[{"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."}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2024_JourExperimBiology_Pal.pdf","access_level":"open_access","content_type":"application/pdf","file_size":594128,"creator":"dernst","relation":"main_file","file_id":"14877","date_created":"2024-01-23T12:08:24Z","date_updated":"2024-01-23T12:08:24Z","checksum":"136325372f6f45abaa62a71e2d23bfb6","success":1}],"title":"Too much information? Males convey parasite levels using more signal modalities than females utilise","ddc":["570"],"status":"public","intvolume":" 227","_id":"14850","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"10","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","keyword":["Insect Science","Molecular Biology","Animal Science and Zoology","Aquatic Science","Physiology","Ecology","Evolution","Behavior and Systematics"],"date_published":"2024-01-10T00:00:00Z","article_type":"original","publication":"Journal of Experimental Biology","citation":{"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","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.","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.","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."},"file_date_updated":"2024-01-23T12:08:24Z","article_number":"jeb246217","date_created":"2024-01-22T08:14:49Z","date_updated":"2024-01-23T12:13:08Z","volume":227,"author":[{"orcid":"0000-0002-4530-8469","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal","first_name":"Arka","full_name":"Pal, Arka"},{"full_name":"Joshi, Mihir","first_name":"Mihir","last_name":"Joshi"},{"full_name":"Thaker, Maria","last_name":"Thaker","first_name":"Maria"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/arka-pal/Cnemaspis-SexualSignaling"}]},"publication_status":"published","publisher":"The Company of Biologists","department":[{"_id":"NiBa"}],"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.","pmid":1,"month":"01","publication_identifier":{"eissn":["0022-0949"],"issn":["1477-9145"]},"language":[{"iso":"eng"}],"doi":"10.1242/jeb.246217","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":{"pmid":["38054353"]},"oa":1},{"day":"19","article_processing_charge":"No","has_accepted_license":"1","page":"183","citation":{"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.","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.","ista":"Olusanya OO. 2024. Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria.","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","ieee":"O. O. Olusanya, “Local adaptation, genetic load and extinction in metapopulations,” Institute of Science and Technology Austria, 2024.","ama":"Olusanya OO. Local adaptation, genetic load and extinction in metapopulations. 2024. doi:10.15479/at:ista:14711"},"date_published":"2024-01-19T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","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."}],"title":"Local adaptation, genetic load and extinction in metapopulations","ddc":["576"],"status":"public","_id":"14711","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","file":[{"creator":"oolusany","content_type":"application/zip","file_size":16986244,"file_name":"FinalSubmission_Thesis_OLUSANYA.zip","access_level":"closed","date_updated":"2024-01-03T18:30:13Z","date_created":"2024-01-03T18:30:13Z","checksum":"de179b1c6758f182ff0c70d8b38c1501","file_id":"14730","relation":"source_file"},{"success":1,"checksum":"0e331585e3cd4823320aab4e69e64ccf","date_created":"2024-01-03T18:31:34Z","date_updated":"2024-01-03T18:31:34Z","file_id":"14731","relation":"main_file","creator":"oolusany","content_type":"application/pdf","file_size":6460403,"access_level":"open_access","file_name":"FinalSubmission2_Thesis_OLUSANYA.pdf"}],"month":"01","publication_identifier":{"issn":["2663 - 337X"]},"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"Causes and consequences of population fragmentation","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","grant_number":"P32896"},{"name":"Polygenic Adaptation in a Metapopulation","_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6","grant_number":"26380"}],"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,"supervisor":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"full_name":"Polechova, Jitka","first_name":"Jitka","last_name":"Polechova"},{"last_name":"Sachdeva","first_name":"Himani","full_name":"Sachdeva, Himani"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:14711","file_date_updated":"2024-01-03T18:31:34Z","ec_funded":1,"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"year":"2024","date_updated":"2024-01-26T12:00:54Z","date_created":"2023-12-26T22:49:53Z","author":[{"id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1971-8314","first_name":"Oluwafunmilola O","last_name":"Olusanya","full_name":"Olusanya, Oluwafunmilola O"}],"related_material":{"record":[{"id":"10658","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10787"},{"relation":"part_of_dissertation","status":"public","id":"14732"}]}},{"volume":383,"date_created":"2024-01-14T23:00:56Z","date_updated":"2024-03-05T09:35:25Z","related_material":{"record":[{"id":"14812","status":"public","relation":"research_data"}],"link":[{"url":"https://ista.ac.at/en/news/the-snail-or-the-egg/","relation":"press_release","description":"News on ISTA Website"}]},"author":[{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean"},{"last_name":"Zagrodzka","first_name":"Zuzanna B.","full_name":"Zagrodzka, Zuzanna B."},{"last_name":"Garlovsky","first_name":"Martin D.","full_name":"Garlovsky, Martin D."},{"last_name":"Pal","first_name":"Arka","orcid":"0000-0002-4530-8469","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","full_name":"Pal, Arka"},{"full_name":"Shipilina, Daria","first_name":"Daria","last_name":"Shipilina","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226"},{"full_name":"Garcia Castillo, Diego Fernando","first_name":"Diego Fernando","last_name":"Garcia Castillo","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701"},{"id":"d6ab5470-2fb3-11ed-8633-986a9b84edac","last_name":"Lifchitz","first_name":"Hila","full_name":"Lifchitz, Hila"},{"full_name":"Le Moan, Alan","last_name":"Le Moan","first_name":"Alan"},{"last_name":"Leder","first_name":"Erica","full_name":"Leder, Erica"},{"first_name":"James","last_name":"Reeve","full_name":"Reeve, James"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"department":[{"_id":"NiBa"},{"_id":"GradSch"}],"publisher":"American Association for the Advancement of Science","publication_status":"published","pmid":1,"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.).","publication_identifier":{"eissn":["1095-9203"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1126/science.adi2982","quality_controlled":"1","external_id":{"pmid":["38175895"]},"issue":"6678","abstract":[{"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.","lang":"eng"}],"type":"journal_article","oa_version":"None","intvolume":" 383","title":"The genetic basis of a recent transition to live-bearing in marine snails","status":"public","_id":"14796","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"05","scopus_import":"1","date_published":"2024-01-05T00:00:00Z","page":"114-119","article_type":"original","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."},"publication":"Science"},{"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","keyword":["Theoretical biology","Optimality","Evolution","Information"],"day":"23","article_processing_charge":"No","has_accepted_license":"1","ddc":["576","519"],"status":"public","title":"Genetic information and biological optimization","_id":"15020","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"date_created":"2024-02-23T13:50:53Z","date_updated":"2024-02-23T13:50:53Z","checksum":"b2d3da47c98d481577a4baf68944fe41","success":1,"relation":"main_file","file_id":"15021","content_type":"application/pdf","file_size":7102089,"creator":"mhledik","file_name":"hledik thesis pdfa 2b.pdf","access_level":"open_access"},{"content_type":"application/zip","file_size":14014790,"creator":"mhledik","file_name":"hledik thesis source.zip","access_level":"closed","date_updated":"2024-02-23T14:20:16Z","date_created":"2024-02-23T13:50:54Z","checksum":"eda9b9430da2610fee7ce1c1419a479a","relation":"source_file","file_id":"15022"}],"oa_version":"Published Version","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"}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"}],"oa":1,"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"ScienComp"}],"supervisor":[{"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":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:15020","month":"02","publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"year":"2024","date_created":"2024-02-23T14:02:04Z","date_updated":"2024-03-06T14:22:52Z","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"},{"relation":"part_of_dissertation","status":"public","id":"12081"},{"id":"7606","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2024-02-23T14:20:16Z","ec_funded":1},{"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."