[{"acknowledgement":"I acknowledge the funding agencies 1Norwegian Research Council RCN project 315287.\r\n2The FIASCO project \"Illuminating range shifts through evolutionary FIASCO: contrasting\r\nFaIling And Successful ColOnizations in replicated wild populations\", funded by the\r\nEuropean Union - Next Generation EU (Piano Nazionale di Ripresa e Resilienza - MUR\r\ncode: P202229JBC, CUP: C53D23007100001). 3Ecotypic formation in Littorina saxatilis\r\nin the Western Atlantic and comparisons across the North Atlantic. University of\r\nGothenburg Research Travel Grant, Tjarno Marine Laboratory, Sweden. $3023 (2018).\r\n4JIN project (Young Researchers, Spanish Ministry of Science, RTI2018-101274-J-I00)","language":[{"iso":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","OA_place":"publisher","year":"2026","publisher":"Institute of Science and Technology Austria","status":"public","citation":{"ama":"Garcia Castillo DF. The genomic architecture of local adaptation in introduced populations. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20991\">10.15479/AT-ISTA-20991</a>","mla":"Garcia Castillo, Diego Fernando. <i>The Genomic Architecture of Local Adaptation in Introduced Populations</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20991\">10.15479/AT-ISTA-20991</a>.","ieee":"D. F. Garcia Castillo, “The genomic architecture of local adaptation in introduced populations,” Institute of Science and Technology Austria, 2026.","short":"D.F. Garcia Castillo, The Genomic Architecture of Local Adaptation in Introduced Populations, Institute of Science and Technology Austria, 2026.","apa":"Garcia Castillo, D. F. (2026). <i>The genomic architecture of local adaptation in introduced populations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20991\">https://doi.org/10.15479/AT-ISTA-20991</a>","ista":"Garcia Castillo DF. 2026. The genomic architecture of local adaptation in introduced populations. Institute of Science and Technology Austria.","chicago":"Garcia Castillo, Diego Fernando. “The Genomic Architecture of Local Adaptation in Introduced Populations.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-20991\">https://doi.org/10.15479/AT-ISTA-20991</a>."},"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"page":"199","author":[{"last_name":"Garcia Castillo","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","first_name":"Diego Fernando","full_name":"Garcia Castillo, Diego Fernando"}],"_id":"20991","related_material":{"record":[{"id":"18498","relation":"research_data","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"18491"}]},"date_created":"2026-01-16T09:47:59Z","tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"day":"16","corr_author":"1","file":[{"checksum":"841f1bc073d667125729b2a017f8c37a","access_level":"closed","file_size":22456421,"relation":"source_file","date_created":"2026-01-16T12:25:13Z","creator":"dgarciac","date_updated":"2026-01-16T12:25:13Z","file_id":"20996","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"2026_Garcia_Diego_Thesis.docx"},{"success":1,"file_size":9556719,"access_level":"open_access","relation":"main_file","checksum":"a1f33d4f183ce7072eee42a6ccf5340b","file_name":"2026_Garcia_Diego_Thesis.pdf","file_id":"20997","content_type":"application/pdf","date_updated":"2026-01-16T12:25:13Z","date_created":"2026-01-16T12:25:13Z","creator":"dgarciac"},{"creator":"dgarciac","date_created":"2026-01-16T13:08:14Z","description":"Source code of the PostgreSQL database, front-end and back-end of the LittorinaDB web application developed as a product of the 4th chapter of the thesis.","date_updated":"2026-01-16T13:08:14Z","file_name":"2026_DiegoGarcia_LittorinaDB Source Code and Protocols.rar","file_id":"20998","content_type":"application/x-compressed","access_level":"closed","file_size":54491433,"relation":"supplementary_material","checksum":"98a80691067174c30fe53f38ce7344e6"},{"content_type":"application/x-compressed","file_id":"20999","file_name":"2026_DiegoGarcia_Thesis-Supplementary_Material.rar","date_updated":"2026-01-16T13:08:14Z","date_created":"2026-01-16T13:08:14Z","creator":"dgarciac","checksum":"99a3cab2fa36666b9a92eefc27d586da","file_size":7982811,"access_level":"open_access","relation":"supplementary_material"},{"file_id":"21000","file_name":"README.txt","content_type":"text/plain","date_updated":"2026-01-16T13:08:59Z","creator":"dgarciac","date_created":"2026-01-16T13:08:59Z","checksum":"255fdf56b2932c46bf27c63aa6106a4f","file_size":732,"access_level":"open_access","relation":"supplementary_material"}],"month":"01","date_published":"2026-01-16T00:00:00Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-077-0"]},"date_updated":"2026-04-16T12:20:37Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","title":"The genomic architecture of local adaptation in introduced populations","abstract":[{"lang":"eng","text":"Rapid local adaptation to new environments is critical for species persistence, especially in introduced populations. The evolutionary success of these populations is fundamentally dictated by the organization of genetic variation—the genomic architecture—in the face of severe demographic constraints, such as the founder effects and genetic bottlenecks that frequently accompany colonization. A central question in evolutionary biology is whether rapid adaptation relies on major-effect loci, such as chromosomal inversions, or on many small-effect loci dispersed across the genome. Furthermore, the genomic architecture strongly influences the extent to which evolutionary outcomes are predictable. Using introduced populations of the marine snail, Littorina saxatilis, as a model, this thesis investigates how genetic variation and genomic structure drive adaptation following introduction. We employed a population genomics approach on experimentally and accidentally introduced populations to dissect the specific genomic features that underpin divergence in newly colonized environments.\r\n\r\nIn Chapter 2, we tested the predictability of local adaptation through an uncommon 30-year transplant experiment in nature. By distinguishing allele and chromosomal inversion frequency changes from neutral expectations, we found that evolutionary change was highly predictable at the macro-scale (phenotypes and chromosomal inversions), but less robust at the level of individual collinear loci. This result demonstrates that evolution can be predictable when a population possesses sufficient standing genetic variation (SGV), with chromosomal inversions acting as key integrated units that facilitate a rapid response to selection. Building on this, Chapter 3 applied whole-genome sequencing to three accidentally introduced populations (Venice, San Francisco, and Redwood City) to investigate their likely source and genomic patterns of divergence. We identified genomic regions of remarkable divergence potentially associated with local adaptation, and likely fuelled by SGV, while explicitly acknowledging the difficulty in disentangling selection signals from the genome-wide effects of demographic processes. Furthermore, we found that the divergence patterns relied extensively on the collinear genome in these introduced populations, and less clearly on the chromosomal inversions. This observation contrasts with local adaptation observed in the experimental system that relied on both collinear loci and highly selected chromosomal inversions, highlighting how demographic history and genomic architecture influence the detectable signature of local adaptation.\r\n\r\nA major limitation to conducting large-scale comparative evolutionary studies is the lack of data standardization, which prevents the integration of community knowledge and high-resolution environmental and genetic data. Chapter 4 addresses this by developing a community database for the Littorina system. This platform implements standardized protocols for the integration of diverse phenotypic and environmental data from multiple Littorina species. Likewise, the platform also centralizes the availability of associated genomic data through links to external repositories. This database represents a crucial tool to test complex, large-scale evolutionary hypotheses.\r\n\r\nCollectively, this thesis strongly reinforces the fundamental importance of SGV as the raw material for successful local adaptation, a conclusion supported by evidence in both experimental and accidental introductions. Furthermore, this work highlights the critical role of the genomic architecture—specifically chromosomal inversions—in driving the predictability and effectiveness of adaptive responses. Our findings underscore how the interplay between SGV and genomic architecture dictates the trajectory and detectability of evolution in colonizing populations, while simultaneously providing a necessary tool to advance comparative evolutionary genomics in emerging model organisms."