[{"date_updated":"2026-06-18T19:05:02Z","_id":"9799","related_material":{"record":[{"id":"6467","relation":"used_in_publication","status":"public"}]},"year":"2020","publisher":"Royal Society of London","title":"Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes","oa_version":"Published Version","day":"15","month":"10","date_created":"2021-08-06T11:26:57Z","status":"public","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"doi":"10.6084/m9.figshare.7957469.v1","abstract":[{"text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations.","lang":"eng"}],"user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7957469.v1","open_access":"1"}],"author":[{"last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Welch","full_name":"Welch, John J.","first_name":"John J."}],"article_processing_charge":"No","citation":{"short":"C. Fraisse, J.J. Welch, (2020).","ama":"Fraisse C, Welch JJ. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. 2020. doi:<a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">10.6084/m9.figshare.7957469.v1</a>","mla":"Fraisse, Christelle, and John J. Welch. <i>Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes</i>. Royal Society of London, 2020, doi:<a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">10.6084/m9.figshare.7957469.v1</a>.","ista":"Fraisse C, Welch JJ. 2020. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, <a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">10.6084/m9.figshare.7957469.v1</a>.","ieee":"C. Fraisse and J. J. Welch, “Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020.","apa":"Fraisse, C., &#38; Welch, J. J. (2020). Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. <a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">https://doi.org/10.6084/m9.figshare.7957469.v1</a>","chicago":"Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. <a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">https://doi.org/10.6084/m9.figshare.7957469.v1</a>."},"OA_place":"publisher","OA_type":"hybrid","type":"research_data_reference","oa":1,"date_published":"2020-10-15T00:00:00Z"},{"type":"journal_article","page":"342-351","pmid":1,"date_published":"2020-03-01T00:00:00Z","oa":1,"publication":"Journal of Evolutionary Biology","publication_status":"published","isi":1,"citation":{"short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R.K. Butlin, Journal of Evolutionary Biology 33 (2020) 342–351.","ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? <i>Journal of Evolutionary Biology</i>. 2020;33(3):342-351. doi:<a href=\"https://doi.org/10.1111/jeb.13570\">10.1111/jeb.13570</a>","mla":"Johannesson, Kerstin, et al. “Is Embryo Abortion a Post-Zygotic Barrier to Gene Flow between Littorina Ecotypes?” <i>Journal of Evolutionary Biology</i>, vol. 33, no. 3, Wiley, 2020, pp. 342–51, doi:<a href=\"https://doi.org/10.1111/jeb.13570\">10.1111/jeb.13570</a>.","ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. K. Butlin, “Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?,” <i>Journal of Evolutionary Biology</i>, vol. 33, no. 3. Wiley, pp. 342–351, 2020.","apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., &#38; Butlin, R. K. (2020). Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.13570\">https://doi.org/10.1111/jeb.13570</a>","ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. 2020. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. 33(3), 342–351.","chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger K. Butlin. “Is Embryo Abortion a Post-Zygotic Barrier to Gene Flow between Littorina Ecotypes?” <i>Journal of Evolutionary Biology</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/jeb.13570\">https://doi.org/10.1111/jeb.13570</a>."},"intvolume":"        33","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","ddc":["570"],"date_created":"2019-12-22T23:00:43Z","external_id":{"isi":["000500954800001"],"pmid":["31724256"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","abstract":[{"lang":"eng","text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis, divergent selection forms strong barriers to gene flow, while the role of post‐zygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Post‐zygotic barriers might include genetic incompatibilities (e.g. Dobzhansky–Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1,011 embryos (mean 130 ± 123), and abortion rates varied between 0% and 100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterized female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index, and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant post‐zygotic barriers contributing to ecotype divergence, and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females."}],"oa_version":"Published Version","day":"01","publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"related_material":{"record":[{"status":"public","relation":"research_data","id":"13067"}]},"scopus_import":"1","file":[{"creator":"dernst","file_size":885611,"file_id":"8553","success":1,"date_updated":"2020-09-22T09:42:18Z","content_type":"application/pdf","relation":"main_file","file_name":"2020_EvolBiology_Johannesson.pdf","date_created":"2020-09-22T09:42:18Z","checksum":"7534ff0839709c0c5265c12d29432f03","access_level":"open_access"}],"file_date_updated":"2020-09-22T09:42:18Z","date_updated":"2025-07-10T11:54:22Z","_id":"7205","issue":"3","author":[{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"full_name":"Zagrodzka, Zuzanna","first_name":"Zuzanna","last_name":"Zagrodzka"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"article_processing_charge":"No","status":"public","doi":"10.1111/jeb.13570","department":[{"_id":"NiBa"}],"title":"Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?","language":[{"iso":"eng"}],"has_accepted_license":"1","month":"03","year":"2020","publisher":"Wiley","volume":33},{"article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Baskett","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","full_name":"Baskett, Carina","orcid":"0000-0002-7354-8574"},{"first_name":"Lucy","full_name":"Schroeder, Lucy","last_name":"Schroeder"},{"full_name":"Weber, Marjorie G.","first_name":"Marjorie G.","last_name":"Weber"},{"last_name":"Schemske","full_name":"Schemske, Douglas W.","first_name":"Douglas W."}],"issue":"1","OA_type":"hybrid","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"volume":90,"year":"2020","publisher":"Wiley","month":"02","has_accepted_license":"1","title":"Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"doi":"10.1002/ecm.1397","status":"public","tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"quality_controlled":"1","intvolume":"        90","citation":{"ama":"Baskett C, Schroeder L, Weber MG, Schemske DW. Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. <i>Ecological Monographs</i>. 2020;90(1). doi:<a href=\"https://doi.org/10.1002/ecm.1397\">10.1002/ecm.1397</a>","short":"C. Baskett, L. Schroeder, M.G. Weber, D.W. Schemske, Ecological Monographs 90 (2020).","chicago":"Baskett, Carina, Lucy Schroeder, Marjorie G. Weber, and Douglas W. Schemske. “Multiple Metrics of Latitudinal Patterns in Insect Pollination and Herbivory for a Tropical‐temperate Congener Pair.” <i>Ecological Monographs</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/ecm.1397\">https://doi.org/10.1002/ecm.1397</a>.","ieee":"C. Baskett, L. Schroeder, M. G. Weber, and D. W. Schemske, “Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair,” <i>Ecological Monographs</i>, vol. 90, no. 1. Wiley, 2020.","ista":"Baskett C, Schroeder L, Weber MG, Schemske DW. 2020. Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. 90(1), e01397.","apa":"Baskett, C., Schroeder, L., Weber, M. G., &#38; Schemske, D. W. (2020). Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. <i>Ecological Monographs</i>. Wiley. <a href=\"https://doi.org/10.1002/ecm.1397\">https://doi.org/10.1002/ecm.1397</a>","mla":"Baskett, Carina, et al. “Multiple Metrics of Latitudinal Patterns in Insect Pollination and Herbivory for a Tropical‐temperate Congener Pair.” <i>Ecological Monographs</i>, vol. 90, no. 1, e01397, Wiley, 2020, doi:<a href=\"https://doi.org/10.1002/ecm.1397\">10.1002/ecm.1397</a>."