}],"type":"journal_article","oa_version":"Published Version","status":"public","ddc":["570"],"title":"Diverse pathways to speciation revealed by marine snails","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15099","day":"22","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","scopus_import":"1","date_published":"2024-02-22T00:00:00Z","article_type":"review","publication":"Trends in Genetics","citation":{"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.","short":"K. Johannesson, R. Faria, A. Le Moan, M. Rafajlović, A.M. Westram, R.K. Butlin, S. Stankowski, Trends in Genetics (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.","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.","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.","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"},"date_created":"2024-03-10T23:00:54Z","date_updated":"2024-03-13T12:08:57Z","author":[{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Alan","last_name":"Le Moan","full_name":"Le Moan, Alan"},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","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"}],"publication_status":"epub_ahead","publisher":"Cell Press","department":[{"_id":"NiBa"}],"year":"2024","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.","pmid":1,"month":"02","publication_identifier":{"issn":["0168-9525"],"eissn":["1362-4555"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.tig.2024.01.002","quality_controlled":"1","external_id":{"pmid":["38395682"]},"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,"main_file_link":[{"url":"https://doi.org/10.1016/j.tig.2024.01.002","open_access":"1"}]},{"file_date_updated":"2023-02-27T07:10:17Z","author":[{"first_name":"Aurélien","last_name":"De Jode","full_name":"De Jode, Aurélien"},{"last_name":"Le Moan","first_name":"Alan","full_name":"Le Moan, Alan"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean","full_name":"Stankowski, Sean"},{"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"},{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle"}],"date_updated":"2023-08-01T12:25:44Z","date_created":"2022-07-03T22:01:33Z","volume":16,"year":"2023","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).","publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"month":"02","publication_identifier":{"eissn":["1752-4571"]},"doi":"10.1111/eva.13428","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000815663700001"]},"quality_controlled":"1","isi":1,"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."}],"issue":"2","type":"journal_article","file":[{"file_name":"2023_EvolutionaryApplications_DeJode.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":2269822,"file_id":"12685","relation":"main_file","date_updated":"2023-02-27T07:10:17Z","date_created":"2023-02-27T07:10:17Z","success":1,"checksum":"d4d6fa9ddf36643af994a6a757919afb"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11479","ddc":["576"],"title":"Ten years of demographic modelling of divergence and speciation in the sea","status":"public","intvolume":" 16","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2023-02-01T00:00:00Z","publication":"Evolutionary Applications","citation":{"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","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.","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","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.","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.","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.","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."},"article_type":"original","page":"542-559"},{"doi":"10.1093/evolut/qpac004","language":[{"iso":"eng"}],"external_id":{"isi":["001021686300024"],"pmid":["36622661"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/evolut/qpac004"}],"oa":1,"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["1558-5646"]},"month":"01","author":[{"last_name":"Bolnick","first_name":"Daniel I.","full_name":"Bolnick, Daniel I."},{"full_name":"Hund, Amanda K.","last_name":"Hund","first_name":"Amanda K."},{"last_name":"Nosil","first_name":"Patrik","full_name":"Nosil, Patrik"},{"last_name":"Peng","first_name":"Foen","full_name":"Peng, Foen"},{"last_name":"Ravinet","first_name":"Mark","full_name":"Ravinet, Mark"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean","full_name":"Stankowski, Sean"},{"first_name":"Swapna","last_name":"Subramanian","full_name":"Subramanian, Swapna"},{"first_name":"Jochen B.W.","last_name":"Wolf","full_name":"Wolf, Jochen B.W."},{"full_name":"Yukilevich, Roman","last_name":"Yukilevich","first_name":"Roman"}],"volume":77,"date_created":"2023-02-05T23:00:59Z","date_updated":"2023-08-01T12:58:30Z","pmid":1,"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.","year":"2023","publisher":"Oxford University Press","department":[{"_id":"NiBa"}],"publication_status":"published","date_published":"2023-01-01T00:00:00Z","citation":{"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.","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","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.","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."},"publication":"Evolution: International journal of organic evolution","page":"318-328","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12514","intvolume":" 77","status":"public","title":"A multivariate view of the speciation continuum","issue":"1","abstract":[{"lang":"eng","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."}],"type":"journal_article"},{"page":"1441-1457","article_type":"original","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.","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.","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","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."},"publication":"Molecular Ecology","date_published":"2023-03-01T00:00:00Z","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","intvolume":" 32","ddc":["570"],"title":"On the origin and structure of haplotype blocks","status":"public","_id":"12159","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":7144607,"file_name":"2023_MolecularEcology_Shipilina.pdf","access_level":"open_access","date_updated":"2023-08-16T08:15:41Z","date_created":"2023-08-16T08:15:41Z","success":1,"checksum":"b10e0f8fa3dc4d72aaf77a557200978a","file_id":"14062","relation":"main_file"}],"type":"journal_article","issue":"6","abstract":[{"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.","lang":"eng"}],"project":[{"name":"The maintenance of alternative adaptive peaks in snapdragons","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327"}],"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"},"oa":1,"external_id":{"isi":["000900762000001"],"pmid":["36433653"]},"language":[{"iso":"eng"}],"doi":"10.1111/mec.16793","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"month":"03","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","pmid":1,"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).","volume":32,"date_created":"2023-01-12T12:09:17Z","date_updated":"2023-08-16T08:18:47Z","author":[{"full_name":"Shipilina, Daria","orcid":"0000-0002-1145-9226","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","last_name":"Shipilina","first_name":"Daria"},{"full_name":"Pal, Arka","first_name":"Arka","last_name":"Pal","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","orcid":"0000-0002-4530-8469"},{"full_name":"Stankowski, Sean","first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"last_name":"Chan","first_name":"Yingguang Frank","full_name":"Chan, Yingguang Frank"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2023-08-16T08:15:41Z"},{"issue":"2","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"}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14469","date_created":"2023-10-30T12:57:53Z","date_updated":"2023-10-30T12:57:53Z","checksum":"3f65b1fbe813e2f4dbb5d2b5e891844a","success":1,"file_name":"2023_Genetics_Barton.pdf","access_level":"open_access","file_size":1439032,"content_type":"application/pdf","creator":"dernst"}],"_id":"14452","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 225","title":"The infinitesimal model with dominance","status":"public","ddc":["570"],"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2023-10-01T00:00:00Z","citation":{"ama":"Barton NH, Etheridge AM, Véber A. The infinitesimal model with dominance. Genetics. 2023;225(2). doi:10.1093/genetics/iyad133","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","ieee":"N. H. Barton, A. M. Etheridge, and A. Véber, “The infinitesimal model with dominance,” Genetics, vol. 225, no. 2. Oxford Academic, 2023.","ista":"Barton NH, Etheridge AM, Véber A. 2023. The infinitesimal model with dominance. Genetics. 225(2), iyad133.","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."},"publication":"Genetics","article_type":"original","ec_funded":1,"file_date_updated":"2023-10-30T12:57:53Z","article_number":"iyad133","related_material":{"record":[{"status":"public","relation":"research_data","id":"12949"}]},"author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Etheridge","first_name":"Alison M.","full_name":"Etheridge, Alison M."