[{"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"}],"type":"research_data_reference","date_updated":"2023-09-19T10:06:07Z","date_created":"2021-08-06T12:03:50Z","oa_version":"Published Version","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"40"}]},"title":"Data from: The consequences of an introgression event","status":"public","department":[{"_id":"NiBa"}],"publisher":"Dryad","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9805","year":"2019","month":"01","day":"09","article_processing_charge":"No","date_published":"2019-01-09T00:00:00Z","doi":"10.5061/dryad.2kb6fh4","citation":{"ama":"Barton NH. Data from: The consequences of an introgression event. 2019. doi:10.5061/dryad.2kb6fh4","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.","short":"N.H. Barton, (2019).","mla":"Barton, Nicholas H. Data from: The Consequences of an Introgression Event. Dryad, 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."},"oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.2kb6fh4","open_access":"1"}]},{"publication_identifier":{"issn":["2663-337X"]},"month":"03","project":[{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"doi":"10.15479/at:ista:th6071","file_date_updated":"2020-07-14T12:47:18Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"publication_status":"published","year":"2019","date_updated":"2023-09-22T10:00:48Z","date_created":"2019-03-06T16:16:10Z","related_material":{"record":[{"id":"1358","status":"public","relation":"part_of_dissertation"},{"id":"955","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Prizak, Roshan","first_name":"Roshan","last_name":"Prizak","id":"4456104E-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","article_processing_charge":"No","day":"11","page":"189","citation":{"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). 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","ieee":"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: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.","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.","short":"R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019."},"date_published":"2019-03-11T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","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"}],"status":"public","ddc":["576"],"title":"Coevolution of transcription factors and their binding sites in sequence space","_id":"6071","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"date_created":"2019-03-06T16:05:07Z","date_updated":"2020-07-14T12:47:18Z","checksum":"e60a72de35d270b31f1a23d50f224ec0","file_id":"6072","relation":"main_file","creator":"rprizak","file_size":20995465,"content_type":"application/pdf","file_name":"Thesis_final_PDFA_RoshanPrizak.pdf","access_level":"open_access"},{"relation":"source_file","title":"Latex files","file_id":"6073","date_created":"2019-03-06T16:09:39Z","date_updated":"2020-07-14T12:47:18Z","checksum":"67c2630333d05ebafef5f018863a8465","file_name":"thesis_v2_merge.zip","access_level":"closed","file_size":85705272,"content_type":"application/zip","creator":"rprizak"}]},{"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","file":[{"checksum":"21e4c95599bbcaf7c483b89954658672","date_created":"2019-11-13T08:15:05Z","date_updated":"2020-07-14T12:47:42Z","file_id":"7011","relation":"main_file","creator":"dernst","file_size":1511958,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_NewPhytologist_Pickup.pdf"}],"oa_version":"Published Version","title":"Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow","ddc":["570"],"status":"public","intvolume":" 224","_id":"6856","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-11-01T00:00:00Z","article_type":"original","page":"1035-1047","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","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","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.","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."},"license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:47:42Z","ec_funded":1,"date_created":"2019-09-07T14:35:40Z","date_updated":"2023-10-18T08:47:08Z","volume":224,"author":[{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda","full_name":"Pickup, Melinda"},{"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":"Brandvain, Yaniv","first_name":"Yaniv","last_name":"Brandvain"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle"},{"last_name":"Yakimowski","first_name":"Sarah","full_name":"Yakimowski, Sarah"},{"last_name":"Dixit","first_name":"Tanmay","full_name":"Dixit, Tanmay"},{"last_name":"Lexer","first_name":"Christian","full_name":"Lexer, Christian"},{"last_name":"Cereghetti","first_name":"Eva","id":"71AA91B4-05ED-11EA-8BEB-F5833E63BD63","full_name":"Cereghetti, Eva"},{"full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field"}],"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","year":"2019","pmid":1,"month":"11","publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"language":[{"iso":"eng"}],"doi":"10.1111/nph.16180","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Mating system and the evolutionary dynamics of hybrid zones","_id":"25B36484-B435-11E9-9278-68D0E5697425","grant_number":"329960"},{"call_identifier":"FWF","name":"Sex chromosomes and species barriers","grant_number":"M02463","_id":"2662AADE-B435-11E9-9278-68D0E5697425"}],"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"]}},{"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.","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.","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","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","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","status":"public","title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6089","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1093/molbev/msy246","project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety"}],"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559","open_access":"1"}],"external_id":{"isi":["000462585100006"],"pmid":["30590559"]},"oa":1,"volume":36,"date_created":"2019-03-10T22:59:19Z","date_updated":"2024-02-21T13:59:17Z","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5757"}]},"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","orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","first_name":"Gemma"},{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"publisher":"Oxford University Press","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2019"},{"date_created":"2019-03-10T22:59:20Z","date_updated":"2024-02-28T13:12:06Z","volume":99,"author":[{"last_name":"Carballo-Pacheco","first_name":"Martín","full_name":"Carballo-Pacheco, Martín"},{"full_name":"Desponds, Jonathan","last_name":"Desponds","first_name":"Jonathan"},{"first_name":"Tatyana","last_name":"Gavrilchenko","full_name":"Gavrilchenko, Tatyana"},{"first_name":"Andreas","last_name":"Mayer","full_name":"Mayer, Andreas"},{"full_name":"Prizak, Roshan","last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Reddy, Gautam","first_name":"Gautam","last_name":"Reddy"},{"full_name":"Nemenman, Ilya","first_name":"Ilya","last_name":"Nemenman"},{"full_name":"Mora, Thierry","last_name":"Mora","first_name":"Thierry"}],"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"year":"2019","article_number":"022423","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.99.022423","isi":1,"quality_controlled":"1","external_id":{"isi":["000459916500007"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/448118v1.abstract"}],"month":"02","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":[{"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."}],"issue":"2","type":"journal_article","date_published":"2019-02-26T00:00:00Z","publication":"Physical Review E","citation":{"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.","short":"M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora, Physical Review E 99 (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.” 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","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.","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"},"day":"26","article_processing_charge":"No","scopus_import":"1"}]