[{"volume":34,"publication":"Molecular Ecology","article_number":"e70051","article_type":"original","publication_status":"published","abstract":[{"text":"Inferring genealogical relationships of wild populations is useful because it gives direct estimates of mating patterns and variance in reproductive success. Inference can be improved by including information about parentage shared between siblings, or by modelling phenotypes or population data related to mating. However, we currently lack a framework to infer parent–offspring relationships, sibships and population parameters in a single analysis. To address this, we here extend a previous method, Fractional Analysis of Paternity and Sibships, to include population data for the case where one parent is known. We illustrate this with the example of pollen dispersal in a natural hybrid zone population of the snapdragon Antirrhinum majus. Pollen dispersal is leptokurtic, with half of mating events occurring within 30 m, but with a long tail of mating events up to 859 m. Using simulations, we find that both sibship and population information substantially improve pedigree reconstruction, and that we can expect to resolve median dispersal distances with high accuracy.","lang":"eng"}],"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","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"},"ddc":["570"],"file":[{"creator":"dernst","content_type":"application/pdf","date_created":"2025-12-30T10:12:17Z","date_updated":"2025-12-30T10:12:17Z","relation":"main_file","success":1,"file_size":1698605,"access_level":"open_access","file_id":"20911","file_name":"2025_MolecularEcology_Ellis.pdf","checksum":"5059ad4d74e6327b84b5282a39d36774"}],"type":"journal_article","date_created":"2025-09-10T05:42:23Z","year":"2025","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","title":"Joint estimation of paternity, sibships and pollen dispersal in a snapdragon hybrid zone","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"citation":{"ama":"Ellis T, Field D, Barton NH. Joint estimation of paternity, sibships and pollen dispersal in a snapdragon hybrid zone. <i>Molecular Ecology</i>. 2025;34(15). doi:<a href=\"https://doi.org/10.1111/mec.70051\">10.1111/mec.70051</a>","chicago":"Ellis, Thomas, David Field, and Nicholas H Barton. “Joint Estimation of Paternity, Sibships and Pollen Dispersal in a Snapdragon Hybrid Zone.” <i>Molecular Ecology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/mec.70051\">https://doi.org/10.1111/mec.70051</a>.","apa":"Ellis, T., Field, D., &#38; Barton, N. H. (2025). Joint estimation of paternity, sibships and pollen dispersal in a snapdragon hybrid zone. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.70051\">https://doi.org/10.1111/mec.70051</a>","short":"T. Ellis, D. Field, N.H. Barton, Molecular Ecology 34 (2025).","ieee":"T. Ellis, D. Field, and N. H. Barton, “Joint estimation of paternity, sibships and pollen dispersal in a snapdragon hybrid zone,” <i>Molecular Ecology</i>, vol. 34, no. 15. Wiley, 2025.","mla":"Ellis, Thomas, et al. “Joint Estimation of Paternity, Sibships and Pollen Dispersal in a Snapdragon Hybrid Zone.” <i>Molecular Ecology</i>, vol. 34, no. 15, e70051, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/mec.70051\">10.1111/mec.70051</a>.","ista":"Ellis T, Field D, Barton NH. 2025. Joint estimation of paternity, sibships and pollen dispersal in a snapdragon hybrid zone. Molecular Ecology. 34(15), e70051."},"_id":"20325","pmid":1,"date_updated":"2025-12-30T10:12:34Z","OA_type":"hybrid","oa":1,"date_published":"2025-09-02T00:00:00Z","external_id":{"pmid":["40751392"],"isi":["001542913000001"]},"quality_controlled":"1","status":"public","department":[{"_id":"NiBa"}],"oa_version":"Published Version","corr_author":"1","acknowledgement":"We thank a large number of field volunteers for maintaining the population sampling, and Tom White for assistance with seed collection. We thank Sylvia Rebel for plating tissue for DNA extraction, as well as Sean Stankowski and two anonymous reviewers for feedback on the manuscript. ","author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ellis","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254"},{"orcid":"0000-0002-4014-8478","last_name":"Field","full_name":"Field, David","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"        34","isi":1,"doi":"10.1111/mec.70051","month":"09","file_date_updated":"2025-12-30T10:12:17Z","day":"02","scopus_import":"1","language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)","OA_place":"publisher","issue":"15","has_accepted_license":"1"},{"quality_controlled":"1","status":"public","oa_version":"Published Version","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"oa":1,"OA_type":"hybrid","date_published":"2025-11-01T00:00:00Z","project":[{"name":"Sexual conflict: resolution, constraints and biomedical implications","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","grant_number":"25817"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327"}],"external_id":{"isi":["001598595000001"]},"intvolume":"       231","isi":1,"acknowledgement":"We thank Tim Connallon for useful discussions and correspondence, Himani Sachdeva and Nick Barton for comments on the manuscript and the Scientific Computing unit at ISTA for technical support. 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). LH received funding from the European Research Council, under the HaplotypeStructure Grant (grant no. 101055327) to Nick Barton.","corr_author":"1","author":[{"last_name":"Puixeu Sala","full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754","first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hayward","full_name":"Hayward, Laura","first_name":"Laura","id":"fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b"}],"month":"11","PlanS_conform":"1","file_date_updated":"2026-01-05T13:03:18Z","doi":"10.1093/genetics/iyaf175","OA_place":"publisher","issue":"3","has_accepted_license":"1","day":"01","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"article_number":"iyaf175","publication_status":"published","article_type":"original","abstract":[{"lang":"eng","text":"The evolution of sexual dimorphism (the difference in average trait values between females and males, SD), is often thought to be constrained by shared genetic architecture between the sexes. Indeed, it is commonly expected that SD should negatively correlate with the intersex correlation (the genetic correlation between effects of segregating variants in females and males, r fm), either because (1) traits with ancestrally low r fm are less constrained in their ability to respond to sex-specific selection and thus evolve to be more dimorphic, or because (2) sex-specific selection, driving sexual dimorphism evolution, also acts to reduce r fm. Despite the intuitive appeal and prominence of these ideas, their generality and the conditions in which they hold remain unclear. Here, we develop models incorporating sex-specific stabilizing selection, mutation and genetic drift to examine the relationship between r fm and SD. We show that the two commonly-discussed mechanisms with the potential to generate a negative correlation between SD and r fm could just as easily generate a positive association, since the standard line of reasoning hinges on a hidden assumption that sex-specific adaptation more frequently favors increased dimorphism than reduced dimorphism. Our results provide, to our knowledge, the first mechanistic framework for understanding the conditions under which a correlation between r fm and SD may arise and offer a compelling explanation for inconsistent empirical evidence. We also make the intriguing observation that—even when selection between the two sexes is identical—drift generates nonzero SD. We quantify this effect and discuss its significance."}],"volume":231,"publication":"Genetics","type":"journal_article","date_created":"2025-09-10T05:48:04Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"ddc":["570"],"file":[{"access_level":"open_access","relation":"main_file","success":1,"file_size":1550562,"file_name":"2025_Genetics_Puixeu.pdf","checksum":"bbb73bbf8617812d4d8db4af92be9538","file_id":"20946","creator":"dernst","date_updated":"2026-01-05T13:03:18Z","date_created":"2026-01-05T13:03:18Z","content_type":"application/pdf"}],"title":"The relationship between sexual dimorphism and intersex correlation: Do models support intuition?","ec_funded":1,"publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","_id":"20330","date_updated":"2026-01-05T13:04:07Z","publication_identifier":{"issn":["1943-2631"]},"citation":{"chicago":"Puixeu Sala, Gemma, and Laura Hayward. “The Relationship between Sexual Dimorphism and Intersex Correlation: Do Models Support Intuition?” <i>Genetics</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/genetics/iyaf175\">https://doi.org/10.1093/genetics/iyaf175</a>.","apa":"Puixeu Sala, G., &#38; Hayward, L. (2025). The relationship between sexual dimorphism and intersex correlation: Do models support intuition? <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyaf175\">https://doi.org/10.1093/genetics/iyaf175</a>","short":"G. Puixeu Sala, L. Hayward, Genetics 231 (2025).","ieee":"G. Puixeu Sala and L. Hayward, “The relationship between sexual dimorphism and intersex correlation: Do models support intuition?,” <i>Genetics</i>, vol. 231, no. 3. Oxford University Press, 2025.","mla":"Puixeu Sala, Gemma, and Laura Hayward. “The Relationship between Sexual Dimorphism and Intersex Correlation: Do Models Support Intuition?” <i>Genetics</i>, vol. 231, no. 3, iyaf175, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/genetics/iyaf175\">10.1093/genetics/iyaf175</a>.","ista":"Puixeu Sala G, Hayward L. 2025. The relationship between sexual dimorphism and intersex correlation: Do models support intuition? Genetics. 231(3), iyaf175.","ama":"Puixeu Sala G, Hayward L. The relationship between sexual dimorphism and intersex correlation: Do models support intuition? <i>Genetics</i>. 2025;231(3). doi:<a href=\"https://doi.org/10.1093/genetics/iyaf175\">10.1093/genetics/iyaf175</a>"}},{"publication_status":"published","article_type":"original","abstract":[{"text":"Plant–plant interactions are key to understanding ecosystem services and shaping restoration strategies, as they can produce either negative or positive effects, determining species establishment and growth. Recognizing these interactions during early-life stages provides valuable insights for restoration in human-disturbed areas. One promising approach is nucleation planting, which establishes small clusters of native species in strategically selected sites, being particularly useful in sites with large herbivores. In southern Patagonia, livestock production has historically been the main economic activity, severely impacting extensive areas of Nothofagus antarctica forest through grazing and intentional burning to increase forage. In this context, nucleation planting with Berberis microphylla, a non-palatable shrub, could foster forest recovery in degraded sites. To evaluate this, we conducted an experiment testing the response of trees to varying shrub number, while also assessing intraspecific effects in both species. We measured survival, biomass, and functional traits. Results showed that the combination of four shrubs surrounding a single tree maintained tree survival at levels comparable to trees growing alone, while seedlings exhibited conspecific negative plant number dependence. Additionally, B. microphylla increased its below- to above-ground biomass ratio under higher plant number, indicating resource reallocation and niche differentiation through spatial separation of root systems.","lang":"eng"}],"volume":226,"publication":"Plant Ecology","type":"journal_article","date_created":"2025-10-05T22:01:36Z","title":"Biotic interactions between trees and colonizing shrubs: Implications for active restoration in southern Patagonian forests","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","_id":"20429","date_updated":"2026-01-05T13:23:57Z","publication_identifier":{"issn":["1385-0237"],"eissn":["1573-5052"]},"citation":{"ama":"Bustamante GN, Arena ME, Selzer L, et al. Biotic interactions between trees and colonizing shrubs: Implications for active restoration in southern Patagonian forests. <i>Plant Ecology</i>. 2025;226:1301-1313. doi:<a href=\"https://doi.org/10.1007/s11258-025-01568-0\">10.1007/s11258-025-01568-0</a>","apa":"Bustamante, G. N., Arena, M. E., Selzer, L., Ruggirello, M., Rodríguez, P., Pedrazzani, S., … Soler Schaller, R. M. (2025). Biotic interactions between trees and colonizing shrubs: Implications for active restoration in southern Patagonian forests. <i>Plant Ecology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11258-025-01568-0\">https://doi.org/10.1007/s11258-025-01568-0</a>","chicago":"Bustamante, Gimena Noemí, Miriam Elisabet Arena, Luciano Selzer, Matthew Ruggirello, Paula Rodríguez, Samuele Pedrazzani, Jose Antonio Navarro-Cano, and Rosina Matilde Soler Schaller. “Biotic Interactions between Trees and Colonizing Shrubs: Implications for Active Restoration in Southern Patagonian Forests.” <i>Plant Ecology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s11258-025-01568-0\">https://doi.org/10.1007/s11258-025-01568-0</a>.","mla":"Bustamante, Gimena Noemí, et al. “Biotic Interactions between Trees and Colonizing Shrubs: Implications for Active Restoration in Southern Patagonian Forests.” <i>Plant Ecology</i>, vol. 226, Springer Nature, 2025, pp. 1301–13, doi:<a href=\"https://doi.org/10.1007/s11258-025-01568-0\">10.1007/s11258-025-01568-0</a>.","ista":"Bustamante GN, Arena ME, Selzer L, Ruggirello M, Rodríguez P, Pedrazzani S, Navarro-Cano JA, Soler Schaller RM. 2025. Biotic interactions between trees and colonizing shrubs: Implications for active restoration in southern Patagonian forests. Plant Ecology. 