}],"oa":1,"ddc":["576"],"alternative_title":["ISTA Thesis"],"supervisor":[{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","first_name":"Anja M"}],"type":"dissertation","degree_awarded":"PhD","oa_version":"Published Version","doi":"10.15479/AT-ISTA-20991","file_date_updated":"2026-01-16T13:08:59Z","publication_status":"published","has_accepted_license":"1"},{"title":"How epistasis and purifying selection shape genetic diversity","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-06-12T12:43:35Z","date_published":"2026-06-07T00:00:00Z","month":"06","file":[{"file_name":"thesis.zip","file_id":"21965","content_type":"application/x-zip-compressed","date_updated":"2026-06-09T08:40:48Z","creator":"kkhudiak","date_created":"2026-06-09T08:34:38Z","checksum":"0cff64ae74f0f9f2d7011700c82f700a","file_size":20549813,"relation":"source_file","access_level":"closed"},{"creator":"kkhudiak","date_created":"2026-06-09T12:28:51Z","embargo_to":"open_access","file_id":"21969","file_name":"2026_Khudiakova_Ksenia_Thesis.pdf","content_type":"application/pdf","date_updated":"2026-06-11T12:14:53Z","relation":"main_file","embargo":"2027-06-10","access_level":"closed","file_size":9387029,"checksum":"547ae42de37cc86894af283f1664dbc8"}],"supervisor":[{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"},{"last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","first_name":"Jan","full_name":"Maas, Jan"}],"alternative_title":["ISTA Thesis"],"ddc":["576"],"project":[{"call_identifier":"H2020","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics"},{"grant_number":"26293","_id":"34d33d68-11ca-11ed-8bc3-ec13763c0ca8","name":"The impact of deleterious mutations on small populations"},{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"publication_status":"published","file_date_updated":"2026-06-11T12:14:53Z","doi":"10.15479/AT-ISTA-21918","has_accepted_license":"1","oa_version":"Published Version","degree_awarded":"PhD","type":"dissertation","acknowledged_ssus":[{"_id":"ScienComp"}],"publisher":"Institute of Science and Technology Austria","year":"2026","article_processing_charge":"No","OA_place":"publisher","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"acknowledgement":"At different stages of my PhD, my work was supported by several grants: the\r\nDOC fellowship of the Austrian Academy of Sciences (26293, awarded to me),\r\nthe FWF-SFB grant (PT1032F06504 n. F65, awarded to Jan Maas), and the ERC\r\ngrant (PR1032ERC01 n. 716117, awarded to Jan Maas). I also appreciate the help\r\nfrom the Scientific Computing unit for their advice on the cluster usage.","ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"citation":{"ieee":"K. Khudiakova, “How epistasis and purifying selection shape genetic diversity,” Institute of Science and Technology Austria, 2026.","mla":"Khudiakova, Kseniia. <i>How Epistasis and Purifying Selection Shape Genetic Diversity</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21918\">10.15479/AT-ISTA-21918</a>.","ama":"Khudiakova K. How epistasis and purifying selection shape genetic diversity. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21918\">10.15479/AT-ISTA-21918</a>","chicago":"Khudiakova, Kseniia. “How Epistasis and Purifying Selection Shape Genetic Diversity.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21918\">https://doi.org/10.15479/AT-ISTA-21918</a>.","ista":"Khudiakova K. 2026. How epistasis and purifying selection shape genetic diversity. Institute of Science and Technology Austria.","short":"K. Khudiakova, How Epistasis and Purifying Selection Shape Genetic Diversity, Institute of Science and Technology Austria, 2026.","apa":"Khudiakova, K. (2026). <i>How epistasis and purifying selection shape genetic diversity</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21918\">https://doi.org/10.15479/AT-ISTA-21918</a>"},"status":"public","date_created":"2026-05-27T06:26:08Z","related_material":{"record":[{"id":"11447","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"deleted","id":"12513"},{"id":"21967","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"21968"}]},"_id":"21918","page":"89","author":[{"orcid":"0000-0002-6246-1465","full_name":"Khudiakova, Kseniia","first_name":"Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","last_name":"Khudiakova"}],"corr_author":"1","day":"07","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"}},{"OA_place":"publisher","article_processing_charge":"No","language":[{"iso":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"ScienComp"}],"year":"2025","status":"public","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>","ieee":"A. Pal, “Using genealogies to study the genomic basis of species divergence,” Institute of Science and Technology Austria, 2025.","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>.","short":"A. Pal, Using Genealogies to Study the Genomic Basis of Species Divergence, Institute of Science and Technology Austria, 2025.","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>","ista":"Pal A. 2025. Using genealogies to study the genomic basis of species divergence. Institute of Science and Technology Austria.","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>."},"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"related_material":{"record":[{"id":"12159","status":"public","relation":"part_of_dissertation"},{"id":"14796","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"20190"}]},"date_created":"2025-11-25T13:19:11Z","author":[{"orcid":"0000-0002-4530-8469","full_name":"Pal, Arka","first_name":"Arka","last_name":"Pal","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425"}],"page":"268","_id":"20694","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"day":"25","corr_author":"1","file":[{"content_type":"application/pdf","date_updated":"2026-03-01T23:30:03Z","file_id":"20721","file_name":"2025_Pal_Arka_Thesis.pdf","creator":"apal","date_created":"2025-12-01T13:53:36Z","checksum":"7a10a738d58524aebb5dcbd9b34c21c5","file_size":42723135,"embargo":"2026-03-01","access_level":"open_access","relation":"main_file"},{"embargo_to":"open_access","file_id":"20722","date_updated":"2026-03-01T23:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"2025_Pal_Arka_Thesis.docx","date_created":"2025-12-01T13:53:39Z","creator":"apal","file_size":60632116,"relation":"source_file","access_level":"closed","checksum":"166d832b08d0434ce407f8f3cb930fe5"}],"month":"11","title":"Using genealogies to study the genomic basis of species divergence","date_published":"2025-11-25T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-04-28T13:20:36Z","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."}],"oa":1,"ddc":["576","578"],"project":[{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"},{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation","grant_number":"P32166"}],"alternative_title":["ISTA Thesis"],"supervisor":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"degree_awarded":"PhD","oa_version":"Published Version","type":"dissertation","publication_status":"published","doi":"10.15479/AT-ISTA-20694","file_date_updated":"2026-03-01T23:30:03Z","has_accepted_license":"1"},{"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10787"},{"status":"public","relation":"part_of_dissertation","id":"10658"},{"status":"public","relation":"part_of_dissertation","id":"14732"}]},"date_created":"2023-12-26T22:49:53Z","author":[{"first_name":"Oluwafunmilola O","full_name":"Olusanya, Oluwafunmilola O","orcid":"0000-0003-1971-8314","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","last_name":"Olusanya"}],"page":"183","_id":"14711","day":"19","corr_author":"1","tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"acknowledged_ssus":[{"_id":"SSU"}],"year":"2024","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","OA_place":"publisher","language":[{"iso":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ec_funded":1,"department":[{"_id":"NiBa"},{"_id":"GradSch"}],"status":"public","citation":{"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>","short":"O.O. Olusanya, Local Adaptation, Genetic Load and Extinction in Metapopulations, Institute of Science and Technology Austria, 2024.","chicago":"Olusanya, Oluwafunmilola O. “Local Adaptation, Genetic Load and Extinction in Metapopulations.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:14711\">https://doi.org/10.15479/at:ista:14711</a>.","ista":"Olusanya OO. 2024. Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria.","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>","ieee":"O. O. Olusanya, “Local adaptation, genetic load and extinction in metapopulations,” Institute of Science and Technology Austria, 2024.","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>."},"alternative_title":["ISTA Thesis"],"supervisor":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jitka","full_name":"Polechova, Jitka","last_name":"Polechova"},{"last_name":"Sachdeva","full_name":"Sachdeva, Himani","first_name":"Himani"}],"ddc":["576"],"project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"},{"_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","name":"Causes and consequences of population fragmentation","grant_number":"P32896"},{"grant_number":"26380","name":"Polygenic Adaptation in a Metapopulation","_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6"}],"has_accepted_license":"1","file_date_updated":"2024-01-03T18:31:34Z","publication_status":"published","doi":"10.15479/at:ista:14711","degree_awarded":"PhD","oa_version":"Published Version","type":"dissertation","title":"Local adaptation, genetic load and extinction in