[{"article_processing_charge":"No","day":"09","month":"01","citation":{"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. https://doi.org/10.5061/dryad.2kb6fh4","ista":"Barton NH. 2019. Data from: The consequences of an introgression event, Dryad, 10.5061/dryad.2kb6fh4.","ama":"Barton NH. Data from: The consequences of an introgression event. 2019. doi: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.","short":"N.H. Barton, (2019).","mla":"Barton, Nicholas H. Data from: The Consequences of an Introgression Event. Dryad, 2019, doi:10.5061/dryad.2kb6fh4."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.2kb6fh4"}],"oa":1,"doi":"10.5061/dryad.2kb6fh4","date_published":"2019-01-09T00:00:00Z","type":"research_data_reference","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"}],"department":[{"_id":"NiBa"}],"publisher":"Dryad","status":"public","title":"Data from: The consequences of an introgression event","_id":"9805","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2019","oa_version":"Published Version","date_created":"2021-08-06T12:03:50Z","date_updated":"2023-09-19T10:06:07Z","related_material":{"record":[{"id":"40","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}]},{"year":"2019","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1358"},{"id":"955","relation":"part_of_dissertation","status":"public"}]},"author":[{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak","first_name":"Roshan","full_name":"Prizak, Roshan"}],"date_created":"2019-03-06T16:16:10Z","date_updated":"2023-09-22T10:00:48Z","file_date_updated":"2020-07-14T12:47:18Z","oa":1,"project":[{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"doi":"10.15479/at:ista:th6071","language":[{"iso":"eng"}],"supervisor":[{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"03","_id":"6071","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["576"],"title":"Coevolution of transcription factors and their binding sites in sequence space","file":[{"access_level":"open_access","file_name":"Thesis_final_PDFA_RoshanPrizak.pdf","creator":"rprizak","file_size":20995465,"content_type":"application/pdf","file_id":"6072","relation":"main_file","checksum":"e60a72de35d270b31f1a23d50f224ec0","date_created":"2019-03-06T16:05:07Z","date_updated":"2020-07-14T12:47:18Z"},{"access_level":"closed","file_name":"thesis_v2_merge.zip","creator":"rprizak","content_type":"application/zip","file_size":85705272,"title":"Latex files","file_id":"6073","relation":"source_file","checksum":"67c2630333d05ebafef5f018863a8465","date_created":"2019-03-06T16:09:39Z","date_updated":"2020-07-14T12:47:18Z"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"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. "}],"citation":{"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.","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","ista":"Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria.","short":"R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019.","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.","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."},"page":"189","date_published":"2019-03-11T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"11"},{"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-11-01T00:00:00Z","publication":"New Phytologist","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.","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.","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.","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","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","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."},"article_type":"original","page":"1035-1047","abstract":[{"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.","lang":"eng"}],"issue":"3","type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"7011","checksum":"21e4c95599bbcaf7c483b89954658672","date_created":"2019-11-13T08:15:05Z","date_updated":"2020-07-14T12:47:42Z","access_level":"open_access","file_name":"2019_NewPhytologist_Pickup.pdf","file_size":1511958,"content_type":"application/pdf","creator":"dernst"}],"_id":"6856","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow","ddc":["570"],"status":"public","intvolume":" 224","month":"11","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"doi":"10.1111/nph.16180","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["31505037"]},"quality_controlled":"1","project":[{"grant_number":"329960","_id":"25B36484-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Mating system and the evolutionary dynamics of hybrid zones"},{"grant_number":"M02463","_id":"2662AADE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosomes and species