[{"has_accepted_license":"1","publication":"Nature Ecology & Evolution","month":"04","project":[{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"oa_version":"Submitted Version","language":[{"iso":"eng"}],"type":"journal_article","date_published":"2020-04-01T00:00:00Z","oa":1,"publication_identifier":{"issn":["2397-334X"]},"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-to-thrive-without-gene-regulation/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"status":"public","relation":"dissertation_contains","id":"8155"},{"status":"public","relation":"research_data","id":"7383"},{"status":"public","id":"7016","relation":"research_data"},{"relation":"used_in_publication","id":"8653","status":"public"}]},"file":[{"creator":"dernst","file_id":"8640","success":1,"relation":"main_file","access_level":"open_access","file_name":"2020_NatureEcolEvo_Tomanek.pdf","content_type":"application/pdf","date_updated":"2020-10-09T09:56:01Z","file_size":745242,"checksum":"ef3bbf42023e30b2c24a6278025d2040","date_created":"2020-10-09T09:56:01Z"}],"issue":"4","author":[{"id":"3981F020-F248-11E8-B48F-1D18A9856A87","full_name":"Tomanek, Isabella","orcid":"0000-0001-6197-363X","last_name":"Tomanek","first_name":"Isabella"},{"orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","first_name":"Rok","last_name":"Grah","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lagator","first_name":"M.","full_name":"Lagator, M."},{"first_name":"A. M. C.","last_name":"Andersson","full_name":"Andersson, A. M. C."},{"orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","first_name":"Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","_id":"7652","intvolume":"         4","title":"Gene amplification as a form of population-level gene expression regulation","date_created":"2020-04-08T15:20:53Z","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"article_processing_charge":"No","publication_status":"published","file_date_updated":"2020-10-09T09:56:01Z","quality_controlled":"1","page":"612-625","article_type":"original","publisher":"Springer Nature","external_id":{"isi":["000519008300005"]},"isi":1,"citation":{"ista":"Tomanek I, Grah R, Lagator M, Andersson AMC, Bollback JP, Tkačik G, Guet CC. 2020. Gene amplification as a form of population-level gene expression regulation. Nature Ecology &#38; Evolution. 4(4), 612–625.","mla":"Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” <i>Nature Ecology &#38; Evolution</i>, vol. 4, no. 4, Springer Nature, 2020, pp. 612–25, doi:<a href=\"https://doi.org/10.1038/s41559-020-1132-7\">10.1038/s41559-020-1132-7</a>.","short":"I. Tomanek, R. Grah, M. Lagator, A.M.C. Andersson, J.P. Bollback, G. Tkačik, C.C. Guet, Nature Ecology &#38; Evolution 4 (2020) 612–625.","ieee":"I. Tomanek <i>et al.</i>, “Gene amplification as a form of population-level gene expression regulation,” <i>Nature Ecology &#38; Evolution</i>, vol. 4, no. 4. Springer Nature, pp. 612–625, 2020.","chicago":"Tomanek, Isabella, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P Bollback, Gašper Tkačik, and Calin C Guet. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” <i>Nature Ecology &#38; Evolution</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41559-020-1132-7\">https://doi.org/10.1038/s41559-020-1132-7</a>.","apa":"Tomanek, I., Grah, R., Lagator, M., Andersson, A. M. C., Bollback, J. P., Tkačik, G., &#38; Guet, C. C. (2020). Gene amplification as a form of population-level gene expression regulation. <i>Nature Ecology &#38; Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41559-020-1132-7\">https://doi.org/10.1038/s41559-020-1132-7</a>","ama":"Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level gene expression regulation. <i>Nature Ecology &#38; Evolution</i>. 2020;4(4):612-625. doi:<a href=\"https://doi.org/10.1038/s41559-020-1132-7\">10.1038/s41559-020-1132-7</a>"},"year":"2020","date_updated":"2024-03-25T23:30:20Z","abstract":[{"lang":"eng","text":"Organisms cope with change by taking advantage of transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. Here, we investigate whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using real-time monitoring of gene-copy-number mutations in Escherichia coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy-number and, therefore, expression-level polymorphisms. This amplification-mediated gene expression tuning (AMGET) occurs on timescales that are similar to canonical gene regulation and can respond to rapid environmental changes. Mathematical modelling shows that amplifications also tune gene expression in stochastic environments in which transcription-factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune the expression of any gene, without leaving any genomic signature."}],"day":"01","doi":"10.1038/s41559-020-1132-7","ddc":["570"],"volume":4,"acknowledgement":"We thank L. Hurst, N. Barton, M. Pleska, M. Steinrück, B. Kavcic and A. Staron for input on the manuscript, and To. Bergmiller and R. Chait for help with microfluidics experiments. I.T. is a recipient the OMV fellowship. R.G. is a recipient of a DOC (Doctoral Fellowship Programme of the Austrian Academy of Sciences) Fellowship of the Austrian Academy of Sciences."},{"language":[{"iso":"eng"}],"publication":"Nature Ecology & Evolution","month":"11","oa_version":"None","project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","date_published":"2019-11-25T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["2397-334X"]},"page":"1632-1641","ec_funded":1,"quality_controlled":"1","article_type":"original","publisher":"Springer Nature","author":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"issue":"12","_id":"7146","scopus_import":"1","title":"Molecular and evolutionary dynamics of animal sex-chromosome turnover","intvolume":"         3","publication_status":"published","article_processing_charge":"No","date_created":"2019-12-04T16:05:25Z","department":[{"_id":"BeVi"}],"volume":3,"isi":1,"external_id":{"isi":["000500728800009"]},"date_updated":"2023-09-06T11:18:59Z","citation":{"ama":"Vicoso B. Molecular and evolutionary dynamics of animal sex-chromosome turnover. <i>Nature Ecology &#38; Evolution</i>. 