226, 1301–1313.","ieee":"G. N. Bustamante <i>et al.</i>, “Biotic interactions between trees and colonizing shrubs: Implications for active restoration in southern Patagonian forests,” <i>Plant Ecology</i>, vol. 226. Springer Nature, pp. 1301–1313, 2025.","short":"G.N. Bustamante, M.E. Arena, L. Selzer, M. Ruggirello, P. Rodríguez, S. Pedrazzani, J.A. Navarro-Cano, R.M. Soler Schaller, Plant Ecology 226 (2025) 1301–1313."},"quality_controlled":"1","status":"public","department":[{"_id":"NiBa"}],"oa_version":"None","OA_type":"closed access","date_published":"2025-12-01T00:00:00Z","external_id":{"isi":["001581599800001"]},"intvolume":"       226","isi":1,"page":"1301-1313","author":[{"full_name":"Bustamante, Gimena Noemí","last_name":"Bustamante","first_name":"Gimena Noemí"},{"last_name":"Arena","full_name":"Arena, Miriam Elisabet","first_name":"Miriam Elisabet"},{"first_name":"Luciano","last_name":"Selzer","full_name":"Selzer, Luciano"},{"last_name":"Ruggirello","full_name":"Ruggirello, Matthew","first_name":"Matthew"},{"last_name":"Rodríguez","full_name":"Rodríguez, Paula","first_name":"Paula"},{"last_name":"Pedrazzani","full_name":"Pedrazzani, Samuele","first_name":"Samuele"},{"full_name":"Navarro-Cano, Jose Antonio","last_name":"Navarro-Cano","first_name":"Jose Antonio"},{"first_name":"Rosina Matilde","full_name":"Soler Schaller, Rosina Matilde","last_name":"Soler Schaller","id":"9e668447-8c32-11ed-b0c7-8dc2d7b80803"}],"month":"12","doi":"10.1007/s11258-025-01568-0","day":"01","scopus_import":"1","article_processing_charge":"No","language":[{"iso":"eng"}]},{"month":"10","doi":"10.1093/evolut/qpaf143","OA_place":"repository","issue":"10","day":"17","main_file_link":[{"url":"https://doi.org/10.1101/2025.01.22.634382","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"article_processing_charge":"No","status":"public","quality_controlled":"1","oa_version":"Preprint","department":[{"_id":"NiBa"}],"OA_type":"green","oa":1,"date_published":"2025-10-17T00:00:00Z","external_id":{"pmid":["40668071"],"isi":["001547542300001"]},"project":[{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}],"intvolume":"        79","isi":1,"page":"2167-2180","acknowledgement":"L.F. is funded by the NOMIS-ISTA Fellowship Program. We thank Colin Olito and two anonymous reviewers for helpful comments, and the bioinformatics and computing services at Roscoff’s Biological Station (Abims platform) and at Institute of Science and Technology Austria for computing time.","author":[{"id":"1676e173-8143-11ed-8927-fe165216a93f","full_name":"Fouqueau, Louise","last_name":"Fouqueau","orcid":"0000-0003-0371-9339","first_name":"Louise"},{"last_name":"Roze","full_name":"Roze, Denis","first_name":"Denis"}],"title":"Deleterious mutations and selection for sex in spatially structured, diploid populations","publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","_id":"20531","pmid":1,"date_updated":"2025-12-01T15:03:54Z","publication_identifier":{"eissn":["1558-5646"]},"citation":{"ista":"Fouqueau L, Roze D. 2025. Deleterious mutations and selection for sex in spatially structured, diploid populations. Evolution. 79(10), 2167–2180.","mla":"Fouqueau, Louise, and Denis Roze. “Deleterious Mutations and Selection for Sex in Spatially Structured, Diploid Populations.” <i>Evolution</i>, vol. 79, no. 10, Oxford University Press, 2025, pp. 2167–80, doi:<a href=\"https://doi.org/10.1093/evolut/qpaf143\">10.1093/evolut/qpaf143</a>.","ieee":"L. Fouqueau and D. Roze, “Deleterious mutations and selection for sex in spatially structured, diploid populations,” <i>Evolution</i>, vol. 79, no. 10. Oxford University Press, pp. 2167–2180, 2025.","short":"L. Fouqueau, D. Roze, Evolution 79 (2025) 2167–2180.","apa":"Fouqueau, L., &#38; Roze, D. (2025). Deleterious mutations and selection for sex in spatially structured, diploid populations. <i>Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolut/qpaf143\">https://doi.org/10.1093/evolut/qpaf143</a>","chicago":"Fouqueau, Louise, and Denis Roze. “Deleterious Mutations and Selection for Sex in Spatially Structured, Diploid Populations.” <i>Evolution</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/evolut/qpaf143\">https://doi.org/10.1093/evolut/qpaf143</a>.","ama":"Fouqueau L, Roze D. Deleterious mutations and selection for sex in spatially structured, diploid populations. <i>Evolution</i>. 2025;79(10):2167-2180. doi:<a href=\"https://doi.org/10.1093/evolut/qpaf143\">10.1093/evolut/qpaf143</a>"},"publication_status":"published","article_type":"original","abstract":[{"lang":"eng","text":"Genetic drift is potentially an important component of selection for sex, as it is a source of statistical associations between alleles at selected loci. By increasing local drift, population structure may thus amplify the evolutionary advantage of sex. However, most previous models have focused either on haploid populations or on diploid populations without spatial structure. In this article, we use two- and three-locus analytical models and multilocus simulations to explore selection for sex in a diploid population structured according to the island model, in the presence of recurrent deleterious mutations. Our results show that selection generally favors an intermediate rate of sex that decreases as the direct cost of sex increases and increases moderately as the degree of population structure increases. Selection for sex is generated by multiple effects involving genetic associations within and between loci. When selection occurs at many loci, it is generally dominated by interference effects involving deleterious alleles at different loci, captured by our three-locus model. In our multilocus simulations, we observed an irreversible spread of asexual mutants under strong costs of sex, and when deleterious mutations are partially recessive. However, population structure may prevent this spread of asexual mutants when dispersal rates are sufficiently small."}],"volume":79,"publication":"Evolution","type":"journal_article","date_created":"2025-10-26T23:01:34Z"},{"abstract":[{"lang":"eng","text":"Understanding the mechanisms underlying speciation is a central aim of evolutionary biology.\r\nA persistent challenge in the field is to identify loci that contribute to reproductive isolation,\r\nwhile disentangling signals of selection from demography, linkage and intrinsic genomic\r\nfeatures. Traditional population genomic approaches that rely on site-based statistics in\r\narbitrary fixed windows face inherent limitations, as they conflate historical and\r\ncontemporary processes of divergence and overlook haplotype structure. Recent advances in\r\nwhole-genome sequencing and methods to infer ancestral recombination graphs (ARGs) now\r\noffer the opportunity to study genealogical relationships explicitly, revealing how lineages\r\ncoalesce and recombine through time. By directly analysing haplotype clustering by species\r\nor phenotype and their patterns of coalescence, ARG-based methods show promise for\r\ndiagnosing sweeps, identifying barrier loci maintained under divergent selection amid gene\r\nflow, and tracing their evolutionary history.\r\nIn this thesis, I explore the utility of genealogical approaches for studying species\r\ndivergence. In chapter 2, I propose a conceptual framework for defining haplotype blocks\r\nthrough the structure of the ARG, using simulations and empirical data to highlight how\r\ngenealogical processes generate rich and often overlooked haplotypic patterns.\r\nIn chapter 3, I examine the genomic basis of a key evolutionary innovation in marine\r\nsnails Littorina. These snails offer a unique opportunity to study an innovation because they\r\ninclude a very recent transition from egg-laying to live bearing, yet snails with the different\r\nreproductive modes are not reciprocally monophyletic. I exploited this by using topology\r\nclustering in ARG-derived local genealogical trees to pinpoint narrow genomic regions or\r\nhaplotype blocks that carry swept alleles, thus revealing that the transition from egg-laying\r\nto live-bearing involves multiple, live-bearer-specific sweeps.\r\nChapter 4 establishes a population-scale, phased genomic resource for Antirrhinum\r\nmajus, using cost-effective haplotagging, then optimizes imputation from low-coverage data\r\nagainst high-accuracy KASP sequencing to maximize sequence completeness with modest\r\naccuracy trade-offs against a traditional short-read sequence pipeline. A hybrid phasing\r\nstrategy combines molecular phasing with statistical phasing to generate phased whole\r\ngenome sequences of 1084 Antirrhinum individuals at a fraction of long-read sequencing\r\ncosts.\r\nIn chapter 5, I analyse hybridising populations from two replicate hybrid zones to find\r\na parallel genetic basis of flower colour, amidst the noise in genomic differentiation landscape\r\ndriven by variation in demographic history. While outlier genome scans of FST failed to dissect\r\nthe causes of differentiation, ARG-based topology clustering revealed a reuse of colour\r\nassociated haplotypes across hybrid zones. In addition to the biological insight, this chapter\r\nalso presents a comparison of the latest ARG inference tools, showing that signals of\r\nAbstract\r\nviii\r\ntopological clustering qualitatively agree between methods, despite differences in the tree\r\nsequences.\r\nNext, in chapter 6, by leveraging ~1000 individuals in one of the hybrid zones, I\r\nintegrated genome-wide association studies of floral pigmentation with genealogical\r\ninference, to test for additional colour loci, and confirm the effect of previously described loci.\r\nThis work demonstrates that flower colour variation is driven by a small number of large effect\r\nloci, while also hinting at the presence of a new candidate regulatory factor.\r\nFinally in chapter 7, in a preliminary analysis, I begin to dissect the genomic island of\r\nspeciation around Rosea/Eluta to understand its evolutionary origins. My results show that it\r\nconsists of 5 highly divergent loci, each of which is associated with flower colour. Using\r\npatterns of coalescence in genealogical trees, I find evidence of staggered selective sweeps\r\nand a persistent localized barrier to gene flow within an otherwise permeable genome.\r\nTogether, these chapters add to the increasing pool of studies using genealogical\r\napproaches to complement and extend site-based statistics to use haplotype structures in\r\nspeciation research. By tracking haplotypes directly and connecting genealogical clustering to\r\npopulation processes, ARG-based inference promises to provide new insights into how local\r\nselective pressures, demographic history, and long-term barriers interact to shape the\r\ngenomic architecture of divergence. By underscoring the value of ARGs in revealing the finescale origins and maintenance of biodiversity, this thesis presents cautious optimism about\r\nthe benefits of using genealogical inference to learn more than what site-based statistics\r\ncould tell us."}],"publication_status":"published","degree_awarded":"PhD","date_created":"2025-11-25T13:19:11Z","type":"dissertation","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","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"},"related_material":{"record":[{"status":"public","id":"12159","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"14796"},{"id":"20190","relation":"part_of_dissertation","status":"public"}]},"file":[{"embargo":"2026-03-01","creator":"apal","date_updated":"2026-03-01T23:30:03Z","date_created":"2025-12-01T13:53:36Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":42723135,"file_name":"2025_Pal_Arka_Thesis.pdf","checksum":"7a10a738d58524aebb5dcbd9b34c21c5","file_id":"20721"},{"file_id":"20722","file_name":"2025_Pal_Arka_Thesis.docx","checksum":"166d832b08d0434ce407f8f3cb930fe5","relation":"source_file","file_size":60632116,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2025-12-01T13:53:39Z","date_updated":"2026-03-01T23:30:03Z","embargo_to":"open_access","creator":"apal"}],"ddc":["576","578"],"title":"Using genealogies to study the genomic basis of species divergence","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","supervisor":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"year":"2025","date_updated":"2026-04-28T13:20:36Z","acknowledged_ssus":[{"_id":"ScienComp"}],"_id":"20694","citation":{"ama":"Pal A. Using genealogies to study the genomic basis of species divergence. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20694\">10.15479/AT-ISTA-20694</a>","apa":"Pal, A. (2025). <i>Using genealogies to study the genomic basis of species divergence</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20694\">https://doi.org/10.15479/AT-ISTA-20694</a>","chicago":"Pal, Arka. “Using Genealogies to Study the Genomic Basis of Species Divergence.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20694\">https://doi.org/10.15479/AT-ISTA-20694</a>.","mla":"Pal, Arka. <i>Using Genealogies to Study the Genomic Basis of Species Divergence</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20694\">10.15479/AT-ISTA-20694</a>.","ista":"Pal A. 2025. Using genealogies to study the genomic basis of species divergence. Institute of Science and Technology Austria.","ieee":"A. Pal, “Using genealogies to study the genomic basis of species divergence,” Institute of Science and Technology Austria, 2025.","short":"A. Pal, Using Genealogies to Study the Genomic Basis of Species Divergence, Institute of Science and Technology Austria, 2025."