[{"type":"journal_article","article_type":"review","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"6858","department":[{"_id":"NiBa"}],"file_date_updated":"2020-10-02T09:16:44Z","date_updated":"2023-08-29T07:51:09Z","ddc":["570"],"scopus_import":"1","month":"03","intvolume":" 6","oa_version":"Published Version","volume":6,"issue":"2","license":"https://creativecommons.org/licenses/by/4.0/","publication_identifier":{"eissn":["2053-714X"],"issn":["2095-5138"]},"publication_status":"published","file":[{"date_created":"2020-10-02T09:16:44Z","file_name":"2019_NSR_Barton.pdf","date_updated":"2020-10-02T09:16:44Z","file_size":106463,"creator":"dernst","checksum":"571d60fa21a568607d1fd04e119da88c","file_id":"8595","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"article_processing_charge":"No","external_id":{"isi":["000467957400025"]},"title":"Is speciation driven by cycles of mixing and isolation?","citation":{"ista":"Barton NH. 2019. Is speciation driven by cycles of mixing and isolation? National Science Review. 6(2), 291–292.","chicago":"Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?” National Science Review. Oxford University Press, 2019. https://doi.org/10.1093/nsr/nwy113.","ieee":"N. H. Barton, “Is speciation driven by cycles of mixing and isolation?,” National Science Review, vol. 6, no. 2. Oxford University Press, pp. 291–292, 2019.","short":"N.H. Barton, National Science Review 6 (2019) 291–292.","apa":"Barton, N. H. (2019). Is speciation driven by cycles of mixing and isolation? National Science Review. Oxford University Press. https://doi.org/10.1093/nsr/nwy113","ama":"Barton NH. Is speciation driven by cycles of mixing and isolation? National Science Review. 2019;6(2):291-292. doi:10.1093/nsr/nwy113","mla":"Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?” National Science Review, vol. 6, no. 2, Oxford University Press, 2019, pp. 291–92, doi:10.1093/nsr/nwy113."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"Oxford University Press","oa":1,"page":"291-292","date_published":"2019-03-01T00:00:00Z","doi":"10.1093/nsr/nwy113","date_created":"2019-09-07T14:43:02Z","has_accepted_license":"1","isi":1,"year":"2019","day":"01","publication":"National Science Review"},{"abstract":[{"text":"Gene Drives are regarded as future tools with a high potential for population control. Due to their inherent ability to overcome the rules of Mendelian inheritance, gene drives (GD) may spread genes rapidly through populations of sexually reproducing organisms. A release of organisms carrying a GD would constitute a paradigm shift in the handling of genetically modified organisms because gene drive organisms (GDO) are designed to drive their transgenes into wild populations and thereby increase the number of GDOs. The rapid development in this field and its focus on wild populations demand a prospective risk assessment with a focus on exposure related aspects. Presently, it is unclear how adequate risk management could be guaranteed to limit the spread of GDs in time and space, in order to avoid potential adverse effects in socio‐ecological systems.\r\n\r\nThe recent workshop on the “Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight into the potential population dynamic behavior of GDs and appropriate measures of control. Scientists from France, Germany, England, and the USA discussed both topics in this meeting on April 4–5, 2019. This article summarizes results of the workshop.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"11","intvolume":" 41","publication_identifier":{"eissn":["1521-1878"]},"publication_status":"published","file":[{"file_id":"6939","checksum":"8cc7551bff70b2658f8d5630f228ee12","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-10-11T06:59:26Z","file_name":"2019_BioEssays_Giese.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:42Z","file_size":193248}],"language":[{"iso":"eng"}],"issue":"11","volume":41,"_id":"6857","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-30T06:56:26Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:42Z","department":[{"_id":"NiBa"}],"quality_controlled":"1","publisher":"Wiley","oa":1,"isi":1,"has_accepted_license":"1","year":"2019","day":"01","publication":"BioEssays","date_published":"2019-11-01T00:00:00Z","doi":"10.1002/bies.201900151","date_created":"2019-09-07T14:40:03Z","article_number":"1900151","citation":{"ama":"Giese B, Friess JL, Schetelig MF, et al. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 2019;41(11). doi:10.1002/bies.201900151","apa":"Giese, B., Friess, J. L., Schetelig, M. F., Barton, N. H., Messer, P., Debarre, F., … Boete, C. (2019). Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. Wiley. https://doi.org/10.1002/bies.201900151","short":"B. Giese, J.L. Friess, M.F. Schetelig, N.H. Barton, P. Messer, F. Debarre, H. Meimberg, N. Windbichler, C. Boete, BioEssays 41 (2019).","ieee":"B. Giese et al., “Gene Drives: Dynamics and regulatory matters – A report from the workshop ‘Evaluation of spatial and temporal control of Gene Drives’, 4 – 5 April 2019, Vienna,” BioEssays, vol. 41, no. 11. Wiley, 2019.","mla":"Giese, B., et al. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays, vol. 41, no. 11, 1900151, Wiley, 2019, doi:10.1002/bies.201900151.","ista":"Giese B, Friess JL, Schetelig MF, Barton NH, Messer P, Debarre F, Meimberg H, Windbichler N, Boete C. 2019. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 41(11), 1900151.","chicago":"Giese, B, J L Friess, M F Schetelig, Nicholas H Barton, Philip Messer, Florence Debarre, H Meimberg, N Windbichler, and C Boete. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays. Wiley, 2019. https://doi.org/10.1002/bies.201900151."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"B","last_name":"Giese","full_name":"Giese, B"},{"last_name":"Friess","full_name":"Friess, J L","first_name":"J L"},{"first_name":"M F ","last_name":"Schetelig","full_name":"Schetelig, M F "},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Philip","full_name":"Messer, Philip","last_name":"Messer"},{"last_name":"Debarre","full_name":"Debarre, Florence","first_name":"Florence"},{"first_name":"H","full_name":"Meimberg, H","last_name":"Meimberg"},{"first_name":"N","full_name":"Windbichler, N","last_name":"Windbichler"},{"full_name":"Boete, C","last_name":"Boete","first_name":"C"}],"external_id":{"isi":["000489502000001"]},"article_processing_charge":"No","title":"Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna"},{"month":"12","publisher":"Dryad","main_file_link":[{"url":"https://doi.org/10.5061/dryad.tb2rbnzwk","open_access":"1"}],"oa":1,"oa_version":"Published Version","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 >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."}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7205"}]},"doi":"10.5061/DRYAD.TB2RBNZWK","date_published":"2019-12-02T00:00:00Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_created":"2023-05-23T16:36:27Z","day":"02","year":"2019","status":"public","type":"research_data_reference","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"_id":"13067","department":[{"_id":"NiBa"}],"title":"Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?","author":[{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna","first_name":"Zuzanna"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_updated":"2023-09-06T14:48:57Z","citation":{"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. https://doi.org/10.5061/DRYAD.TB2RBNZWK.","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, 10.5061/DRYAD.TB2RBNZWK.","mla":"Johannesson, Kerstin, et al. Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes? Dryad, 2019, doi:10.5061/DRYAD.TB2RBNZWK.","apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. (2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? Dryad. https://doi.org/10.5061/DRYAD.TB2RBNZWK","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:10.5061/DRYAD.TB2RBNZWK","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.","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019)."}},{"title":"Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast","article_processing_charge":"No","external_id":{"pmid":["31840052"],"isi":["000505069600008"]},"author":[{"first_name":"Hernán E.","full_name":"Morales, Hernán E.","last_name":"Morales"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"first_name":"Tomas","full_name":"Larsson, Tomas","last_name":"Larsson"},{"first_name":"Marina","full_name":"Panova, Marina","last_name":"Panova"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Morales HE, Faria R, Johannesson K, Larsson T, Panova M, Westram AM, Butlin RK. 2019. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 5(12), eaav9963.","chicago":"Morales, Hernán E., Rui Faria, Kerstin Johannesson, Tomas Larsson, Marina Panova, Anja M Westram, and Roger K. Butlin. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances. AAAS, 2019. https://doi.org/10.1126/sciadv.aav9963.","ieee":"H. E. Morales et al., “Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast,” Science Advances, vol. 5, no. 12. AAAS, 2019.","short":"H.E. Morales, R. Faria, K. Johannesson, T. Larsson, M. Panova, A.M. Westram, R.K. Butlin, Science Advances 5 (2019).","apa":"Morales, H. E., Faria, R., Johannesson, K., Larsson, T., Panova, M., Westram, A. M., & Butlin, R. K. (2019). Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. AAAS. https://doi.org/10.1126/sciadv.aav9963","ama":"Morales HE, Faria R, Johannesson K, et al. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 2019;5(12). doi:10.1126/sciadv.aav9963","mla":"Morales, Hernán E., et al. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances, vol. 5, no. 12, eaav9963, AAAS, 2019, doi:10.1126/sciadv.aav9963."},"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Theoretical and empirical approaches to understanding Parallel Adaptation","grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"eaav9963","date_created":"2020-01-29T15:58:27Z","date_published":"2019-12-04T00:00:00Z","doi":"10.1126/sciadv.aav9963","publication":"Science Advances","day":"04","year":"2019","has_accepted_license":"1","isi":1,"oa":1,"publisher":"AAAS","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:57Z","department":[{"_id":"NiBa"}],"ddc":["570"],"date_updated":"2023-09-06T15:35:56Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"article_type":"original","type":"journal_article","_id":"7393","license":"https://creativecommons.org/licenses/by-nc/4.0/","ec_funded":1,"issue":"12","volume":5,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"af99a5dcdc66c6d6102051faf3be48d8","file_id":"7442","file_size":1869449,"date_updated":"2020-07-14T12:47:57Z","creator":"dernst","file_name":"2019_ScienceAdvances_Morales.pdf","date_created":"2020-02-03T13:33:25Z"}],"publication_status":"published","publication_identifier":{"issn":["2375-2548"]},"intvolume":" 5","month":"12","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow.","lang":"eng"}]},{"day":"29","publication":"Handbook of statistical genomics","isi":1,"year":"2019","date_published":"2019-07-29T00:00:00Z","doi":"10.1002/9781119487845.ch4","date_created":"2020-08-21T04:25:39Z","page":"115-144","quality_controlled":"1","publisher":"Wiley","edition":"4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Barton NH, Etheridge A. 2019.Mathematical models in population genetics. In: Handbook of statistical genomics. , 115–144.","chicago":"Barton, Nicholas H, and Alison Etheridge. “Mathematical Models in Population Genetics.” In Handbook of Statistical Genomics, edited by David Balding, Ida Moltke, and John Marioni, 4th ed., 115–44. Wiley, 2019. https://doi.org/10.1002/9781119487845.ch4.","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.","ieee":"N. H. Barton and A. Etheridge, “Mathematical models in population genetics,” in Handbook of statistical genomics, 4th ed., D. Balding, I. Moltke, and J. Marioni, Eds. Wiley, 2019, pp. 115–144.","ama":"Barton NH, Etheridge A. Mathematical models in population genetics. In: Balding D, Moltke I, Marioni J, eds. Handbook of Statistical Genomics. 4th ed. Wiley; 2019:115-144. doi:10.1002/9781119487845.ch4","apa":"Barton, N. H., & Etheridge, A. (2019). Mathematical models in population genetics. In D. Balding, I. Moltke, & J. Marioni (Eds.), Handbook of statistical genomics (4th ed., pp. 115–144). Wiley. https://doi.org/10.1002/9781119487845.ch4","mla":"Barton, Nicholas H., and Alison Etheridge. “Mathematical Models in Population Genetics.” Handbook of Statistical Genomics, edited by David Balding et al., 4th ed., Wiley, 2019, pp. 115–44, doi:10.1002/9781119487845.ch4."},"title":"Mathematical models in population genetics","editor":[{"full_name":"Balding, David","last_name":"Balding","first_name":"David"},{"first_name":"Ida","last_name":"Moltke","full_name":"Moltke, Ida"},{"first_name":"John","full_name":"Marioni, John","last_name":"Marioni"}],"author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"}],"external_id":{"isi":["000261343000003"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781119429142"]},"publication_status":"published","oa_version":"None","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."