prada. RKB and ADJ were supported by the European Research Council. MR was supported by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243; to MR) and Formas (grant number 2019-00882; to KJ and MR), and by additional grants from the European Research Council (to RKB) and Vetenskapsrådet (to KJ) through the Centre for Marine Evolutionary Biology (https://www.gu.se/en/cemeb-marine-evolutionary-biology).","year":"2023","volume":16,"date_created":"2022-07-03T22:01:33Z","date_updated":"2023-08-01T12:25:44Z","author":[{"last_name":"De Jode","first_name":"Aurélien","full_name":"De Jode, Aurélien"},{"first_name":"Alan","last_name":"Le Moan","full_name":"Le Moan, Alan"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"full_name":"Stankowski, Sean","first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"},{"full_name":"Rafajlović, Marina","first_name":"Marina","last_name":"Rafajlović"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle"}],"publication_identifier":{"eissn":["1752-4571"]},"month":"02","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000815663700001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/eva.13428","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results."}],"intvolume":" 16","title":"Ten years of demographic modelling of divergence and speciation in the sea","ddc":["576"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11479","file":[{"date_updated":"2023-02-27T07:10:17Z","date_created":"2023-02-27T07:10:17Z","checksum":"d4d6fa9ddf36643af994a6a757919afb","success":1,"relation":"main_file","file_id":"12685","file_size":2269822,"content_type":"application/pdf","creator":"dernst","file_name":"2023_EvolutionaryApplications_DeJode.pdf","access_level":"open_access"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"542-559","article_type":"original","citation":{"ieee":"A. De Jode et al., “Ten years of demographic modelling of divergence and speciation in the sea,” Evolutionary Applications, vol. 16, no. 2. Wiley, pp. 542–559, 2023.","apa":"De Jode, A., Le Moan, A., Johannesson, K., Faria, R., Stankowski, S., Westram, A. M., … Fraisse, C. (2023). Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. Wiley. https://doi.org/10.1111/eva.13428","ista":"De Jode A, Le Moan A, Johannesson K, Faria R, Stankowski S, Westram AM, Butlin RK, Rafajlović M, Fraisse C. 2023. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 16(2), 542–559.","ama":"De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 2023;16(2):542-559. doi:10.1111/eva.13428","chicago":"De Jode, Aurélien, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski, Anja M Westram, Roger K. Butlin, Marina Rafajlović, and Christelle Fraisse. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications. Wiley, 2023. https://doi.org/10.1111/eva.13428.","short":"A. De Jode, A. Le Moan, K. Johannesson, R. Faria, S. Stankowski, A.M. Westram, R.K. Butlin, M. Rafajlović, C. Fraisse, Evolutionary Applications 16 (2023) 542–559.","mla":"De Jode, Aurélien, et al. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications, vol. 16, no. 2, Wiley, 2023, pp. 542–59, doi:10.1111/eva.13428."},"publication":"Evolutionary Applications","date_published":"2023-02-01T00:00:00Z"},{"date_published":"2023-01-01T00:00:00Z","article_type":"original","page":"318-328","publication":"Evolution: International journal of organic evolution","citation":{"ama":"Bolnick DI, Hund AK, Nosil P, et al. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 2023;77(1):318-328. doi:10.1093/evolut/qpac004","ieee":"D. I. Bolnick et al., “A multivariate view of the speciation continuum,” Evolution: International journal of organic evolution, vol. 77, no. 1. Oxford University Press, pp. 318–328, 2023.","apa":"Bolnick, D. I., Hund, A. K., Nosil, P., Peng, F., Ravinet, M., Stankowski, S., … Yukilevich, R. (2023). A multivariate view of the speciation continuum. Evolution: International Journal of Organic Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpac004","ista":"Bolnick DI, Hund AK, Nosil P, Peng F, Ravinet M, Stankowski S, Subramanian S, Wolf JBW, Yukilevich R. 2023. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 77(1), 318–328.","short":"D.I. Bolnick, A.K. Hund, P. Nosil, F. Peng, M. Ravinet, S. Stankowski, S. Subramanian, J.B.W. Wolf, R. Yukilevich, Evolution: International Journal of Organic Evolution 77 (2023) 318–328.","mla":"Bolnick, Daniel I., et al. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution, vol. 77, no. 1, Oxford University Press, 2023, pp. 318–28, doi:10.1093/evolut/qpac004.","chicago":"Bolnick, Daniel I., Amanda K. Hund, Patrik Nosil, Foen Peng, Mark Ravinet, Sean Stankowski, Swapna Subramanian, Jochen B.W. Wolf, and Roman Yukilevich. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution. Oxford University Press, 2023. https://doi.org/10.1093/evolut/qpac004."