barriers"}],"file_date_updated":"2020-07-14T12:47:42Z","ec_funded":1,"license":"https://creativecommons.org/licenses/by/4.0/","author":[{"full_name":"Pickup, Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","first_name":"Melinda","last_name":"Pickup"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"},{"full_name":"Brandvain, Yaniv","last_name":"Brandvain","first_name":"Yaniv"},{"full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse"},{"full_name":"Yakimowski, Sarah","first_name":"Sarah","last_name":"Yakimowski"},{"first_name":"Tanmay","last_name":"Dixit","full_name":"Dixit, Tanmay"},{"full_name":"Lexer, Christian","first_name":"Christian","last_name":"Lexer"},{"id":"71AA91B4-05ED-11EA-8BEB-F5833E63BD63","first_name":"Eva","last_name":"Cereghetti","full_name":"Cereghetti, Eva"},{"last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David"}],"date_created":"2019-09-07T14:35:40Z","date_updated":"2023-10-18T08:47:08Z","volume":224,"year":"2019","pmid":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}]},{"volume":36,"date_created":"2019-03-10T22:59:19Z","date_updated":"2024-02-21T13:59:17Z","related_material":{"record":[{"id":"5757","relation":"popular_science","status":"public"}]},"author":[{"full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Puixeu Sala, Gemma","first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz"}],"publisher":"Oxford University Press","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2019","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1093/molbev/msy246","project":[{"grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559"}],"external_id":{"isi":["000462585100006"],"pmid":["30590559"]},"issue":"3","abstract":[{"lang":"eng","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."}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 36","title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","status":"public","_id":"6089","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-03-01T00:00:00Z","page":"500-515","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.","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.","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.","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","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"},"publication":"Molecular biology and evolution"},{"date_published":"2019-02-26T00:00:00Z","publication":"Physical Review E","citation":{"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.","short":"M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora, Physical Review E 99 (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.","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.","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","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.","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"},"day":"26","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","title":"Receptor crosstalk improves concentration sensing of multiple ligands","status":"public","intvolume":" 99","_id":"6090","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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"}],"issue":"2","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.99.022423","quality_controlled":"1","isi":1,"external_id":{"isi":["000459916500007"]},"oa":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/448118v1.abstract","open_access":"1"}],"month":"02","date_updated":"2024-02-28T13:12:06Z","date_created":"2019-03-10T22:59:20Z","volume":99,"author":[{"full_name":"Carballo-Pacheco, Martín","first_name":"Martín","last_name":"Carballo-Pacheco"},{"full_name":"Desponds, Jonathan","last_name":"Desponds","first_name":"Jonathan"},{"full_name":"Gavrilchenko, Tatyana","last_name":"Gavrilchenko","first_name":"Tatyana"},{"last_name":"Mayer","first_name":"Andreas","full_name":"Mayer, Andreas"},{"full_name":"Prizak, Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak","first_name":"Roshan"},{"full_name":"Reddy, Gautam","last_name":"Reddy","first_name":"Gautam"},{"last_name":"Nemenman","first_name":"Ilya","full_name":"Nemenman, Ilya"},{"full_name":"Mora, Thierry","first_name":"Thierry","last_name":"Mora"}],"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"year":"2019","article_number":"022423"},{"file_date_updated":"2020-07-14T12:47:38Z","article_number":"e42014","author":[{"last_name":"Castro","first_name":"João Pl","full_name":"Castro, João Pl"},{"first_name":"Michelle N.","last_name":"Yancoskie","full_name":"Yancoskie, Michelle N."},{"full_name":"Marchini, Marta","last_name":"Marchini","first_name":"Marta"},{"full_name":"Belohlavy, Stefanie","orcid":"0000-0002-9849-498X","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","last_name":"Belohlavy","first_name":"Stefanie"},{"first_name":"Layla","last_name":"Hiramatsu","full_name":"Hiramatsu, Layla"},{"last_name":"Kučka","first_name":"Marek","full_name":"Kučka, Marek"},{"first_name":"William H.","last_name":"Beluch","full_name":"Beluch, William H."