},"isi":1,"publication_status":"published","article_number":"e01397","publication":"Ecological Monographs","oa":1,"date_published":"2020-02-01T00:00:00Z","OA_place":"publisher","type":"journal_article","_id":"7236","file_date_updated":"2020-07-14T12:47:54Z","file":[{"file_size":537941,"creator":"dernst","date_updated":"2020-07-14T12:47:54Z","content_type":"application/pdf","file_id":"7469","date_created":"2020-02-10T08:18:14Z","relation":"main_file","file_name":"2020_EcologMono_Baskett.pdf","checksum":"ab8130c6e68101f5a091d05324c36f08","access_level":"open_access"}],"date_updated":"2025-04-14T07:44:07Z","scopus_import":"1","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","day":"01","publication_identifier":{"issn":["0012-9615"],"eissn":["1557-7015"]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The biotic interactions hypothesis posits that biotic interactions are more important drivers of adaptation closer to the equator, evidenced by “stronger” contemporary interactions (e.g. greater interaction rates) and/or patterns of trait evolution consistent with a history of stronger interactions. Support for the hypothesis is mixed, but few studies span tropical and temperate regions while experimentally controlling for evolutionary history. Here, we integrate field observations and common garden experiments to quantify the relative importance of pollination and herbivory in a pair of tropical‐temperate congeneric perennial herbs. Phytolacca rivinoides and P. americana are pioneer species native to the Neotropics and the eastern USA, respectively. We compared plant‐pollinator and plant‐herbivore interactions between three tropical populations of P. rivinoides from Costa Rica and three temperate populations of P. americana from its northern range edge in Michigan and Ohio. For some metrics of interaction importance, we also included three subtropical populations of P. americana from its southern range edge in Florida. This approach confounds species and region but allows us, uniquely, to measure complementary proxies of interaction importance across a tropical‐temperate range in one system. To test the prediction that lower‐latitude plants are more reliant on insect pollinators, we quantified floral display and reward, insect visitation rates, and self‐pollination ability (autogamy). To test the prediction that lower‐latitude plants experience more herbivore pressure, we quantified herbivory rates, herbivore abundance, and leaf palatability. We found evidence supporting the biotic interactions hypothesis for most comparisons between P. rivinoides and north‐temperate P. americana (floral display, insect visitation, autogamy, herbivory, herbivore abundance, and young‐leaf palatability). Results for subtropical P. americana populations, however, were typically not intermediate between P. rivinoides and north‐temperate P. americana, as would be predicted by a linear latitudinal gradient in interaction importance. Subtropical young‐leaf palatability was intermediate, but subtropical mature leaves were the least palatable, and pollination‐related traits did not differ between temperate and subtropical regions. These nonlinear patterns of interaction importance suggest future work to relate interaction importance to climatic or biotic thresholds. In sum, we found that the biotic interactions hypothesis was more consistently supported at the larger spatial scale of our study."}],"user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","article_type":"original","external_id":{"isi":["000508511600001"]},"date_created":"2020-01-07T12:47:07Z","ddc":["570"]},{"publication_identifier":{"issn":["1742-5689"],"eissn":["1742-5662"]},"day":"01","oa_version":"Published Version","abstract":[{"text":"The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. We have developed a way to infer a set of developmentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods.","lang":"eng"}],"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-04-08T15:19:17Z","ddc":["570"],"_id":"7651","file":[{"file_size":1556190,"creator":"dernst","file_id":"7660","content_type":"application/pdf","date_updated":"2020-07-14T12:48:01Z","relation":"main_file","file_name":"2020_JournRoyalSociety_Larsson.pdf","date_created":"2020-04-14T12:31:16Z","checksum":"4eb102304402f5c56432516b84df86d6","access_level":"open_access"}],"date_updated":"2026-08-12T14:06:19Z","file_date_updated":"2020-07-14T12:48:01Z","scopus_import":"1","publication_status":"published","publication":"Journal of the Royal Society Interface","article_number":"20190721","oa":1,"date_published":"2020-02-01T00:00:00Z","type":"journal_article","quality_controlled":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        17","citation":{"mla":"Larsson, J., et al. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” <i>Journal of the Royal Society Interface</i>, vol. 17, no. 163, 20190721, Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rsif.2019.0721\">10.1098/rsif.2019.0721</a>.","apa":"Larsson, J., Westram, A. M., Bengmark, S., Lundh, T., &#38; Butlin, R. K. (2020). A developmentally descriptive method for quantifying shape in gastropod shells. <i>Journal of the Royal Society Interface</i>. Royal Society. <a href=\"https://doi.org/10.1098/rsif.2019.0721\">https://doi.org/10.1098/rsif.2019.0721</a>","ista":"Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. 2020. A developmentally descriptive method for quantifying shape in gastropod shells. Journal of the Royal Society Interface. 17(163), 20190721.","ieee":"J. Larsson, A. M. Westram, S. Bengmark, T. Lundh, and R. K. Butlin, “A developmentally descriptive method for quantifying shape in gastropod shells,” <i>Journal of the Royal Society Interface</i>, vol. 17, no. 163. Royal Society, 2020.","chicago":"Larsson, J., Anja M Westram, S. Bengmark, T. Lundh, and R. K. Butlin. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” <i>Journal of the Royal Society Interface</i>. Royal Society, 2020. <a href=\"https://doi.org/10.1098/rsif.2019.0721\">https://doi.org/10.1098/rsif.2019.0721</a>.","short":"J. Larsson, A.M. Westram, S. Bengmark, T. Lundh, R.K. Butlin, Journal of the Royal Society Interface 17 (2020).","ama":"Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. A developmentally descriptive method for quantifying shape in gastropod shells. <i>Journal of the Royal Society Interface</i>. 2020;17(163). doi:<a href=\"https://doi.org/10.1098/rsif.2019.0721\">10.1098/rsif.2019.0721</a>"},"month":"02","has_accepted_license":"1","language":[{"iso":"eng"}],"title":"A developmentally descriptive method for quantifying shape in gastropod shells","department":[{"_id":"NiBa"}],"doi":"10.1098/rsif.2019.0721","status":"public","volume":17,"year":"2020","publisher":"Royal Society","article_processing_charge":"No","author":[{"full_name":"Larsson, J.","first_name":"J.","last_name":"Larsson"},{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"last_name":"Bengmark","first_name":"S.","full_name":"Bengmark, S."},{"first_name":"T.","full_name":"Lundh, T.","last_name":"Lundh"},{"full_name":"Butlin, R. K.","first_name":"R. K.","last_name":"Butlin"}],"issue":"163"},{"citation":{"mla":"Johannesson, Kerstin, et al. <i>Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes?</i> Dryad, 2019, doi:<a href=\"https://doi.org/10.5061/DRYAD.TB2RBNZWK\">10.5061/DRYAD.TB2RBNZWK</a>.","chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes?” Dryad, 2019. <a href=\"https://doi.org/10.5061/DRYAD.TB2RBNZWK\">https://doi.org/10.5061/DRYAD.TB2RBNZWK</a>.","ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.TB2RBNZWK\">10.5061/DRYAD.TB2RBNZWK</a>.","apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., &#38; Butlin, R. (2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? Dryad. <a href=\"https://doi.org/10.5061/DRYAD.TB2RBNZWK\">https://doi.org/10.5061/DRYAD.TB2RBNZWK</a>","ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. Butlin, “Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?” Dryad, 2019.","ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? 2019. doi:<a href=\"https://doi.org/10.5061/DRYAD.TB2RBNZWK\">10.5061/DRYAD.TB2RBNZWK</a>","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019)."},"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"article_processing_charge":"No","author":[{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna","first_name":"Zuzanna"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram"},{"last_name":"Butlin","full_name":"Butlin, Roger","first_name":"Roger"}],"oa":1,"date_published":"2019-12-02T00:00:00Z","type":"research_data_reference","related_material":{"record":[{"status":"public","id":"7205","relation":"used_in_publication"}]},"publisher":"Dryad","license":"https://creativecommons.org/publicdomain/zero/1.0/","year":"2019","_id":"13067","date_updated":"2025-07-10T11:54:22Z","department":[{"_id":"NiBa"}],"abstract":[{"lang":"eng","text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis divergent selection forms strong barriers to gene flow, while the role of postzygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Postzygotic barriers might include genetic incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of &gt;500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterised female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant postzygotic barriers contributing to ecotype divergence and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females."