metapopulations","date_published":"2024-01-19T00:00:00Z","date_updated":"2026-04-07T12:54:29Z","publication_identifier":{"issn":["2663-337X"]},"file":[{"relation":"source_file","access_level":"closed","file_size":16986244,"checksum":"de179b1c6758f182ff0c70d8b38c1501","date_created":"2024-01-03T18:30:13Z","creator":"oolusany","content_type":"application/zip","file_id":"14730","date_updated":"2024-01-03T18:30:13Z","file_name":"FinalSubmission_Thesis_OLUSANYA.zip"},{"date_updated":"2024-01-03T18:31:34Z","file_id":"14731","content_type":"application/pdf","file_name":"FinalSubmission2_Thesis_OLUSANYA.pdf","date_created":"2024-01-03T18:31:34Z","creator":"oolusany","success":1,"checksum":"0e331585e3cd4823320aab4e69e64ccf","file_size":6460403,"access_level":"open_access","relation":"main_file"}],"month":"01","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"}],"oa":1},{"day":"23","corr_author":"1","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7606"},{"status":"public","relation":"part_of_dissertation","id":"12081"},{"id":"7553","relation":"part_of_dissertation","status":"public"}]},"date_created":"2024-02-23T14:02:04Z","author":[{"full_name":"Hledik, Michal","first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik"}],"page":"158","_id":"15020","status":"public","citation":{"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>.","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.","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>","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>.","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","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>"},"ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"article_processing_charge":"No","OA_place":"publisher","language":[{"iso":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledged_ssus":[{"_id":"ScienComp"}],"year":"2024","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","oa_version":"Published Version","type":"dissertation","file_date_updated":"2024-02-23T14:20:16Z","has_accepted_license":"1","publication_status":"published","doi":"10.15479/at:ista:15020","ddc":["576","519"],"project":[{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"},{"name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327"}],"keyword":["Theoretical biology","Optimality","Evolution","Information"],"alternative_title":["ISTA Thesis"],"supervisor":[{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"},{"last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","first_name":"Gašper"}],"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"}],"oa":1,"file":[{"creator":"mhledik","date_created":"2024-02-23T13:50:53Z","file_name":"hledik thesis pdfa 2b.pdf","content_type":"application/pdf","file_id":"15021","date_updated":"2024-02-23T13:50:53Z","file_size":7102089,"relation":"main_file","access_level":"open_access","checksum":"b2d3da47c98d481577a4baf68944fe41","success":1},{"checksum":"eda9b9430da2610fee7ce1c1419a479a","relation":"source_file","access_level":"closed","file_size":14014790,"date_created":"2024-02-23T13:50:54Z","creator":"mhledik","date_updated":"2024-02-23T14:20:16Z","file_id":"15022","file_name":"hledik thesis source.zip","content_type":"application/zip"}],"month":"02","title":"Genetic information and biological optimization","date_published":"2024-02-23T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-04-07T12:59:25Z"},{"tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"corr_author":"1","day":"07","date_created":"2024-11-06T21:25:37Z","_id":"18515","page":"219","author":[{"last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87","full_name":"Surendranadh, Parvathy","first_name":"Parvathy","orcid":"0000-0001-6395-386X"}],"citation":{"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>","short":"P. Surendranadh, Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange, Institute of Science and Technology Austria, 2024.","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>.","ista":"Surendranadh P. 2024. Effect of population structure on neutral genetic variation and barriers to gene exchange. Institute of Science and Technology Austria.","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>","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>.","ieee":"P. Surendranadh, “Effect of population structure on neutral genetic variation and barriers to gene exchange,” Institute of Science and Technology Austria, 2024."},"status":"public","OA_type":"gold","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"article_processing_charge":"No","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"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.","year":"2024","acknowledged_ssus":[{"_id":"ScienComp"}],"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","degree_awarded":"PhD","type":"dissertation","publication_status":"published","file_date_updated":"2024-11-07T10:59:42Z","doi":"10.15479/at:ista:18515","has_accepted_license":"1","ddc":["576"],"project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation","grant_number":"P32166"},{"name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327"}],"supervisor":[{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"alternative_title":["ISTA Thesis"],"oa":1,"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"}],"month":"11","file":[{"checksum":"c32cf7bc75748d9c551d8eb70178bbec","access_level":"open_access","relation":"main_file","file_size":37019760,"success":1,"date_created":"2024-11-07T10:59:29Z","creator":"psurendr","content_type":"application/pdf","date_updated":"2024-11-07T10:59:29Z","file_id":"18519","file_name":"PhD_Thesis__Parvathy_071124_PDFA.pdf"},{"content_type":"application/zip","file_name":"PhD Thesis- Parvathy_071124.zip","file_id":"18520","date_updated":"2024-11-07T10:59:42Z","date_created":"2024-11-07T10:59:42Z","creator":"psurendr","checksum":"4417e02d54084d89e75734e18caaa96d","access_level":"closed","file_size":41198857,"relation":"source_file"}],"title":"Effect of population structure on neutral genetic variation and barriers to gene exchange","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-04-07T12:56:52Z","date_published":"2024-11-07T00:00:00Z"},{"project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"},{"grant_number":"25817","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","name":"Sexual conflict: resolution, constraints and biomedical implications"}],"ddc":["576"],"alternative_title":["ISTA Thesis"],"supervisor":[{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","first_name":"Beatriz","orcid":"0000-0002-4579-8306"},{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","degree_awarded":"PhD","oa_version":"Published Version","file_date_updated":"2023-08-18T10:47:55Z","has_accepted_license":"1","doi":"10.15479/at:ista:14058","publication_status":"published","file":[{"file_name":"Thesis_latex_forpdfa.zip","file_id":"14075","content_type":"application/zip","date_updated":"2023-08-17T06:55:24Z","date_created":"2023-08-16T18:15:17Z","creator":"gpuixeus","checksum":"4e44e169f2724ee8c9324cd60bcc2b71","relation":"source_file","access_level":"closed","file_size":10891454},{"creator":"gpuixeus","date_created":"2023-08-18T10:47:55Z","date_updated":"2023-08-18T10:47:55Z","file_name":"PhDThesis_PuixeuG.pdf","content_type":"application/pdf","file_id":"14079","success":1,"file_size":19856686,"access_level":"open_access","relation":"main_file","checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8"}],"month":"08","date_published":"2023-08-15T00:00:00Z","publication_identifier":{"isbn":["978-3-99078-035-0"],"issn":["2663-337X"]},"date_updated":"2026-04-07T13:25:34Z","title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation","abstract":[{"lang":"eng","text":"Females and males across species are subject to divergent selective pressures arising\r\nfrom di↵erent reproductive interests and ecological niches. This often translates into a\r\nintricate array of sex-specific natural and sexual selection on traits that have a shared\r\ngenetic basis between both sexes, causing a genetic sexual conflict. The resolution of\r\nthis conflict mostly relies on the evolution of sex-specific expression of the shared genes,\r\nleading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought\r\nto evolve via modifications of the genetic networks ultimately linked to sex-determining\r\ntranscription factors. Although much empirical and theoretical evidence supports this\r\nstandard picture of the molecular basis of sexual conflict resolution, there still are a\r\nfew open questions regarding the complex array of selective forces driving phenotypic\r\ndi↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis.\r\nFirst, how do patterns of phenotypic sexual dimorphism vary within populations,\r\nas a response to the temporal and spatial changes in sex-specific selective forces? To\r\ntackle this question, I analyze the patterns of sex-specific phenotypic variation along\r\nthree life stages and across populations spanning the whole geographical range of Rumex\r\nhastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis.\r\nSecond, how do gene expression patterns lead to phenotypic dimorphism, and what\r\nare the molecular mechanisms underlying the observed transcriptomic variation? I\r\naddress this question by examining the sex- and tissue-specific expression variation in\r\nnewly-generated datasets of sex-specific expression in heads and gonads of Drosophila\r\nmelanogaster. I additionally used two complementary approaches for the study of the\r\ngenetic basis of sex di↵erences in gene expression in the second and third Chapters of\r\nthe thesis.\r\nThird, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual\r\ndimorphism? I develop models of sex-specific stabilizing selection, mutation and drift\r\nto formalize common intuition regarding the patterns of covariation between intersex\r\ncorrelation and sexual dimorphism in the fourth Chapter of the thesis.\r\nAlltogether, the work described in this PhD thesis provides useful insights into the\r\nlinks between genetic, transcriptomic and phenotypic layers of sex-specific variation,\r\nand contributes to our general understanding of the dynamics of sexual dimorphism\r\nevolution."