},"publication_identifier":{"issn":["2663-337X"]},"status":"public","oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"date_published":"2025-11-25T00:00:00Z","project":[{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"},{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation"}],"oa":1,"alternative_title":["ISTA Thesis"],"corr_author":"1","author":[{"id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","first_name":"Arka","full_name":"Pal, Arka","last_name":"Pal","orcid":"0000-0002-4530-8469"}],"page":"268","file_date_updated":"2026-03-01T23:30:03Z","month":"11","doi":"10.15479/AT-ISTA-20694","has_accepted_license":"1","OA_place":"publisher","language":[{"iso":"eng"}],"article_processing_charge":"No","day":"25"},{"year":"2025","title":"Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Wiley","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"citation":{"ieee":"A. Pal <i>et al.</i>, “Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum,” <i>Molecular Ecology</i>, vol. 34, no. 22. Wiley, 2025.","short":"A. Pal, D. Shipilina, A. Le Moan, A.J. Mcnairn, J.K. Grenier, M. Kucka, G. Coop, Y.F. Chan, N.H. Barton, D. Field, S. Stankowski, Molecular Ecology 34 (2025).","mla":"Pal, Arka, et al. “Genealogical Analysis of Replicate Flower Colour Hybrid Zones in Antirrhinum.” <i>Molecular Ecology</i>, vol. 34, no. 22, e70067, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/mec.70067\">10.1111/mec.70067</a>.","ista":"Pal A, Shipilina D, Le Moan A, Mcnairn AJ, Grenier JK, Kucka M, Coop G, Chan YF, Barton NH, Field D, Stankowski S. 2025. Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. Molecular Ecology. 34(22), e70067.","chicago":"Pal, Arka, Daria Shipilina, Alan Le Moan, Adrian J. Mcnairn, Jennifer K. Grenier, Marek Kucka, Graham Coop, et al. “Genealogical Analysis of Replicate Flower Colour Hybrid Zones in Antirrhinum.” <i>Molecular Ecology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/mec.70067\">https://doi.org/10.1111/mec.70067</a>.","apa":"Pal, A., Shipilina, D., Le Moan, A., Mcnairn, A. J., Grenier, J. K., Kucka, M., … Stankowski, S. (2025). Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.70067\">https://doi.org/10.1111/mec.70067</a>","ama":"Pal A, Shipilina D, Le Moan A, et al. Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. <i>Molecular Ecology</i>. 2025;34(22). doi:<a href=\"https://doi.org/10.1111/mec.70067\">10.1111/mec.70067</a>"},"acknowledged_ssus":[{"_id":"ScienComp"}],"_id":"20190","date_updated":"2026-08-25T22:30:41Z","volume":34,"publication":"Molecular Ecology","article_number":"e70067","publication_status":"published","article_type":"original","abstract":[{"text":"A major goal of speciation research is identifying loci that underpin barriers to gene flow. Population genomics takes a ‘bottom-up’ approach, scanning the genome for molecular signatures of processes that drive or maintain divergence. However, interpreting the ‘genomic landscape’ of speciation is complicated, because genome scans conflate multiple processes, most of which are not informative about gene flow. However, studying replicated population contrasts, including multiple incidences of secondary contact, can strengthen inferences. In this paper, we use linked-read sequencing (haplotagging), FST scans and genealogical methods to characterise the genomic landscape associated with replicate hybrid zone formation. We studied two flower colour varieties of the common snapdragon, Antirrhinum majus subspecies majus, that form secondary hybrid zones in multiple independent valleys in the Pyrenees. Consistent with past work, we found very low differentiation at one well-studied zone (Planoles). However, at a second zone (Avellanet), we found stronger differentiation and greater heterogeneity, which we argue is due to differences in the amount of introgression following secondary contact. Topology weighting of genealogical trees identified loci where haplotype diversity was associated with the two snapdragon varieties. Two of the strongest associations were at previously identified flower colour loci: Flavia, that affects yellow pigmentation, and Rosea/Eluta, two linked loci that affect magenta pigmentation. Preliminary analysis of coalescence times provides additional evidence for selective sweeps at these loci and barriers to gene flow. Our study highlights the impact of demographic history on the differentiation landscape, emphasising the need to distinguish between historical divergence and recent introgression.","lang":"eng"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/snapdragon-secrets/","relation":"press_release","description":"News on ISTA website"}],"record":[{"id":"20694","relation":"dissertation_contains","status":"public"}]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"creator":"dernst","date_updated":"2026-01-05T13:47:47Z","date_created":"2026-01-05T13:47:47Z","content_type":"application/pdf","access_level":"open_access","success":1,"relation":"main_file","file_size":9886694,"file_name":"2025_MolecEcology_Pal.pdf","checksum":"c586fc674df4e7dd6e43aef87a52c6f6","file_id":"20958"}],"ddc":["570"],"type":"journal_article","date_created":"2025-08-17T22:01:37Z","doi":"10.1111/mec.70067","month":"11","file_date_updated":"2026-01-05T13:47:47Z","PlanS_conform":"1","day":"01","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"OA_place":"publisher","issue":"22","has_accepted_license":"1","oa":1,"OA_type":"hybrid","date_published":"2025-11-01T00:00:00Z","project":[{"name":"Snapdragon Speciation","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166"},{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"external_id":{"isi":["001546622100001"]},"status":"public","quality_controlled":"1","oa_version":"Published Version","department":[{"_id":"NiBa"}],"corr_author":"1","acknowledgement":"We thank ESEB Godfrey Hewitt Mobility Award for supporting AP’s research stay at UC Davis. We thank Tom Ellis, Parvathy Surendranadh, and other Barton Group and Coop Lab members for stimulating discussions. We are grateful to all the interns and volunteers who have helped us with fieldwork. We thank Eva Salmerón Mateu for her assistance in fieldwork logistics at the field station, El Serrat. We are grateful to Enrico Coen and his research group for providing the Antirrhinum molle PoolSeq data used in the allele polarisation. We are also thankful to Enrico Coen and Cristophe Thébaud for discovering the Avellanet hybrid zone, followed up with sampling led by D.L.F. in 2017. The study was supported by Austrian Science Fund (FWF) Grant (Snapdragon Speciation P32166, awarded to D.L.F.); ERC (Advanced Grant HaplotypeStructure 101055327, awarded to NHB); ERC (POC Grant 101069216, awarded to Y.F.C.) and the National Institutes of Health (NIH R35 GM136290, awarded to G.C.). Y.F.C. was supported by the Max Planck Society. Computing infrastructure for bioinformatics and analyses was provided by ISTA High Performance Cluster. ","author":[{"id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal","full_name":"Pal, Arka","orcid":"0000-0002-4530-8469","first_name":"Arka"},{"orcid":"0000-0002-1145-9226","full_name":"Shipilina, Daria","last_name":"Shipilina","first_name":"Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Le Moan, Alan","last_name":"Le Moan","first_name":"Alan"},{"full_name":"Mcnairn, Adrian J.","last_name":"Mcnairn","first_name":"Adrian J."},{"first_name":"Jennifer K.","full_name":"Grenier, Jennifer K.","last_name":"Grenier"},{"full_name":"Kucka, Marek","last_name":"Kucka","first_name":"Marek"},{"first_name":"Graham","full_name":"Coop, Graham","last_name":"Coop"},{"first_name":"Yingguang Frank","last_name":"Chan","full_name":"Chan, Yingguang Frank"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478","first_name":"David"},{"first_name":"Sean","full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"}],"intvolume":"        34","isi":1},{"ec_funded":1,"title":"Genealogies under purifying selection","month":"10","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2024","doi":"10.1101/2024.10.15.618444","date_updated":"2026-06-12T12:43:34Z","_id":"21967","citation":{"mla":"Khudiakova, Kseniia, et al. “Genealogies under Purifying Selection.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.10.15.618444\">10.1101/2024.10.15.618444</a>.","ista":"Khudiakova K, Boenkost F, Tourniaire JN. Genealogies under purifying selection. bioRxiv, <a href=\"https://doi.org/10.1101/2024.10.15.618444\">10.1101/2024.10.15.618444</a>.","short":"K. Khudiakova, F. Boenkost, J.N. Tourniaire, BioRxiv (n.d.).","ieee":"K. Khudiakova, F. Boenkost, and J. N. Tourniaire, “Genealogies under purifying selection,” <i>bioRxiv</i>. .","apa":"Khudiakova, K., Boenkost, F., &#38; Tourniaire, J. N. (n.d.). Genealogies under purifying selection. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.10.15.618444\">https://doi.org/10.1101/2024.10.15.618444</a>","chicago":"Khudiakova, Kseniia, Florin Boenkost, and Julie N Tourniaire. “Genealogies under Purifying Selection.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.10.15.618444\">https://doi.org/10.1101/2024.10.15.618444</a>.","ama":"Khudiakova K, Boenkost F, Tourniaire JN. Genealogies under purifying selection. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.10.15.618444\">10.1101/2024.10.15.618444</a>"},"language":[{"iso":"eng"}],"article_processing_charge":"No","day":"18","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.10.15.618444"}],"status":"public","abstract":[{"lang":"eng","text":"Selection against deleterious mutations, called purifying selection, plays a central role in evolution and acts in all populations. It is known that the genetic patterns observed in genomic regions undergoing purifying selection differ from those resulting from neutral evolution. However, a comprehensive understanding of the underlying mechanisms shaping those patterns is still lacking.\r\n\r\nIn the present work, we use simulations combined with a genealogical approach to identify the effect of purifying selection on the ancestry and thus on the genetic diversity. Our analysis relies on the postulate that the genealogy belongs to the universality class of Beta-coalescents. Under this assumption, we derive statistics measuring the distortion of the genealogy. This approach allows us to consider a wide range of regimes (i.e. arbitrary selection and mutation strengths) and uncover a rich phase diagram. We find that, for strong selection, the limiting genealogy is given by Kingman’s coalescent on a polynomial timescale. As selection gets weaker, Muller’s ratchet starts operating, setting off the emergence of multiple mergers in the genealogical structures. Our results show that while multiple-merger coalescents are often interpreted as the signature of selective sweeps in rapidly adapting populations, these structures can also appear in the context of Muller’s ratchet."}],"department":[{"_id":"NiBa"},{"_id":"JaMa"}],"oa_version":"Preprint","publication_status":"draft","date_published":"2024-10-18T00:00:00Z","publication":"bioRxiv","project":[{"grant_number":"26293","name":"The impact of deleterious mutations on small populations","_id":"34d33d68-11ca-11ed-8bc3-ec13763c0ca8"},{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"OA_type":"green","oa":1,"date_created":"2026-06-09T12:14:08Z","type":"preprint","acknowledgement":"This work was supported by the Austrian Academy of Science, DOC fellowship No 26293 (K.K.) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413 (J.T.). Simulations were performed on the ISTA High-performance Computing Cluster.","corr_author":"1","author":[{"id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","first_name":"Kseniia","orcid":"0000-0002-6246-1465","full_name":"Khudiakova, Kseniia","last_name":"Khudiakova"},{"first_name":"Florin","full_name":"Boenkost, Florin","last_name":"Boenkost"},{"full_name":"Tourniaire, Julie N","last_name":"Tourniaire","first_name":"Julie N","id":"5dc06dd8-8e51-11ec-9170-8d9c450cc216"}],"related_material":{"record":[{"id":"21918","relation":"dissertation_contains","status":"public"}]},"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","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"}},{"OA_type":"hybrid","oa":1,"external_id":{"pmid":["37843465"],"isi":["001085119000001"]},"date_published":"2024-12-01T00:00:00Z","department":[{"_id":"NiBa"}],"oa_version":"Published Version","quality_controlled":"1","status":"public","author":[{"first_name":"James","last_name":"Reeve","full_name":"Reeve, James"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."},{"first_name":"Eva L.","full_name":"Koch, Eva L.","last_name":"Koch"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"}],"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).","isi":1,"intvolume":"        33","doi":"10.1111/mec.17160","month":"12","file_date_updated":"2025-01-09T07:52:12Z","day":"01","article_processing_charge":"Yes (in subscription journal)","language":[{"iso":"eng"}],"scopus_import":"1","issue":"24","OA_place":"publisher","has_accepted_license":"1","volume":33,"publication":"Molecular Ecology","publication_status":"published","article_type":"original","article_number":"e17160","abstract":[{"lang":"eng","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."}],"ddc":["570"],"file":[{"relation":"main_file","success":1,"file_size":6228700,"access_level":"open_access","file_id":"18785","file_name":"2024_MolecularEcology_Reeve.pdf","checksum":"686576036663f489c2d079df3079d126","creator":"dernst","content_type":"application/pdf","date_updated":"2025-01-09T07:52:12Z","date_created":"2025-01-09T07:52:12Z"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"type":"journal_article","date_created":"2023-10-29T23:01:17Z","year":"2024","publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana)","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"citation":{"mla":"Reeve, James, et al. “Chromosomal Inversion Polymorphisms Are Widespread across the Species Ranges of Rough Periwinkles (Littorina Saxatilis and L. Arcana).” <i>Molecular Ecology</i>, vol. 33, no. 24, e17160, Wiley, 2024, doi:<a href=\"https://doi.org/10.1111/mec.17160\">10.1111/mec.17160</a>.","ista":"Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. 