}],"month":"07","ddc":["576"],"date_updated":"2023-09-08T11:24:15Z","department":[{"_id":"NiBa"}],"_id":"8281","status":"public","type":"book_chapter"},{"day":"09","year":"2019","date_created":"2021-08-06T12:03:50Z","related_material":{"record":[{"id":"40","status":"public","relation":"used_in_publication"}]},"doi":"10.5061/dryad.2kb6fh4","date_published":"2019-01-09T00:00:00Z","oa_version":"Published Version","abstract":[{"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?","lang":"eng"}],"month":"01","main_file_link":[{"url":"https://doi.org/10.5061/dryad.2kb6fh4","open_access":"1"}],"oa":1,"publisher":"Dryad","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-19T10:06:07Z","citation":{"apa":"Barton, N. H. (2019). Data from: The consequences of an introgression event. Dryad. https://doi.org/10.5061/dryad.2kb6fh4","ama":"Barton NH. Data from: The consequences of an introgression event. 2019. doi:10.5061/dryad.2kb6fh4","short":"N.H. Barton, (2019).","ieee":"N. H. Barton, “Data from: The consequences of an introgression event.” Dryad, 2019.","mla":"Barton, Nicholas H. Data from: The Consequences of an Introgression Event. Dryad, 2019, doi:10.5061/dryad.2kb6fh4.","ista":"Barton NH. 2019. Data from: The consequences of an introgression event, Dryad, 10.5061/dryad.2kb6fh4.","chicago":"Barton, Nicholas H. “Data from: The Consequences of an Introgression Event.” Dryad, 2019. https://doi.org/10.5061/dryad.2kb6fh4."},"department":[{"_id":"NiBa"}],"title":"Data from: The consequences of an introgression event","article_processing_charge":"No","author":[{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"_id":"9805","status":"public","type":"research_data_reference"},{"author":[{"last_name":"Prizak","full_name":"Prizak, Roshan","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Coevolution of transcription factors and their binding sites in sequence space","citation":{"chicago":"Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th6071.","ista":"Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria.","mla":"Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites in Sequence Space. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th6071.","apa":"Prizak, R. (2019). Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th6071","ama":"Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:10.15479/at:ista:th6071","ieee":"R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” Institute of Science and Technology Austria, 2019.","short":"R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"page":"189","date_published":"2019-03-11T00:00:00Z","doi":"10.15479/at:ista:th6071","date_created":"2019-03-06T16:16:10Z","has_accepted_license":"1","year":"2019","day":"11","publisher":"Institute of Science and Technology Austria","oa":1,"file_date_updated":"2020-07-14T12:47:18Z","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"supervisor":[{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"date_updated":"2023-09-22T10:00:48Z","ddc":["576"],"type":"dissertation","status":"public","_id":"6071","related_material":{"record":[{"relation":"part_of_dissertation","id":"1358","status":"public"},{"relation":"part_of_dissertation","id":"955","status":"public"}]},"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"e60a72de35d270b31f1a23d50f224ec0","file_id":"6072","creator":"rprizak","date_updated":"2020-07-14T12:47:18Z","file_size":20995465,"date_created":"2019-03-06T16:05:07Z","file_name":"Thesis_final_PDFA_RoshanPrizak.pdf"},{"date_updated":"2020-07-14T12:47:18Z","file_size":85705272,"creator":"rprizak","title":"Latex files","date_created":"2019-03-06T16:09:39Z","file_name":"thesis_v2_merge.zip","content_type":"application/zip","access_level":"closed","relation":"source_file","checksum":"67c2630333d05ebafef5f018863a8465","file_id":"6073"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"03","abstract":[{"lang":"eng","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. "}],"oa_version":"Published Version"},{"project":[{"call_identifier":"FP7","_id":"25B36484-B435-11E9-9278-68D0E5697425","name":"Mating system and the evolutionary dynamics of hybrid zones","grant_number":"329960"},{"grant_number":"M02463","name":"Sex chromosomes and species barriers","_id":"2662AADE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M. Pickup, N.H. Barton, Y. Brandvain, C. Fraisse, S. Yakimowski, T. Dixit, C. Lexer, E. Cereghetti, D. Field, New Phytologist 224 (2019) 1035–1047.","ieee":"M. Pickup et al., “Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow,” New Phytologist, vol. 224, no. 3. Wiley, pp. 1035–1047, 2019.","apa":"Pickup, M., Barton, N. H., Brandvain, Y., Fraisse, C., Yakimowski, S., Dixit, T., … Field, D. (2019). Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. Wiley. https://doi.org/10.1111/nph.16180","ama":"Pickup M, Barton NH, Brandvain Y, et al. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 2019;224(3):1035-1047. doi:10.1111/nph.16180","mla":"Pickup, Melinda, et al. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” New Phytologist, vol. 224, no. 3, Wiley, 2019, pp. 1035–47, doi:10.1111/nph.16180.","ista":"Pickup M, Barton NH, Brandvain Y, Fraisse C, Yakimowski S, Dixit T, Lexer C, Cereghetti E, Field D. 2019. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 224(3), 1035–1047.","chicago":"Pickup, Melinda, Nicholas H Barton, Yaniv Brandvain, Christelle Fraisse, Sarah Yakimowski, Tanmay Dixit, Christian Lexer, Eva Cereghetti, and David Field. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16180."},"title":"Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow","article_processing_charge":"No","external_id":{"pmid":["31505037"]},"author":[{"orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"first_name":"Yaniv","full_name":"Brandvain, Yaniv","last_name":"Brandvain"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse"},{"last_name":"Yakimowski","full_name":"Yakimowski, Sarah","first_name":"Sarah"},{"last_name":"Dixit","full_name":"Dixit, Tanmay","first_name":"Tanmay"},{"first_name":"Christian","last_name":"Lexer","full_name":"Lexer, Christian"},{"first_name":"Eva","id":"71AA91B4-05ED-11EA-8BEB-F5833E63BD63","last_name":"Cereghetti","full_name":"Cereghetti, Eva"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478"}],"oa":1,"quality_controlled":"1","publisher":"Wiley","publication":"New Phytologist","day":"01","year":"2019","has_accepted_license":"1","date_created":"2019-09-07T14:35:40Z","date_published":"2019-11-01T00:00:00Z","doi":"10.1111/nph.16180","page":"1035-1047","_id":"6856","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["570"],"date_updated":"2023-10-18T08:47:08Z","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:42Z","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Plant mating systems play a key role in structuring genetic variation both within and between species. In hybrid zones, the outcomes and dynamics of hybridization are usually interpreted as the balance between gene flow and selection against hybrids. Yet, mating systems can introduce selective forces that alter these expectations; with diverse outcomes for the level and direction of gene flow depending on variation in outcrossing and whether the mating systems of the species pair are the same or divergent. We present a survey of hybridization in 133 species pairs from 41 plant families and examine how patterns of hybridization vary with mating system. We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and the frequency of reproductive isolating barriers vary in relation to mating system/s of the species pair. We combine these results with a simulation model and examples from the literature to address two general themes: (i) the two‐way interaction between introgression and the evolution of reproductive systems, and (ii) how mating system can facilitate or restrict interspecific gene flow. We conclude that examining mating system with hybridization provides unique opportunities to understand divergence and the processes underlying reproductive isolation."