},{"last_name":"Naumann","first_name":"Ronald","full_name":"Naumann, Ronald"},{"full_name":"Skuplik, Isabella","first_name":"Isabella","last_name":"Skuplik"},{"last_name":"Cobb","first_name":"John","full_name":"Cobb, John"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rolian, Campbell","last_name":"Rolian","first_name":"Campbell"},{"first_name":"Yingguang Frank","last_name":"Chan","full_name":"Chan, Yingguang Frank"}],"related_material":{"record":[{"id":"9804","relation":"research_data","status":"public"},{"status":"public","relation":"dissertation_contains","id":"11388"}]},"date_created":"2019-07-28T21:59:17Z","date_updated":"2024-03-28T23:30:23Z","volume":8,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"eLife Sciences Publications","month":"06","doi":"10.7554/eLife.42014","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000473588700001"],"pmid":["31169497"]},"quality_controlled":"1","isi":1,"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."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"6721","relation":"main_file","date_updated":"2020-07-14T12:47:38Z","date_created":"2019-07-29T07:41:18Z","checksum":"fa0936fe58f0d9e3f8e75038570e5a17","file_name":"2019_eLife_Castro.pdf","access_level":"open_access","creator":"apreinsp","file_size":6748249,"content_type":"application/pdf"}],"_id":"6713","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["576"],"title":"An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","status":"public","intvolume":" 8","day":"06","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-06-06T00:00:00Z","publication":"eLife","citation":{"chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42014.","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, ELife 8 (2019).","mla":"Castro, João Pl, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” ELife, vol. 8, e42014, eLife Sciences Publications, 2019, doi:10.7554/eLife.42014.","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.42014","ieee":"J. P. Castro et al., “An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice,” eLife, vol. 8. eLife Sciences Publications, 2019.","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. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 8, e42014.","ama":"Castro JP, Yancoskie MN, Marchini M, et al. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 2019;8. doi:10.7554/eLife.42014"}},{"scopus_import":1,"has_accepted_license":"1","day":"15","citation":{"chicago":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005372.","mla":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology, vol. 16, no. 6, e2005372, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005372.","short":"J. Polechova, PLoS Biology 16 (2018).","ista":"Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372.","apa":"Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005372","ieee":"J. Polechova, “Is the sky the limit? On the expansion threshold of a species’ range,” PLoS Biology, vol. 16, no. 6. Public Library of Science, 2018.","ama":"Polechova J. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 2018;16(6). doi:10.1371/journal.pbio.2005372"},"publication":"PLoS Biology","date_published":"2018-06-15T00:00:00Z","type":"journal_article","issue":"6","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."}],"intvolume":" 16","status":"public","ddc":["576"],"title":"Is the sky the limit? On the expansion threshold of a species’ range","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"315","oa_version":"Published Version","file":[{"file_name":"2017_PLOS_Polechova.pdf","access_level":"open_access","content_type":"application/pdf","file_size":6968201,"creator":"dernst","relation":"main_file","file_id":"5870","date_updated":"2020-07-14T12:46:01Z","date_created":"2019-01-22T08:30:03Z","checksum":"908c52751bba30c55ed36789e5e4c84d"}],"publication_identifier":{"issn":["15449173"]},"month":"06","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.2005372","article_number":"e2005372","publist_id":"7550","file_date_updated":"2020-07-14T12:46:01Z","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2018","volume":16,"date_updated":"2023-02-23T14:10:16Z","date_created":"2018-12-11T11:45:46Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9839"}]},"author":[{"full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","first_name":"Jitka"}]},{"oa":1,"citation":{"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. 2018. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes, Dryad, 10.5061/dryad.72cg113.","ieee":"R. Faria et al., “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Dryad. https://doi.org/10.5061/dryad.72cg113","ama":"Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:10.5061/dryad.72cg113","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. https://doi.org/10.5061/dryad.72cg113.","mla":"Faria, Rui, et al. Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes. Dryad, 2018, doi:10.5061/dryad.72cg113.","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, (2018)."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.72cg113"}],"date_published":"2018-10-09T00:00:00Z","doi":"10.5061/dryad.72cg113","day":"09","month":"10","article_processing_charge":"No","status":"public","title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","publisher":"Dryad","department":[{"_id":"NiBa"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9837","year":"2018","date_updated":"2023-08-24T14:50:26Z","date_created":"2021-08-09T12:46:39Z","oa_version":"Published Version","author":[{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"first_name":"Pragya","last_name":"Chaube","full_name":"Chaube, Pragya"},{"full_name":"Morales, Hernán E.","last_name":"Morales","first_name":"Hernán E."