}],"doi":"10.5061/DRYAD.TB2RBNZWK","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.tb2rbnzwk"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_created":"2023-05-23T16:36:27Z","ddc":["570"],"day":"02","month":"12","oa_version":"Published Version","title":"Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?"},{"citation":{"ama":"Faria R, Johannesson K, Butlin RK, Westram AM. Evolving inversions. <i>Trends in Ecology and Evolution</i>. 2019;34(3):239-248. doi:<a href=\"https://doi.org/10.1016/j.tree.2018.12.005\">10.1016/j.tree.2018.12.005</a>","short":"R. Faria, K. Johannesson, R.K. Butlin, A.M. Westram, Trends in Ecology and Evolution 34 (2019) 239–248.","mla":"Faria, Rui, et al. “Evolving Inversions.” <i>Trends in Ecology and Evolution</i>, vol. 34, no. 3, Elsevier, 2019, pp. 239–48, doi:<a href=\"https://doi.org/10.1016/j.tree.2018.12.005\">10.1016/j.tree.2018.12.005</a>.","chicago":"Faria, Rui, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram. “Evolving Inversions.” <i>Trends in Ecology and Evolution</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.tree.2018.12.005\">https://doi.org/10.1016/j.tree.2018.12.005</a>.","ista":"Faria R, Johannesson K, Butlin RK, Westram AM. 2019. Evolving inversions. Trends in Ecology and Evolution. 34(3), 239–248.","ieee":"R. Faria, K. Johannesson, R. K. Butlin, and A. M. Westram, “Evolving inversions,” <i>Trends in Ecology and Evolution</i>, vol. 34, no. 3. Elsevier, pp. 239–248, 2019.","apa":"Faria, R., Johannesson, K., Butlin, R. K., &#38; Westram, A. M. (2019). Evolving inversions. <i>Trends in Ecology and Evolution</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tree.2018.12.005\">https://doi.org/10.1016/j.tree.2018.12.005</a>"},"isi":1,"intvolume":"        34","quality_controlled":"1","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"page":"239-248","type":"journal_article","oa":1,"date_published":"2019-03-01T00:00:00Z","publication":"Trends in Ecology and Evolution","publication_status":"published","ec_funded":1,"scopus_import":"1","date_updated":"2026-04-16T09:48:52Z","file_date_updated":"2020-07-14T12:47:13Z","file":[{"creator":"cziletti","file_size":1946795,"date_updated":"2020-07-14T12:47:13Z","content_type":"application/pdf","file_id":"7245","date_created":"2020-01-09T10:55:58Z","relation":"main_file","file_name":"2019_Trends_Evolution_Faria.pdf","checksum":"ef24572d6ebcc1452c067e05410cc4a2","access_level":"open_access"}],"_id":"5911","external_id":{"isi":["000459899000013"]},"date_created":"2019-02-03T22:59:15Z","ddc":["570"],"abstract":[{"text":"Empirical data suggest that inversions in many species contain genes important for intraspecific divergence and speciation, yet mechanisms of evolution remain unclear. While genes inside an inversion are tightly linked, inversions are not static but evolve separately from the rest of the genome by new mutations, recombination within arrangements, and gene flux between arrangements. Inversion polymorphisms are maintained by different processes, for example, divergent or balancing selection, or a mix of multiple processes. Moreover, the relative roles of selection, drift, mutation, and recombination will change over the lifetime of an inversion and within its area of distribution. We believe inversions are central to the evolution of many species, but we need many more data and new models to understand the complex mechanisms involved.","lang":"eng"}],"article_type":"original","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","publication_identifier":{"issn":["0169-5347"]},"day":"01","issue":"3","author":[{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"},{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","publisher":"Elsevier","year":"2019","volume":34,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"status":"public","doi":"10.1016/j.tree.2018.12.005","department":[{"_id":"NiBa"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"title":"Evolving inversions","month":"03"},{"type":"journal_article","date_published":"2019-02-07T00:00:00Z","oa":1,"article_number":"e2005902","publication":"PLoS Biology","publication_status":"published","citation":{"ieee":"R. M. Merrill <i>et al.</i>, “Genetic dissection of assortative mating behavior,” <i>PLoS Biology</i>, vol. 17, no. 2. Public Library of Science, 2019.","ista":"Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Genetic dissection of assortative mating behavior. PLoS Biology. 17(2), e2005902.","apa":"Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Genetic dissection of assortative mating behavior. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2005902\">https://doi.org/10.1371/journal.pbio.2005902</a>","chicago":"Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Genetic Dissection of Assortative Mating Behavior.” <i>PLoS Biology</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pbio.2005902\">https://doi.org/10.1371/journal.pbio.2005902</a>.","mla":"Merrill, Richard M., et al. “Genetic Dissection of Assortative Mating Behavior.” <i>PLoS Biology</i>, vol. 17, no. 2, e2005902, Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005902\">10.1371/journal.pbio.2005902</a>.","short":"R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, PLoS Biology 17 (2019).","ama":"Merrill RM, Rastas P, Martin SH, et al. Genetic dissection of assortative mating behavior. <i>PLoS Biology</i>. 2019;17(2). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005902\">10.1371/journal.pbio.2005902</a>"},"isi":1,"intvolume":"        17","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"quality_controlled":"1","ddc":["570"],"date_created":"2019-02-17T22:59:21Z","external_id":{"isi":["000460317100001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"The evolution of new species is made easier when traits under divergent ecological selection are also mating cues. Such ecological mating cues are now considered more common than previously thought, but we still know little about the genetic changes underlying their evolution or more generally about the genetic basis for assortative mating behaviors. Both tight physical linkage and the existence of large-effect preference loci will strengthen genetic associations between behavioral and ecological barriers, promoting the evolution of assortative mating. The warning patterns of Heliconius melpomene and H. cydno are under disruptive selection due to increased predation of nonmimetic hybrids and are used during mate recognition. We carried out a genome-wide quantitative trait locus (QTL) analysis of preference behaviors between these species and showed that divergent male preference has a simple genetic basis. We identify three QTLs that together explain a large proportion (approximately 60%) of the difference in preference behavior observed between the parental species. One of these QTLs is just 1.2 (0-4.8) centiMorgans (cM) from the major color pattern gene optix, and, individually, all three have a large effect on the preference phenotype. Genomic divergence between H. cydno and H. melpomene is high but broadly heterogenous, and admixture is reduced at the preference-optix color pattern locus but not the other preference QTLs. The simple genetic architecture we reveal will facilitate the evolution and maintenance of new species despite ongoing gene flow by coupling behavioral and ecological aspects of reproductive isolation.","lang":"eng"}],"oa_version":"Published Version","day":"07","related_material":{"record":[{"relation":"research_data","id":"9801","status":"public"}]},"scopus_import":"1","date_updated":"2023-08-24T14:46:23Z","file_date_updated":"2020-07-14T12:47:17Z","file":[{"file_size":2005949,"creator":"dernst","date_updated":"2020-07-14T12:47:17Z","content_type":"application/pdf","file_id":"6036","date_created":"2019-02-18T14:57:24Z","relation":"main_file","file_name":"2019_PLOS_Merrill.pdf","access_level":"open_access","checksum":"5f34001617ee729314ca520c049b1112"}],"_id":"6022","issue":"2","author":[{"last_name":"Merrill","first_name":"Richard M.","full_name":"Merrill, Richard M."