2024. Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology. 33(24), e17160.","short":"J. Reeve, R.K. Butlin, E.L. Koch, S. Stankowski, R. Faria, Molecular Ecology 33 (2024).","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),” <i>Molecular Ecology</i>, vol. 33, no. 24. Wiley, 2024.","apa":"Reeve, J., Butlin, R. K., Koch, E. L., Stankowski, S., &#38; Faria, R. (2024). Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.17160\">https://doi.org/10.1111/mec.17160</a>","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).” <i>Molecular Ecology</i>. Wiley, 2024. <a href=\"https://doi.org/10.1111/mec.17160\">https://doi.org/10.1111/mec.17160</a>.","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). <i>Molecular Ecology</i>. 2024;33(24). doi:<a href=\"https://doi.org/10.1111/mec.17160\">10.1111/mec.17160</a>"},"_id":"14463","pmid":1,"date_updated":"2025-01-09T07:53:18Z"},{"month":"01","file_date_updated":"2024-01-03T18:31:34Z","doi":"10.15479/at:ista:14711","OA_place":"publisher","has_accepted_license":"1","day":"19","article_processing_charge":"No","language":[{"iso":"eng"}],"oa_version":"Published Version","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"status":"public","oa":1,"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"},{"_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","name":"Causes and consequences of population fragmentation","grant_number":"P32896"},{"_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6","name":"Polygenic Adaptation in a Metapopulation","grant_number":"26380"}],"date_published":"2024-01-19T00:00:00Z","alternative_title":["ISTA Thesis"],"page":"183","author":[{"first_name":"Oluwafunmilola O","orcid":"0000-0003-1971-8314","full_name":"Olusanya, Oluwafunmilola O","last_name":"Olusanya","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87"}],"corr_author":"1","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ec_funded":1,"title":"Local adaptation, genetic load and extinction in metapopulations","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","year":"2024","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"full_name":"Polechova, Jitka","last_name":"Polechova","first_name":"Jitka"},{"last_name":"Sachdeva","full_name":"Sachdeva, Himani","first_name":"Himani"}],"acknowledged_ssus":[{"_id":"SSU"}],"_id":"14711","date_updated":"2026-04-07T12:54:29Z","publication_identifier":{"issn":["2663-337X"]},"citation":{"ista":"Olusanya OO. 2024. Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria.","mla":"Olusanya, Oluwafunmilola O. <i>Local Adaptation, Genetic Load and Extinction in Metapopulations</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:14711\">10.15479/at:ista:14711</a>.","short":"O.O. Olusanya, Local Adaptation, Genetic Load and Extinction in Metapopulations, Institute of Science and Technology Austria, 2024.","ieee":"O. O. Olusanya, “Local adaptation, genetic load and extinction in metapopulations,” Institute of Science and Technology Austria, 2024.","apa":"Olusanya, O. O. (2024). <i>Local adaptation, genetic load and extinction in metapopulations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14711\">https://doi.org/10.15479/at:ista:14711</a>","chicago":"Olusanya, Oluwafunmilola O. “Local Adaptation, Genetic Load and Extinction in Metapopulations.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:14711\">https://doi.org/10.15479/at:ista:14711</a>.","ama":"Olusanya OO. Local adaptation, genetic load and extinction in metapopulations. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:14711\">10.15479/at:ista:14711</a>"},"publication_status":"published","abstract":[{"text":"In nature, different species find their niche in a range of environments, each with its unique characteristics. While some thrive in uniform (homogeneous) landscapes where environmental conditions stay relatively consistent across space, others traverse the complexities of spatially heterogeneous terrains. Comprehending how species are distributed and how they interact within these landscapes holds the key to gaining insights into their evolutionary dynamics while also informing conservation and management strategies.\r\n\r\nFor species inhabiting heterogeneous landscapes, when the rate of dispersal is low compared to spatial fluctuations in selection pressure, localized adaptations may emerge. Such adaptation in response to varying selection strengths plays an important role in the persistence of populations in our rapidly changing world. Hence, species in nature are continuously in a struggle to adapt to local environmental conditions, to ensure their continued survival. Natural populations can often adapt in time scales short enough for evolutionary changes to influence ecological dynamics and vice versa, thereby creating a feedback between evolution and demography. The analysis of this feedback and the relative contributions of gene flow, demography, drift, and natural selection to genetic variation and differentiation has remained a recurring theme in evolutionary biology. Nevertheless, the effective role of these forces in maintaining variation and shaping patterns of diversity is not fully understood. Even in homogeneous environments devoid of local adaptations, such understanding remains elusive. Understanding this feedback is crucial, for example in determining the conditions under which extinction risk can be mitigated in peripheral populations subject to deleterious mutation accumulation at the edges of species’ ranges\r\nas well as in highly fragmented populations.\r\n\r\nIn this thesis we explore both uniform and spatially heterogeneous metapopulations, investigating and providing theoretical insights into the dynamics of local adaptation in the latter and examining the dynamics of load and extinction as well as the impact of joint ecological and evolutionary (eco-evolutionary) dynamics in the former. The thesis is divided into 5 chapters.\r\n\r\nChapter 1 provides a general introduction into the subject matter, clarifying concepts and ideas used throughout the thesis. In chapter 2, we explore how fast a species distributed across a heterogeneous landscape adapts to changing conditions marked by alterations in carrying capacity, selection pressure, and migration rate.\r\n\r\nIn chapter 3, we investigate how migration selection and drift influences adaptation and the maintenance of variation in a metapopulation with three habitats, an extension of previous models of adaptation in two habitats. We further develop analytical approximations for the critical threshold required for polymorphism to persist.\r\n\r\nThe focus of chapter 4 of the thesis is on understanding the interplay between ecology and evolution as coupled processes. We investigate how eco-evolutionary feedback between migration, selection, drift, and demography influences eco-evolutionary outcomes in marginal populations subject to deleterious mutation accumulation. Using simulations as well as theoretical approximations of the coupled dynamics of population size and allele frequency, we analyze how gene flow from a large mainland source influences genetic load and population size on an island (i.e., in a marginal population) under genetically realistic assumptions. Analyses of this sort are important because small isolated populations, are repeatedly affected by complex interactions between ecological and evolutionary processes, which can lead to their death. Understanding these interactions can therefore provide an insight into the conditions under which extinction risk can be mitigated in peripheral populations thus, contributing to conservation and restoration efforts.\r\n\r\nChapter 5 extends the analysis in chapter 4 to consider the dynamics of load (due to deleterious mutation accumulation) and extinction risk in a metapopulation. We explore the role of gene flow, selection, and dominance on load and extinction risk and further pinpoint critical thresholds required for metapopulation persistence.\r\n\r\nOverall this research contributes to our understanding of ecological and evolutionary mechanisms that shape species’ persistence in fragmented landscapes, a crucial foundation for successful conservation efforts and biodiversity management.","lang":"eng"}],"degree_awarded":"PhD","type":"dissertation","date_created":"2023-12-26T22:49:53Z","file":[{"file_id":"14730","file_name":"FinalSubmission_Thesis_OLUSANYA.zip","checksum":"de179b1c6758f182ff0c70d8b38c1501","relation":"source_file","file_size":16986244,"access_level":"closed","content_type":"application/zip","date_updated":"2024-01-03T18:30:13Z","date_created":"2024-01-03T18:30:13Z","creator":"oolusany"},{"file_size":6460403,"relation":"main_file","success":1,"access_level":"open_access","file_id":"14731","checksum":"0e331585e3cd4823320aab4e69e64ccf","file_name":"FinalSubmission2_Thesis_OLUSANYA.pdf","creator":"oolusany","content_type":"application/pdf","date_created":"2024-01-03T18:31:34Z","date_updated":"2024-01-03T18:31:34Z"}],"ddc":["576"],"tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10787"},{"relation":"part_of_dissertation","id":"10658","status":"public"},{"id":"14732","relation":"part_of_dissertation","status":"public"}]}},{"isi":1,"intvolume":"       227","author":[{"id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","orcid":"0000-0002-4530-8469","last_name":"Pal","full_name":"Pal, Arka","first_name":"Arka"},{"full_name":"Joshi, Mihir","last_name":"Joshi","first_name":"Mihir"},{"first_name":"Maria","last_name":"Thaker","full_name":"Thaker, Maria"}],"corr_author":"1","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.","department":[{"_id":"NiBa"}],"oa_version":"Published Version","status":"public","quality_controlled":"1","external_id":{"isi":["001214515700016"],"pmid":["38054353"]},"date_published":"2024-01-10T00:00:00Z","oa":1,"has_accepted_license":"1","issue":"1","article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"scopus_import":"1","day":"10","file_date_updated":"2024-01-23T12:08:24Z","month":"01","doi":"10.1242/jeb.246217","date_created":"2024-01-22T08:14:49Z","type":"journal_article","file":[{"access_level":"open_access","file_size":594128,"relation":"main_file","success":1,"checksum":"136325372f6f45abaa62a71e2d23bfb6","file_name":"2024_JourExperimBiology_Pal.pdf","file_id":"14877","creator":"dernst","date_updated":"2024-01-23T12:08:24Z","date_created":"2024-01-23T12:08:24Z","content_type":"application/pdf"}],"ddc":["570"],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"related_material":{"link":[{"url":"https://github.com/arka-pal/Cnemaspis-SexualSignaling","relation":"software"}]},"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.</jats:p>"}],"article_type":"original","publication_status":"published","article_number":"jeb246217","publication":"Journal of Experimental Biology","keyword":["Insect Science","Molecular Biology","Animal Science and Zoology","Aquatic Science","Physiology","Ecology","Evolution","Behavior and Systematics"],"volume":227,"pmid":1,"date_updated":"2025-09-04T11:50:21Z","_id":"14850","citation":{"short":"A. Pal, M. Joshi, M. Thaker, Journal of Experimental Biology 227 (2024).","ieee":"A. Pal, M. Joshi, and M. Thaker, “Too much information? Males convey parasite levels using more signal modalities than females utilise,” <i>Journal of Experimental Biology</i>, vol. 227, no. 1. The Company of Biologists, 2024.","mla":"Pal, Arka, et al. “Too Much Information? Males Convey Parasite Levels Using More Signal Modalities than Females Utilise.” <i>Journal of Experimental Biology</i>, vol. 227, no. 1, jeb246217, The Company of Biologists, 2024, doi:<a href=\"https://doi.org/10.1242/jeb.246217\">10.1242/jeb.246217</a>.","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.","chicago":"Pal, Arka, Mihir Joshi, and Maria Thaker. “Too Much Information? Males Convey Parasite Levels Using More Signal Modalities than Females Utilise.” <i>Journal of Experimental Biology</i>. The Company of Biologists, 2024. <a href=\"https://doi.org/10.1242/jeb.246217\">https://doi.org/10.1242/jeb.246217</a>.","apa":"Pal, A., Joshi, M., &#38; Thaker, M. (2024). Too much information? Males convey parasite levels using more signal modalities than females utilise. <i>Journal of Experimental Biology</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jeb.246217\">https://doi.org/10.1242/jeb.246217</a>","ama":"Pal A, Joshi M, Thaker M. Too much information? Males convey parasite levels using more signal modalities than females utilise. <i>Journal of Experimental Biology</i>. 2024;227(1). doi:<a href=\"https://doi.org/10.1242/jeb.246217\">10.1242/jeb.246217</a>"},"publication_identifier":{"issn":["1477-9145"],"eissn":["0022-0949"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"The Company of Biologists","title":"Too much information? Males convey parasite levels using more signal modalities than females utilise","year":"2024"},{"article_processing_charge":"No","language":[{"iso":"eng"}],"day":"23","has_accepted_license":"1","OA_place":"publisher","doi":"10.15479/at:ista:15020","file_date_updated":"2024-02-23T14:20:16Z","month":"02","corr_author":"1","author":[{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik","full_name":"Hledik, Michal","first_name":"Michal"}],"page":"158","alternative_title":["ISTA Thesis"],"date_published":"2024-02-23T00:00:00Z","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"},{"grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"},{"grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes"}],"oa":1,"status":"public","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"oa_version":"Published Version","citation":{"mla":"Hledik, Michal. <i>Genetic Information and Biological Optimization</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>.","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.","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","apa":"Hledik, M. (2024). <i>Genetic information and biological optimization</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>","chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>.","ama":"Hledik M. Genetic information and biological optimization. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>"},"publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-04-07T12:59:25Z","_id":"15020","acknowledged_ssus":[{"_id":"ScienComp"}],"year":"2024","supervisor":[{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"title":"Genetic information and biological optimization","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"record":[{"relation":"part_of_dissertation","id":"7606","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"12081"},{"status":"public","id":"7553","relation":"part_of_dissertation"}]},"file":[{"file_size":7102089,"relation":"main_file","success":1,"access_level":"open_access","file_id":"15021","checksum":"b2d3da47c98d481577a4baf68944fe41","file_name":"hledik thesis pdfa 2b.pdf","creator":"mhledik","content_type":"application/pdf","date_created":"2024-02-23T13:50:53Z","date_updated":"2024-02-23T13:50:53Z"},{"creator":"mhledik","date_created":"2024-02-23T13:50:54Z","date_updated":"2024-02-23T14:20:16Z","content_type":"application/zip","access_level":"closed","file_size":14014790,"relation":"source_file","checksum":"eda9b9430da2610fee7ce1c1419a479a","file_name":"hledik thesis source.zip","file_id":"15022"}],"ddc":["576","519"],"date_created":"2024-02-23T14:02:04Z","type":"dissertation","keyword":["Theoretical biology","Optimality","Evolution","Information"],"degree_awarded":"PhD","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"}],"publication_status":"published"},{"intvolume":"        40","isi":1,"acknowledgement":"KJ, MR, and RKB were supported by grants from the Swedish Research Council (2021-0419, 2021-05243, and 2018-03695, respectively). RKB was also supported by the Leverhulme Trust (RPG-2021-141), RF by FCT- Portuguese Science Foundation (PTDC/BIA-EVL/1614/2021 and 2020.00275.CEECIND), and AMW by Norwegian Research Council RCN (Project number 315287). We thank the members of the Integration of Speciation Research network for stimulating discussions, the Littorina research community for important contributions of data and analyses, and Cynthia Riginos for useful comments on an earlier draft.","author":[{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"first_name":"Alan","full_name":"Le Moan, Alan","last_name":"Le Moan"},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","last_name":"Westram","full_name":"Westram, Anja M","first_name":"Anja M"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean"}],"page":"337-351","status":"public","quality_controlled":"1","department":[{"_id":"NiBa"}],"oa_version":"Published Version","date_published":"2024-04-01T00:00:00Z","external_id":{"isi":["001224671300001"],"pmid":["38395682"]},"oa":1,"has_accepted_license":"1","issue":"4","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","language":[{"iso":"eng"}],"day":"01","file_date_updated":"2024-07-22T12:05:58Z","month":"04","doi":"10.1016/j.tig.2024.01.002","date_created":"2024-03-10T23:00:54Z","type":"journal_article","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"creator":"dernst","content_type":"application/pdf","date_created":"2024-07-22T12:05:58Z","date_updated":"2024-07-22T12:05:58Z","relation":"main_file","success":1,"file_size":2288340,"access_level":"open_access","file_id":"17313","file_name":"2024_TrendsGenetics_Johannesson.pdf","checksum":"3077ea808c4cdc24d02dc58aced7eb35"}],"ddc":["570"],"abstract":[{"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.","lang":"eng"}],"publication_status":"published","article_type":"review","publication":"Trends in Genetics","volume":40,"pmid":1,"date_updated":"2025-09-04T12:18:08Z","_id":"15099","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.” <i>Trends in Genetics</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.tig.2024.01.002\">https://doi.org/10.1016/j.tig.2024.01.002</a>.","apa":"Johannesson, K., Faria, R., Le Moan, A., Rafajlović, M., Westram, A. M., Butlin, R. K., &#38; Stankowski, S. (2024). Diverse pathways to speciation revealed by marine snails. <i>Trends in Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tig.2024.01.002\">https://doi.org/10.1016/j.tig.2024.01.002</a>","short":"K. Johannesson, R. Faria, A. Le Moan, M. Rafajlović, A.M. Westram, R.K. Butlin, S. Stankowski, Trends in Genetics 40 (2024) 337–351.","ieee":"K. Johannesson <i>et al.</i>, “Diverse pathways to speciation revealed by marine snails,” <i>Trends in Genetics</i>, vol. 40, no. 4. Elsevier, pp. 337–351, 2024.","mla":"Johannesson, Kerstin, et al. “Diverse Pathways to Speciation Revealed by Marine Snails.” <i>Trends in Genetics</i>, vol. 40, no. 4, Elsevier, 2024, pp. 337–51, doi:<a href=\"https://doi.org/10.1016/j.tig.2024.01.002\">10.1016/j.tig.2024.01.002</a>.","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. 40(4), 337–351.","ama":"Johannesson K, Faria R, Le Moan A, et al. Diverse pathways to speciation revealed by marine snails. <i>Trends in Genetics</i>. 2024;40(4):337-351. doi:<a href=\"https://doi.org/10.1016/j.tig.2024.01.002\">10.1016/j.tig.2024.01.002</a>"},"publication_identifier":{"issn":["0168-9525"],"eissn":["1362-4555"]},"title":"Diverse pathways to speciation revealed by marine snails","publisher":"Elsevier","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024"},{"department":[{"_id":"NiBa"}],"oa_version":"Published Version","quality_controlled":"1","status":"public","external_id":{"pmid":["38643838"],"isi":["001237016800001"]},"project":[{"grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes"}],"date_published":"2024-06-01T00:00:00Z","oa":1,"isi":1,"intvolume":"       157","author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Himani","full_name":"Sachdeva, Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"We thank Emmanuel Schertzer and two reviewers for comments on this manuscript. NB thanks the European Research Council for support via the grant “HaplotypeStructure” 101055327. We would also like to give our sincere thanks to Alison Etheridge for her insight, inspiration and support over the years.","corr_author":"1","page":"129-137","file_date_updated":"2024-05-13T08:22:21Z","month":"06","doi":"10.1016/j.tpb.2024.04.001","has_accepted_license":"1","language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)","scopus_import":"1","day":"01","abstract":[{"text":"We consider how a population of N haploid individuals responds to directional selection on standing variation, with no new variation from recombination or mutation. Individuals have trait values z1,…,zN, which are drawn from a distribution ψ; the fitness of individual i is proportional to [Formula: see text] . For illustration, we consider the Laplace and Gaussian distributions, which are parametrised only by the variance V0, and show that for large N, there is a scaling limit which depends on a single parameter NV0. When selection is weak relative to drift (NV0≪1), the variance decreases exponentially at rate 1/N, and the expected ultimate gain in log fitness (scaled by V0), is just NV0, which is the same as Robertson's (1960) prediction for a sexual population. In contrast, when selection is strong relative to drift (NV0≫1), the ultimate gain can be found by approximating the establishment of alleles by a branching process in which each allele competes independently with the population mean and the fittest allele to establish is certain to fix. Then, if the probability of survival to time t∼1/V0 of an allele with value z is P(z), with mean P¯, the winning allele is the fittest of NP¯ survivors drawn from a distribution ψP/P¯. The expected ultimate change is ∼2log(1.15NV0) for a Gaussian distribution, and ∼-12log0.36NV0-log-log0.36NV0 for a Laplace distribution. This approach also predicts the variability of the process, and its dynamics; we show that in the strong selection regime, the expected genetic variance decreases as ∼t-3 at large times. We discuss how these results may be related to selection on standing variation that is spread along a linear chromosome.","lang":"eng"}],"publication_status":"published","article_type":"original","publication":"Theoretical Population Biology","volume":157,"date_created":"2024-05-05T22:01:03Z","type":"journal_article","file":[{"success":1,"relation":"main_file","file_size":1098292,"access_level":"open_access","file_id":"15383","file_name":"2024_TheorPopulationBiology_Barton.pdf","checksum":"78f36488d24f868d5913624e9c8d88bf","creator":"dernst","content_type":"application/pdf","date_created":"2024-05-13T08:22:21Z","date_updated":"2024-05-13T08:22:21Z"}],"ddc":["570"],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"publisher":"Elsevier","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Limits to selection on standing variation in an asexual population","year":"2024","pmid":1,"date_updated":"2025-09-04T13:56:11Z","_id":"15358","citation":{"mla":"Barton, Nicholas H., and Himani Sachdeva. “Limits to Selection on Standing Variation in an Asexual Population.” <i>Theoretical Population Biology</i>, vol. 157, Elsevier, 2024, pp. 129–37, doi:<a href=\"https://doi.org/10.1016/j.tpb.2024.04.001\">10.1016/j.tpb.2024.04.001</a>.","ista":"Barton NH, Sachdeva H. 2024. Limits to selection on standing variation in an asexual population. Theoretical Population Biology. 157, 129–137.","ieee":"N. H. Barton and H. Sachdeva, “Limits to selection on standing variation in an asexual population,” <i>Theoretical Population Biology</i>, vol. 157. Elsevier, pp. 129–137, 2024.","short":"N.H. Barton, H. Sachdeva, Theoretical Population Biology 157 (2024) 129–137.","apa":"Barton, N. H., &#38; Sachdeva, H. (2024). Limits to selection on standing variation in an asexual population. <i>Theoretical Population Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tpb.2024.04.001\">https://doi.org/10.1016/j.tpb.2024.04.001</a>","chicago":"Barton, Nicholas H, and Himani Sachdeva. “Limits to Selection on Standing Variation in an Asexual Population.” <i>Theoretical Population Biology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.tpb.2024.04.001\">https://doi.org/10.1016/j.tpb.2024.04.001</a>.","ama":"Barton NH, Sachdeva H. Limits to selection on standing variation in an asexual population. <i>Theoretical Population Biology</i>. 2024;157:129-137. doi:<a href=\"https://doi.org/10.1016/j.tpb.2024.04.001\">10.1016/j.tpb.2024.04.001</a>"},"publication_identifier":{"issn":["0040-5809"],"eissn":["1096-0325"]}},{"corr_author":"1","acknowledgement":"This work was received funding from the following: Norwegian Research Council RCN project 315287 (A.M.W.), Swedish Research Council 2021-04191 (K.J.), European Research Council grant 101055327 HaplotypeStructure (N.B.), Austrian Science Fund FWF; P 32166-B32 Snapdragon Speciation (N.B.), European Research Council (R.B.), and Portuguese Foundation for Science and Technology FCT: 2020.00275.CEECIND and PTDC/BIA-EVL/1614/2021 (R.F.).","author":[{"first_name":"Diego Fernando","last_name":"Garcia Castillo","full_name":"Garcia Castillo, Diego Fernando","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"first_name":"Jenny","last_name":"Larsson","full_name":"Larsson, Jenny"},{"last_name":"Stankowski","full_name":"Stankowski, Sean","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Westram, Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"        10","isi":1,"date_published":"2024-10-11T00:00:00Z","project":[{"grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes"},{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation","grant_number":"P32166"},{"call_identifier":"FWF","name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"external_id":{"isi":["001354405400018"]},"oa":1,"OA_type":"gold","quality_controlled":"1","status":"public","oa_version":"Published Version","department":[{"_id":"NiBa"}],"scopus_import":"1","language":[{"iso":"eng"}],"article_processing_charge":"Yes","day":"11","has_accepted_license":"1","OA_place":"publisher","issue":"41","doi":"10.1126/sciadv.adp2102","PlanS_conform":"1","file_date_updated":"2024-11-04T09:35:49Z","month":"10","related_material":{"link":[{"relation":"software","url":"https://github.com/fernandoGarcia21/littorina_saxatilis_skerry"}],"record":[{"id":"18498","relation":"research_data","status":"public"},{"id":"20991","relation":"dissertation_contains","status":"public"}]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"ddc":["570"],"file":[{"file_size":1154107,"relation":"main_file","success":1,"access_level":"open_access","file_id":"18499","checksum":"96aa0d3640fa9401975138e59054f84e","file_name":"2024_ScienceAdv_Castillo.pdf","creator":"dernst","content_type":"application/pdf","date_created":"2024-11-04T09:35:49Z","date_updated":"2024-11-04T09:35:49Z"}],"date_created":"2024-11-03T23:01:44Z","type":"journal_article","publication":"Science Advances","volume":10,"abstract":[{"text":"Predicting the outcomes of adaptation is a major goal of evolutionary biology. When temporal changes in the environment mirror spatial gradients, it opens up the potential for predicting the course of adaptive evolution over time based on patterns of spatial genetic and phenotypic variation. We assessed this approach in a 30-year transplant experiment in the intertidal snail Littorina saxatilis. In 1992, snails were transplanted from a predation-dominated environment to one dominated by wave action. On the basis of spatial patterns, we predicted transitions in shell size and morphology, allele frequencies at positions throughout the genome, and chromosomal rearrangement frequencies. Observed changes closely agreed with predictions and transformation was both dramatic and rapid. Hence, adaptation can be predicted from knowledge of the phenotypic and genetic variation among populations.","lang":"eng"}],"article_number":"eadp2102","article_type":"original","publication_status":"published","citation":{"ama":"Garcia Castillo DF, Barton NH, Faria R, et al. Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails. <i>Science Advances</i>. 2024;10(41). doi:<a href=\"https://doi.org/10.1126/sciadv.adp2102\">10.1126/sciadv.adp2102</a>","ista":"Garcia Castillo DF, Barton NH, Faria R, Larsson J, Stankowski S, Butlin R, Johannesson K, Westram AM. 2024. Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails. Science Advances. 10(41), eadp2102.","mla":"Garcia Castillo, Diego Fernando, et al. “Predicting Rapid Adaptation in Time from Adaptation in Space: A 30-Year Field Experiment in Marine Snails.” <i>Science Advances</i>, vol. 10, no. 41, eadp2102, AAAS, 2024, doi:<a href=\"https://doi.org/10.1126/sciadv.adp2102\">10.1126/sciadv.adp2102</a>.","ieee":"D. F. Garcia Castillo <i>et al.</i>, “Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails,” <i>Science Advances</i>, vol. 10, no. 41. AAAS, 2024.","short":"D.F. Garcia Castillo, N.H. Barton, R. Faria, J. Larsson, S. Stankowski, R. Butlin, K. Johannesson, A.M. Westram, Science Advances 10 (2024).","apa":"Garcia Castillo, D. F., Barton, N. H., Faria, R., Larsson, J., Stankowski, S., Butlin, R., … Westram, A. M. (2024). Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails. <i>Science Advances</i>. AAAS. <a href=\"https://doi.org/10.1126/sciadv.adp2102\">https://doi.org/10.1126/sciadv.adp2102</a>","chicago":"Garcia Castillo, Diego Fernando, Nicholas H Barton, Rui Faria, Jenny Larsson, Sean Stankowski, Roger Butlin, Kerstin Johannesson, and Anja M Westram. “Predicting Rapid Adaptation in Time from Adaptation in Space: A 30-Year Field Experiment in Marine Snails.” <i>Science Advances</i>. AAAS, 2024. <a href=\"https://doi.org/10.1126/sciadv.adp2102\">https://doi.org/10.1126/sciadv.adp2102</a>."},"APC_amount":"4569,23 EUR","publication_identifier":{"eissn":["2375-2548"]},"date_updated":"2026-04-07T11:42:09Z","_id":"18491","DOAJ_listed":"1","year":"2024","title":"Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"AAAS"},{"date_published":"2024-06-19T00:00:00Z","oa":1,"department":[{"_id":"NiBa"}],"oa_version":"Published Version","abstract":[{"text":"Scripts and data used in the research study Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails. https://doi.org/10.1101/2023.09.27.559715","lang":"eng"}],"status":"public","author":[{"full_name":"Garcia Castillo, Diego Fernando","last_name":"Garcia Castillo","first_name":"Diego Fernando","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701"},{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"first_name":"Jenny","full_name":"Larsson, Jenny","last_name":"Larsson"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram","full_name":"Westram, Anja M"}],"corr_author":"1","ddc":["570"],"related_material":{"record":[{"status":"public","id":"20991","relation":"used_in_publication"},{"id":"18491","relation":"used_in_publication","status":"public"}]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"date_created":"2024-11-04T09:33:17Z","type":"research_data_reference","doi":"10.5281/ZENODO.12159343","year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Zenodo","month":"06","title":"Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails","article_processing_charge":"No","citation":{"chicago":"Garcia Castillo, Diego Fernando, Nicholas H Barton, Rui Faria, Jenny Larsson, Sean Stankowski, Roger Butlin, Kerstin Johannesson, and Anja M Westram. “Data and Code for: Predicting Rapid Adaptation in Time from Adaptation in Space: A 30-Year Field Experiment in Marine Snails.” Zenodo, 2024. <a href=\"https://doi.org/10.5281/ZENODO.12159343\">https://doi.org/10.5281/ZENODO.12159343</a>.","apa":"Garcia Castillo, D. F., Barton, N. H., Faria, R., Larsson, J., Stankowski, S., Butlin, R., … Westram, A. M. (2024). Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.12159343\">https://doi.org/10.5281/ZENODO.12159343</a>","short":"D.F. Garcia Castillo, N.H. Barton, R. Faria, J. Larsson, S. Stankowski, R. Butlin, K. Johannesson, A.M. Westram, (2024).","ieee":"D. F. Garcia Castillo <i>et al.</i>, “Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails.” Zenodo, 2024.","mla":"Garcia Castillo, Diego Fernando, et al. <i>Data and Code for: Predicting Rapid Adaptation in Time from Adaptation in Space: A 30-Year Field Experiment in Marine Snails</i>. Zenodo, 2024, doi:<a href=\"https://doi.org/10.5281/ZENODO.12159343\">10.5281/ZENODO.12159343</a>.","ista":"Garcia Castillo DF, Barton NH, Faria R, Larsson J, Stankowski S, Butlin R, Johannesson K, Westram AM. 2024. Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.12159343\">10.5281/ZENODO.12159343</a>.","ama":"Garcia Castillo DF, Barton NH, Faria R, et al. Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails. 2024. doi:<a href=\"https://doi.org/10.5281/ZENODO.12159343\">10.5281/ZENODO.12159343</a>"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.12159344"}],"day":"19","date_updated":"2026-04-16T12:20:37Z","has_accepted_license":"1","_id":"18498","OA_place":"repository"},{"abstract":[{"text":"Understanding the role of evolutionary processes in shaping genetic variation has been a\r\nprimary goal in evolutionary genetics. In this regard, a key question is how genetically\r\ndistinct populations evolve in the face of gene flow, thereby generating genetic and\r\nphenotypic divergence and reproductive isolation (RI). This requires quantifying the role\r\nand relative contributions of prezygotic and postzygotic isolating mechanisms on the\r\nreduction of gene exchange between populations, and identifying regions in the genome\r\nthat mediate RI, which is often polygenic. Further, this needs distinguishing neutral and\r\nselected regions in the genome, and discerning how selection influences patterns of neutral\r\ndivergence.\r\nPopulation structure, defined as any deviation from panmixia, such as geographic distribution, movement and mating patterns of individuals, influences how genetic variation is\r\nstructured in space and shapes the neutral null model. Availability of large scale spatial\r\ngenomic datasets now enables us to detect signatures of population structure in genetic\r\ndata and infer population genetic parameters. Such inferences are crucial and have wide\r\napplications in biodiversity, conservation genetics, population management and medical\r\ngenetics. However, inferences are based on assumptions that do not always match the\r\ncomplex reality, thus leading to erroneous conclusions. Moreover, the role and interaction\r\nof heterogeneous population density and dispersal, which are ubiquitous in nature, has\r\nbeen challenging to study owing to their mathematical complexity. In such scenarios,\r\nfeedback between theory, data and simulations can prove to be useful.\r\nIn this thesis, I examine the effect of population structure on neutral genetic variation\r\nand barriers to gene exchange in hybridising populations, thereby bridging together the\r\nfields of spatial population genetics and speciation.\r\nDespite being a key concept in speciation, reproductive isolation (RI) lacks a quantitative\r\ndefinition and has been used and measured differently across different fields. Chapter 2\r\ngives a quantitative definition of RI, in terms of the effect of genetic differences on gene\r\nflow. We give analytical predictions for RI in a range of scenarios, in terms of effective migration rates for discrete populations and barrier strength for continuous populations.\r\nIn addition to this, we discuss current measures of RI and their limitations, and propose\r\nthe need for new measures that combine organismal and genetic perspectives of RI.\r\nIn chapter 3, I examine the combined effect of assortative mating, sexual selection\r\nand viability selection on RI. For this, we consider a polygenic ‘magic’ trait under a\r\nmainland-island model. We obtain novel theoretical predictions for molecular divergence\r\nin terms of effective migration rates, which bears a simple relationship to measurable\r\nfitness components of migrants and various early generation hybrids. We explore the\r\nconditions under which local adaptation can be maintained despite maladaptive gene flow\r\nand quantify the relative contributions of viability and sexual selection to genome-wide\r\nbarriers to gene flow.\r\nThe next two chapters of the thesis focus on a hybrid zone of Antirrhinum majus that\r\nconsist of two subspecies- the magenta flowered A. m. pseudomajus and the yellow\r\nflowered A.m. striatum. Previous studies have suggested that flower colour is target of\r\npollinator mediated selection and is influenced only by few genes. While these regions\r\nshow high genetic differentiation between the subspecies, the rest of the genome is seen\r\nto be well mixed. Chapter 4 examines the effects of heterogeneous population density\r\nand leptokurtic dispersal on isolation by distance and the distribution of heterozygosity\r\nby focusing on non-flower colour markers.\r\nChapter 5 analyses cline shapes and associations among 6 focal flower colour markers to\r\nunderstand how selection and dispersal maintain this hybrid zone. We see sharp coincident\r\nstepped clines at all loci and positive associations throughout the hybrid zone, contrary to\r\nthe expected patterns from diffusive gene flow. With a novel scheme of inferring dispersal\r\ncombined with multilocus simulations, we show that stepped clines do not reflect genetic\r\nbarriers to gene flow, but are rather a result of long-distance migration. This framework\r\nallows us to get realistic estimates gene flow and selection and shows how traditional cline\r\nanalysis may lead to inaccurate conclusions when assumptions of the theory are not met.\r\nOverall, this thesis investigates how different features of population structure leave\r\ndetectable signatures in genetic variation, namely in patterns of isolation by distance,\r\nlinkage disequilibrium and genetic divergence. It also highlights how effective migration\r\nrates provide useful way of analysing polygenic architectures and shed new light into\r\nhybrid zones. In doing so, I identify scenarios when simple models become insufficient\r\nand suggest possibe directions by combining genetic data with simulations.","lang":"eng"}],"publication_status":"published","degree_awarded":"PhD","date_created":"2024-11-06T21:25:37Z","type":"dissertation","tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"file":[{"creator":"psurendr","date_updated":"2024-11-07T10:59:29Z","date_created":"2024-11-07T10:59:29Z","content_type":"application/pdf","access_level":"open_access","success":1,"relation":"main_file","file_size":37019760,"file_name":"PhD_Thesis__Parvathy_071124_PDFA.pdf","checksum":"c32cf7bc75748d9c551d8eb70178bbec","file_id":"18519"},{"access_level":"closed","relation":"source_file","file_size":41198857,"file_name":"PhD Thesis- Parvathy_071124.zip","checksum":"4417e02d54084d89e75734e18caaa96d","file_id":"18520","creator":"psurendr","date_created":"2024-11-07T10:59:42Z","date_updated":"2024-11-07T10:59:42Z","content_type":"application/zip"}],"ddc":["576"],"title":"Effect of population structure on neutral genetic variation and barriers to gene exchange","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","year":"2024","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"date_updated":"2026-04-07T12:56:52Z","acknowledged_ssus":[{"_id":"ScienComp"}],"_id":"18515","citation":{"ama":"Surendranadh P. Effect of population structure on neutral genetic variation and barriers to gene exchange. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18515\">10.15479/at:ista:18515</a>","chicago":"Surendranadh, Parvathy. “Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18515\">https://doi.org/10.15479/at:ista:18515</a>.","apa":"Surendranadh, P. (2024). <i>Effect of population structure on neutral genetic variation and barriers to gene exchange</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18515\">https://doi.org/10.15479/at:ista:18515</a>","ieee":"P. Surendranadh, “Effect of population structure on neutral genetic variation and barriers to gene exchange,” Institute of Science and Technology Austria, 2024.","short":"P. Surendranadh, Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange, Institute of Science and Technology Austria, 2024.","mla":"Surendranadh, Parvathy. <i>Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18515\">10.15479/at:ista:18515</a>.","ista":"Surendranadh P. 2024. Effect of population structure on neutral genetic variation and barriers to gene exchange. Institute of Science and Technology Austria."