}],"oa":1,"page":"230","author":[{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","orcid":"0000-0001-8330-1754","first_name":"Gemma","full_name":"Puixeu Sala, Gemma"}],"_id":"14058","related_material":{"record":[{"id":"9803","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"12933"},{"relation":"part_of_dissertation","status":"public","id":"6831"},{"id":"14077","relation":"part_of_dissertation","status":"public"}]},"date_created":"2023-08-15T10:20:40Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"15","corr_author":"1","language":[{"iso":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","OA_place":"publisher","year":"2023","publisher":"Institute of Science and Technology Austria","status":"public","citation":{"ieee":"G. Puixeu Sala, “The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation,” Institute of Science and Technology Austria, 2023.","mla":"Puixeu Sala, Gemma. <i>The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14058\">10.15479/at:ista:14058</a>.","ama":"Puixeu Sala G. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14058\">10.15479/at:ista:14058</a>","chicago":"Puixeu Sala, Gemma. “The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14058\">https://doi.org/10.15479/at:ista:14058</a>.","ista":"Puixeu Sala G. 2023. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria.","apa":"Puixeu Sala, G. (2023). <i>The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14058\">https://doi.org/10.15479/at:ista:14058</a>","short":"G. Puixeu Sala, The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation, Institute of Science and Technology Austria, 2023."},"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"ec_funded":1},{"file_date_updated":"2023-12-14T08:58:18Z","has_accepted_license":"1","doi":"10.15479/at:ista:14651","publication_status":"published","type":"dissertation","oa_version":"Published Version","degree_awarded":"PhD","supervisor":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"alternative_title":["ISTA Thesis"],"project":[{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"ddc":["570"],"oa":1,"abstract":[{"text":"For self-incompatibility (SI) to be stable in a population, theory predicts that sufficient inbreeding depression (ID) is required: the fitness of offspring from self-mated individuals must be low enough to prevent the spread of self-compatibility (SC). Reviews of natural plant populations have supported this theory, with SI species generally showing high levels of ID. However, there is thought to be an under-sampling of self-incompatible taxa in the current literature. In this thesis, I study inbreeding depression in the SI plant species Antirrhinum majus using both greenhouse crosses and a large collected field dataset. Additionally, the gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus making assembly and discovery of S-alleles very difficult. Here, 206 new alleles of the male component SLFs are presented, along with a phylogeny showing the high conservation with alleles from another Antirrhinum species. Lastly, selected sites within the protein structure of SLFs are investigated, with one site in particular highlighted as potentially being involved in the SI recognition mechanism.","lang":"eng"}],"date_updated":"2026-04-07T13:28:30Z","publication_identifier":{"issn":["2663-337X"]},"date_published":"2023-12-12T00:00:00Z","title":"Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus","month":"12","file":[{"date_created":"2023-12-13T15:37:55Z","creator":"larathoo","file_id":"14684","date_updated":"2023-12-13T15:37:55Z","content_type":"application/pdf","file_name":"Phd_Thesis_LA.pdf","success":1,"access_level":"open_access","relation":"main_file","file_size":34101468,"checksum":"520bdb61e95e66070e02824947d2c5fa"},{"date_created":"2023-12-13T15:42:23Z","creator":"larathoo","content_type":"application/zip","file_name":"Phd_Thesis_LA.zip","date_updated":"2023-12-14T08:58:18Z","file_id":"14685","checksum":"d8e59afd0817c98fba2564a264508e5c","access_level":"closed","file_size":31052872,"relation":"source_file"},{"checksum":"9a778c949932286f4519e1f1fca2820d","file_size":10713896,"access_level":"closed","relation":"supplementary_material","date_updated":"2023-12-14T08:58:18Z","file_id":"14681","content_type":"application/zip","file_name":"Supplementary_Materials.zip","creator":"larathoo","date_created":"2023-12-11T19:24:59Z"}],"corr_author":"1","day":"12","_id":"14651","author":[{"orcid":"0000-0003-1771-714X","full_name":"Arathoon, Louise S","first_name":"Louise S","last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"}],"page":"96","date_created":"2023-12-11T19:30:37Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11411"}]},"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"ec_funded":1,"citation":{"apa":"Arathoon, L. S. (2023). <i>Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14651\">https://doi.org/10.15479/at:ista:14651</a>","short":"L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023.","ista":"Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria.","chicago":"Arathoon, Louise S. “Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14651\">https://doi.org/10.15479/at:ista:14651</a>.","ama":"Arathoon LS. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14651\">10.15479/at:ista:14651</a>","ieee":"L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023.","mla":"Arathoon, Louise S. <i>Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14651\">10.15479/at:ista:14651</a>."},"status":"public","acknowledged_ssus":[{"_id":"ScienComp"}],"year":"2023","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"article_processing_charge":"No","OA_place":"publisher"},{"file":[{"access_level":"closed","file_size":52795,"relation":"supplementary_material","checksum":"b76cf6d69f2093d8248f6a3f9d4654a4","embargo_to":"open_access","date_updated":"2023-06-02T22:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_id":"12805","file_name":"Dispersaldata.xlsx","date_created":"2023-04-06T06:09:40Z","creator":"mjulseth"},{"checksum":"5a13b6d204371572e249f03795bc0d04","access_level":"open_access","embargo":"2023-06-01","file_size":787239,"relation":"supplementary_material","date_created":"2023-04-06T06:11:27Z","creator":"mjulseth","content_type":"application/vnd.wolfram.nb","file_id":"12806","file_name":"2023_MSc_ThesisMaraJulseth_Notebook.nb","date_updated":"2023-06-02T22:30:04Z"},{"file_id":"12812","file_name":"ThesisMaraJulseth_04_23.docx","date_updated":"2023-06-02T22:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","creator":"mjulseth","date_created":"2023-04-06T08:26:12Z","relation":"source_file","file_size":1061763,"access_level":"closed","checksum":"c3ec842839ed1e66bf2618ae33047df8"},{"date_created":"2023-04-06T08:26:37Z","creator":"mjulseth","file_name":"ThesisMaraJulseth_04_23.pdf","file_id":"12813","date_updated":"2023-06-02T22:30:04Z","content_type":"application/pdf","checksum":"3132cc998fbe3ae2a3a83c2a69367f37","relation":"main_file","file_size":1741364,"embargo":"2023-06-01","access_level":"open_access"}],"month":"04","date_published":"2023-04-05T00:00:00Z","publication_identifier":{"issn":["2791-4585"]},"date_updated":"2026-04-07T14:01:51Z","title":"The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone","abstract":[{"lang":"eng","text":"The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. "}],"oa":1,"ddc":["576"],"alternative_title":["ISTA Master's Thesis"],"supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"type":"dissertation","degree_awarded":"MS","oa_version":"Published Version","has_accepted_license":"1","doi":"10.15479/at:ista:12800","publication_status":"published","file_date_updated":"2023-06-02T22:30:04Z","language":[{"iso":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","year":"2023","status":"public","citation":{"apa":"Julseth, M. (2023). <i>The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12800\">https://doi.org/10.15479/at:ista:12800</a>","short":"M. Julseth, The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology Austria, 2023.","chicago":"Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12800\">https://doi.org/10.15479/at:ista:12800</a>.","ista":"Julseth M. 2023. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria.","ama":"Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12800\">10.15479/at:ista:12800</a>","ieee":"M. Julseth, “The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone,” Institute of Science and Technology Austria, 2023.","mla":"Julseth, Mara. <i>The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12800\">10.15479/at:ista:12800</a>."},"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"page":"21","author":[{"first_name":"Mara","full_name":"Julseth, Mara","id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","last_name":"Julseth"}],"_id":"12800","date_created":"2023-04-04T18:57:11Z","day":"05","corr_author":"1"},{"oa":1,"abstract":[{"lang":"eng","text":"Although we often see studies focusing on simple or even discrete traits in studies of colouration,\r\nthe variation of “appearance” phenotypes found in nature is often more complex, continuous\r\nand high-dimensional. Therefore, we developed automated methods suitable for large datasets\r\nof genomes and images, striving to account for their complex nature, while minimising human\r\nbias. We used these methods on a dataset of more than 20, 000 plant SNP genomes and\r\ncorresponding fower images from a hybrid zone of two subspecies of Antirrhinum majus with\r\ndistinctly coloured fowers to improve our understanding of the genetic nature of the fower\r\ncolour in our study system.