},{"first_name":"Pasi","full_name":"Rastas, Pasi","last_name":"Rastas"},{"first_name":"Simon H.","full_name":"Martin, Simon H.","last_name":"Martin"},{"last_name":"Melo Hurtado","full_name":"Melo Hurtado, Maria C","id":"386D7308-F248-11E8-B48F-1D18A9856A87","first_name":"Maria C"},{"last_name":"Barker","full_name":"Barker, Sarah","first_name":"Sarah"},{"first_name":"John","full_name":"Davey, John","last_name":"Davey"},{"first_name":"W. Owen","full_name":"Mcmillan, W. Owen","last_name":"Mcmillan"},{"full_name":"Jiggins, Chris D.","first_name":"Chris D.","last_name":"Jiggins"}],"article_processing_charge":"No","status":"public","department":[{"_id":"NiBa"}],"doi":"10.1371/journal.pbio.2005902","title":"Genetic dissection of assortative mating behavior","language":[{"iso":"eng"}],"has_accepted_license":"1","month":"02","year":"2019","publisher":"Public Library of Science","volume":17},{"alternative_title":["ISTA Thesis"],"supervisor":[{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"corr_author":"1","citation":{"mla":"Prizak, Roshan. <i>Coevolution of Transcription Factors and Their Binding Sites in Sequence Space</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/at:ista:th6071\">10.15479/at:ista:th6071</a>.","ieee":"R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” Institute of Science and Technology Austria, 2019.","ista":"Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria.","apa":"Prizak, R. (2019). <i>Coevolution of transcription factors and their binding sites in sequence space</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:th6071\">https://doi.org/10.15479/at:ista:th6071</a>","chicago":"Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/at:ista:th6071\">https://doi.org/10.15479/at:ista:th6071</a>.","short":"R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019.","ama":"Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:<a href=\"https://doi.org/10.15479/at:ista:th6071\">10.15479/at:ista:th6071</a>"},"publication_status":"published","oa":1,"date_published":"2019-03-11T00:00:00Z","OA_place":"publisher","page":"189","type":"dissertation","_id":"6071","file":[{"checksum":"e60a72de35d270b31f1a23d50f224ec0","access_level":"open_access","date_created":"2019-03-06T16:05:07Z","relation":"main_file","file_name":"Thesis_final_PDFA_RoshanPrizak.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:18Z","file_id":"6072","file_size":20995465,"creator":"rprizak"},{"access_level":"closed","title":"Latex files","checksum":"67c2630333d05ebafef5f018863a8465","relation":"source_file","file_name":"thesis_v2_merge.zip","date_created":"2019-03-06T16:09:39Z","file_id":"6073","date_updated":"2020-07-14T12:47:18Z","content_type":"application/zip","creator":"rprizak","file_size":85705272}],"file_date_updated":"2020-07-14T12:47:18Z","date_updated":"2026-04-08T13:54:25Z","degree_awarded":"PhD","related_material":{"record":[{"id":"955","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"1358","relation":"part_of_dissertation"}]},"day":"11","publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","abstract":[{"text":"Transcription factors, by binding to specific sequences on the DNA, control the precise spatio-temporal expression of genes inside a cell. However, this specificity is limited, leading to frequent incorrect binding of transcription factors that might have deleterious consequences on the cell. By constructing a biophysical model of TF-DNA binding in the context of gene regulation, I will first explore how regulatory constraints can strongly shape the distribution of a population in sequence space. Then, by directly linking this to a picture of multiple types of transcription factors performing their functions simultaneously inside the cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions between transcription factors and binding sites that lead to erroneous regulatory states -- and understand the constraints this places on the design of regulatory systems. I will then develop a generic theoretical framework to investigate the coevolution of multiple transcription factors and multiple binding sites, in the context of a gene regulatory network that performs a certain function. As a particular tractable version of this problem, I will consider the evolution of two transcription factors when they transmit upstream signals to downstream target genes. Specifically, I will describe the evolutionary steady states and the evolutionary pathways involved, along with their timescales, of a system that initially undergoes a transcription factor duplication event. To connect this important theoretical model to the prominent biological event of transcription factor duplication giving rise to paralogous families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription factors, a major family in humans, and focus on the patterns of evolution that paralogs have undergone in their various protein domains in the recent past. ","lang":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2019-03-06T16:16:10Z","ddc":["576"],"article_processing_charge":"No","author":[{"last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan"}],"project":[{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"publisher":"Institute of Science and Technology Austria","year":"2019","month":"03","has_accepted_license":"1","title":"Coevolution of transcription factors and their binding sites in sequence space","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"doi":"10.15479/at:ista:th6071","status":"public"},{"issue":"3","author":[{"last_name":"Fraisse","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"last_name":"Puixeu Sala","first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso"}],"article_processing_charge":"No","year":"2019","publisher":"Oxford University Press","volume":36,"project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF"}],"status":"public","doi":"10.1093/molbev/msy246","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559","open_access":"1"}],"language":[{"iso":"eng"}],"title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","month":"03","citation":{"chicago":"Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/molbev/msy246\">https://doi.org/10.1093/molbev/msy246</a>.","ista":"Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 36(3), 500–515.","ieee":"C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy of selection in drosophila melanogaster,” <i>Molecular biology and evolution</i>, vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019.","apa":"Fraisse, C., Puixeu Sala, G., &#38; Vicoso, B. (2019). Pleiotropy modulates the efficacy of selection in drosophila melanogaster. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msy246\">https://doi.org/10.1093/molbev/msy246</a>","mla":"Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” <i>Molecular Biology and Evolution</i>, vol. 36, no. 3, Oxford University Press, 2019, pp. 500–15, doi:<a href=\"https://doi.org/10.1093/molbev/msy246\">10.1093/molbev/msy246</a>.","ama":"Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. <i>Molecular biology and evolution</i>. 2019;36(3):500-515. doi:<a href=\"https://doi.org/10.1093/molbev/msy246\">10.1093/molbev/msy246</a>","short":"C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 500–515."},"isi":1,"intvolume":"        36","quality_controlled":"1","pmid":1,"page":"500-515","type":"journal_article","oa":1,"date_published":"2019-03-01T00:00:00Z","publication":"Molecular biology and evolution","publication_status":"published","related_material":{"record":[{"relation":"popular_science","id":"5757","status":"public"}]},"scopus_import":"1","date_updated":"2025-04-15T08:18:38Z","_id":"6089","external_id":{"pmid":["30590559"],"isi":["000462585100006"]},"date_created":"2019-03-10T22:59:19Z","abstract":[{"text":"Pleiotropy is the well-established idea that a single mutation affects multiple phenotypes. If a mutation has opposite effects on fitness when expressed in different contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce the efficacy of selection by limiting the fixation of beneficial mutations through adaptation, and the removal of deleterious mutations through purifying selection. Although this has been widely discussed, in particular in the context of a putative “gender load,” it has yet to be systematically quantified. In this work, we empirically estimate to which extent different pleiotropic regimes impede the efficacy of selection in Drosophila melanogaster. We use whole-genome polymorphism data from a single African population and divergence data from D. simulans to estimate the fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction of selection (DoS). After controlling for confounding covariates, we find that the different pleiotropic regimes have a relatively small, but significant, effect on selection efficacy. Specifically, our results suggest that pleiotropic sexual antagonism may restrict the efficacy of selection, but that this conflict can be resolved by limiting the expression of genes to the sex where they are beneficial. Intermediate levels of pleiotropy across tissues and life stages can also lead to maladaptation in D. melanogaster, due to inefficient purifying selection combined with low frequency of mutations that confer a selective advantage. Thus, our study highlights the need to consider the efficacy of selection in the context of antagonistic pleiotropy, and of genetic conflict in general.