}],"intvolume":" 224","month":"11","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_id":"7011","checksum":"21e4c95599bbcaf7c483b89954658672","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2019_NewPhytologist_Pickup.pdf","date_created":"2019-11-13T08:15:05Z","creator":"dernst","file_size":1511958,"date_updated":"2020-07-14T12:47:42Z"}],"publication_status":"published","publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"ec_funded":1,"volume":224,"issue":"3"},{"oa":1,"publisher":"Oxford University Press","quality_controlled":"1","year":"2019","isi":1,"publication":"Molecular biology and evolution","day":"01","page":"500-515","date_created":"2019-03-10T22:59:19Z","doi":"10.1093/molbev/msy246","date_published":"2019-03-01T00:00:00Z","project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22"}],"citation":{"chicago":"Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/molbev/msy246.","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.","mla":"Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution, vol. 36, no. 3, Oxford University Press, 2019, pp. 500–15, doi:10.1093/molbev/msy246.","short":"C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 500–515.","ieee":"C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy of selection in drosophila melanogaster,” Molecular biology and evolution, vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019.","ama":"Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 2019;36(3):500-515. doi:10.1093/molbev/msy246","apa":"Fraisse, C., Puixeu Sala, G., & Vicoso, B. (2019). Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy246"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["30590559"],"isi":["000462585100006"]},"article_processing_charge":"No","author":[{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","first_name":"Gemma"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","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"}],"oa_version":"Submitted Version","pmid":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559"}],"scopus_import":"1","intvolume":" 36","month":"03","publication_status":"published","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"language":[{"iso":"eng"}],"volume":36,"issue":"3","related_material":{"record":[{"id":"5757","status":"public","relation":"popular_science"}]},"_id":"6089","type":"journal_article","status":"public","date_updated":"2024-02-21T13:59:17Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}]},{"article_number":"022423","external_id":{"isi":["000459916500007"]},"article_processing_charge":"No","author":[{"last_name":"Carballo-Pacheco","full_name":"Carballo-Pacheco, Martín","first_name":"Martín"},{"first_name":"Jonathan","last_name":"Desponds","full_name":"Desponds, Jonathan"},{"last_name":"Gavrilchenko","full_name":"Gavrilchenko, Tatyana","first_name":"Tatyana"},{"first_name":"Andreas","full_name":"Mayer, Andreas","last_name":"Mayer"},{"full_name":"Prizak, Roshan","last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Reddy","full_name":"Reddy, Gautam","first_name":"Gautam"},{"first_name":"Ilya","last_name":"Nemenman","full_name":"Nemenman, Ilya"},{"full_name":"Mora, Thierry","last_name":"Mora","first_name":"Thierry"}],"title":"Receptor crosstalk improves concentration sensing of multiple ligands","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.","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.” Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/PhysRevE.99.022423.","ama":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 2019;99(2). doi:10.1103/PhysRevE.99.022423","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. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.99.022423","short":"M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).","ieee":"M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration sensing of multiple ligands,” Physical Review E, vol. 99, no. 2. American Physical Society, 2019.","mla":"Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E, vol. 99, no. 2, 022423, American Physical Society, 2019, doi:10.1103/PhysRevE.99.022423."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"American Physical Society","quality_controlled":"1","date_created":"2019-03-10T22:59:20Z","date_published":"2019-02-26T00:00:00Z","doi":"10.1103/PhysRevE.99.022423","year":"2019","isi":1,"publication":"Physical Review E","day":"26","type":"journal_article","status":"public","_id":"6090","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"date_updated":"2024-02-28T13:12:06Z","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/448118v1.abstract"}],"scopus_import":"1","intvolume":" 99","month":"02","abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","volume":99,"issue":"2","publication_status":"published","language":[{"iso":"eng"}]}]