},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","status":"public","title":"A multivariate view of the speciation continuum","intvolume":" 77","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12514","abstract":[{"text":"The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model.","lang":"eng"}],"issue":"1","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1093/evolut/qpac004","quality_controlled":"1","isi":1,"external_id":{"isi":["001021686300024"],"pmid":["36622661"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1093/evolut/qpac004","open_access":"1"}],"month":"01","publication_identifier":{"eissn":["1558-5646"]},"date_created":"2023-02-05T23:00:59Z","date_updated":"2023-08-01T12:58:30Z","volume":77,"author":[{"full_name":"Bolnick, Daniel I.","last_name":"Bolnick","first_name":"Daniel I."},{"full_name":"Hund, Amanda K.","first_name":"Amanda K.","last_name":"Hund"},{"first_name":"Patrik","last_name":"Nosil","full_name":"Nosil, Patrik"},{"first_name":"Foen","last_name":"Peng","full_name":"Peng, Foen"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"},{"last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"full_name":"Subramanian, Swapna","last_name":"Subramanian","first_name":"Swapna"},{"full_name":"Wolf, Jochen B.W.","first_name":"Jochen B.W.","last_name":"Wolf"},{"first_name":"Roman","last_name":"Yukilevich","full_name":"Yukilevich, Roman"}],"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","year":"2023","acknowledgement":"The authors of this article were supported by LMU Munich (J.B.W.W.), a James S. McDonnell Foundation postdoctoral fellowship (A.K.H.). P.N. received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant agreement No. 770826 EE-Dynamics).\r\nWe thank participants in the 2019 Gordon Conference on Speciation for the extensive conversation on this topic. Thanks to Dan Funk for providing permission to use data from Funk et al. 2006, and for comments on the manuscript.","pmid":1},{"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","year":"2023","acknowledgement":"We thank the Barton group for useful discussion and feedback during the writing of this article. Comments from Roger Butlin, Molly Schumer's Group, the tskit development team, editors and three reviewers greatly improved the manuscript. Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).","pmid":1,"date_created":"2023-01-12T12:09:17Z","date_updated":"2023-08-16T08:18:47Z","volume":32,"author":[{"id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226","first_name":"Daria","last_name":"Shipilina","full_name":"Shipilina, Daria"},{"id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","orcid":"0000-0002-4530-8469","first_name":"Arka","last_name":"Pal","full_name":"Pal, Arka"},{"last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"last_name":"Chan","first_name":"Yingguang Frank","full_name":"Chan, Yingguang Frank"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"file_date_updated":"2023-08-16T08:15:41Z","quality_controlled":"1","isi":1,"project":[{"name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000900762000001"],"pmid":["36433653"]},"language":[{"iso":"eng"}],"doi":"10.1111/mec.16793","month":"03","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"ddc":["570"],"status":"public","title":"On the origin and structure of haplotype blocks","intvolume":" 32","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12159","file":[{"relation":"main_file","file_id":"14062","date_updated":"2023-08-16T08:15:41Z","date_created":"2023-08-16T08:15:41Z","checksum":"b10e0f8fa3dc4d72aaf77a557200978a","success":1,"file_name":"2023_MolecularEcology_Shipilina.pdf","access_level":"open_access","file_size":7144607,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The term “haplotype block” is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies."}],"issue":"6","article_type":"original","page":"1441-1457","publication":"Molecular Ecology","citation":{"ista":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.","apa":"Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023). On the origin and structure of haplotype blocks. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16793","ieee":"D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the origin and structure of haplotype blocks,” Molecular Ecology, vol. 32, no. 6. Wiley, pp. 1441–1457, 2023.","ama":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793","chicago":"Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793.","mla":"Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793.","short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457."