},{"full_name":"Véber, Amandine","first_name":"Amandine","last_name":"Véber"}],"volume":225,"date_created":"2023-10-29T23:01:15Z","date_updated":"2023-10-30T13:04:11Z","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.","year":"2023","department":[{"_id":"NiBa"}],"publisher":"Oxford Academic","publication_status":"published","publication_identifier":{"eissn":["1943-2631"],"issn":["0016-6731"]},"month":"10","doi":"10.1093/genetics/iyad133","language":[{"iso":"eng"}],"external_id":{"arxiv":["2211.03515"]},"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,"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes"}],"quality_controlled":"1"},{"scopus_import":"1","day":"08","article_processing_charge":"No","has_accepted_license":"1","publication":"Journal of Evolutionary Biology","citation":{"chicago":"Berdan, Emma L., Nicholas H Barton, Roger Butlin, Brian Charlesworth, Rui Faria, Inês Fragata, Kimberly J. Gilbert, et al. “How Chromosomal Inversions Reorient the Evolutionary Process.” Journal of Evolutionary Biology. Wiley, 2023. https://doi.org/10.1111/jeb.14242.","short":"E.L. Berdan, N.H. Barton, R. Butlin, B. Charlesworth, R. Faria, I. Fragata, K.J. Gilbert, P. Jay, M. Kapun, K.E. Lotterhos, C. Mérot, E. Durmaz Mitchell, M. Pascual, C.L. Peichel, M. Rafajlović, A.M. Westram, S.W. Schaeffer, K. Johannesson, T. Flatt, Journal of Evolutionary Biology (2023).","mla":"Berdan, Emma L., et al. “How Chromosomal Inversions Reorient the Evolutionary Process.” Journal of Evolutionary Biology, 14242, Wiley, 2023, doi:10.1111/jeb.14242.","ieee":"E. L. Berdan et al., “How chromosomal inversions reorient the evolutionary process,” Journal of Evolutionary Biology. Wiley, 2023.","apa":"Berdan, E. L., Barton, N. H., Butlin, R., Charlesworth, B., Faria, R., Fragata, I., … Flatt, T. (2023). How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14242","ista":"Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. 2023. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology., 14242.","ama":"Berdan EL, Barton NH, Butlin R, et al. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology. 2023. doi:10.1111/jeb.14242"},"article_type":"review","date_published":"2023-11-08T00:00:00Z","type":"journal_article","abstract":[{"text":"Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14556","status":"public","title":"How chromosomal inversions reorient the evolutionary process","ddc":["570"],"oa_version":"Published Version","month":"11","publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jeb.14242"}],"oa":1,"quality_controlled":"1","doi":"10.1111/jeb.14242","language":[{"iso":"eng"}],"article_number":"14242","license":"https://creativecommons.org/licenses/by-nc/4.0/","acknowledgement":"We are grateful to two referees and Luke Holman for valuable comments on a previous version of our manuscript. This paper was conceived at the ESEB Progress Meeting ‘Disentangling neutral versus adaptive evolution in chromosomal inversions’, organized by ELB, KJ and TF and held at Tjärnö Marine Laboratory (Sweden) between 28 February and 3 March 2022. We are indebted to ESEB for sponsoring our workshop and to the following funding bodies for supporting our research: ERC AdG 101055327 to NHB; Swedish Research Council (VR) 2018-03695 and Leverhulme Trust RPG-2021-141 to RKB; Fundação para a Ciência e a Tecnologia (FCT) contract 2020.00275.CEECIND and research project PTDC/BIA-1232 EVL/1614/2021 to RF; Fundação para a Ciência e a Tecnologia (FCT) junior researcher contract CEECIND/02616/2018 to IF; Swiss National Science Foundation (SNSF) Ambizione #PZ00P3_185952 to KJG; National Science Foundation NSF-OCE 2043905 and NSF-DEB 1655701 to KEL; Swiss National Science Foundation (SNSF) 310030_204681 to CLP; Swedish Research Council (VR) 2021-05243 to MR; Norwegian Research Council grant 315287 to AMW; Swiss National Science Foundation (SNSF) 31003A-182262 and FZEB-0-214654 to TF. We also thank Luca Ferretti for the discussion and Eliane Zinn (Flatt lab) for help with reference formatting.","year":"2023","publication_status":"epub_ahead","department":[{"_id":"NiBa"}],"publisher":"Wiley","author":[{"full_name":"Berdan, Emma L.","last_name":"Berdan","first_name":"Emma L."},{"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":"Butlin","first_name":"Roger","full_name":"Butlin, Roger"},{"first_name":"Brian","last_name":"Charlesworth","full_name":"Charlesworth, Brian"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"full_name":"Fragata, Inês","last_name":"Fragata","first_name":"Inês"},{"full_name":"Gilbert, Kimberly J.","last_name":"Gilbert","first_name":"Kimberly J."},{"full_name":"Jay, Paul","last_name":"Jay","first_name":"Paul"},{"full_name":"Kapun, Martin","first_name":"Martin","last_name":"Kapun"},{"last_name":"Lotterhos","first_name":"Katie E.","full_name":"Lotterhos, Katie E."},{"full_name":"Mérot, Claire","first_name":"Claire","last_name":"Mérot"},{"first_name":"Esra","last_name":"Durmaz Mitchell","full_name":"Durmaz Mitchell, Esra"},{"full_name":"Pascual, Marta","last_name":"Pascual","first_name":"Marta"},{"first_name":"Catherine L.","last_name":"Peichel","full_name":"Peichel, Catherine L."},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"first_name":"Stephen W.","last_name":"Schaeffer","full_name":"Schaeffer, Stephen W."},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"first_name":"Thomas","last_name":"Flatt","full_name":"Flatt, Thomas"}],"date_updated":"2023-11-20T08:51:09Z","date_created":"2023-11-19T23:00:55Z"},{"day":"09","article_processing_charge":"No","scopus_import":"1","date_published":"2023-11-09T00:00:00Z","article_type":"original","page":"679-683","publication":"Science","citation":{"short":"M.L. Robinson, P.G. Hahn, B.D. Inouye, N. Underwood, S.R. Whitehead, K.C. Abbott, E.M. Bruna, N.I. Cacho, L.A. Dyer, L. Abdala-Roberts, W.J. Allen, J.F. Andrade, D.F. Angulo, D. Anjos, D.N. Anstett, R. Bagchi, S. Bagchi, M. Barbosa, S. Barrett, C. Baskett, E. Ben-Simchon, K.J. Bloodworth, J.L. Bronstein, Y.M. Buckley, K.T. Burghardt, C. Bustos-Segura, E.S. Calixto, R.L. Carvalho, B. Castagneyrol, M.C. Chiuffo, D. Cinoğlu, E. Cinto Mejía, M.C. Cock, R. Cogni, O.L. Cope, T. Cornelissen, D.R. Cortez, D.W. Crowder, C. Dallstream, W. Dáttilo, J.K. Davis, R.D. Dimarco, H.E. Dole, I.N. Egbon, M. Eisenring, A. Ejomah, B.D. Elderd, M.J. Endara, M.D. Eubanks, S.E. Everingham, K.N. Farah, R.P. Farias, A.P. Fernandes, G.W. Fernandes, M. Ferrante, A. Finn, G.A. Florjancic, M.L. Forister, Q.N. Fox, E. Frago, F.M. França, A.S. Getman-Pickering, Z. Getman-Pickering, E. Gianoli, B. Gooden, M.M. Gossner, K.A. Greig, S. Gripenberg, R. Groenteman, P. Grof-Tisza, N. Haack, L. Hahn, S.M. Haq, A.M. Helms, J. Hennecke, S.L. Hermann, L.M. Holeski, S. Holm, M.C. Hutchinson, E.E. Jackson, S. Kagiya, A. Kalske, M. Kalwajtys, R. Karban, R. Kariyat, T. Keasar, M.F. Kersch-Becker, H.M. Kharouba, T.N. Kim, D.M. Kimuyu, J. Kluse, S.E. Koerner, K.J. Komatsu, S. Krishnan, M. Laihonen, L. Lamelas-López, M.C. Lascaleia, N. Lecomte, C.R. Lehn, X. Li, R.L. Lindroth, E.F. Lopresti, M. Losada, A.M. Louthan, V.J. Luizzi, S.C. Lynch, J.S. Lynn, N.J. Lyon, L.F. Maia, R.A. Maia, T.L. Mannall, B.S. Martin, T.J. Massad, A.C. Mccall, K. Mcgurrin, A.C. Merwin, Z. Mijango-Ramos, C.H. Mills, A.T. Moles, C.M. Moore, X. Moreira, C.R. Morrison, M.C. Moshobane, A. Muola, R. Nakadai, K. Nakajima, S. Novais, C.O. Ogbebor, H. Ohsaki, V.S. Pan, N.A. Pardikes, M. Pareja, N. Parthasarathy, R.R. Pawar, Q. Paynter, I.S. Pearse, R.M. Penczykowski, A.A. Pepi, C.C. Pereira, S.S. Phartyal, F.I. Piper, K. Poveda, E.G. Pringle, J. Puy, T. Quijano, C. Quintero, S. Rasmann, C. Rosche, L.Y. Rosenheim, J.A. Rosenheim, J.B. Runyon, A. Sadeh, Y. Sakata, D.M. Salcido, C. Salgado-Luarte, B.A. Santos, Y. Sapir, Y. Sasal, Y. Sato, M. Sawant, H. Schroeder, I. Schumann, M. Segoli, H. Segre, O. Shelef, N. Shinohara, R.P. Singh, D.S. Smith, M. Sobral, G.C. Stotz, A.J.M. Tack, M. Tayal, J.F. Tooker, D. Torrico-Bazoberry, K. Tougeron, A.M. Trowbridge, S. Utsumi, O. Uyi, J.L. Vaca-Uribe, A. Valtonen, L.J.A. Van Dijk, V. Vandvik, J. Villellas, L.P. Waller, M.G. Weber, A. Yamawo, S. Yim, P.L. Zarnetske, L.N. Zehr, Z. Zhong, W.C. Wetzel, Science 382 (2023) 679–683.","mla":"Robinson, M. L., et al. “Plant Size, Latitude, and Phylogeny Explain within-Population Variability in Herbivory.” Science, vol. 382, no. 6671, AAAS, 2023, pp. 679–83, doi:10.1126/science.adh8830.","chicago":"Robinson, M. L., P. G. Hahn, B. D. Inouye, N. Underwood, S. R. Whitehead, K. C. Abbott, E. M. Bruna, et al. “Plant Size, Latitude, and Phylogeny Explain within-Population Variability in Herbivory.” Science. AAAS, 2023. https://doi.org/10.1126/science.adh8830.","ama":"Robinson ML, Hahn PG, Inouye BD, et al. Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science. 2023;382(6671):679-683. doi:10.1126/science.adh8830","apa":"Robinson, M. L., Hahn, P. G., Inouye, B. D., Underwood, N., Whitehead, S. R., Abbott, K. C., … Wetzel, W. C. (2023). Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science. AAAS. https://doi.org/10.1126/science.adh8830","ieee":"M. L. Robinson et al., “Plant size, latitude, and phylogeny explain within-population variability in herbivory,” Science, vol. 382, no. 6671. AAAS, pp. 679–683, 2023.","ista":"Robinson ML et al. 2023. Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science. 382(6671), 679–683."},"abstract":[{"text":"Interactions between plants and herbivores are central in most ecosystems, but their strength is highly variable. The amount of variability within a system is thought to influence most aspects of plant-herbivore biology, from ecological stability to plant defense evolution. Our understanding of what influences variability, however, is limited by sparse data. We collected standardized surveys of herbivory for 503 plant species at 790 sites across 116° of latitude. With these data, we show that within-population variability in herbivory increases with latitude, decreases with plant size, and is phylogenetically structured. Differences in the magnitude of variability are thus central to how plant-herbivore biology varies across macroscale gradients. We argue that increased focus on interaction variability will advance understanding of patterns of life on Earth.","lang":"eng"}],"issue":"6671","type":"journal_article","oa_version":"None","status":"public","title":"Plant size, latitude, and phylogeny explain within-population variability in herbivory","intvolume":" 382","_id":"14552","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"11","publication_identifier":{"eissn":["1095-9203"]},"language":[{"iso":"eng"}],"doi":"10.1126/science.adh8830","quality_controlled":"1","external_id":{"pmid":["37943897"]},"date_updated":"2023-11-20T11:17:34Z","date_created":"2023-11-19T23:00:54Z","volume":382,"author":[{"full_name":"Robinson, M. L.","last_name":"Robinson","first_name":"M. L."