},"publication_identifier":{"issn":["2663-337X"]},"status":"public","oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"date_published":"2024-11-07T00:00:00Z","project":[{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"}],"OA_type":"gold","oa":1,"alternative_title":["ISTA Thesis"],"corr_author":"1","acknowledgement":"I also acknowledge the funding agencies Marie Curie COFUND Doctoral Fellowship,\r\nAustrian Science Fund FWF (grant P32166) and ERC (grant PR1000ERC02) for financially\r\nsupporting my research over the years.","author":[{"first_name":"Parvathy","full_name":"Surendranadh, Parvathy","last_name":"Surendranadh","orcid":"0000-0001-6395-386X","id":"455235B8-F248-11E8-B48F-1D18A9856A87"}],"page":"219","file_date_updated":"2024-11-07T10:59:42Z","month":"11","doi":"10.15479/at:ista:18515","has_accepted_license":"1","OA_place":"publisher","language":[{"iso":"eng"}],"article_processing_charge":"No","day":"07"},{"department":[{"_id":"NiBa"}],"oa_version":"Published Version","quality_controlled":"1","status":"public","external_id":{"isi":["001206532900001"],"pmid":["39479507"]},"date_published":"2024-04-23T00:00:00Z","oa":1,"OA_type":"gold","isi":1,"intvolume":"         8","author":[{"first_name":"Alan","full_name":"Le Moan, Alan","last_name":"Le Moan"},{"last_name":"Stankowski","full_name":"Stankowski, Sean","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"first_name":"Olga","full_name":"Ortega-Martinez, Olga","last_name":"Ortega-Martinez"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"last_name":"Butlin","full_name":"Butlin, Roger K","first_name":"Roger K"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"}],"acknowledgement":"The computations and data handling were enabled by resources provided by the Swedish National Infrastructure for Computing at UPPMAX partially funded by the Swedish Research Council through grant agreement no. 2018-05973. We thank all the member of the Littorina team for the stimulating discussions about the manuscripts, James Reeves for his help the implementation of Hsplit, and Thomas Broquet for his useful comments in the latter stage of manuscript revisions.","page":"575-586","file_date_updated":"2025-01-27T13:33:14Z","month":"04","doi":"10.1093/evlett/qrae014","has_accepted_license":"1","issue":"4","OA_place":"publisher","language":[{"iso":"eng"}],"article_processing_charge":"Yes","scopus_import":"1","day":"23","abstract":[{"text":"Chromosomal rearrangements can lead to the coupling of reproductive barriers, but whether and how they contribute to the completion of speciation remains unclear. Marine snails of the genus Littorina repeatedly form hybrid zones between populations segregating for multiple inversion arrangements, providing opportunities to study their barrier effects. Here, we analyzed 2 adjacent transects across hybrid zones between 2 ecotypes of Littorina fabalis (“large” and “dwarf”) adapted to different wave exposure conditions on a Swedish island. Applying whole-genome sequencing, we found 12 putative inversions on 9 of 17 chromosomes. Nine of the putative inversions reached near differential fixation between the 2 ecotypes, and all were in strong linkage disequilibrium. These inversions cover 20% of the genome and carry 93% of divergent single nucleotide polymorphisms (SNPs). Bimodal hybrid zones in both transects indicated that the 2 ecotypes of Littorina fabalis maintain their genetic and phenotypic integrity following contact. The bimodality reflects the strong coupling between inversion clines and the extension of the barrier effect across the whole genome. Demographic inference suggests that coupling arose during a period of allopatry and has been maintained for &amp;gt; 1,000 generations after secondary contact. Overall, this study shows that the coupling of multiple chromosomal inversions contributes to strong reproductive isolation. Notably, 2 of the putative inversions overlap with inverted genomic regions associated with ecotype differences in a closely related species (Littorina saxatilis), suggesting the same regions, with similar structural variants, repeatedly contribute to ecotype evolution in distinct species.","lang":"eng"}],"publication_status":"published","article_type":"letter_note","publication":"Evolution Letters","volume":8,"date_created":"2025-01-27T13:30:27Z","type":"journal_article","ddc":["570"],"file":[{"date_updated":"2025-01-27T13:33:14Z","date_created":"2025-01-27T13:33:14Z","content_type":"application/pdf","creator":"dernst","file_name":"2024_EvolutionLetter_Moan.pdf","checksum":"2f7780b7b6b3489755f1815f476639c6","file_id":"18909","access_level":"open_access","relation":"main_file","success":1,"file_size":24356661}],"tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"publisher":"Oxford University Press","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes","license":"https://creativecommons.org/licenses/by-nc/4.0/","year":"2024","pmid":1,"date_updated":"2025-09-09T12:05:51Z","_id":"18908","citation":{"ama":"Le Moan A, Stankowski S, Rafajlović M, et al. Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes. <i>Evolution Letters</i>. 2024;8(4):575-586. doi:<a href=\"https://doi.org/10.1093/evlett/qrae014\">10.1093/evlett/qrae014</a>","short":"A. Le Moan, S. Stankowski, M. Rafajlović, O. Ortega-Martinez, R. Faria, R.K. Butlin, K. Johannesson, Evolution Letters 8 (2024) 575–586.","ieee":"A. Le Moan <i>et al.</i>, “Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes,” <i>Evolution Letters</i>, vol. 8, no. 4. Oxford University Press, pp. 575–586, 2024.","ista":"Le Moan A, Stankowski S, Rafajlović M, Ortega-Martinez O, Faria R, Butlin RK, Johannesson K. 2024. Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes. Evolution Letters. 8(4), 575–586.","mla":"Le Moan, Alan, et al. “Coupling of Twelve Putative Chromosomal Inversions Maintains a Strong Barrier to Gene Flow between Snail Ecotypes.” <i>Evolution Letters</i>, vol. 8, no. 4, Oxford University Press, 2024, pp. 575–86, doi:<a href=\"https://doi.org/10.1093/evlett/qrae014\">10.1093/evlett/qrae014</a>.","chicago":"Le Moan, Alan, Sean Stankowski, Marina Rafajlović, Olga Ortega-Martinez, Rui Faria, Roger K Butlin, and Kerstin Johannesson. “Coupling of Twelve Putative Chromosomal Inversions Maintains a Strong Barrier to Gene Flow between Snail Ecotypes.” <i>Evolution Letters</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/evlett/qrae014\">https://doi.org/10.1093/evlett/qrae014</a>.","apa":"Le Moan, A., Stankowski, S., Rafajlović, M., Ortega-Martinez, O., Faria, R., Butlin, R. K., &#38; Johannesson, K. (2024). Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes. <i>Evolution Letters</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evlett/qrae014\">https://doi.org/10.1093/evlett/qrae014</a>"},"publication_identifier":{"issn":["2056-3744"]}},{"OA_place":"repository","day":"25","main_file_link":[{"open_access":"1","url":"https://inria.hal.science/hal-04624490/"}],"scopus_import":"1","language":[{"iso":"eng"}],"article_processing_charge":"No","month":"07","doi":"10.3354/meps14640","intvolume":"       740","page":"23-42","corr_author":"1","author":[{"id":"1676e173-8143-11ed-8927-fe165216a93f","first_name":"Louise","orcid":"0000-0003-0371-9339","last_name":"Fouqueau","full_name":"Fouqueau, Louise"},{"first_name":"L","last_name":"Reynes","full_name":"Reynes, L"},{"last_name":"Tempera","full_name":"Tempera, F","first_name":"F"},{"full_name":"Bajjouk, T","last_name":"Bajjouk","first_name":"T"},{"last_name":"Blanfuné","full_name":"Blanfuné, A","first_name":"A"},{"first_name":"C","last_name":"Chevalier","full_name":"Chevalier, C"},{"full_name":"Laurans, M","last_name":"Laurans","first_name":"M"},{"full_name":"Mauger, S","last_name":"Mauger","first_name":"S"},{"last_name":"Sourisseau","full_name":"Sourisseau, M","first_name":"M"},{"first_name":"J","last_name":"Assis","full_name":"Assis, J"},{"last_name":"Lévêque","full_name":"Lévêque, L","first_name":"L"},{"first_name":"M","last_name":"Valero","full_name":"Valero, M"}],"status":"public","quality_controlled":"1","oa_version":"Submitted Version","department":[{"_id":"NiBa"}],"OA_type":"green","oa":1,"date_published":"2024-07-25T00:00:00Z","_id":"18944","date_updated":"2025-01-29T09:12:34Z","publication_identifier":{"issn":["0171-8630"],"eissn":["1616-1599"]},"citation":{"short":"L. Fouqueau, L. Reynes, F. Tempera, T. Bajjouk, A. Blanfuné, C. Chevalier, M. Laurans, S. Mauger, M. Sourisseau, J. Assis, L. Lévêque, M. Valero, Marine Ecology Progress Series 740 (2024) 23–42.","ieee":"L. Fouqueau <i>et al.</i>, “Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes,” <i>Marine Ecology Progress Series</i>, vol. 740. Inter-Research Science Center, pp. 23–42, 2024.","ista":"Fouqueau L, Reynes L, Tempera F, Bajjouk T, Blanfuné A, Chevalier C, Laurans M, Mauger S, Sourisseau M, Assis J, Lévêque L, Valero M. 2024. Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes. Marine Ecology Progress Series. 740, 23–42.","mla":"Fouqueau, Louise, et al. “Seascape Genetic Study on Laminaria Digitata Underscores the Critical Role of Sampling Schemes.” <i>Marine Ecology Progress Series</i>, vol. 740, Inter-Research Science Center, 2024, pp. 23–42, doi:<a href=\"https://doi.org/10.3354/meps14640\">10.3354/meps14640</a>.","chicago":"Fouqueau, Louise, L Reynes, F Tempera, T Bajjouk, A Blanfuné, C Chevalier, M Laurans, et al. “Seascape Genetic Study on Laminaria Digitata Underscores the Critical Role of Sampling Schemes.” <i>Marine Ecology Progress Series</i>. Inter-Research Science Center, 2024. <a href=\"https://doi.org/10.3354/meps14640\">https://doi.org/10.3354/meps14640</a>.","apa":"Fouqueau, L., Reynes, L., Tempera, F., Bajjouk, T., Blanfuné, A., Chevalier, C., … Valero, M. (2024). Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes. <i>Marine Ecology Progress Series</i>. Inter-Research Science Center. <a href=\"https://doi.org/10.3354/meps14640\">https://doi.org/10.3354/meps14640</a>","ama":"Fouqueau L, Reynes L, Tempera F, et al. Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes. <i>Marine Ecology Progress Series</i>. 2024;740:23-42. doi:<a href=\"https://doi.org/10.3354/meps14640\">10.3354/meps14640</a>"},"title":"Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Inter-Research Science Center","year":"2024","type":"journal_article","date_created":"2025-01-29T09:09:10Z","publication_status":"published","article_type":"original","abstract":[{"text":"Understanding connectivity patterns exhibited by endangered species living in fragmented habitats is fundamental to improving management and conservation actions. Such improvements can be particularly pressing at the trailing edges of these habitats, where populations are facing the greatest challenges from climate change, and appear even more crucial if the species is commercially harvested. Seascape genetics have been increasingly used to meet these needs. In this study, we examined connectivity patterns among 32 populations of the oarweed kelp <jats:italic>Lam</jats:italic><jats:italic>inaria digitata</jats:italic> located at the species’ southern range limit. The distance (or sampling gap) between neighboring populations ranged from a few km to a few 100s of km. By genotyping 11 microsatellite markers, we aimed to (1) refine analyses of population structure; (2) test whether on-shelf islands are genetically more differentiated than mainland populations; (3) evaluate the relative importance of various abiotic conditions in shaping the genetic structure; and (4) evaluate if the relative importance of each environmental factor varied according to sampling schemes. Our analyses revealed a positive relationship between connectivity links and genetic diversity: populations with high levels of connectivity were genetically enriched while isolated populations showed signs of genetic erosion. The genetically impoverished populations corresponded to the southernmost populations as well as populations along the northern coast of Brittany (Locquirec, Saint-Malo Bay) and the northernmost population in Pas-de-Calais. By performing distance-based redundancy analysis on various sampling schemes, geographic distance appeared as the dominant factor influencing connectivity between populations separated by great distances, while hydrodynamic processes were the main factor when analyzing at a final spatial resolution.","lang":"eng"}],"volume":740,"publication":"Marine Ecology Progress Series"},{"type":"journal_article","date_created":"2025-01-29T10:38:17Z","ddc":["570"],"file":[{"creator":"dernst","date_updated":"2025-01-29T10:52:40Z","date_created":"2025-01-29T10:52:40Z","content_type":"application/pdf","access_level":"open_access","file_size":3935454,"success":1,"relation":"main_file","checksum":"db08120a92527acaef476bd93f2b87f9","file_name":"2024_EvolJourLinneanSoc_Stankowski.pdf","file_id":"18950"}],"tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"article_type":"original","publication_status":"published","article_number":"kzae001","abstract":[{"text":"Speciation research—the scientific field focused on understanding the origin and diversity of species—has a long and complex history. While relevant to one another, the specific goals and activities of speciation researchers are highly diverse, and scattered across a collection of different perspectives. Thus, our understanding of speciation will benefit from efforts to bridge scientific findings and the diverse people who do the work. In this paper, we outline two ways of integrating speciation research: (i) scientific integration, through the bringing together of ideas, data, and approaches; and (ii) social integration, by creating ways for a diversity of researchers to participate in the scientific process. We then discuss five challenges to integration: (i) the multidisciplinary nature of speciation research, (ii) the complex language of speciation; (iii) a bias toward certain study systems; (iv) the challenges of working across scales; and (v) inconsistent measures and reporting standards. We provide practical steps that individuals and groups can take to help overcome these challenges, and argue that integration is a team effort in which we all have a role to play.","lang":"eng"}],"volume":3,"publication":"Evolutionary Journal of the Linnean Society","_id":"18949","date_updated":"2025-01-29T10:55:54Z","publication_identifier":{"issn":["2752-938X"]},"citation":{"apa":"Stankowski, S., Cutter, A. D., Satokangas, I., Lerch, B. A., Rolland, J., Smadja, C. M., … Kulmuni, J. (2024). Toward the integration of speciation research. <i>Evolutionary Journal of the Linnean Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolinnean/kzae001\">https://doi.org/10.1093/evolinnean/kzae001</a>","chicago":"Stankowski, Sean, Asher D Cutter, Ina Satokangas, Brian A Lerch, Jonathan Rolland, Carole M Smadja, J Carolina Segami Marzal, et al. “Toward the Integration of Speciation Research.” <i>Evolutionary Journal of the Linnean Society</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/evolinnean/kzae001\">https://doi.org/10.1093/evolinnean/kzae001</a>.","mla":"Stankowski, Sean, et al. “Toward the Integration of Speciation Research.” <i>Evolutionary Journal of the Linnean Society</i>, vol. 3, no. 1, kzae001, Oxford University Press, 2024, doi:<a href=\"https://doi.org/10.1093/evolinnean/kzae001\">10.1093/evolinnean/kzae001</a>.","ista":"Stankowski S, Cutter AD, Satokangas I, Lerch BA, Rolland J, Smadja CM, Segami Marzal JC, Cooney CR, Feulner PGD, Domingos FMCB, North HL, Yamaguchi R, Butlin RK, Wolf JBW, Coughlan J, Heidbreder P, Hernández-Gutiérrez R, Barnard-Kubow KB, Peede D, Rancilhac L, Salvador RB, Thompson KA, Stacy EA, Moyle LC, Garlovsky MD, Maulana A, Kantelinen A, Cacho NI, Schneemann H, Domínguez M, Dopman EB, Lohse K, Rometsch SJ, Comeault AA, Merrill RM, Scordato ESC, Singhal S, Pärssinen V, Lackey ACR, Kumar S, Meier JI, Barton NH, Fraisse C, Ravinet M, Kulmuni J. 2024. Toward the integration of speciation research. Evolutionary Journal of the Linnean Society. 