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"day":"01"},{"author":[{"full_name":"Carballo-Pacheco, Martín","first_name":"Martín","last_name":"Carballo-Pacheco"},{"first_name":"Jonathan","full_name":"Desponds, Jonathan","last_name":"Desponds"},{"first_name":"Tatyana","full_name":"Gavrilchenko, Tatyana","last_name":"Gavrilchenko"},{"full_name":"Mayer, Andreas","first_name":"Andreas","last_name":"Mayer"},{"last_name":"Prizak","full_name":"Prizak, Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan"},{"full_name":"Reddy, Gautam","first_name":"Gautam","last_name":"Reddy"},{"last_name":"Nemenman","full_name":"Nemenman, Ilya","first_name":"Ilya"},{"last_name":"Mora","first_name":"Thierry","full_name":"Mora, Thierry"}],"article_processing_charge":"No","issue":"2","title":"Receptor crosstalk improves concentration sensing of multiple ligands","language":[{"iso":"eng"}],"month":"02","status":"public","doi":"10.1103/PhysRevE.99.022423","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/448118v1.abstract","open_access":"1"}],"volume":99,"year":"2019","publisher":"American Physical Society","publication":"Physical Review E","article_number":"022423","publication_status":"published","type":"journal_article","oa":1,"date_published":"2019-02-26T00:00:00Z","quality_controlled":"1","citation":{"ista":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G, Nemenman I, Mora T. 2019. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 99(2), 022423.","apa":"Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R., Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing of multiple ligands. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.99.022423\">https://doi.org/10.1103/PhysRevE.99.022423</a>","ieee":"M. Carballo-Pacheco <i>et al.</i>, “Receptor crosstalk improves concentration sensing of multiple ligands,” <i>Physical Review E</i>, vol. 99, no. 2. American Physical Society, 2019.","chicago":"Carballo-Pacheco, Martín, Jonathan Desponds, Tatyana Gavrilchenko, Andreas Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” <i>Physical Review E</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/PhysRevE.99.022423\">https://doi.org/10.1103/PhysRevE.99.022423</a>.","mla":"Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” <i>Physical Review E</i>, vol. 99, no. 2, 022423, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/PhysRevE.99.022423\">10.1103/PhysRevE.99.022423</a>.","short":"M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).","ama":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves concentration sensing of multiple ligands. <i>Physical Review E</i>. 2019;99(2). doi:<a href=\"https://doi.org/10.1103/PhysRevE.99.022423\">10.1103/PhysRevE.99.022423</a>"},"isi":1,"intvolume":"        99","oa_version":"Preprint","day":"26","external_id":{"isi":["000459916500007"]},"date_created":"2019-03-10T22:59:20Z","abstract":[{"text":"Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems, leading to crosstalk between ligand-receptor pairs. Crosstalk is often thought of as a deviation from optimal specific recognition, as the binding of noncognate ligands can interfere with the detection of the receptor's cognate ligand, possibly leading to a false triggering of a downstream signaling pathway. Here we quantify the optimal precision of sensing the concentrations of multiple ligands by a collection of promiscuous receptors. We demonstrate that crosstalk can improve precision in concentration sensing and discrimination tasks. To achieve superior precision, the additional information about ligand concentrations contained in short binding events of the noncognate ligand should be exploited. We present a proofreading scheme to realize an approximate estimation of multiple ligand concentrations that reaches a precision close to the derived optimal bounds. Our results help rationalize the observed ubiquity of receptor crosstalk in molecular sensing.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-28T13:12:06Z","_id":"6090","scopus_import":"1"},{"year":"2019","publisher":"Wiley","volume":28,"doi":"10.1111/mec.14972","department":[{"_id":"NiBa"}],"status":"public","month":"03","has_accepted_license":"1","title":"Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","language":[{"iso":"eng"}],"issue":"6","article_processing_charge":"No","author":[{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"full_name":"Chaube, Pragya","first_name":"Pragya","last_name":"Chaube"},{"full_name":"Morales, Hernán E.","first_name":"Hernán E.","last_name":"Morales"},{"last_name":"Larsson","full_name":"Larsson, Tomas","first_name":"Tomas"},{"last_name":"Lemmon","first_name":"Alan R.","full_name":"Lemmon, Alan R."},{"last_name":"Lemmon","full_name":"Lemmon, Emily M.","first_name":"Emily M."},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"last_name":"Panova","first_name":"Marina","full_name":"Panova, Marina"},{"first_name":"Mark","full_name":"Ravinet, Mark","last_name":"Ravinet"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"}],"scopus_import":"1","related_material":{"record":[{"relation":"research_data","id":"9837","status":"public"}]},"_id":"6095","file_date_updated":"2020-07-14T12:47:19Z","date_updated":"2023-08-24T14:50:27Z","file":[{"file_id":"6097","date_updated":"2020-07-14T12:47:19Z","content_type":"application/pdf","creator":"dernst","file_size":1510715,"checksum":"f915885756057ec0ca5912a41f46a887","access_level":"open_access","file_name":"2019_MolecularEcology_Faria.pdf","relation":"main_file","date_created":"2019-03-11T16:12:54Z"}],"abstract":[{"lang":"eng","text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000465219200013"]},"date_created":"2019-03-10T22:59:21Z","ddc":["570"],"day":"01","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"oa_version":"Published Version","intvolume":"        28","citation":{"short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, Molecular Ecology 28 (2019) 1375–1393.","ama":"Faria R, Chaube P, Morales HE, et al. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. <i>Molecular Ecology</i>. 2019;28(6):1375-1393. doi:<a href=\"https://doi.org/10.1111/mec.14972\">10.1111/mec.14972</a>","ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2019. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. 28(6), 1375–1393.","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2019). Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.14972\">https://doi.org/10.1111/mec.14972</a>","ieee":"R. Faria <i>et al.</i>, “Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes,” <i>Molecular Ecology</i>, vol. 28, no. 6. Wiley, pp. 1375–1393, 2019.","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” <i>Molecular Ecology</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/mec.14972\">https://doi.org/10.1111/mec.14972</a>.","mla":"Faria, Rui, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” <i>Molecular Ecology</i>, vol. 28, no. 6, Wiley, 2019, pp. 1375–93, doi:<a href=\"https://doi.org/10.1111/mec.14972\">10.1111/mec.14972</a>."},"isi":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","oa":1,"date_published":"2019-03-01T00:00:00Z","page":"1375-1393","type":"journal_article","publication_status":"published","publication":"Molecular Ecology"},{"quality_controlled":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"         8","isi":1,"citation":{"ieee":"N. H. Barton, J. Hermisson, and M. Nordborg, “Why structure matters,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","ista":"Barton NH, Hermisson J, Nordborg M. 2019. Why structure matters. eLife. 8, e45380.","apa":"Barton, N. H., Hermisson, J., &#38; Nordborg, M. (2019). Why structure matters. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.45380\">https://doi.org/10.7554/eLife.45380</a>","chicago":"Barton, Nicholas H, Joachim Hermisson, and Magnus Nordborg. “Why Structure Matters.