},{"last_name":"Hahn","first_name":"P. G.","full_name":"Hahn, P. G."},{"full_name":"Inouye, B. D.","last_name":"Inouye","first_name":"B. D."},{"last_name":"Underwood","first_name":"N.","full_name":"Underwood, N."},{"full_name":"Whitehead, S. R.","first_name":"S. R.","last_name":"Whitehead"},{"first_name":"K. C.","last_name":"Abbott","full_name":"Abbott, K. C."},{"full_name":"Bruna, E. M.","first_name":"E. M.","last_name":"Bruna"},{"full_name":"Cacho, N. I.","first_name":"N. I.","last_name":"Cacho"},{"last_name":"Dyer","first_name":"L. A.","full_name":"Dyer, L. A."},{"first_name":"L.","last_name":"Abdala-Roberts","full_name":"Abdala-Roberts, L."},{"last_name":"Allen","first_name":"W. J.","full_name":"Allen, W. J."},{"last_name":"Andrade","first_name":"J. F.","full_name":"Andrade, J. F."},{"full_name":"Angulo, D. F.","last_name":"Angulo","first_name":"D. F."},{"full_name":"Anjos, D.","last_name":"Anjos","first_name":"D."},{"first_name":"D. N.","last_name":"Anstett","full_name":"Anstett, D. N."},{"first_name":"R.","last_name":"Bagchi","full_name":"Bagchi, R."},{"last_name":"Bagchi","first_name":"S.","full_name":"Bagchi, S."},{"first_name":"M.","last_name":"Barbosa","full_name":"Barbosa, M."},{"full_name":"Barrett, S.","last_name":"Barrett","first_name":"S."},{"full_name":"Baskett, Carina","orcid":"0000-0002-7354-8574","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","first_name":"Carina"},{"full_name":"Ben-Simchon, E.","first_name":"E.","last_name":"Ben-Simchon"},{"first_name":"K. J.","last_name":"Bloodworth","full_name":"Bloodworth, K. J."},{"full_name":"Bronstein, J. L.","last_name":"Bronstein","first_name":"J. L."},{"last_name":"Buckley","first_name":"Y. M.","full_name":"Buckley, Y. M."},{"first_name":"K. T.","last_name":"Burghardt","full_name":"Burghardt, K. T."},{"first_name":"C.","last_name":"Bustos-Segura","full_name":"Bustos-Segura, C."},{"last_name":"Calixto","first_name":"E. S.","full_name":"Calixto, E. S."},{"first_name":"R. L.","last_name":"Carvalho","full_name":"Carvalho, R. L."},{"first_name":"B.","last_name":"Castagneyrol","full_name":"Castagneyrol, B."},{"last_name":"Chiuffo","first_name":"M. C.","full_name":"Chiuffo, M. C."},{"last_name":"Cinoğlu","first_name":"D.","full_name":"Cinoğlu, D."},{"first_name":"E.","last_name":"Cinto Mejía","full_name":"Cinto Mejía, E."},{"first_name":"M. C.","last_name":"Cock","full_name":"Cock, M. C."},{"full_name":"Cogni, R.","last_name":"Cogni","first_name":"R."},{"first_name":"O. L.","last_name":"Cope","full_name":"Cope, O. L."},{"full_name":"Cornelissen, T.","last_name":"Cornelissen","first_name":"T."},{"full_name":"Cortez, D. R.","last_name":"Cortez","first_name":"D. R."},{"full_name":"Crowder, D. W.","last_name":"Crowder","first_name":"D. W."},{"full_name":"Dallstream, C.","last_name":"Dallstream","first_name":"C."},{"full_name":"Dáttilo, W.","last_name":"Dáttilo","first_name":"W."},{"full_name":"Davis, J. K.","first_name":"J. K.","last_name":"Davis"},{"full_name":"Dimarco, R. D.","first_name":"R. D.","last_name":"Dimarco"},{"last_name":"Dole","first_name":"H. E.","full_name":"Dole, H. E."},{"full_name":"Egbon, I. N.","first_name":"I. N.","last_name":"Egbon"},{"first_name":"M.","last_name":"Eisenring","full_name":"Eisenring, M."},{"full_name":"Ejomah, A.","last_name":"Ejomah","first_name":"A."},{"full_name":"Elderd, B. D.","last_name":"Elderd","first_name":"B. D."},{"full_name":"Endara, M. J.","last_name":"Endara","first_name":"M. J."},{"first_name":"M. D.","last_name":"Eubanks","full_name":"Eubanks, M. D."},{"full_name":"Everingham, S. E.","last_name":"Everingham","first_name":"S. E."},{"full_name":"Farah, K. N.","last_name":"Farah","first_name":"K. N."},{"full_name":"Farias, R. P.","last_name":"Farias","first_name":"R. P."},{"full_name":"Fernandes, A. P.","last_name":"Fernandes","first_name":"A. P."},{"full_name":"Fernandes, G. W.","first_name":"G. W.","last_name":"Fernandes"},{"first_name":"M.","last_name":"Ferrante","full_name":"Ferrante, M."},{"first_name":"A.","last_name":"Finn","full_name":"Finn, A."},{"first_name":"G. A.","last_name":"Florjancic","full_name":"Florjancic, G. A."},{"full_name":"Forister, M. L.","last_name":"Forister","first_name":"M. L."},{"last_name":"Fox","first_name":"Q. N.","full_name":"Fox, Q. N."},{"last_name":"Frago","first_name":"E.","full_name":"Frago, E."},{"full_name":"França, F. M.","last_name":"França","first_name":"F. M."},{"last_name":"Getman-Pickering","first_name":"A. S.","full_name":"Getman-Pickering, A. S."},{"last_name":"Getman-Pickering","first_name":"Z.","full_name":"Getman-Pickering, Z."},{"first_name":"E.","last_name":"Gianoli","full_name":"Gianoli, E."},{"first_name":"B.","last_name":"Gooden","full_name":"Gooden, B."},{"first_name":"M. M.","last_name":"Gossner","full_name":"Gossner, M. M."},{"full_name":"Greig, K. A.","first_name":"K. A.","last_name":"Greig"},{"full_name":"Gripenberg, S.","first_name":"S.","last_name":"Gripenberg"},{"last_name":"Groenteman","first_name":"R.","full_name":"Groenteman, R."},{"full_name":"Grof-Tisza, P.","last_name":"Grof-Tisza","first_name":"P."},{"first_name":"N.","last_name":"Haack","full_name":"Haack, N."},{"first_name":"L.","last_name":"Hahn","full_name":"Hahn, L."},{"last_name":"Haq","first_name":"S. M.","full_name":"Haq, S. M."},{"full_name":"Helms, A. M.","first_name":"A. M.","last_name":"Helms"},{"first_name":"J.","last_name":"Hennecke","full_name":"Hennecke, J."},{"full_name":"Hermann, S. L.","last_name":"Hermann","first_name":"S. L."},{"first_name":"L. M.","last_name":"Holeski","full_name":"Holeski, L. M."},{"first_name":"S.","last_name":"Holm","full_name":"Holm, S."},{"full_name":"Hutchinson, M. C.","first_name":"M. C.","last_name":"Hutchinson"},{"last_name":"Jackson","first_name":"E. E.","full_name":"Jackson, E. E."},{"last_name":"Kagiya","first_name":"S.","full_name":"Kagiya, S."},{"first_name":"A.","last_name":"Kalske","full_name":"Kalske, A."},{"last_name":"Kalwajtys","first_name":"M.","full_name":"Kalwajtys, M."},{"full_name":"Karban, R.","last_name":"Karban","first_name":"R."},{"last_name":"Kariyat","first_name":"R.","full_name":"Kariyat, R."},{"full_name":"Keasar, T.","last_name":"Keasar","first_name":"T."},{"last_name":"Kersch-Becker","first_name":"M. F.","full_name":"Kersch-Becker, M. F."},{"full_name":"Kharouba, H. M.","last_name":"Kharouba","first_name":"H. M."},{"first_name":"T. N.","last_name":"Kim","full_name":"Kim, T. N."},{"full_name":"Kimuyu, D. M.","last_name":"Kimuyu","first_name":"D. M."},{"full_name":"Kluse, J.","first_name":"J.","last_name":"Kluse"},{"last_name":"Koerner","first_name":"S. E.","full_name":"Koerner, S. E."},{"first_name":"K. J.","last_name":"Komatsu","full_name":"Komatsu, K. 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A."},{"full_name":"Sapir, Y.","last_name":"Sapir","first_name":"Y."},{"first_name":"Y.","last_name":"Sasal","full_name":"Sasal, Y."},{"full_name":"Sato, Y.","last_name":"Sato","first_name":"Y."},{"first_name":"M.","last_name":"Sawant","full_name":"Sawant, M."},{"full_name":"Schroeder, H.","last_name":"Schroeder","first_name":"H."},{"full_name":"Schumann, I.","last_name":"Schumann","first_name":"I."},{"last_name":"Segoli","first_name":"M.","full_name":"Segoli, M."},{"full_name":"Segre, H.","last_name":"Segre","first_name":"H."},{"full_name":"Shelef, O.","last_name":"Shelef","first_name":"O."},{"full_name":"Shinohara, N.","first_name":"N.","last_name":"Shinohara"},{"last_name":"Singh","first_name":"R. P.","full_name":"Singh, R. P."},{"last_name":"Smith","first_name":"D. S.","full_name":"Smith, D. S."},{"full_name":"Sobral, M.","first_name":"M.","last_name":"Sobral"},{"last_name":"Stotz","first_name":"G. C.","full_name":"Stotz, G. C."},{"full_name":"Tack, A. J.M.","first_name":"A. J.M.","last_name":"Tack"},{"full_name":"Tayal, M.","first_name":"M.","last_name":"Tayal"},{"full_name":"Tooker, J. F.","first_name":"J. F.","last_name":"Tooker"},{"last_name":"Torrico-Bazoberry","first_name":"D.","full_name":"Torrico-Bazoberry, D."},{"full_name":"Tougeron, K.","first_name":"K.","last_name":"Tougeron"},{"last_name":"Trowbridge","first_name":"A. M.","full_name":"Trowbridge, A. M."},{"full_name":"Utsumi, S.","first_name":"S.","last_name":"Utsumi"},{"last_name":"Uyi","first_name":"O.","full_name":"Uyi, O."},{"full_name":"Vaca-Uribe, J. L.","last_name":"Vaca-Uribe","first_name":"J. L."},{"last_name":"Valtonen","first_name":"A.","full_name":"Valtonen, A."},{"full_name":"Van Dijk, L. J.A.","last_name":"Van Dijk","first_name":"L. J.A."},{"first_name":"V.","last_name":"Vandvik","full_name":"Vandvik, V."},{"full_name":"Villellas, J.","last_name":"Villellas","first_name":"J."},{"full_name":"Waller, L. P.","last_name":"Waller","first_name":"L. P."},{"full_name":"Weber, M. G.","last_name":"Weber","first_name":"M. G."},{"full_name":"Yamawo, A.","last_name":"Yamawo","first_name":"A."},{"full_name":"Yim, S.","first_name":"S.","last_name":"Yim"},{"first_name":"P. L.","last_name":"Zarnetske","full_name":"Zarnetske, P. L."},{"first_name":"L. N.","last_name":"Zehr","full_name":"Zehr, L. N."},{"last_name":"Zhong","first_name":"Z.","full_name":"Zhong, Z."},{"last_name":"Wetzel","first_name":"W. C.","full_name":"Wetzel, W. C."