},{"full_name":"Larsson, Tomas","first_name":"Tomas","last_name":"Larsson"},{"full_name":"Lemmon, Alan R.","first_name":"Alan R.","last_name":"Lemmon"},{"last_name":"Lemmon","first_name":"Emily M.","full_name":"Lemmon, Emily M."},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"full_name":"Panova, Marina","first_name":"Marina","last_name":"Panova"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"related_material":{"record":[{"id":"6095","relation":"used_in_publication","status":"public"}]},"type":"research_data_reference","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."}]},{"language":[{"iso":"eng"}],"doi":"10.7554/eLife.32035","quality_controlled":"1","isi":1,"project":[{"grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000431035800001"]},"month":"03","date_created":"2018-12-11T11:46:23Z","date_updated":"2023-09-11T12:49:17Z","volume":7,"author":[{"last_name":"Payne","first_name":"Pavel","orcid":"0000-0002-2711-9453","id":"35F78294-F248-11E8-B48F-1D18A9856A87","full_name":"Payne, Pavel"},{"full_name":"Geyrhofer, Lukas","first_name":"Lukas","last_name":"Geyrhofer"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bollback, Jonathan P","last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9840"}]},"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"acknowledgement":"We are grateful to Remy Chait for his help and assistance with establishing our experimental setups and to Tobias Bergmiller for valuable insights into some specific experimental details. We thank Luciano Marraffini for donating us the pCas9 plasmid used in this study. We also want to express our gratitude to Seth Barribeau, Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable discussions on the manuscript. Finally, we would like to thank the \r\neditors and reviewers for their helpful comments and suggestions.","year":"2018","file_date_updated":"2020-07-14T12:46:25Z","ec_funded":1,"publist_id":"7400","article_number":"e32035","date_published":"2018-03-09T00:00:00Z","publication":"eLife","citation":{"short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).","mla":"Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife, vol. 7, e32035, eLife Sciences Publications, 2018, doi:10.7554/eLife.32035.","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32035.","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 2018;7. doi:10.7554/eLife.32035","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd immunity can limit phage epidemics in bacterial populations,” eLife, vol. 7. eLife Sciences Publications, 2018.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32035","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 7, e32035."},"day":"09","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":3533881,"file_name":"2018_eLife_Payne.pdf","access_level":"open_access","date_created":"2018-12-17T10:36:07Z","date_updated":"2020-07-14T12:46:25Z","checksum":"447cf6e680bdc3c01062a8737d876569","file_id":"5689","relation":"main_file"}],"ddc":["576"],"title":"CRISPR-based herd immunity can limit phage epidemics in bacterial populations","status":"public","intvolume":" 7","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"423","abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"type":"journal_article"},{"abstract":[{"text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity.","lang":"eng"}],"type":"research_data_reference","author":[{"full_name":"Payne, Pavel","orcid":"0000-0002-2711-9453","id":"35F78294-F248-11E8-B48F-1D18A9856A87","last_name":"Payne","first_name":"Pavel"},{"full_name":"Geyrhofer, Lukas","first_name":"Lukas","last_name":"Geyrhofer"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P"}],"related_material":{"record":[{"id":"423","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-09T13:10:02Z","date_updated":"2023-09-11T12:49:17Z","oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9840","year":"2018","status":"public","title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","publisher":"Dryad","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"month":"03","day":"12","article_processing_charge":"No","doi":"10.5061/dryad.42n44","date_published":"2018-03-12T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.42n44"}],"oa":1,"citation":{"ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:10.5061/dryad.42n44","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. https://doi.org/10.5061/dryad.42n44","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations, Dryad, 10.5061/dryad.42n44.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).","mla":"Payne, Pavel, et al. Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations. Dryad, 2018, doi:10.5061/dryad.42n44.","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.” Dryad, 2018. https://doi.org/10.5061/dryad.42n44."}}]