\r\nFirstly, we use the advantage of large numbers of genotyped plants to estimate the haplotypes in\r\nthe main fower colour regulating region. We study colour- and geography-related characteristics\r\nof the estimated haplotypes and how they connect to their relatedness. We show discrepancies\r\nfrom the expected fower colour distributions given the genotype and identify particular\r\nhaplotypes leading to unexpected phenotypes. We also confrm a signifcant defcit of the\r\ndouble recessive recombinant and quite surprisingly, we show that haplotypes of the most\r\nfrequent parental type are much less variable than others.\r\nSecondly, we introduce our pipeline capable of processing tens of thousands of full fower\r\nimages without human interaction and summarising each image into a set of informative scores.\r\nWe show the compatibility of these machine-measured fower colour scores with the previously\r\nused manual scores and study impact of external efect on the resulting scores. Finally, we use\r\nthe machine-measured fower colour scores to ft and examine a phenotype cline across the\r\nhybrid zone in Planoles using full fower images as opposed to discrete, manual scores and\r\ncompare it with the genotypic cline."}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-016-9"]},"date_updated":"2026-04-07T14:12:19Z","date_published":"2022-04-06T00:00:00Z","title":"Genetic basis of flower colour as a model for adaptive evolution","month":"04","file":[{"checksum":"e9609bc4e8f8e20146fc1125fd4f1bf7","access_level":"open_access","relation":"main_file","file_size":11906472,"file_name":"LenkaPhD_Official_PDFA.pdf","date_updated":"2022-04-07T08:11:34Z","file_id":"11129","content_type":"application/pdf","date_created":"2022-04-07T08:11:34Z","creator":"cchlebak"},{"checksum":"99d67040432fd07a225643a212ee8588","relation":"source_file","access_level":"closed","file_size":23036766,"content_type":"application/x-zip-compressed","file_name":"LenkaPhD Official_source.zip","file_id":"11130","date_updated":"2022-04-07T08:11:51Z","date_created":"2022-04-07T08:11:51Z","creator":"cchlebak"}],"doi":"10.15479/at:ista:11128","file_date_updated":"2022-04-07T08:11:51Z","publication_status":"published","has_accepted_license":"1","type":"dissertation","oa_version":"Published Version","degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"alternative_title":["ISTA Thesis"],"ddc":["576","582"],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"citation":{"chicago":"Matejovicova, Lenka. “Genetic Basis of Flower Colour as a Model for Adaptive Evolution.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11128\">https://doi.org/10.15479/at:ista:11128</a>.","ista":"Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria.","short":"L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution, Institute of Science and Technology Austria, 2022.","apa":"Matejovicova, L. (2022). <i>Genetic basis of flower colour as a model for adaptive evolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11128\">https://doi.org/10.15479/at:ista:11128</a>","mla":"Matejovicova, Lenka. <i>Genetic Basis of Flower Colour as a Model for Adaptive Evolution</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11128\">10.15479/at:ista:11128</a>.","ieee":"L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,” Institute of Science and Technology Austria, 2022.","ama":"Matejovicova L. Genetic basis of flower colour as a model for adaptive evolution. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11128\">10.15479/at:ista:11128</a>"},"status":"public","publisher":"Institute of Science and Technology Austria","year":"2022","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"OA_place":"publisher","article_processing_charge":"No","corr_author":"1","day":"06","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"_id":"11128","page":"112","author":[{"last_name":"Matejovicova","id":"2DFDEC72-F248-11E8-B48F-1D18A9856A87","first_name":"Lenka","full_name":"Matejovicova, Lenka"}],"date_created":"2022-04-07T08:19:54Z"},{"OA_place":"publisher","article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"year":"2022","publisher":"Institute of Science and Technology Austria","citation":{"chicago":"Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11388\">https://doi.org/10.15479/at:ista:11388</a>.","ista":"Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria.","apa":"Belohlavy, S. (2022). <i>The genetic basis of complex traits studied via analysis of evolve and resequence experiments</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11388\">https://doi.org/10.15479/at:ista:11388</a>","short":"S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments, Institute of Science and Technology Austria, 2022.","ieee":"S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” Institute of Science and Technology Austria, 2022.","mla":"Belohlavy, Stefanie. <i>The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11388\">10.15479/at:ista:11388</a>.","ama":"Belohlavy S. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11388\">10.15479/at:ista:11388</a>"},"status":"public","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"date_created":"2022-05-16T16:49:18Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6713"}]},"_id":"11388","author":[{"id":"43FE426A-F248-11E8-B48F-1D18A9856A87","last_name":"Belohlavy","orcid":"0000-0002-9849-498X","full_name":"Belohlavy, Stefanie","first_name":"Stefanie"}],"page":"98","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"corr_author":"1","day":"18","month":"05","file":[{"embargo":"2023-05-19","relation":"main_file","file_size":8247240,"access_level":"open_access","checksum":"4d75e6a619df7e8a9d6e840aee182380","content_type":"application/pdf","file_name":"thesis_sb_final_pdfa.pdf","file_id":"11398","date_updated":"2023-05-20T22:30:03Z","creator":"sbelohla","date_created":"2022-05-19T13:03:13Z"},{"access_level":"closed","relation":"source_file","file_size":7094,"checksum":"7a5d8b6dd0ca00784f860075b0a7d8f0","embargo_to":"open_access","date_updated":"2023-05-20T22:30:03Z","file_name":"thesis_sb_final.zip","content_type":"application/x-zip-compressed","file_id":"11399","creator":"sbelohla","date_created":"2022-05-19T13:07:47Z"}],"title":"The genetic basis of complex traits studied via analysis of evolve and resequence experiments","publication_identifier":{"isbn":["978-3-99078-018-3"]},"date_updated":"2026-04-07T14:29:57Z","date_published":"2022-05-18T00:00:00Z","oa":1,"abstract":[{"lang":"eng","text":"In evolve and resequence experiments, a population is sequenced, subjected to selection and\r\nthen sequenced again, so that genetic changes before and after selection can be observed at\r\nthe genetic level. Here, I use these studies to better understand the genetic basis of complex\r\ntraits - traits which depend on more than a few genes.\r\nIn the first chapter, I discuss the first evolve and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\" mice, were selected for tibia length while their body mass\r\nwas kept constant. The full pedigree is known. We observed a selection response on all\r\nchromosomes and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber of genes with infinitesimally small effect sizes, as a null model. Results implied a very\r\npolygenic basis with a few loci of major effect standing out and changing in parallel. There\r\nwas large variability between the different chromosomes in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving an equation based on the initial allele frequencies, average\r\npairwise LD, and the first four moments of the haplotype block copy number distribution. I\r\ndescribe this distribution by referring back to the founder generation. I then demonstrate\r\nhow to infer selection via a maximum likelihood scheme on the example of a single locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations. The experiment was highly replicated with 27 lines selected within family and a\r\nknown pedigree. We observed a phenotypic selection response of over one standard deviation.\r\nI describe the patterns in allele frequency data, including allele frequency changes and patterns\r\nof heterozygosity, and give ideas for future work."}],"ddc":["576"],"supervisor":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"alternative_title":["ISTA Thesis"],"oa_version":"Published Version","degree_awarded":"PhD","type":"dissertation","publication_status":"published","file_date_updated":"2023-05-20T22:30:03Z","doi":"10.15479/at:ista:11388","has_accepted_license":"1"},{"citation":{"mla":"Szep, Eniko. <i>Local Adaptation in Metapopulations</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8574\">10.15479/AT:ISTA:8574</a>.","ieee":"E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology Austria, 2020.","ama":"Szep E. Local adaptation in metapopulations. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8574\">10.15479/AT:ISTA:8574</a>","chicago":"Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8574\">https://doi.org/10.15479/AT:ISTA:8574</a>.","ista":"Szep E. 2020. Local adaptation in metapopulations. Institute of Science and Technology Austria.","short":"E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology Austria, 2020.","apa":"Szep, E. (2020). <i>Local adaptation in metapopulations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8574\">https://doi.org/10.15479/AT:ISTA:8574</a>"},"status":"public","department":[{"_id":"NiBa"}],"OA_place":"publisher","article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","year":"2020","corr_author":"1","day":"20","date_created":"2020-09-28T07:33:38Z","_id":"8574","page":"158","author":[{"last_name":"Szep","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","first_name":"Eniko","full_name":"Szep, Eniko"}],"oa":1,"abstract":[{"lang":"eng","text":"This thesis concerns itself with the interactions of evolutionary and ecological forces and the consequences on genetic diversity and the ultimate survival of populations. It is important to understand what signals processes \r\nleave on the genome and what we can infer from such data, which is usually abundant but noisy. Furthermore, understanding how and when populations adapt or go extinct is important for practical purposes,  such as the genetic management of populations, as well as for theoretical questions, since local adaptation can be the first step toward speciation. \r\nIn Chapter 2, we introduce the method of maximum entropy to approximate the demographic changes of a population in a simple setting, namely the logistic growth model with immigration. We show that this method is not only a powerful \r\ntool in physics but can be gainfully applied in an ecological framework. We investigate how well it approximates the real \r\nbehavior of the system, and find that is does so, even in unexpected situations. Finally, we illustrate how it can model changing environments.\r\nIn Chapter 3, we analyze the co-evolution of allele frequencies and population sizes in an infinite island model.\r\nWe give conditions under which polygenic adaptation to a rare habitat is possible. The model we use is based on the diffusion approximation, considers eco-evolutionary feedback mechanisms (hard selection), and treats both \r\ndrift and environmental fluctuations explicitly. We also look at limiting scenarios, for which we derive analytical expressions. \r\nIn Chapter 4, we present a coalescent based simulation tool to obtain patterns of diversity in a spatially explicit subdivided population, in which the demographic history of each subpopulation can be specified. We compare \r\nthe results to existing predictions, and explore the relative importance of time and space under a variety of spatial arrangements and demographic histories, such as expansion and extinction. \r\nIn the last chapter, we give a brief outlook to further research. "}],"month":"09","file":[{"checksum":"20e71f015fbbd78fea708893ad634ed0","access_level":"open_access","relation":"main_file","file_size":6354833,"success":1,"date_updated":"2020-09-28T07:25:35Z","file_name":"thesis_EnikoSzep_final.pdf","file_id":"8575","content_type":"application/pdf","creator":"dernst","date_created":"2020-09-28T07:25:35Z"},{"file_name":"thesisFiles_EnikoSzep.zip","content_type":"application/x-zip-compressed","file_id":"8576","date_updated":"2020-09-28T07:25:37Z","date_created":"2020-09-28T07:25:37Z","creator":"dernst","checksum":"a8de2c14a1bb4e53c857787efbb289e1","relation":"source_file","access_level":"closed","file_size":23020401}],"title":"Local adaptation in metapopulations","publication_identifier":{"eissn":["2663-337X"]},"date_updated":"2026-04-08T07:21:44Z","date_published":"2020-09-20T00:00:00Z","oa_version":"Published Version","degree_awarded":"PhD","type":"dissertation","doi":"10.15479/AT:ISTA:8574","file_date_updated":"2020-09-28T07:25:37Z","has_accepted_license":"1","publication_status":"published","ddc":["570"],"supervisor":[{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"alternative_title":["ISTA Thesis"]},{"file_date_updated":"2020-07-14T12:45:23Z","has_accepted_license":"1","publist_id":"7713","doi":"10.15479/AT:ISTA:th_963","publication_status":"published","type":"dissertation","oa_version":"Published Version","degree_awarded":"PhD","supervisor":[{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"ddc":["576"],"oa":1,"abstract":[{"text":"This thesis is concerned with the inference of current population structure based on geo-referenced genetic data. The underlying idea is that population structure affects its spatial genetic structure. Therefore, genotype information can be utilized to estimate important demographic parameters such as migration rates. These indirect estimates of population structure have become very attractive, as genotype data is now widely available. However, there also has been much concern about these approaches. Importantly, genetic structure can be influenced by many complex patterns, which often cannot be disentangled. Moreover, many methods merely fit heuristic patterns of genetic structure, and do not build upon population genetics theory. Here, I describe two novel inference methods that address these shortcomings. In Chapter 2, I introduce an inference scheme based on a new type of signal, identity by descent (IBD) blocks. Recently, it has become feasible to detect such long blocks of genome shared between pairs of samples. These blocks are direct traces of recent coalescence events. As such, they contain ample signal for inferring recent demography. I examine sharing of IBD blocks in two-dimensional populations with local migration. Using a diffusion approximation, I derive formulas for an isolation by distance pattern of long IBD blocks and show that sharing of long IBD blocks approaches rapid exponential decay for growing sample distance. I describe an inference scheme based on these results. It can robustly estimate the dispersal rate and population density, which is demonstrated on simulated data. I also show an application to estimate mean migration and the rate of recent population growth within Eastern Europe. Chapter 3 is about a novel method to estimate barriers to gene flow in a two dimensional population. This inference scheme utilizes geographically localized allele frequency fluctuations - a classical isolation by distance signal. The strength of these local fluctuations increases on average next to a barrier, and there is less correlation across it. I again use a framework of diffusion of ancestral lineages to model this effect, and provide an efficient numerical implementation to fit the results to geo-referenced biallelic SNP data. This inference scheme is able to robustly estimate strong barriers to gene flow, as tests on simulated data confirm.","lang":"eng"}],"date_updated":"2026-04-08T14:06:37Z","publication_identifier":{"issn":["2663-337X"]},"date_published":"2018-02-21T00:00:00Z","pubrep_id":"963","title":"Inferring recent demography from spatial genetic structure","month":"02","file":[{"content_type":"application/pdf","file_name":"IST-2018-963-v1+1_thesis.pdf","file_id":"5111","date_updated":"2020-07-14T12:45:23Z","creator":"system","date_created":"2018-12-12T10:14:55Z","access_level":"open_access","file_size":5792935,"relation":"main_file","checksum":"8cc534d2b528ae017acf80874cce48c9"},{"file_size":113365,"relation":"source_file","access_level":"closed","checksum":"6af18d7e5a7e2728ceda2f41ee24f628","content_type":"application/zip","file_name":"2018_thesis_ringbauer_source.zip","date_updated":"2020-07-14T12:45:23Z","file_id":"6224","creator":"dernst","date_created":"2019-04-05T09:30:12Z"}],"corr_author":"1","day":"21","tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"_id":"200","author":[{"last_name":"Ringbauer","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","full_name":"Ringbauer, Harald","first_name":"Harald","orcid":"0000-0002-4884-9682"}],"page":"146","date_created":"2018-12-11T11:45:10Z","related_material":{"record":[{"id":"563","relation":"part_of_dissertation","status":"public"},{"id":"1074","status":"public","relation":"part_of_dissertation"}]},"department":[{"_id":"NiBa"}],"citation":{"chicago":"Ringbauer, Harald. “Inferring Recent Demography from Spatial Genetic Structure.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">https://doi.org/10.15479/AT:ISTA:th_963</a>.","ista":"Ringbauer H. 2018. Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria.","short":"H. Ringbauer, Inferring Recent Demography from Spatial Genetic Structure, Institute of Science and Technology Austria, 2018.","apa":"Ringbauer, H. (2018). <i>Inferring recent demography from spatial genetic structure</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">https://doi.org/10.15479/AT:ISTA:th_963</a>","mla":"Ringbauer, Harald. <i>Inferring Recent Demography from Spatial Genetic Structure</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">10.15479/AT:ISTA:th_963</a>.","ieee":"H. Ringbauer, “Inferring recent demography from spatial genetic structure,” Institute of Science and Technology Austria, 2018.","ama":"Ringbauer H. Inferring recent demography from spatial genetic structure. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">10.15479/AT:ISTA:th_963</a>"},"status":"public","publisher":"Institute of Science and Technology Austria","year":"2018","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"OA_place":"publisher","article_processing_charge":"No"},{"oa":1,"abstract":[{"lang":"eng","text":"Bacteria and their pathogens – phages – are the most abundant living entities on Earth. Throughout their coevolution, bacteria have evolved multiple immune systems to overcome the ubiquitous threat from the phages. Although the molecu- lar details of these immune systems’ functions are relatively well understood, their epidemiological consequences for the phage-bacterial communities have been largely neglected. In this thesis we employed both experimental and theoretical methods to explore whether herd and social immunity may arise in bacterial popu- lations. Using our experimental system consisting of Escherichia coli strains with a CRISPR based immunity to the T7 phage we show that herd immunity arises in phage-bacterial communities and that it is accentuated when the populations are spatially structured. By fitting a mathematical model, we inferred expressions for the herd immunity threshold and the velocity of spread of a phage epidemic in partially resistant bacterial populations, which both depend on the bacterial growth rate, phage burst size and phage latent period. We also investigated the poten- tial for social immunity in Streptococcus thermophilus and its phage 2972 using a bioinformatic analysis of potentially coding short open reading frames with a signalling signature, encoded within the CRISPR associated genes. Subsequently, we tested one identified potentially signalling peptide and found that its addition to a phage-challenged culture increases probability of survival of bacteria two fold, although the results were only marginally significant. Together, these results demonstrate that the ubiquitous arms races between bacteria and phages have further consequences at the level of the population."