}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"14579"}]},"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"AAAS","year":"2023","acknowledgement":"The authors acknowledge funding for central project coordination from NSF Research Coordination Network grant DEB-2203582; the Ecology, Evolution, and Behavior Program at Michigan State University; and AgBioResearch at Michigan State University. Site-specific funding is listed in the supplementary materials.","pmid":1},{"_id":"14579","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","title":"HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0","ddc":["570"],"status":"public","publisher":"Zenodo","department":[{"_id":"NiBa"}],"author":[{"first_name":"William","last_name":"Wetzel","full_name":"Wetzel, William"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14552"}]},"date_updated":"2023-11-20T11:17:33Z","date_created":"2023-11-20T11:07:45Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"text":"This is associated with our paper \"Plant size, latitude, and phylogeny explain within-population variability in herbivory\" published in Science.\r\n","lang":"eng"}],"citation":{"ama":"Wetzel W. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. 2023. doi:10.5281/ZENODO.8133117","apa":"Wetzel, W. (2023). HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. Zenodo. https://doi.org/10.5281/ZENODO.8133117","ieee":"W. Wetzel, “HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0.” Zenodo, 2023.","ista":"Wetzel W. 2023. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0, Zenodo, 10.5281/ZENODO.8133117.","short":"W. Wetzel, (2023).","mla":"Wetzel, William. HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0. Zenodo, 2023, doi:10.5281/ZENODO.8133117.","chicago":"Wetzel, William. “HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8133117."},"oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133118","open_access":"1"}],"date_published":"2023-07-11T00:00:00Z","doi":"10.5281/ZENODO.8133117","day":"11","month":"07","article_processing_charge":"No"},{"article_processing_charge":"No","has_accepted_license":"1","day":"15","date_published":"2023-08-15T00:00:00Z","citation":{"ama":"Puixeu Sala G. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. 2023. doi:10.15479/at:ista:14058","ista":"Puixeu Sala G. 2023. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria.","ieee":"G. Puixeu Sala, “The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation,” Institute of Science and Technology Austria, 2023.","apa":"Puixeu Sala, G. (2023). The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14058","mla":"Puixeu Sala, Gemma. The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14058.","short":"G. Puixeu Sala, The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation, Institute of Science and Technology Austria, 2023.","chicago":"Puixeu Sala, Gemma. “The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14058."},"page":"230","abstract":[{"text":"Females and males across species are subject to divergent selective pressures arising\r\nfrom di↵erent reproductive interests and ecological niches. This often translates into a\r\nintricate array of sex-specific natural and sexual selection on traits that have a shared\r\ngenetic basis between both sexes, causing a genetic sexual conflict. The resolution of\r\nthis conflict mostly relies on the evolution of sex-specific expression of the shared genes,\r\nleading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought\r\nto evolve via modifications of the genetic networks ultimately linked to sex-determining\r\ntranscription factors. Although much empirical and theoretical evidence supports this\r\nstandard picture of the molecular basis of sexual conflict resolution, there still are a\r\nfew open questions regarding the complex array of selective forces driving phenotypic\r\ndi↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis.\r\nFirst, how do patterns of phenotypic sexual dimorphism vary within populations,\r\nas a response to the temporal and spatial changes in sex-specific selective forces? To\r\ntackle this question, I analyze the patterns of sex-specific phenotypic variation along\r\nthree life stages and across populations spanning the whole geographical range of Rumex\r\nhastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis.\r\nSecond, how do gene expression patterns lead to phenotypic dimorphism, and what\r\nare the molecular mechanisms underlying the observed transcriptomic variation? I\r\naddress this question by examining the sex- and tissue-specific expression variation in\r\nnewly-generated datasets of sex-specific expression in heads and gonads of Drosophila\r\nmelanogaster. I additionally used two complementary approaches for the study of the\r\ngenetic basis of sex di↵erences in gene expression in the second and third Chapters of\r\nthe thesis.\r\nThird, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual\r\ndimorphism? I develop models of sex-specific stabilizing selection, mutation and drift\r\nto formalize common intuition regarding the patterns of covariation between intersex\r\ncorrelation and sexual dimorphism in the fourth Chapter of the thesis.\r\nAlltogether, the work described in this PhD thesis provides useful insights into the\r\nlinks between genetic, transcriptomic and phenotypic layers of sex-specific variation,\r\nand contributes to our general understanding of the dynamics of sexual dimorphism\r\nevolution.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"date_updated":"2023-08-17T06:55:24Z","date_created":"2023-08-16T18:15:17Z","checksum":"4e44e169f2724ee8c9324cd60bcc2b71","file_id":"14075","relation":"source_file","creator":"gpuixeus","file_size":10891454,"content_type":"application/zip","file_name":"Thesis_latex_forpdfa.zip","access_level":"closed"},{"file_name":"PhDThesis_PuixeuG.pdf","access_level":"open_access","creator":"gpuixeus","file_size":19856686,"content_type":"application/pdf","file_id":"14079","relation":"main_file","date_created":"2023-08-18T10:47:55Z","date_updated":"2023-08-18T10:47:55Z","success":1,"checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8"}],"_id":"14058","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["576"],"title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation","status":"public","publication_identifier":{"isbn":["978-3-99078-035-0"],"issn":["2663-337X"]},"month":"08","doi":"10.15479/at:ista:14058","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"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"},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"grant_number":"25817","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","name":"Sexual conflict: resolution, constraints and biomedical implications"}],"ec_funded":1,"file_date_updated":"2023-08-18T10:47:55Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"9803"},{"id":"12933","relation":"research_data","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6831"},{"relation":"part_of_dissertation","status":"public","id":"14077"}]},"author":[{"last_name":"Puixeu Sala","first_name":"Gemma","orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","full_name":"Puixeu Sala, Gemma"}],"date_created":"2023-08-15T10:20:40Z","date_updated":"2023-12-13T12:15:36Z","year":"2023","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"publication_status":"published"},{"file":[{"creator":"dernst","content_type":"application/pdf","file_size":845642,"access_level":"open_access","file_name":"2023_G3_Puixeu.pdf","success":1,"checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","date_updated":"2023-11-07T09:00:19Z","date_created":"2023-11-07T09:00:19Z","file_id":"14498","relation":"main_file"}],"oa_version":"Published Version","_id":"14077","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 13","title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","status":"public","ddc":["570"],"issue":"8","abstract":[{"text":"The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed\r\nso far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues\r\nand biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila\r\nmelanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate\r\ncrosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand,\r\ntestes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that\r\nhave been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation\r\nof genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression\r\nand can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis\r\nvariation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary\r\nexpression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance\r\nas well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled\r\nexperimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns.","lang":"eng"}],"type":"journal_article","date_published":"2023-08-01T00:00:00Z","citation":{"ieee":"G. Puixeu Sala, A. Macon, and B. Vicoso, “Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster,” G3: Genes, Genomes, Genetics, vol. 13, no. 8. Oxford University Press, 2023.","apa":"Puixeu Sala, G., Macon, A., & Vicoso, B. (2023). Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. Oxford University Press. https://doi.org/10.1093/g3journal/jkad121","ista":"Puixeu Sala G, Macon A, Vicoso B. 2023. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 13(8).","ama":"Puixeu Sala G, Macon A, Vicoso B. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 2023;13(8). doi:10.1093/g3journal/jkad121","chicago":"Puixeu Sala, Gemma, Ariana Macon, and Beatriz Vicoso. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” G3: Genes, Genomes, Genetics. Oxford University Press, 2023. https://doi.org/10.1093/g3journal/jkad121.","short":"G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023).","mla":"Puixeu Sala, Gemma, et al. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” G3: Genes, Genomes, Genetics, vol. 13, no. 8, Oxford University Press, 2023, doi:10.1093/g3journal/jkad121."},"publication":"G3: Genes, Genomes, Genetics","article_type":"original","article_processing_charge":"Yes","has_accepted_license":"1","day":"01","scopus_import":"1","keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"related_material":{"record":[{"status":"public","relation":"research_data","id":"12933"},{"relation":"dissertation_contains","status":"public","id":"14058"}]},"author":[{"orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","first_name":"Gemma","full_name":"Puixeu Sala, Gemma"},{"last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana"},{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"volume":13,"date_updated":"2023-12-13T12:15:37Z","date_created":"2023-08-18T06:52:14Z","acknowledgement":"We thank members of the Vicoso Group for comments on the manuscript, the Scientific Computing Unit at ISTA for technical support, and 2 anonymous reviewers for useful feedback. GP is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (DOC 25817) and received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant (agreement no. 665385).","year":"2023","publisher":"Oxford University Press","department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2023-11-07T09:00:19Z","doi":"10.1093/g3journal/jkad121","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"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":["001002997200001"]},"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"},{"name":"Sexual conflict: resolution, constraints and biomedical implications","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","grant_number":"25817"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["2160-1836"]},"month":"08"},{"doi":"10.1111/mec.17160","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/mec.17160"}],"external_id":{"pmid":["37843465"],"isi":["001085119000001"]},"oa":1,"quality_controlled":"1","isi":1,"month":"10","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"author":[{"first_name":"James","last_name":"Reeve","full_name":"Reeve, James"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."},{"last_name":"Koch","first_name":"Eva L.","full_name":"Koch, Eva L."},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean","full_name":"Stankowski, Sean"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"}],"date_updated":"2023-12-13T13:05:27Z","date_created":"2023-10-29T23:01:17Z","year":"2023","acknowledgement":"We would like to thank members of the Littorina team for their advice and feedback during this project. In particular, we thank Alan Le Moan, who inspired us to look at heterozygosity differences to identify inversions, and Katherine Hearn for helping with the PCA scripts. We thank Edinburgh Genomics for library preparation and sequencing. Sample collections, sequencing and data preparation were supported by the European Research Council (ERC-2015-AdG-693030- BARRIERS) and the Natural Environment Research Council (NE/P001610/1). The analysis was supported by the Swedish Research Council (vetenskaprådet; 2018-03695_VR) and the Portuguese Foundation for Science and Technology (Fundación para a Ciência e Tecnologia) through a research project (PTDC/BIA-EVL/1614/2021) and CEEC contract (2020.00275.CEECIND).","pmid":1,"publication_status":"epub_ahead","department":[{"_id":"NiBa"}],"publisher":"Wiley","date_published":"2023-10-16T00:00:00Z","publication":"Molecular Ecology","citation":{"short":"J. Reeve, R.K. Butlin, E.L. Koch, S. Stankowski, R. Faria, Molecular Ecology (2023).","mla":"Reeve, James, et al. “Chromosomal Inversion Polymorphisms Are Widespread across the Species Ranges of Rough Periwinkles (Littorina Saxatilis and L. Arcana).” Molecular Ecology, Wiley, 2023, doi:10.1111/mec.17160.","chicago":"Reeve, James, Roger K. Butlin, Eva L. Koch, Sean Stankowski, and Rui Faria. “Chromosomal Inversion Polymorphisms Are Widespread across the Species Ranges of Rough Periwinkles (Littorina Saxatilis and L. Arcana).” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.17160.","ama":"Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology. 2023. doi:10.1111/mec.17160","apa":"Reeve, J., Butlin, R. K., Koch, E. L., Stankowski, S., & Faria, R. (2023). Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology. Wiley. https://doi.org/10.1111/mec.17160","ieee":"J. Reeve, R. K. Butlin, E. L. Koch, S. Stankowski, and R. Faria, “Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana),” Molecular Ecology. Wiley, 2023.","ista":"Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. 2023. Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology."},"article_type":"original","day":"16","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","oa_version":"Published Version","_id":"14463","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana)","abstract":[{"text":"Inversions are thought to play a key role in adaptation and speciation, suppressing recombination between diverging populations. Genes influencing adaptive traits cluster in inversions, and changes in inversion frequencies are associated with environmental differences. However, in many organisms, it is unclear if inversions are geographically and taxonomically widespread. The intertidal snail, Littorina saxatilis, is one such example. Strong associations between putative polymorphic inversions and phenotypic differences have been demonstrated between two ecotypes of L. saxatilis in Sweden and inferred elsewhere, but no direct evidence for inversion polymorphism currently exists across the species range. Using whole genome data from 107 snails, most inversion polymorphisms were found to be widespread across the species range. The frequencies of some inversion arrangements were significantly different among ecotypes, suggesting a parallel adaptive role. Many inversions were also polymorphic in the sister species, L. arcana, hinting at an ancient origin.","lang":"eng"}],"type":"journal_article"},{"citation":{"apa":"Arathoon, L. S. (2023). Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14651","ieee":"L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023.","ista":"Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria.","ama":"Arathoon LS. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. 2023. doi:10.15479/at:ista:14651","chicago":"Arathoon, Louise S. “Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14651.","short":"L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023.","mla":"Arathoon, Louise S. Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14651."},"page":"96","date_published":"2023-12-12T00:00:00Z","day":"12","has_accepted_license":"1","article_processing_charge":"No","_id":"14651","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["570"],"title":"Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus","status":"public","file":[{"date_updated":"2023-12-13T15:37:55Z","date_created":"2023-12-13T15:37:55Z","success":1,"checksum":"520bdb61e95e66070e02824947d2c5fa","file_id":"14684","relation":"main_file","creator":"larathoo","file_size":34101468,"content_type":"application/pdf","file_name":"Phd_Thesis_LA.pdf","access_level":"open_access"},{"file_id":"14685","relation":"source_file","date_updated":"2023-12-14T08:58:18Z","date_created":"2023-12-13T15:42:23Z","checksum":"d8e59afd0817c98fba2564a264508e5c","file_name":"Phd_Thesis_LA.zip","access_level":"closed","creator":"larathoo","content_type":"application/zip","file_size":31052872},{"relation":"supplementary_material","file_id":"14681","checksum":"9a778c949932286f4519e1f1fca2820d","date_created":"2023-12-11T19:24:59Z","date_updated":"2023-12-14T08:58:18Z","access_level":"closed","file_name":"Supplementary_Materials.zip","content_type":"application/zip","file_size":10713896,"creator":"larathoo"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"For self-incompatibility (SI) to be stable in a population, theory predicts that sufficient inbreeding depression (ID) is required: the fitness of offspring from self-mated individuals must be low enough to prevent the spread of self-compatibility (SC). Reviews of natural plant populations have supported this theory, with SI species generally showing high levels of ID. However, there is thought to be an under-sampling of self-incompatible taxa in the current literature. In this thesis, I study inbreeding depression in the SI plant species Antirrhinum majus using both greenhouse crosses and a large collected field dataset. Additionally, the gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus making assembly and discovery of S-alleles very difficult. Here, 206 new alleles of the male component SLFs are presented, along with a phylogeny showing the high conservation with alleles from another Antirrhinum species. Lastly, selected sites within the protein structure of SLFs are investigated, with one site in particular highlighted as potentially being involved in the SI recognition mechanism.","lang":"eng"}],"oa":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/at:ista:14651","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"ScienComp"}],"supervisor":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"language":[{"iso":"eng"}],"month":"12","publication_identifier":{"issn":["2663 - 337X"]},"year":"2023","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Arathoon, Louise S","last_name":"Arathoon","first_name":"Louise S","orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11411"}]},"date_updated":"2023-12-22T11:04:45Z","date_created":"2023-12-11T19:30:37Z","file_date_updated":"2023-12-14T08:58:18Z","ec_funded":1},{"article_number":"a041447","author":[{"full_name":"Lucek, Kay","first_name":"Kay","last_name":"Lucek"},{"first_name":"Mabel D.","last_name":"Giménez","full_name":"Giménez, Mabel D."