3(1), kzae001.","short":"S. Stankowski, A.D. Cutter, I. Satokangas, B.A. Lerch, J. Rolland, C.M. Smadja, J.C. Segami Marzal, C.R. Cooney, P.G.D. Feulner, F.M.C.B. Domingos, H.L. North, R. Yamaguchi, R.K. Butlin, J.B.W. Wolf, J. Coughlan, P. Heidbreder, R. Hernández-Gutiérrez, K.B. Barnard-Kubow, D. Peede, L. Rancilhac, R.B. Salvador, K.A. Thompson, E.A. Stacy, L.C. Moyle, M.D. Garlovsky, A. Maulana, A. Kantelinen, N.I. Cacho, H. Schneemann, M. Domínguez, E.B. Dopman, K. Lohse, S.J. Rometsch, A.A. Comeault, R.M. Merrill, E.S.C. Scordato, S. Singhal, V. Pärssinen, A.C.R. Lackey, S. Kumar, J.I. Meier, N.H. Barton, C. Fraisse, M. Ravinet, J. Kulmuni, Evolutionary Journal of the Linnean Society 3 (2024).","ieee":"S. Stankowski <i>et al.</i>, “Toward the integration of speciation research,” <i>Evolutionary Journal of the Linnean Society</i>, vol. 3, no. 1. Oxford University Press, 2024.","ama":"Stankowski S, Cutter AD, Satokangas I, et al. Toward the integration of speciation research. <i>Evolutionary Journal of the Linnean Society</i>. 2024;3(1). doi:<a href=\"https://doi.org/10.1093/evolinnean/kzae001\">10.1093/evolinnean/kzae001</a>"},"publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Toward the integration of speciation research","year":"2024","intvolume":"         3","author":[{"last_name":"Stankowski","full_name":"Stankowski, Sean","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"first_name":"Asher D","full_name":"Cutter, Asher D","last_name":"Cutter"},{"last_name":"Satokangas","full_name":"Satokangas, Ina","first_name":"Ina"},{"first_name":"Brian A","last_name":"Lerch","full_name":"Lerch, Brian A"},{"last_name":"Rolland","full_name":"Rolland, Jonathan","first_name":"Jonathan"},{"full_name":"Smadja, Carole M","last_name":"Smadja","first_name":"Carole M"},{"first_name":"J Carolina","last_name":"Segami Marzal","full_name":"Segami Marzal, J Carolina"},{"last_name":"Cooney","full_name":"Cooney, Christopher R","first_name":"Christopher R"},{"last_name":"Feulner","full_name":"Feulner, Philine G D","first_name":"Philine G D"},{"last_name":"Domingos","full_name":"Domingos, Fabricius Maia Chaves Bicalho","first_name":"Fabricius Maia Chaves Bicalho"},{"first_name":"Henry L","full_name":"North, Henry L","last_name":"North"},{"full_name":"Yamaguchi, Ryo","last_name":"Yamaguchi","first_name":"Ryo"},{"full_name":"Butlin, Roger K","last_name":"Butlin","first_name":"Roger K"},{"first_name":"Jochen B W","last_name":"Wolf","full_name":"Wolf, Jochen B W"},{"first_name":"Jenn","last_name":"Coughlan","full_name":"Coughlan, Jenn"},{"full_name":"Heidbreder, Patrick","last_name":"Heidbreder","first_name":"Patrick"},{"first_name":"Rebeca","last_name":"Hernández-Gutiérrez","full_name":"Hernández-Gutiérrez, Rebeca"},{"first_name":"Karen B","last_name":"Barnard-Kubow","full_name":"Barnard-Kubow, Karen B"},{"first_name":"David","full_name":"Peede, David","last_name":"Peede"},{"last_name":"Rancilhac","full_name":"Rancilhac, Loïs","first_name":"Loïs"},{"last_name":"Salvador","full_name":"Salvador, Rodrigo Brincalepe","first_name":"Rodrigo Brincalepe"},{"first_name":"Ken A","last_name":"Thompson","full_name":"Thompson, Ken A"},{"first_name":"Elizabeth A","full_name":"Stacy, Elizabeth A","last_name":"Stacy"},{"last_name":"Moyle","full_name":"Moyle, Leonie C","first_name":"Leonie C"},{"full_name":"Garlovsky, Martin D","last_name":"Garlovsky","first_name":"Martin D"},{"first_name":"Arif","full_name":"Maulana, Arif","last_name":"Maulana"},{"first_name":"Annina","last_name":"Kantelinen","full_name":"Kantelinen, Annina"},{"first_name":"N Ivalú","last_name":"Cacho","full_name":"Cacho, N Ivalú"},{"full_name":"Schneemann, Hilde","last_name":"Schneemann","first_name":"Hilde"},{"full_name":"Domínguez, Marisol","last_name":"Domínguez","first_name":"Marisol"},{"last_name":"Dopman","full_name":"Dopman, Erik B","first_name":"Erik B"},{"first_name":"Konrad","last_name":"Lohse","full_name":"Lohse, Konrad"},{"full_name":"Rometsch, Sina J","last_name":"Rometsch","first_name":"Sina J"},{"last_name":"Comeault","full_name":"Comeault, Aaron A","first_name":"Aaron A"},{"first_name":"Richard M","full_name":"Merrill, Richard M","last_name":"Merrill"},{"last_name":"Scordato","full_name":"Scordato, Elizabeth S C","first_name":"Elizabeth S C"},{"first_name":"Sonal","full_name":"Singhal, Sonal","last_name":"Singhal"},{"first_name":"Varpu","last_name":"Pärssinen","full_name":"Pärssinen, Varpu"},{"full_name":"Lackey, Alycia C R","last_name":"Lackey","first_name":"Alycia C R"},{"first_name":"Sanghamitra","last_name":"Kumar","full_name":"Kumar, Sanghamitra"},{"first_name":"Joana I","full_name":"Meier, Joana I","last_name":"Meier"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"},{"last_name":"Kulmuni","full_name":"Kulmuni, Jonna","first_name":"Jonna"}],"corr_author":"1","acknowledgement":"We thank the staff of the Tvärminne Zoological Station (University of Helsinki) for their hospitality during the workshop. We are also grateful to everyone who applied to attend the workshop.\r\nFunding for the workshop was provided by the European Society for Evolutionary Biology through the Special Topic Network (STN) funding scheme.","oa_version":"Published Version","department":[{"_id":"NiBa"}],"quality_controlled":"1","status":"public","oa":1,"OA_type":"gold","date_published":"2024-02-16T00:00:00Z","issue":"1","OA_place":"publisher","has_accepted_license":"1","day":"16","language":[{"iso":"eng"}],"article_processing_charge":"Yes","scopus_import":"1","month":"02","file_date_updated":"2025-01-29T10:52:40Z","doi":"10.1093/evolinnean/kzae001"},{"year":"2024","doi":"10.1101/2024.09.20.614050","month":"09","title":"Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"27","main_file_link":[{"url":"https://doi.org/10.1101/2024.09.20.614050","open_access":"1"}],"citation":{"apa":"Vijatovic, D., Toma, F. A., Harrington, Z. P., Sommer, C. M., Hauschild, R., Trevisan, A. J., … Sweeney, L. B. (n.d.). Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.09.20.614050\">https://doi.org/10.1101/2024.09.20.614050</a>","chicago":"Vijatovic, David, Florina Alexandra  Toma, Zoe P Harrington, Christoph M Sommer, Robert Hauschild, Alexandra J. Trevisan, Phillip Chapman, et al. “Spinal Neuron Diversity Scales Exponentially with Swim-to-Limb Transformation during Frog Metamorphosis.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.09.20.614050\">https://doi.org/10.1101/2024.09.20.614050</a>.","ista":"Vijatovic D, Toma FA, Harrington ZP, Sommer CM, Hauschild R, Trevisan AJ, Chapman P, Julseth M, Brenner-Morton S, Gabitto MI, Dasen JS, Bikoff JB, Sweeney LB. Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis. bioRxiv, <a href=\"https://doi.org/10.1101/2024.09.20.614050\">10.1101/2024.09.20.614050</a>.","mla":"Vijatovic, David, et al. “Spinal Neuron Diversity Scales Exponentially with Swim-to-Limb Transformation during Frog Metamorphosis.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.09.20.614050\">10.1101/2024.09.20.614050</a>.","ieee":"D. Vijatovic <i>et al.</i>, “Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis,” <i>bioRxiv</i>. .","short":"D. Vijatovic, F.A. Toma, Z.P. Harrington, C.M. Sommer, R. Hauschild, A.J. Trevisan, P. Chapman, M. Julseth, S. Brenner-Morton, M.I. Gabitto, J.S. Dasen, J.B. Bikoff, L.B. Sweeney, BioRxiv (n.d.).","ama":"Vijatovic D, Toma FA, Harrington ZP, et al. Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.09.20.614050\">10.1101/2024.09.20.614050</a>"},"language":[{"iso":"eng"}],"article_processing_charge":"No","OA_place":"repository","acknowledged_ssus":[{"_id":"Bio"}],"_id":"19520","date_updated":"2025-05-14T11:40:13Z","oa":1,"OA_type":"green","date_published":"2024-09-27T00:00:00Z","publication":"bioRxiv","project":[{"name":"Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis","_id":"bd73af52-d553-11ed-ba76-912049f0ac7a","grant_number":"FTI21-D-046"},{"name":"Development and Evolution of Tetrapod Motor Circuits","_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae","grant_number":"101041551"},{"_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473","name":"Tools for automation and feedback microscopy","grant_number":"CZI01"}],"publication_status":"submitted","status":"public","oa_version":"Preprint","abstract":[{"text":"Vertebrates exhibit a wide range of motor behaviors, ranging from swimming to complex limb-based movements. Here we take advantage of frog metamorphosis, which captures a swim-to-limb-based movement transformation during the development of a single organism, to explore changes in the underlying spinal circuits. We find that the tadpole spinal cord contains small and largely homogeneous populations of motor neurons (MNs) and V1 interneurons (V1s) at early escape swimming stages. These neuronal populations only modestly increase in number and subtype heterogeneity with the emergence of free swimming. In contrast, during frog metamorphosis and the emergence of limb movement, there is a dramatic expansion of MN and V1 interneuron number and transcriptional heterogeneity, culminating in cohorts of neurons that exhibit striking molecular similarity to mammalian motor circuits. CRISPR/Cas9-mediated gene disruption of the limb MN and V1 determinants FoxP1 and Engrailed-1, respectively, results in severe but selective deficits in tail and limb function. Our work thus demonstrates that neural diversity scales exponentially with increasing behavioral complexity and illustrates striking evolutionary conservation in the molecular organization and function of motor circuits across species.","lang":"eng"}],"department":[{"_id":"LoSw"},{"_id":"TiVo"},{"_id":"Bio"},{"_id":"NiBa"}],"corr_author":"1","acknowledgement":"We would like to thank the members of the Sweeney Lab (especially Stavros Papadopoulos and\r\nSophie Gobeil) for their contributions to this project and, in addition to the lab, Graziana Gatto\r\nand Mario de Bono, for discussion, and support. We are also grateful to Tom Jessell and Chris\r\nKintner for their scientific insight and mentorship during the conception of this project. This\r\nproject would also not have been possible with the technical support of the Matthias Nowak,\r\nVerena Mayer and the Aquatics as well as the Imaging and Optics Facility support teams\r\n(ISTA). In addition, we thank our funding sources for providing the resources to do these\r\nexperiments: FTI Strategy Lower Austria Dissertation Grant Number FT121-D-046 (D.V.);\r\nHorizon Europe ERC Starting Grant Number 101041551 (L.B.S., F.A.T. and D.V); Special\r\nResearch Program (SFB) of the Austrian Science Fund (FWF) Project number F7814-B (L.B.S);\r\nNINDS 5R35NS116858 (J.S.D); CZI grant DAF2020-225401 (DOI): 10.37921/120055ratwvi\r\n(R.H.); NIH grant number R01NS123116 (J.B.B); American Lebanese Syrian Associated\r\nCharities (ALSAC) (J.B.B.); German Academic Exchange Service (DAAD) IFI Grant Number\r\n57515251-91853472 (Z.H.); and Project A.L.S. (S.B-M.). ","author":[{"id":"cf391e77-ec3c-11ea-a124-d69323410b58","first_name":"David","full_name":"Vijatovic, David","last_name":"Vijatovic"},{"id":"2f73f876-f128-11eb-9611-b96b5a30cb0e","first_name":"Florina Alexandra ","full_name":"Toma, Florina Alexandra ","last_name":"Toma"},{"first_name":"Zoe P","full_name":"Harrington, Zoe P","last_name":"Harrington","orcid":"0009-0008-0158-4032","id":"a8144562-32c9-11ee-b5ce-d9800628bda2"},{"first_name":"Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522","first_name":"Robert"},{"full_name":"Trevisan, Alexandra J.","last_name":"Trevisan","first_name":"Alexandra J."},{"first_name":"Phillip","last_name":"Chapman","full_name":"Chapman, Phillip"},{"first_name":"Mara","last_name":"Julseth","full_name":"Julseth, Mara","id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1"},{"first_name":"Susan","last_name":"Brenner-Morton","full_name":"Brenner-Morton, Susan"},{"first_name":"Mariano I.","last_name":"Gabitto","full_name":"Gabitto, Mariano I."},{"full_name":"Dasen, Jeremy S.","last_name":"Dasen","first_name":"Jeremy S."},{"full_name":"Bikoff, Jay B.","last_name":"Bikoff","first_name":"Jay B."},{"id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","orcid":"0000-0001-9242-5601","last_name":"Sweeney","full_name":"Sweeney, Lora Beatrice Jaeger","first_name":"Lora Beatrice Jaeger"}],"type":"preprint","date_created":"2025-04-07T08:48:28Z"}]