}],"publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-04-08T14:16:28Z","date_published":"2017-02-01T00:00:00Z","title":"Bacterial herd and social immunity to phages","month":"02","file":[{"checksum":"a0fc5c26a89c0ea759947ffba87d0d8f","relation":"main_file","file_size":3025175,"access_level":"closed","creator":"dernst","date_created":"2019-04-09T15:15:32Z","file_name":"thesis_pavel_payne_final_w_signature_page.pdf","file_id":"6292","date_updated":"2020-07-14T12:47:27Z","content_type":"application/pdf"},{"content_type":"application/pdf","file_id":"9187","date_updated":"2021-02-22T13:45:59Z","file_name":"2017_Payne_Thesis.pdf","date_created":"2021-02-22T13:45:59Z","creator":"dernst","access_level":"open_access","file_size":3111536,"relation":"main_file","checksum":"af531e921a7f64a9e0af4cd8783b2226","success":1}],"file_date_updated":"2021-02-22T13:45:59Z","has_accepted_license":"1","publication_status":"published","type":"dissertation","oa_version":"Published Version","degree_awarded":"PhD","supervisor":[{"last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","full_name":"Bollback, Jonathan P"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"alternative_title":["ISTA Thesis"],"ddc":["570"],"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"citation":{"ieee":"P. Payne, “Bacterial herd and social immunity to phages,” Institute of Science and Technology Austria, 2017.","mla":"Payne, Pavel. <i>Bacterial Herd and Social Immunity to Phages</i>. Institute of Science and Technology Austria, 2017.","ama":"Payne P. Bacterial herd and social immunity to phages. 2017.","chicago":"Payne, Pavel. “Bacterial Herd and Social Immunity to Phages.” Institute of Science and Technology Austria, 2017.","ista":"Payne P. 2017. Bacterial herd and social immunity to phages. Institute of Science and Technology Austria.","apa":"Payne, P. (2017). <i>Bacterial herd and social immunity to phages</i>. Institute of Science and Technology Austria.","short":"P. Payne, Bacterial Herd and Social Immunity to Phages, Institute of Science and Technology Austria, 2017."},"status":"public","publisher":"Institute of Science and Technology Austria","year":"2017","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"OA_place":"publisher","article_processing_charge":"No","corr_author":"1","day":"01","_id":"6291","author":[{"id":"35F78294-F248-11E8-B48F-1D18A9856A87","last_name":"Payne","full_name":"Payne, Pavel","first_name":"Pavel","orcid":"0000-0002-2711-9453"}],"page":"83","date_created":"2019-04-09T15:16:45Z"},{"file_date_updated":"2021-02-22T13:42:47Z","has_accepted_license":"1","publist_id":"6235","publication_status":"published","oa_version":"Published Version","degree_awarded":"PhD","type":"dissertation","supervisor":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"ddc":["576"],"oa":1,"abstract":[{"text":"Natural environments are never constant but subject to spatial and temporal change on\r\nall scales, increasingly so due to human activity. Hence, it is crucial to understand the\r\nimpact of environmental variation on evolutionary processes. In this thesis, I present\r\nthree topics that share the common theme of environmental variation, yet illustrate its\r\neffect from different perspectives.\r\nFirst, I show how a temporally fluctuating environment gives rise to second-order\r\nselection on a modifier for stress-induced mutagenesis. Without fluctuations, when\r\npopulations are adapted to their environment, mutation rates are minimized. I argue\r\nthat a stress-induced mutator mechanism may only be maintained if the population is\r\nrepeatedly subjected to diverse environmental challenges, and I outline implications of\r\nthe presented results to antibiotic treatment strategies.\r\nSecond, I discuss my work on the evolution of dispersal. Besides reproducing\r\nknown results about the effect of heterogeneous habitats on dispersal, it identifies\r\nspatial changes in dispersal type frequencies as a source for selection for increased\r\npropensities to disperse. This concept contains effects of relatedness that are known\r\nto promote dispersal, and I explain how it identifies other forces selecting for dispersal\r\nand puts them on a common scale.\r\nThird, I analyse genetic variances of phenotypic traits under multivariate stabilizing\r\nselection. For the case of constant environments, I generalize known formulae of\r\nequilibrium variances to multiple traits and discuss how the genetic variance of a focal\r\ntrait is influenced by selection on background traits. I conclude by presenting ideas and\r\npreliminary work aiming at including environmental fluctuations in the form of moving\r\ntrait optima into the model.","lang":"eng"}],"title":"Evolutionary proccesses in variable emvironments","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-04-09T14:25:34Z","date_published":"2016-07-01T00:00:00Z","month":"07","file":[{"file_size":3564901,"access_level":"closed","relation":"main_file","checksum":"81dcc838dfcf7aa0b1a27ecf4fe2da4e","creator":"dernst","date_created":"2019-08-13T09:01:00Z","file_id":"6811","date_updated":"2019-08-13T09:01:00Z","content_type":"application/pdf","file_name":"Novak_thesis.pdf"},{"access_level":"open_access","relation":"main_file","file_size":2814384,"checksum":"30808d2f7ca920e09f63a95cdc49bffd","success":1,"creator":"dernst","date_created":"2021-02-22T13:42:47Z","content_type":"application/pdf","file_name":"2016_Novak_Thesis.pdf","date_updated":"2021-02-22T13:42:47Z","file_id":"9186"}],"corr_author":"1","day":"01","date_created":"2018-12-11T11:50:17Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"2023"}]},"_id":"1125","page":"124","author":[{"full_name":"Novak, Sebastian","first_name":"Sebastian","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak"}],"department":[{"_id":"NiBa"}],"citation":{"ista":"Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria.","chicago":"Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute of Science and Technology Austria, 2016.","apa":"Novak, S. (2016). <i>Evolutionary proccesses in variable emvironments</i>. Institute of Science and Technology Austria.","short":"S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of Science and Technology Austria, 2016.","ieee":"S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of Science and Technology Austria, 2016.","mla":"Novak, Sebastian. <i>Evolutionary Proccesses in Variable Emvironments</i>. Institute of Science and Technology Austria, 2016.","ama":"Novak S. Evolutionary proccesses in variable emvironments. 2016."},"status":"public","year":"2016","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}]},{"citation":{"ieee":"M. Tugrul, “Evolution of transcriptional regulatory sequences,” Institute of Science and Technology Austria, 2016.","mla":"Tugrul, Murat. <i>Evolution of Transcriptional Regulatory Sequences</i>. Institute of Science and Technology Austria, 2016.","ama":"Tugrul M. Evolution of transcriptional regulatory sequences. 2016.","chicago":"Tugrul, Murat. “Evolution of Transcriptional Regulatory Sequences.” Institute of Science and Technology Austria, 2016.","ista":"Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria.","apa":"Tugrul, M. (2016). <i>Evolution of transcriptional regulatory sequences</i>. Institute of Science and Technology Austria.","short":"M. Tugrul, Evolution of Transcriptional Regulatory Sequences, Institute of Science and Technology Austria, 2016."},"status":"public","department":[{"_id":"NiBa"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"acknowledgement":"This PhD thesis may not have been completed without the help and care I received from some peo- ple during my PhD life. I am especially grateful to Tiago Paixao, Gasper Tkacik, Nick Barton, not only for their scientific advices but also for their patience and support. I thank Calin Guet and Jonathan Bollback for allowing me to “play around” in their labs and get some experience on experimental evolution. I thank Magdalena Steinrueck and Fabienne Jesse for collaborating and sharing their experimental data with me. I thank Johannes Jaeger for reviewing my thesis. I thank all members of Barton group (aka bartonians) for their feedback, and all workers of IST Austria for making the best working conditions. Lastly, I thank two special women, Nejla Sag ̆lam and Setenay Dog ̆an, for their continuous support and encouragement. I truly had a great chance of having right people around me.","article_processing_charge":"No","OA_place":"publisher","publisher":"Institute of Science and Technology Austria","year":"2016","corr_author":"1","day":"01","_id":"1131","page":"89","author":[{"orcid":"0000-0002-8523-0758","first_name":"Murat","full_name":"Tugrul, Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","last_name":"Tugrul"}],"date_created":"2018-12-11T11:50:19Z","related_material":{"record":[{"id":"5554","relation":"research_data","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"1666"}]},"oa":1,"abstract":[{"text":"Evolution of gene regulation is important for phenotypic evolution and diversity. Sequence-specific binding of regulatory proteins is one of the key regulatory mechanisms determining gene expression. Although there has been intense interest in evolution of regulatory binding sites in the last decades, a theoretical understanding is far from being complete. In this thesis, I aim at a better understanding of the evolution of transcriptional regulatory binding sequences by using biophysical and population genetic models.