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/eLife.45380\">https://doi.org/10.7554/eLife.45380</a>.","mla":"Barton, Nicholas H., et al. “Why Structure Matters.” <i>ELife</i>, vol. 8, e45380, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/eLife.45380\">10.7554/eLife.45380</a>.","short":"N.H. Barton, J. Hermisson, M. Nordborg, ELife 8 (2019).","ama":"Barton NH, Hermisson J, Nordborg M. Why structure matters. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/eLife.45380\">10.7554/eLife.45380</a>"},"publication_status":"published","publication":"eLife","article_number":"e45380","oa":1,"date_published":"2019-03-21T00:00:00Z","type":"journal_article","_id":"6230","date_updated":"2026-04-02T14:03:15Z","file":[{"access_level":"open_access","checksum":"130d7544b57df4a6787e1263c2d7ea43","relation":"main_file","file_name":"2019_eLife_Barton.pdf","date_created":"2019-04-11T11:43:38Z","file_id":"6293","content_type":"application/pdf","date_updated":"2020-07-14T12:47:24Z","file_size":298466,"creator":"dernst"}],"file_date_updated":"2020-07-14T12:47:24Z","scopus_import":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/body-height-bmi-disease-risk-co/","description":"News on IST Homepage","relation":"press_release"}]},"day":"21","publication_identifier":{"eissn":["2050-084X"]},"oa_version":"Published Version","abstract":[{"text":"Great care is needed when interpreting claims about the genetic basis of human variation based on data from genome-wide association studies.","lang":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","external_id":{"isi":["000461988300001"]},"date_created":"2019-04-07T21:59:15Z","ddc":["570"],"article_processing_charge":"No","author":[{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hermisson","full_name":"Hermisson, Joachim","first_name":"Joachim"},{"full_name":"Nordborg, Magnus","first_name":"Magnus","last_name":"Nordborg"}],"volume":8,"year":"2019","publisher":"eLife Sciences Publications","month":"03","has_accepted_license":"1","language":[{"iso":"eng"}],"title":"Why structure matters","doi":"10.7554/eLife.45380","department":[{"_id":"NiBa"}],"status":"public"},{"scopus_import":"1","_id":"8281","date_updated":"2024-10-21T06:02:39Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"We review the history of population genetics, starting with its origins a century ago from the synthesis between Mendel and Darwin's ideas, through to the recent development of sophisticated schemes of inference from sequence data, based on the coalescent. We explain the close relation between the coalescent and a diffusion process, which we illustrate by their application to understand spatial structure. We summarise the powerful methods available for analysis of multiple loci, when linkage equilibrium can be assumed, and then discuss approaches to the more challenging case, where associations between alleles require that we follow genotype, rather than allele, frequencies. Though we can hardly cover the whole of population genetics, we give an overview of the current state of the subject, and future challenges to it."}],"ddc":["576"],"date_created":"2020-08-21T04:25:39Z","external_id":{"isi":["000261343000003"]},"day":"29","publication_identifier":{"isbn":["9781119429142"]},"oa_version":"None","citation":{"short":"N.H. Barton, A. Etheridge, in:, D. Balding, I. Moltke, J. Marioni (Eds.), Handbook of Statistical Genomics, 4th ed., Wiley, 2019, pp. 115–144.","ama":"Barton NH, Etheridge A. Mathematical models in population genetics. In: Balding D, Moltke I, Marioni J, eds. <i>Handbook of Statistical Genomics</i>. 4th ed. Wiley; 2019:115-144. doi:<a href=\"https://doi.org/10.1002/9781119487845.ch4\">10.1002/9781119487845.ch4</a>","mla":"Barton, Nicholas H., and Alison Etheridge. “Mathematical Models in Population Genetics.” <i>Handbook of Statistical Genomics</i>, edited by David Balding et al., 4th ed., Wiley, 2019, pp. 115–44, doi:<a href=\"https://doi.org/10.1002/9781119487845.ch4\">10.1002/9781119487845.ch4</a>.","ista":"Barton NH, Etheridge A. 2019.Mathematical models in population genetics. In: Handbook of statistical genomics. , 115–144.","apa":"Barton, N. H., &#38; Etheridge, A. (2019). Mathematical models in population genetics. In D. Balding, I. Moltke, &#38; J. Marioni (Eds.), <i>Handbook of statistical genomics</i> (4th ed., pp. 115–144). Wiley. <a href=\"https://doi.org/10.1002/9781119487845.ch4\">https://doi.org/10.1002/9781119487845.ch4</a>","ieee":"N. H. Barton and A. Etheridge, “Mathematical models in population genetics,” in <i>Handbook of statistical genomics</i>, 4th ed., D. Balding, I. Moltke, and J. Marioni, Eds. Wiley, 2019, pp. 115–144.","chicago":"Barton, Nicholas H, and Alison Etheridge. “Mathematical Models in Population Genetics.” In <i>Handbook of Statistical Genomics</i>, edited by David Balding, Ida Moltke, and John Marioni, 4th ed., 115–44. Wiley, 2019. <a href=\"https://doi.org/10.1002/9781119487845.ch4\">https://doi.org/10.1002/9781119487845.ch4</a>."},"isi":1,"quality_controlled":"1","date_published":"2019-07-29T00:00:00Z","type":"book_chapter","page":"115-144","publication_status":"published","publication":"Handbook of statistical genomics","publisher":"Wiley","year":"2019","department":[{"_id":"NiBa"}],"doi":"10.1002/9781119487845.ch4","status":"public","month":"07","language":[{"iso":"eng"}],"title":"Mathematical models in population genetics","edition":"4","editor":[{"last_name":"Balding","first_name":"David","full_name":"Balding, David"},{"full_name":"Moltke, Ida","first_name":"Ida","last_name":"Moltke"},{"first_name":"John","full_name":"Marioni, John","last_name":"Marioni"}],"article_processing_charge":"No","author":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Alison","full_name":"Etheridge, Alison","last_name":"Etheridge"}]},{"date_published":"2019-02-07T00:00:00Z","type":"research_data_reference","article_processing_charge":"No","author":[{"first_name":"Richard M.","full_name":"Merrill, Richard M.","last_name":"Merrill"},{"last_name":"Rastas","full_name":"Rastas, Pasi","first_name":"Pasi"},{"last_name":"Martin","first_name":"Simon H.","full_name":"Martin, Simon H."},{"last_name":"Melo Hurtado","first_name":"Maria C","id":"386D7308-F248-11E8-B48F-1D18A9856A87","full_name":"Melo Hurtado, Maria C"},{"last_name":"Barker","full_name":"Barker, Sarah","first_name":"Sarah"},{"last_name":"Davey","full_name":"Davey, John","first_name":"John"},{"first_name":"W. Owen","full_name":"Mcmillan, W. Owen","last_name":"Mcmillan"},{"last_name":"Jiggins","first_name":"Chris D.","full_name":"Jiggins, Chris D."}],"citation":{"apa":"Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Raw behavioral data. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2005902.s006\">https://doi.org/10.1371/journal.pbio.2005902.s006</a>","ista":"Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Raw behavioral data, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2005902.s006\">10.1371/journal.pbio.2005902.s006</a>.","ieee":"R. M. Merrill <i>et al.</i>, “Raw behavioral data.” Public Library of Science, 2019.","chicago":"Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Raw Behavioral Data.” Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pbio.2005902.s006\">https://doi.org/10.1371/journal.pbio.2005902.s006</a>.","mla":"Merrill, Richard M., et al. <i>Raw Behavioral Data</i>. Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005902.s006\">10.1371/journal.pbio.2005902.s006</a>.","short":"R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, (2019).","ama":"Merrill RM, Rastas P, Martin SH, et al. Raw behavioral data. 2019. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005902.s006\">10.1371/journal.pbio.2005902.s006</a>"},"day":"07","month":"02","oa_version":"Published Version","title":"Raw behavioral data","department":[{"_id":"NiBa"}],"doi":"10.1371/journal.pbio.2005902.s006","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","date_created":"2021-08-06T11:34:56Z","_id":"9801","date_updated":"2023-08-24T14:46:23Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6022"}]},"publisher":"Public Library of Science","year":"2019"},{"status":"public","date_created":"2021-08-06T11:45:11Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.8tp0900"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"NiBa"}],"abstract":[{"lang":"eng","text":"This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation-selection balance in a large, partially selfing source population under selection involving multiple non-identical loci. I then use individual-based simulations to study the eco-evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long-term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed."}],"doi":"10.5061/dryad.8tp0900","oa_version":"Published Version","title":"Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat","month":"07","day":"16","publisher":"Dryad","year":"2019","related_material":{"record":[{"status":"public","id":"6680","relation":"used_in_publication"}]},"date_updated":"2024-10-09T20:58:56Z","_id":"9802","type":"research_data_reference","date_published":"2019-07-16T00:00:00Z","oa":1,"citation":{"ama":"Sachdeva H. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. 2019. doi:<a href=\"https://doi.org/10.5061/dryad.8tp0900\">10.5061/dryad.8tp0900</a>","short":"H. Sachdeva, (2019).","mla":"Sachdeva, Himani. <i>Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat</i>. Dryad, 2019, doi:<a href=\"https://doi.org/10.5061/dryad.8tp0900\">10.5061/dryad.8tp0900</a>.","chicago":"Sachdeva, Himani. “Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Dryad, 2019. <a href=\"https://doi.org/10.5061/dryad.8tp0900\">https://doi.org/10.5061/dryad.8tp0900</a>.","ista":"Sachdeva H. 2019. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat, Dryad, <a href=\"https://doi.org/10.5061/dryad.8tp0900\">10.5061/dryad.8tp0900</a>.","ieee":"H. Sachdeva, “Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat.” Dryad, 2019.","apa":"Sachdeva, H. (2019). Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. Dryad. <a href=\"https://doi.org/10.5061/dryad.8tp0900\">https://doi.org/10.5061/dryad.8tp0900</a>"},"author":[{"last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","full_name":"Sachdeva, Himani"}],"article_processing_charge":"No"},{"status":"public","date_created":"2021-08-06T11:48:42Z","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"doi":"10.5061/dryad.n1701c9","abstract":[{"text":"Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life-cycle dynamics. Here, we investigate patterns of genetically-based sexual dimorphism in vegetative and reproductive traits of a wind-pollinated dioecious plant, Rumex hastatulus, across three life-cycle stages using open-pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY1Y2) of the species. The direction and degree of sexual dimorphism was highly variable among populations and life-cycle stages. Sex-specific differences in reproductive function explained a significant amount of temporal change in sexual dimorphism. For several traits, geographical variation in sexual dimorphism was associated with bioclimatic parameters, likely due to the differential responses of the sexes to climate. We found no systematic differences in sexual dimorphism between chromosome races. Sex-specific trait differences in dioecious plants largely result from a balance between sexual and natural selection on resource allocation. Our results indicate that abiotic factors associated with geographical context also play a role in modifying sexual dimorphism during the plant life cycle.","lang":"eng"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.n1701c9"}],"oa_version":"Published Version","title":"Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics","day":"22","month":"07","related_material":{"record":[{"status":"public","id":"6831","relation":"used_in_publication"},{"relation":"used_in_publication","id":"14058","status":"public"}]},"publisher":"Dryad","year":"2019","date_updated":"2026-04-07T13:25:33Z","_id":"9803","type":"research_data_reference","oa":1,"date_published":"2019-07-22T00:00:00Z","citation":{"ama":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics. 2019. doi:<a href=\"https://doi.org/10.5061/dryad.n1701c9\">10.5061/dryad.n1701c9</a>","short":"G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, (2019).","chicago":"Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett. “Data from: Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” Dryad, 2019. <a href=\"https://doi.org/10.5061/dryad.n1701c9\">https://doi.org/10.5061/dryad.n1701c9</a>.","ieee":"G. Puixeu Sala, M. Pickup, D. Field, and S. C. H. Barrett, “Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics.” Dryad, 2019.","ista":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics, Dryad, <a href=\"https://doi.org/10.5061/dryad.n1701c9\">10.5061/dryad.n1701c9</a>.","apa":"Puixeu Sala, G., Pickup, M., Field, D., &#38; Barrett, S. C. H. (2019). Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics. Dryad. <a href=\"https://doi.org/10.5061/dryad.n1701c9\">https://doi.org/10.5061/dryad.n1701c9</a>","mla":"Puixeu Sala, Gemma, et al. <i>Data from: Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics</i>. Dryad, 2019, doi:<a href=\"https://doi.org/10.5061/dryad.n1701c9\">10.5061/dryad.n1701c9</a>."},"author":[{"last_name":"Puixeu Sala","first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma"},{"last_name":"Pickup","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541"},{"full_name":"Field, David","first_name":"David","last_name":"Field"},{"first_name":"Spencer C.H.","full_name":"Barrett, Spencer C.H.","last_name":"Barrett"}],"article_processing_charge":"No"},{"department":[{"_id":"NiBa"}],"doi":"10.5061/dryad.0q2h6tk","abstract":[{"lang":"eng","text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response."}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.0q2h6tk","open_access":"1"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","date_created":"2021-08-06T11:52:54Z","day":"06","month":"06","title":"Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","oa_version":"Published Version","related_material":{"record":[{"id":"6713","relation":"used_in_publication","status":"public"}]},"publisher":"Dryad","year":"2019","_id":"9804","date_updated":"2023-08-29T06:41:51Z","oa":1,"date_published":"2019-06-06T00:00:00Z","type":"research_data_reference","citation":{"short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, (2019).","ama":"Castro JP, Yancoskie MN, Marchini M, et al. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. 2019. doi:<a href=\"https://doi.org/10.5061/dryad.0q2h6tk\">10.5061/dryad.0q2h6tk</a>","mla":"Castro, João Pl, et al. <i>Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice</i>. Dryad, 2019, doi:<a href=\"https://doi.org/10.5061/dryad.0q2h6tk\">10.5061/dryad.0q2h6tk</a>.","ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice, Dryad, <a href=\"https://doi.org/10.5061/dryad.0q2h6tk\">10.5061/dryad.0q2h6tk</a>.","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. Dryad. <a href=\"https://doi.org/10.5061/dryad.0q2h6tk\">https://doi.org/10.5061/dryad.0q2h6tk</a>","ieee":"J. P. Castro <i>et al.</i>, “Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice.” Dryad, 2019.","chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” Dryad, 2019. <a href=\"https://doi.org/10.5061/dryad.0q2h6tk\">https://doi.org/10.5061/dryad.0q2h6tk</a>."},"article_processing_charge":"No","author":[{"full_name":"Castro, João Pl","first_name":"João Pl","last_name":"Castro"},{"full_name":"Yancoskie, Michelle N.","first_name":"Michelle N.","last_name":"Yancoskie"},{"first_name":"Marta","full_name":"Marchini, Marta","last_name":"Marchini"},{"full_name":"Belohlavy, Stefanie","orcid":"0000-0002-9849-498X","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefanie","last_name":"Belohlavy"},{"first_name":"Layla","full_name":"Hiramatsu, Layla","last_name":"Hiramatsu"},{"first_name":"Marek","full_name":"Kučka, Marek","last_name":"Kučka"},{"full_name":"Beluch, William H.","first_name":"William H.","last_name":"Beluch"},{"last_name":"Naumann","first_name":"Ronald","full_name":"Naumann, Ronald"},{"full_name":"Skuplik, Isabella","first_name":"Isabella","last_name":"Skuplik"},{"full_name":"Cobb, John","first_name":"John","last_name":"Cobb"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"},{"last_name":"Rolian","full_name":"Rolian, Campbell","first_name":"Campbell"},{"last_name":"Chan","full_name":"Chan, Yingguang Frank","first_name":"Yingguang Frank"}]},{"citation":{"short":"N.H. Barton, (2019).","ama":"Barton NH. Data from: The consequences of an introgression event. 2019. doi:<a href=\"https://doi.org/10.5061/dryad.2kb6fh4\">10.5061/dryad.2kb6fh4</a>","ieee":"N. H. Barton, “Data from: The consequences of an introgression event.” Dryad, 2019.","apa":"Barton, N. H. (2019). Data from: The consequences of an introgression event. Dryad. <a href=\"https://doi.org/10.5061/dryad.2kb6fh4\">https://doi.org/10.5061/dryad.2kb6fh4</a>","ista":"Barton NH. 2019. Data from: The consequences of an introgression event, Dryad, <a href=\"https://doi.org/10.5061/dryad.2kb6fh4\">10.5061/dryad.2kb6fh4</a>.","chicago":"Barton, Nicholas H. “Data from: The Consequences of an Introgression Event.” Dryad, 2019. <a href=\"https://doi.org/10.5061/dryad.2kb6fh4\">https://doi.org/10.5061/dryad.2kb6fh4</a>.","mla":"Barton, Nicholas H. <i>Data from: The Consequences of an Introgression Event</i>. Dryad, 2019, doi:<a href=\"https://doi.org/10.5061/dryad.2kb6fh4\">10.5061/dryad.2kb6fh4</a>."