},"date_published":"2023-03-01T00:00:00Z","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)"},{"quality_controlled":"1","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"name":"Understanding the evolution of continuous genomes","grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2211.03515"]},"language":[{"iso":"eng"}],"doi":"10.1093/genetics/iyad133","month":"10","publication_identifier":{"issn":["0016-6731"],"eissn":["1943-2631"]},"publication_status":"published","publisher":"Oxford Academic","department":[{"_id":"NiBa"}],"year":"2023","acknowledgement":"NHB was supported in part by ERC Grants 250152 and 101055327. AV was partly supported by the chaire Modélisation Mathématique et Biodiversité of Veolia Environment—Ecole Polytechnique—Museum National d’Histoire Naturelle—Fondation X.","date_updated":"2023-10-30T13:04:11Z","date_created":"2023-10-29T23:01:15Z","volume":225,"author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"last_name":"Etheridge","first_name":"Alison M.","full_name":"Etheridge, Alison M."},{"first_name":"Amandine","last_name":"Véber","full_name":"Véber, Amandine"}],"related_material":{"record":[{"id":"12949","status":"public","relation":"research_data"}]},"article_number":"iyad133","file_date_updated":"2023-10-30T12:57:53Z","ec_funded":1,"article_type":"original","publication":"Genetics","citation":{"short":"N.H. Barton, A.M. Etheridge, A. Véber, Genetics 225 (2023).","mla":"Barton, Nicholas H., et al. “The Infinitesimal Model with Dominance.” Genetics, vol. 225, no. 2, iyad133, Oxford Academic, 2023, doi:10.1093/genetics/iyad133.","chicago":"Barton, Nicholas H, Alison M. Etheridge, and Amandine Véber. “The Infinitesimal Model with Dominance.” Genetics. Oxford Academic, 2023. https://doi.org/10.1093/genetics/iyad133.","ama":"Barton NH, Etheridge AM, Véber A. The infinitesimal model with dominance. Genetics. 2023;225(2). doi:10.1093/genetics/iyad133","ieee":"N. H. Barton, A. M. Etheridge, and A. Véber, “The infinitesimal model with dominance,” Genetics, vol. 225, no. 2. Oxford Academic, 2023.","apa":"Barton, N. H., Etheridge, A. M., & Véber, A. (2023). The infinitesimal model with dominance. Genetics. Oxford Academic. https://doi.org/10.1093/genetics/iyad133","ista":"Barton NH, Etheridge AM, Véber A. 2023. The infinitesimal model with dominance. Genetics. 225(2), iyad133."},"date_published":"2023-10-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","ddc":["570"],"title":"The infinitesimal model with dominance","status":"public","intvolume":" 225","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14452","oa_version":"Published Version","file":[{"file_size":1439032,"content_type":"application/pdf","creator":"dernst","file_name":"2023_Genetics_Barton.pdf","access_level":"open_access","date_created":"2023-10-30T12:57:53Z","date_updated":"2023-10-30T12:57:53Z","checksum":"3f65b1fbe813e2f4dbb5d2b5e891844a","success":1,"relation":"main_file","file_id":"14469"}],"type":"journal_article","abstract":[{"text":"The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and an environmental component, and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the parental traits. In previous work, we showed that when trait values are determined by the sum of a large number of additive Mendelian factors, each of small effect, one can justify the infinitesimal model as a limit of Mendelian inheritance. In this paper, we show that this result extends to include dominance. We define the model in terms of classical quantities of quantitative genetics, before justifying it as a limit of Mendelian inheritance as the number, M, of underlying loci tends to infinity. As in the additive case, the multivariate normal distribution of trait values across the pedigree can be expressed in terms of variance components in an ancestral population and probabilities of identity by descent determined by the pedigree. Now, with just first-order dominance effects, we require two-, three-, and four-way identities. We also show that, even if we condition on parental trait values, the “shared” and “residual” components of trait values within each family will be asymptotically normally distributed as the number of loci tends to infinity, with an error of order 1/M−−√. We illustrate our results with some numerical examples.","lang":"eng"}],"issue":"2"},{"author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14452"}]},"contributor":[{"first_name":"Amandine","contributor_type":"researcher","last_name":"Veber"},{"last_name":"Etheridge","contributor_type":"researcher","first_name":"Alison"}],"date_created":"2023-05-13T09:49:09Z","date_updated":"2023-10-30T13:04:11Z","file":[{"date_created":"2023-05-13T09:36:33Z","date_updated":"2023-05-13T09:36:33Z","checksum":"b0ce7d4b1ee7e7265430ceed36fc3336","success":1,"relation":"main_file","file_id":"12950","file_size":13662,"content_type":"application/octet-stream","creator":"nbarton","file_name":"Neutral identities 16th Jan","access_level":"open_access"},{"creator":"nbarton","file_size":181619928,"content_type":"application/octet-stream","file_name":"p, zA, zD, N=30 neutral III","access_level":"open_access","date_updated":"2023-05-13T09:38:17Z","date_created":"2023-05-13T09:38:17Z","success":1,"checksum":"ad5035ad4f7d3b150a252c79884f6a83","file_id":"12951","relation":"main_file"},{"success":1,"checksum":"62182a1de796256edd6f4223704312ef","date_updated":"2023-05-13T09:41:59Z","date_created":"2023-05-13T09:41:59Z","file_id":"12952","relation":"main_file","creator":"nbarton","content_type":"application/octet-stream","file_size":605902074,"access_level":"open_access","file_name":"p, zA, zD, N=30 