\r\nIn the first part of the thesis, I discuss how to formulate the evolutionary dynamics of binding se- quences in a single isolated binding site and in promoter/enhancer regions. I develop a theoretical framework bridging between a thermodynamical model for transcription and a mutation-selection-drift model for monomorphic populations. I mainly address the typical evolutionary rates, and how they de- pend on biophysical parameters (e.g. binding length and specificity) and population genetic parameters (e.g. population size and selection strength).\r\nIn the second part of the thesis, I analyse empirical data for a better evolutionary and biophysical understanding of sequence-specific binding of bacterial RNA polymerase. First, I infer selection on regulatory and non-regulatory binding sites of RNA polymerase in the E. coli K12 genome. Second, I infer the chemical potential of RNA polymerase, an important but unknown physical parameter defining the threshold energy for strong binding. Furthermore, I try to understand the relation between the lac promoter sequence diversity and the LacZ activity variation among 20 bacterial isolates by constructing a simple but biophysically motivated gene expression model. Lastly, I lay out a statistical framework to predict adaptive point mutations in de novo promoter evolution in a selection experiment.","lang":"eng"}],"month":"07","file":[{"date_created":"2019-08-13T08:53:52Z","creator":"dernst","file_name":"Tugrul_thesis_w_signature_page.pdf","content_type":"application/pdf","date_updated":"2019-08-13T08:53:52Z","file_id":"6810","relation":"main_file","file_size":3695257,"access_level":"closed","checksum":"66cb61a59943e4fb7447c6a86be5ef51"},{"creator":"dernst","date_created":"2021-02-22T11:45:20Z","file_name":"2016_Tugrul_Thesis.pdf","content_type":"application/pdf","file_id":"9182","date_updated":"2021-02-22T11:45:20Z","success":1,"checksum":"293e388d70563760f6b24c3e66283dda","relation":"main_file","access_level":"open_access","file_size":3880811}],"date_updated":"2026-04-09T10:52:40Z","publication_identifier":{"issn":["2663-337X"]},"date_published":"2016-07-01T00:00:00Z","title":"Evolution of transcriptional regulatory sequences","type":"dissertation","oa_version":"Published Version","degree_awarded":"PhD","has_accepted_license":"1","publication_status":"published","file_date_updated":"2021-02-22T11:45:20Z","publist_id":"6229","ddc":["576"],"supervisor":[{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"alternative_title":["ISTA Thesis"]},{"publist_id":"5809","has_accepted_license":"1","publication_status":"published","doi":"10.15479/AT:ISTA:TH_526 ","file_date_updated":"2025-07-03T06:24:39Z","degree_awarded":"PhD","oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"supervisor":[{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"ddc":["576"],"abstract":[{"text":"Hybrid zones represent evolutionary laboratories, where recombination brings together alleles in combinations which have not previously been tested by selection. This provides an excellent opportunity to test the effect of molecular variation on fitness, and how this variation is able to spread through populations in a natural context. The snapdragon Antirrhinum majus is polymorphic in the wild for two loci controlling the distribution of yellow and magenta floral pigments. Where the yellow A. m. striatum and the magenta A. m. pseudomajus meet along a valley in the Spanish Pyrenees they form a stable hybrid zone Alleles at these loci recombine to give striking transgressive variation for flower colour. The sharp transition in phenotype over ~1km implies strong selection maintaining the hybrid zone. An indirect assay of pollinator visitation in the field found that pollinators forage in a positive-frequency dependent manner on Antirrhinum, matching previous data on fruit set. Experimental arrays and paternity analysis of wild-pollinated seeds demonstrated assortative mating for pigmentation alleles, and that pollinator behaviour alone is sufficient to explain this pattern. Selection by pollinators should be sufficiently strong to maintain the hybrid zone, although other mechanisms may be at work. At a broader scale I examined evolutionary transitions between yellow and anthocyanin pigmentation in the tribe Antirrhinae, and found that selection has acted strate that pollinators are a major determinant of reproductive success and mating patterns in wild Antirrhinum.","lang":"eng"}],"oa":1,"title":"The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone","pubrep_id":"526","date_published":"2016-02-18T00:00:00Z","date_updated":"2026-04-09T10:52:07Z","publication_identifier":{"issn":["2663-337X"]},"file":[{"access_level":"open_access","relation":"main_file","file_size":7590862,"checksum":"f0f7c260e19ec1416824b165afe2d5fd","creator":"dernst","date_created":"2025-07-03T06:24:17Z","file_name":"2016_Thesis_Ellis_noSignatures.pdf","date_updated":"2025-07-03T06:24:17Z","content_type":"application/pdf","file_id":"19957"},{"file_id":"5106","content_type":"application/pdf","file_name":"IST-2016-526-v1+1_Ellis_signed_thesis.pdf","date_updated":"2025-07-03T06:24:39Z","date_created":"2018-12-12T10:14:51Z","creator":"system","checksum":"a89b17ff27cf92c9a15f6b3d46bd7e53","relation":"main_file","access_level":"closed","file_size":11928241}],"month":"02","day":"18","corr_author":"1","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"5553"},{"id":"5551","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"5552"}]},"date_created":"2018-12-11T11:51:47Z","author":[{"first_name":"Thomas","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis"}],"page":"130","_id":"1398","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"status":"public","citation":{"ieee":"T. Ellis, “The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone,” Institute of Science and Technology Austria, 2016.","mla":"Ellis, Thomas. <i>The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">10.15479/AT:ISTA:TH_526 </a>.","ama":"Ellis T. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">10.15479/AT:ISTA:TH_526 </a>","chicago":"Ellis, Thomas. “The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">https://doi.org/10.15479/AT:ISTA:TH_526 </a>.","ista":"Ellis T. 2016. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute of Science and Technology Austria.","short":"T. Ellis, The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone, Institute of Science and Technology Austria, 2016.","apa":"Ellis, T. (2016). <i>The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">https://doi.org/10.15479/AT:ISTA:TH_526 </a>"},"year":"2016","publisher":"Institute of Science and Technology Austria","OA_place":"publisher","article_processing_charge":"No","language":[{"iso":"eng"}],"acknowledgement":"I am indebted to many people for their support during my PhD, but I particularly wish to thank Nick Barton for his guidance and intuition, and for encouraging me to take the time to look beyond the immediate topic of my PhD to understand the broader context. I am also especially grateful to David Field his bottomless patience, invaluable advice on experimental design, analysis and scientific writing, and for tireless work on the population surveys and genomic work without most of my thesis could not have happened. \r\n\r\nIt has been a pleasure to work with the combined strengths of the groups at The John Innes Centre, University of Toulouse and IST Austria. Thanks to Enrico Coen and his group for hosting me in Norwich in 2011 and especially for setting up the tag experiment. \r\n\r\nI thank David Field, Desmond Bradley and Maria Clara Melo-Hurtado for organising field collections, as well as Monique Burrus and Christophe Andalo and a large number of volunteers for their e ff orts helping with the field work. Furthermore I thank Coline Jaworski for providing seeds and for her input into the design of the experimental arrays, and Matthew Couchman for maintaining the database of. \r\n\r\nIn addition to those mentioned above, I am grateful to Melinda Pickup, Spencer Barrett, and four anonymous reviewers for their insightful comments on sections of this manuscript. I also thank Jana Porsche for her e ff orts in tracking down the more obscure references for chapter 5, and Jon Bollback for his advice about the analysis. \r\n\r\nI am indebted to Jon Ågren for his patience whilst I finished this thesis, and to Sylvia Cremer and Magnus Nordborg for taking the time to read and evaluate the thesis given a shorter deadline than was fair. \r\n\r\nA very positive aspect of my PhD has been the supportive atmosphere of IST. In particular, I have come to appreciate the enormous support from our group assistants Nicole Hotzy, Julia Asimakis, Christine Ostermann and Jerneja Beslagic. I also thank Christian Chaloupka and Stefan Hipfinger for their enthusiasm and readiness to help where possible in setting up our greenhouse and experiments. ","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"}]