},{"first_name":"Mathieu","last_name":"Joron","full_name":"Joron, Mathieu"},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"last_name":"Searle","first_name":"Jeremy B.","full_name":"Searle, Jeremy B."},{"last_name":"Walden","first_name":"Nora","full_name":"Walden, Nora"},{"full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"}],"volume":15,"date_updated":"2024-01-08T12:52:29Z","date_created":"2024-01-08T12:43:48Z","pmid":1,"year":"2023","acknowledgement":"K.L. was funded by a Swiss National Science Foundation Eccellenza project: The evolution of strong reproductive barriers towards the completion of speciation (PCEFP3_202869). R.F.\r\nwas funded by an FCT CEEC (Fundação para a Ciênca e a Tecnologia, Concurso Estímulo ao\r\nEmprego Científico) contract (2020.00275. CEECIND) and by an FCT research project\r\n(PTDC/BIA-EVL/1614/2021). M.R. was funded by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243). A.M.W. was partly funded by the Norwegian Research Council RCN. We thank Luis Silva for his help preparing Figure 1. We are grateful to Maren Wellenreuther, Daniel Bolnick, and two anonymous reviewers for their constructive feedback on an earlier version of this paper.","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"publisher":"Cold Spring Harbor Laboratory","publication_status":"published","publication_identifier":{"issn":["1943-0264"]},"month":"11","doi":"10.1101/cshperspect.a041447","language":[{"iso":"eng"}],"external_id":{"pmid":["37604585"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1101/cshperspect.a041447","open_access":"1"}],"quality_controlled":"1","issue":"11","abstract":[{"lang":"eng","text":"Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics.\r\nWhile an important role for CRs in speciation has been suggested, evidence primarily stems\r\nfrom theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon\r\npairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at\r\na macroevolutionary level has been supported by associations between species diversity and\r\nrates of evolution of CRs across phylogenies, these findings are limited to a restricted range of\r\nCRs and taxa. Now that more broadly applicable and precise CR detection approaches have\r\nbecome available, we address the challenges in filling some of the conceptual and empirical\r\ngaps between micro- and macroevolutionary studies on the role of CRs in speciation. We\r\nsynthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life."}],"type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14742","intvolume":" 15","status":"public","title":"The impact of chromosomal rearrangements in speciation: From micro- to macroevolution","article_processing_charge":"No","day":"01","scopus_import":"1","keyword":["General Biochemistry","Genetics and Molecular Biology"],"date_published":"2023-11-01T00:00:00Z","citation":{"ista":"Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram AM, Faria R. 2023. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 15(11), a041447.","apa":"Lucek, K., Giménez, M. D., Joron, M., Rafajlović, M., Searle, J. B., Walden, N., … Faria, R. (2023). The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory. https://doi.org/10.1101/cshperspect.a041447","ieee":"K. Lucek et al., “The impact of chromosomal rearrangements in speciation: From micro- to macroevolution,” Cold Spring Harbor Perspectives in Biology, vol. 15, no. 11. Cold Spring Harbor Laboratory, 2023.","ama":"Lucek K, Giménez MD, Joron M, et al. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 2023;15(11). doi:10.1101/cshperspect.a041447","chicago":"Lucek, Kay, Mabel D. Giménez, Mathieu Joron, Marina Rafajlović, Jeremy B. Searle, Nora Walden, Anja M Westram, and Rui Faria. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory, 2023. https://doi.org/10.1101/cshperspect.a041447.","mla":"Lucek, Kay, et al. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” Cold Spring Harbor Perspectives in Biology, vol. 15, no. 11, a041447, Cold Spring Harbor Laboratory, 2023, doi:10.1101/cshperspect.a041447.","short":"K. Lucek, M.D. Giménez, M. Joron, M. Rafajlović, J.B. Searle, N. Walden, A.M. Westram, R. Faria, Cold Spring Harbor Perspectives in Biology 15 (2023)."},"publication":"Cold Spring Harbor Perspectives in Biology","article_type":"original"},{"article_processing_charge":"No","day":"01","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"date_published":"2023-04-01T00:00:00Z","page":"2041-2054","article_type":"original","citation":{"chicago":"Stankowski, Sean, Madeline A. Chase, Hanna McIntosh, and Matthew A. Streisfeld. “Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid Zone.” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16849.","mla":"Stankowski, Sean, et al. “Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid Zone.” Molecular Ecology, vol. 32, no. 8, Wiley, 2023, pp. 2041–54, doi:10.1111/mec.16849.","short":"S. Stankowski, M.A. Chase, H. McIntosh, M.A. Streisfeld, Molecular Ecology 32 (2023) 2041–2054.","ista":"Stankowski S, Chase MA, McIntosh H, Streisfeld MA. 2023. Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. Molecular Ecology. 32(8), 2041–2054.","ieee":"S. Stankowski, M. A. Chase, H. McIntosh, and M. A. Streisfeld, “Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone,” Molecular Ecology, vol. 32, no. 8. Wiley, pp. 2041–2054, 2023.","apa":"Stankowski, S., Chase, M. A., McIntosh, H., & Streisfeld, M. A. (2023). Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16849","ama":"Stankowski S, Chase MA, McIntosh H, Streisfeld MA. Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. Molecular Ecology. 2023;32(8):2041-2054. doi:10.1111/mec.16849"},"publication":"Molecular Ecology","issue":"8","abstract":[{"lang":"eng","text":"Understanding the phenotypic and genetic architecture of reproductive isolation is a long‐standing goal of speciation research. In several systems, large‐effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine “top‐down” and “bottom‐up” approaches with demographic modelling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to gene flow between two divergent red‐ and yellow‐flowered ecotypes ofMimulus aurantiacus. Several candidate isolating traits and anonymous single nucleotide polymorphism loci under divergent selection have been identified, but their genomic positions remain unknown. Here, we report findings from demographic analyses that indicate this hybrid zone formed by secondary contact, but that subsequent gene flow was restricted by widespread barrier loci across the genome. Using a novel, geographic cline‐based genome scan, we demonstrate that candidate barrier loci are broadly distributed across the genome, rather than mapping to one or a few “islands of speciation.” Quantitative trait locus (QTL) mapping reveals that most floral traits are highly polygenic, with little evidence that QTL colocalize, indicating that most traits are genetically independent. Finally, we find little evidence that QTL and candidate barrier loci overlap, suggesting that some loci contribute to other forms of reproductive isolation. Our findings highlight the challenges of understanding the genetic architecture of reproductive isolation and reveal that barriers to gene flow other than pollinator isolation may play an important role in this system."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 32","status":"public","title":"Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14787","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"month":"04","language":[{"iso":"eng"}],"doi":"10.1111/mec.16849","isi":1,"quality_controlled":"1","oa":1,"external_id":{"pmid":["36651268"],"isi":["000919244600001"]},"main_file_link":[{"url":"https://doi.org/10.1101/2022.01.28.478139","open_access":"1"}],"volume":32,"date_updated":"2024-01-16T10:10:00Z","date_created":"2024-01-10T10:44:45Z","author":[{"full_name":"Stankowski, Sean","first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Chase, Madeline A.","last_name":"Chase","first_name":"Madeline A."},{"full_name":"McIntosh, Hanna","last_name":"McIntosh","first_name":"Hanna"},{"full_name":"Streisfeld, Matthew A.","last_name":"Streisfeld","first_name":"Matthew A."}],"department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","pmid":1,"acknowledgement":"We thank Julian Catchen for making modifications to Stacks to aid this project. Peter L. Ralph, Thomas Nelson, Roger K. Butlin, Anja M. Westram and Nicholas H. Barton provided advice, stimulating discussion and critical feedback. The project was supported by National Science Foundation grant DEB-1258199.","year":"2023"},{"day":"17","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publication":"Evolutionary Journal of the Linnean Society","citation":{"mla":"Stankowski, Sean, et al. “Whole-Genome Phylogeography of the Intertidal Snail Littorina Saxatilis.” Evolutionary Journal of the Linnean Society, vol. 2, no. 1, kzad002, Oxford University Press, 2023, doi:10.1093/evolinnean/kzad002.","short":"S. Stankowski, Z.B. Zagrodzka, J. Galindo, M. Montaño-Rendón, R. Faria, N. Mikhailova, A.M.H. Blakeslee, E. Arnason, T. Broquet, H.E. Morales, J.W. Grahame, A.M. Westram, K. Johannesson, R.K. Butlin, Evolutionary Journal of the Linnean Society 2 (2023).","chicago":"Stankowski, Sean, Zuzanna B Zagrodzka, Juan Galindo, Mauricio Montaño-Rendón, Rui Faria, Natalia Mikhailova, April M H Blakeslee, et al. “Whole-Genome Phylogeography of the Intertidal Snail Littorina Saxatilis.” Evolutionary Journal of the Linnean Society. Oxford University Press, 2023. https://doi.org/10.1093/evolinnean/kzad002.","ama":"Stankowski S, Zagrodzka ZB, Galindo J, et al. Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. 2023;2(1). doi:10.1093/evolinnean/kzad002","ista":"Stankowski S, Zagrodzka ZB, Galindo J, Montaño-Rendón M, Faria R, Mikhailova N, Blakeslee AMH, Arnason E, Broquet T, Morales HE, Grahame JW, Westram AM, Johannesson K, Butlin RK. 2023. Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. 2(1), kzad002.","ieee":"S. Stankowski et al., “Whole-genome phylogeography of the intertidal snail Littorina saxatilis,” Evolutionary Journal of the Linnean Society, vol. 2, no. 1. Oxford University Press, 2023.","apa":"Stankowski, S., Zagrodzka, Z. B., Galindo, J., Montaño-Rendón, M., Faria, R., Mikhailova, N., … Butlin, R. K. (2023). Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. Oxford University Press. https://doi.org/10.1093/evolinnean/kzad002"},"article_type":"original","date_published":"2023-08-17T00:00:00Z","type":"journal_article","abstract":[{"text":"Understanding the factors that have shaped the current distributions and diversity of species is a central and longstanding aim of evolutionary biology. The recent inclusion of genomic data into phylogeographic studies has dramatically improved our understanding in organisms where evolutionary relationships have been challenging to infer. We used whole-genome sequences to study the phylogeography of the intertidal snail Littorina saxatilis, which has successfully colonized and diversified across a broad range of coastal environments in the Northern Hemisphere amid repeated cycles of glaciation. Building on past studies based on short DNA sequences, we used genome-wide data to provide a clearer picture of the relationships among samples spanning most of the species natural range. Our results confirm the trans-Atlantic colonization of North America from Europe, and have allowed us to identify rough locations of glacial refugia and to infer likely routes of colonization within Europe. We also investigated the signals in different datasets to account for the effects of genomic architecture and non-neutral evolution, which provides new insights about diversification of four ecotypes of L. saxatilis (the crab, wave, barnacle, and brackish ecotypes) at different spatial scales. Overall, we provide a much clearer picture of the biogeography of L. saxatilis, providing a foundation for more detailed phylogenomic and demographic studies.","lang":"eng"}],"issue":"1","_id":"14833","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Whole-genome phylogeography of the intertidal snail Littorina saxatilis","ddc":["570"],"intvolume":" 2","file":[{"date_updated":"2024-01-23T08:10:00Z","date_created":"2024-01-23T08:10:00Z","success":1,"checksum":"ba6f9102d3a9fe6631c4fa398c5e4313","file_id":"14875","relation":"main_file","creator":"dernst","file_size":3408944,"content_type":"application/pdf","file_name":"2023_EvolJourLinneanSociety_Stankowski.pdf","access_level":"open_access"}],"oa_version":"Published Version","month":"08","publication_identifier":{"eissn":["2752-938X"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"quality_controlled":"1","doi":"10.1093/evolinnean/kzad002","language":[{"iso":"eng"}],"article_number":"kzad002","file_date_updated":"2024-01-23T08:10:00Z","acknowledgement":"Isobel Eyres, Richard Turney, Graciela Sotelo, Jenny Larson, and Stéphane Loisel helped with the collection and processing of samples. Petri Kemppainen kindly provided samples from Trondheim Fjord. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield high-performance computing cluster, ShARC. Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council (ERC). J.G. was funded by a Juntas Industriales y Navales (JIN) project (Ministerio de Ciencia, Innovación y Universidades, code RTI2018-101274-J-I00).","year":"2023","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"NiBa"}],"author":[{"full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Zagrodzka, Zuzanna B","last_name":"Zagrodzka","first_name":"Zuzanna B"},{"last_name":"Galindo","first_name":"Juan","full_name":"Galindo, Juan"},{"first_name":"Mauricio","last_name":"Montaño-Rendón","full_name":"Montaño-Rendón, Mauricio"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Natalia","last_name":"Mikhailova","full_name":"Mikhailova, Natalia"},{"full_name":"Blakeslee, April M H","first_name":"April M H","last_name":"Blakeslee"},{"first_name":"Einar","last_name":"Arnason","full_name":"Arnason, Einar"},{"full_name":"Broquet, Thomas","first_name":"Thomas","last_name":"Broquet"},{"full_name":"Morales, Hernán E","last_name":"Morales","first_name":"Hernán E"},{"last_name":"Grahame","first_name":"John W","full_name":"Grahame, John W"},{"first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger K","first_name":"Roger K","last_name":"Butlin"}],"date_created":"2024-01-18T07:54:10Z","date_updated":"2024-01-23T08:13:43Z","volume":2},{"_id":"14732","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2023","department":[{"_id":"NiBa"},{"_id":"JaMa"}],"status":"public","title":"Genetic load, eco-evolutionary feedback and extinction in a metapopulation","publication_status":"submitted","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14711"}]},"author":[{"full_name":"Olusanya, Oluwafunmilola O","orcid":"0000-0003-1971-8314","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","last_name":"Olusanya","first_name":"Oluwafunmilola O"},{"id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0002-6246-1465","first_name":"Kseniia","last_name":"Khudiakova","full_name":"Khudiakova, Kseniia"},{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","first_name":"Himani","full_name":"Sachdeva, Himani"}],"oa_version":"Preprint","date_updated":"2024-01-26T12:00:53Z","date_created":"2024-01-04T09:35:54Z","type":"preprint","abstract":[{"lang":"eng","text":"Fragmented landscapes pose a significant threat to the persistence of species as they are highly susceptible to heightened risk of extinction due to the combined effects of genetic and demographic factors such as genetic drift and demographic stochasticity. This paper explores the intricate interplay between genetic load and extinction risk within metapopulations with a focus on understanding the impact of eco-evolutionary feedback mechanisms. We distinguish between two models of selection: soft selection, characterised by subpopulations maintaining carrying capacity despite load, and hard selection, where load can significantly affect population size. Within the soft selection framework, we investigate the impact of gene flow on genetic load at a single locus, while also considering the effect of selection strength and dominance coefficient. We subsequently build on this to examine how gene flow influences both population size and load under hard selection as well as identify critical thresholds for metapopulation persistence. Our analysis employs the diffusion, semi-deterministic and effective migration approximations. Our findings reveal that under soft selection, even modest levels of migration can significantly alleviate the burden of load. In sharp contrast, with hard selection, a much higher degree of gene flow is required to mitigate load and prevent the collapse of the metapopulation. Overall, this study sheds light into the crucial role migration plays in shaping the dynamics of genetic load and extinction risk in fragmented landscapes, offering valuable insights for conservation strategies and the preservation of diversity in a changing world."}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"citation":{"mla":"Olusanya, Oluwafunmilola O., et al. “Genetic Load, Eco-Evolutionary Feedback and Extinction in a Metapopulation.” BioRxiv, doi:10.1101/2023.12.02.569702.","short":"O.O. Olusanya, K. Khudiakova, H. Sachdeva, BioRxiv (n.d.).","chicago":"Olusanya, Oluwafunmilola O, Kseniia Khudiakova, and Himani Sachdeva. “Genetic Load, Eco-Evolutionary Feedback and Extinction in a Metapopulation.” BioRxiv, n.d. https://doi.org/10.1101/2023.12.02.569702.","ama":"Olusanya OO, Khudiakova K, Sachdeva H. Genetic load, eco-evolutionary feedback and extinction in a metapopulation. bioRxiv. doi:10.1101/2023.12.02.569702","ista":"Olusanya OO, Khudiakova K, Sachdeva H. Genetic load, eco-evolutionary feedback and extinction in a metapopulation. bioRxiv, 10.1101/2023.12.02.569702.","ieee":"O. O. Olusanya, K. Khudiakova, and H. Sachdeva, “Genetic load, eco-evolutionary feedback and extinction in a metapopulation,” bioRxiv. .","apa":"Olusanya, O. O., Khudiakova, K., & Sachdeva, H. (n.d.). Genetic load, eco-evolutionary feedback and extinction in a metapopulation. bioRxiv. https://doi.org/10.1101/2023.12.02.569702"},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2023.12.02.569702v1","open_access":"1"}],"oa":1,"publication":"bioRxiv","project":[{"grant_number":"P32896","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","name":"Causes and consequences of population fragmentation"},{"name":"The impact of deleterious mutations on small populations","_id":"34d33d68-11ca-11ed-8bc3-ec13763c0ca8","grant_number":"26293"},{"_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6","grant_number":"26380","name":"Polygenic Adaptation in a Metapopulation"}],"date_published":"2023-12-04T00:00:00Z","doi":"10.1101/2023.12.02.569702","language":[{"iso":"eng"}],"article_processing_charge":"No","day":"04","month":"12"}]