neutral IV"},{"date_updated":"2023-05-13T09:46:52Z","date_created":"2023-05-13T09:46:52Z","checksum":"af775dda5c4f6859cb1e5a81ec40a667","success":1,"relation":"main_file","file_id":"12953","file_size":1018238746,"content_type":"application/octet-stream","creator":"nbarton","file_name":"p, zA, zD, N=30 selected k=5","access_level":"open_access"},{"checksum":"af26f3394c387d3ada14b434cd68b1e5","success":1,"date_created":"2023-05-13T09:42:05Z","date_updated":"2023-05-13T09:42:05Z","relation":"main_file","file_id":"12954","file_size":3197160,"content_type":"application/octet-stream","creator":"nbarton","access_level":"open_access","file_name":"Pairwise F N=30 neutral II"},{"file_name":"Pedigrees N=30 neutral II","access_level":"open_access","content_type":"application/octet-stream","file_size":55492,"creator":"nbarton","relation":"main_file","file_id":"12955","date_updated":"2023-05-13T09:42:06Z","date_created":"2023-05-13T09:42:06Z","checksum":"d5da7dc0e7282dd48222e26d12e34220","success":1},{"checksum":"00f386d80677590e29f6235d49cba58d","success":1,"date_updated":"2023-05-13T09:46:06Z","date_created":"2023-05-13T09:46:06Z","relation":"main_file","file_id":"12956","file_size":474003467,"content_type":"application/octet-stream","creator":"nbarton","access_level":"open_access","file_name":"selected reps N=30 selected k=1,2 300 reps III"},{"access_level":"open_access","file_name":"Algorithm for caclulating identities.nb","creator":"nbarton","file_size":121209,"content_type":"application/octet-stream","file_id":"12957","relation":"main_file","success":1,"checksum":"658cef3eaea6136a4d24da4f074191d7","date_updated":"2023-05-13T09:46:08Z","date_created":"2023-05-13T09:46:08Z"},{"date_created":"2023-05-13T09:46:08Z","date_updated":"2023-05-13T09:46:08Z","success":1,"checksum":"db9b6dddd7a596d974e25f5e78f5c45c","file_id":"12958","relation":"main_file","creator":"nbarton","file_size":1803898,"content_type":"application/octet-stream","file_name":"Infinitesimal with dominance.nb","access_level":"open_access"},{"file_id":"12967","relation":"main_file","success":1,"checksum":"91f80a9fb58cae8eef2d8bf59fe30189","date_created":"2023-05-16T04:09:08Z","date_updated":"2023-05-16T04:09:08Z","access_level":"open_access","file_name":"ReadMe.txt","creator":"nbarton","file_size":990,"content_type":"text/plain"}],"oa_version":"Published Version","_id":"12949","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The infinitesimal model with dominance","ddc":["576"],"status":"public","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-05-16T04:09:08Z","abstract":[{"text":"The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and a non-genetic (environmental) component and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the trait values of the parents. Although the trait distribution across the whole population can be far from normal, the trait distributions within families are normally distributed with a variance-covariance matrix that is determined entirely by that in the ancestral population and the probabilities of identity determined by the pedigree. Moreover, conditioning on some of the trait values within the pedigree has predictable effects on the mean and variance within and between families. In previous work, Barton et al. (2017), we showed that when trait values are determined by the sum of a large number of Mendelian factors, each of small effect, one can justify the infinitesimal model as limit of Mendelian inheritance. It was also shown that under some forms of epistasis, trait values within a family are still normally distributed.","lang":"eng"}],"type":"research_data","date_published":"2023-05-13T00:00:00Z","doi":"10.15479/AT:ISTA:12949","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"citation":{"ieee":"N. H. Barton, “The infinitesimal model with dominance.” Institute of Science and Technology Austria, 2023.","apa":"Barton, N. H. (2023). The infinitesimal model with dominance. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12949","ista":"Barton NH. 2023. The infinitesimal model with dominance, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12949.","ama":"Barton NH. The infinitesimal model with dominance. 2023. doi:10.15479/AT:ISTA:12949","chicago":"Barton, Nicholas H. “The Infinitesimal Model with Dominance.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12949.","short":"N.H. Barton, (2023).","mla":"Barton, Nicholas H. The Infinitesimal Model with Dominance. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12949."},"project":[{"grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes"}],"month":"05","day":"13","has_accepted_license":"1","article_processing_charge":"No","keyword":["Quantitative genetics","infinitesimal model"]}]