},"article_processing_charge":"No","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"date_published":"2019-01-09T00:00:00Z","oa":1,"type":"research_data_reference","year":"2019","publisher":"Dryad","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"40"}]},"_id":"9805","date_updated":"2025-07-10T11:52:34Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"url":"https://doi.org/10.5061/dryad.2kb6fh4","open_access":"1"}],"doi":"10.5061/dryad.2kb6fh4","department":[{"_id":"NiBa"}],"abstract":[{"lang":"eng","text":"The spread of adaptive alleles is fundamental to evolution, and in theory, this process is well‐understood. However, only rarely can we follow this process—whether it originates from the spread of a new mutation, or by introgression from another population. In this issue of Molecular Ecology, Hanemaaijer et al. (2018) report on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP). The species are usually reproductively isolated from each other, but in 2002 and 2006, bursts of hybridization were observed, when F1 hybrids became abundant. Alleles backcrossed from A. gambiae into A. coluzzi, but after the first event, these declined over the following years. In contrast, after 2006, an insecticide resistance allele that had established in A. gambiae spread into A. coluzzi, and rose to high frequency there, over 6 years (~75 generations). Whole genome sequences of 74 individuals showed that A. gambiae SNP from across the genome had become common in the A. coluzzi population, but that most of these were clustered in 34 genes around the resistance locus. A new set of SNP from 25 of these genes were assayed over time; over the 4 years since near‐fixation of the resistance allele; some remained common, whereas others declined. What do these patterns tell us about this introgression event?"}],"status":"public","date_created":"2021-08-06T12:03:50Z","month":"01","day":"09","oa_version":"Published Version","title":"Data from: The consequences of an introgression event"},{"citation":{"ama":"Polechova J. Data from: Is the sky the limit? On the expansion threshold of a species’ range. 2019. doi:<a href=\"https://doi.org/10.5061/dryad.5vv37\">10.5061/dryad.5vv37</a>","short":"J. Polechova, (2019).","chicago":"Polechova, Jitka. “Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” Dryad, 2019. <a href=\"https://doi.org/10.5061/dryad.5vv37\">https://doi.org/10.5061/dryad.5vv37</a>.","ieee":"J. Polechova, “Data from: Is the sky the limit? On the expansion threshold of a species’ range.” Dryad, 2019.","apa":"Polechova, J. (2019). Data from: Is the sky the limit? On the expansion threshold of a species’ range. Dryad. <a href=\"https://doi.org/10.5061/dryad.5vv37\">https://doi.org/10.5061/dryad.5vv37</a>","ista":"Polechova J. 2019. Data from: Is the sky the limit? On the expansion threshold of a species’ range, Dryad, <a href=\"https://doi.org/10.5061/dryad.5vv37\">10.5061/dryad.5vv37</a>.","mla":"Polechova, Jitka. <i>Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range</i>. Dryad, 2019, doi:<a href=\"https://doi.org/10.5061/dryad.5vv37\">10.5061/dryad.5vv37</a>."},"article_processing_charge":"No","author":[{"last_name":"Polechova","first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112","full_name":"Polechova, Jitka"}],"oa":1,"date_published":"2019-06-22T00:00:00Z","type":"research_data_reference","related_material":{"record":[{"id":"315","relation":"used_in_publication","status":"public"}]},"year":"2019","publisher":"Dryad","_id":"9839","date_updated":"2025-07-10T11:52:26Z","abstract":[{"lang":"eng","text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range."}],"department":[{"_id":"NiBa"}],"doi":"10.5061/dryad.5vv37","main_file_link":[{"url":"https://doi.org/10.5061/dryad.5vv37","open_access":"1"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","date_created":"2021-08-09T13:07:28Z","day":"22","month":"06","oa_version":"Published Version","title":"Data from: Is the sky the limit? On the expansion threshold of a species' range"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","abstract":[{"lang":"eng","text":"One of the most striking and consistent results in speciation genomics is the heterogeneous divergence observed across the genomes of closely related species. This pattern was initially attributed to different levels of gene exchange—with divergence preserved at loci generating a barrier to gene flow but homogenized at unlinked neutral loci. Although there is evidence to support this model, it is now recognized that interpreting patterns of divergence across genomes is not so straightforward. One \r\nproblem is that heterogenous divergence between populations can also be generated by other processes (e.g. recurrent selective sweeps or background selection) without any involvement of differential gene flow. Thus, integrated studies that identify which loci are likely subject to divergent selection are required to shed light on the interplay between selection and gene flow during the early phases of speciation. In this issue of Molecular Ecology, Rifkin et al. (2019) confront this challenge using a pair of sister morning glory species. They wisely design their sampling to take the geographic context of individuals into account, including geographically isolated (allopatric) and co‐occurring (sympatric) populations. This enabled them to show that individuals are phenotypically less differentiated in sympatry. They also found that the loci that resist introgression are enriched for those most differentiated in allopatry and loci that exhibit signals of divergent selection. One great strength of the \r\nstudy is the combination of methods from population genetics and molecular evolution, including the development of a model to simultaneously infer admixture proportions and selfing rates."}],"ddc":["580","576"],"external_id":{"isi":["000474808300001"]},"date_created":"2019-05-19T21:59:15Z","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"day":"01","oa_version":"Published Version","scopus_import":"1","_id":"6466","date_updated":"2026-04-16T08:33:17Z","file":[{"file_name":"2019_MolecularEcology_Field.pdf","relation":"main_file","date_created":"2019-05-20T11:49:06Z","checksum":"521e3aff3e9263ddf2ffbfe0b6157715","access_level":"open_access","file_size":367711,"creator":"dernst","file_id":"6472","date_updated":"2020-07-14T12:47:31Z","content_type":"application/pdf"}],"file_date_updated":"2020-07-14T12:47:31Z","date_published":"2019-04-01T00:00:00Z","oa":1,"type":"journal_article","page":"1579-1581","publication_status":"published","publication":"Molecular ecology","intvolume":"        28","citation":{"ieee":"D. Field and C. Fraisse, “Breaking down barriers in morning glories,” <i>Molecular ecology</i>, vol. 28, no. 7. Wiley, pp. 1579–1581, 2019.","ista":"Field D, Fraisse C. 2019. Breaking down barriers in morning glories. Molecular ecology. 28(7), 1579–1581.","apa":"Field, D., &#38; Fraisse, C. (2019). Breaking down barriers in morning glories. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.15048\">https://doi.org/10.1111/mec.15048</a>","chicago":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” <i>Molecular Ecology</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/mec.15048\">https://doi.org/10.1111/mec.15048</a>.","mla":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” <i>Molecular Ecology</i>, vol. 28, no. 7, Wiley, 2019, pp. 1579–81, doi:<a href=\"https://doi.org/10.1111/mec.15048\">10.1111/mec.15048</a>.","short":"D. Field, C. Fraisse, Molecular Ecology 28 (2019) 1579–1581.","ama":"Field D, Fraisse C. Breaking down barriers in morning glories. <i>Molecular ecology</i>. 2019;28(7):1579-1581. doi:<a href=\"https://doi.org/10.1111/mec.15048\">10.1111/mec.15048</a>"},"isi":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","department":[{"_id":"NiBa"}],"doi":"10.1111/mec.15048","status":"public","month":"04","title":"Breaking down barriers in morning glories","language":[{"iso":"eng"}],"has_accepted_license":"1","publisher":"Wiley","year":"2019","volume":28,"issue":"7","article_processing_charge":"No","author":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field"},{"last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"}]}]