2019;3(12):1632-1641. doi:<a href=\"https://doi.org/10.1038/s41559-019-1050-8\">10.1038/s41559-019-1050-8</a>","apa":"Vicoso, B. (2019). Molecular and evolutionary dynamics of animal sex-chromosome turnover. <i>Nature Ecology &#38; Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41559-019-1050-8\">https://doi.org/10.1038/s41559-019-1050-8</a>","ieee":"B. Vicoso, “Molecular and evolutionary dynamics of animal sex-chromosome turnover,” <i>Nature Ecology &#38; Evolution</i>, vol. 3, no. 12. Springer Nature, pp. 1632–1641, 2019.","chicago":"Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome Turnover.” <i>Nature Ecology &#38; Evolution</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41559-019-1050-8\">https://doi.org/10.1038/s41559-019-1050-8</a>.","short":"B. Vicoso, Nature Ecology &#38; Evolution 3 (2019) 1632–1641.","mla":"Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome Turnover.” <i>Nature Ecology &#38; Evolution</i>, vol. 3, no. 12, Springer Nature, 2019, pp. 1632–41, doi:<a href=\"https://doi.org/10.1038/s41559-019-1050-8\">10.1038/s41559-019-1050-8</a>.","ista":"Vicoso B. 2019. Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology &#38; Evolution. 3(12), 1632–1641."},"year":"2019","abstract":[{"text":"Prevailing models of sex-chromosome evolution were largely inspired by the stable and highly differentiated XY pairs of model organisms, such as those of mammals and flies. Recent work has uncovered an incredible diversity of sex-determining systems, bringing some of the assumptions of these traditional models into question. One particular question that has arisen is what drives some sex chromosomes to be maintained over millions of years and differentiate fully, while others are replaced by new sex-determining chromosomes before differentiation has occurred. Here, I review recent data on the variability of sex-determining genes and sex chromosomes in different non-model vertebrates and invertebrates, and discuss some theoretical models that have been put forward to account for this diversity.","lang":"eng"}],"doi":"10.1038/s41559-019-1050-8","day":"25"},{"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","volume":2,"date_published":"2017-11-27T00:00:00Z","type":"journal_article","date_updated":"2021-01-12T08:15:07Z","citation":{"short":"J. Reger, M.I. Lind, M.R. Robinson, A.P. Beckerman, Nature Ecology &#38; Evolution 2 (2017) 100–107.","mla":"Reger, Julia, et al. “Predation Drives Local Adaptation of Phenotypic Plasticity.” <i>Nature Ecology &#38; Evolution</i>, vol. 2, Springer Nature, 2017, pp. 100–07, doi:<a href=\"https://doi.org/10.1038/s41559-017-0373-6\">10.1038/s41559-017-0373-6</a>.","ista":"Reger J, Lind MI, Robinson MR, Beckerman AP. 2017. Predation drives local adaptation of phenotypic plasticity. Nature Ecology &#38; Evolution. 2, 100–107.","ama":"Reger J, Lind MI, Robinson MR, Beckerman AP. Predation drives local adaptation of phenotypic plasticity. <i>Nature Ecology &#38; Evolution</i>. 2017;2:100-107. doi:<a href=\"https://doi.org/10.1038/s41559-017-0373-6\">10.1038/s41559-017-0373-6</a>","apa":"Reger, J., Lind, M. I., Robinson, M. R., &#38; Beckerman, A. P. (2017). Predation drives local adaptation of phenotypic plasticity. <i>Nature Ecology &#38; Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41559-017-0373-6\">https://doi.org/10.1038/s41559-017-0373-6</a>","chicago":"Reger, Julia, Martin I. Lind, Matthew Richard Robinson, and Andrew P. Beckerman. “Predation Drives Local Adaptation of Phenotypic Plasticity.” <i>Nature Ecology &#38; Evolution</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/s41559-017-0373-6\">https://doi.org/10.1038/s41559-017-0373-6</a>.","ieee":"J. Reger, M. I. Lind, M. R. Robinson, and A. P. Beckerman, “Predation drives local adaptation of phenotypic plasticity,” <i>Nature Ecology &#38; Evolution</i>, vol. 2. Springer Nature, pp. 100–107, 2017."},"year":"2017","abstract":[{"lang":"eng","text":"Phenotypic plasticity is the ability of an individual genotype to alter aspects of its phenotype depending on the current environment. It is central to the persistence, resistance and resilience of populations facing variation in physical or biological factors. Genetic variation in plasticity is pervasive, which suggests its local adaptation is plausible. Existing studies on the adaptation of plasticity typically focus on single traits and a few populations, while theory about interactions among genes (for example, pleiotropy) suggests that a multi-trait, landscape scale (for example, multiple populations) perspective is required. We present data from a landscape scale, replicated, multi-trait experiment using a classic predator–prey system centred on the water flea Daphnia pulex. We find predator regime-driven differences in genetic variation of multivariate plasticity. These differences are associated with strong divergent selection linked to a predation regime. Our findings are evidence for local adaptation of plasticity, suggesting that responses of populations to environmental variation depend on the conditions in which they evolved in the past."}],"doi":"10.1038/s41559-017-0373-6","day":"27","publication_identifier":{"issn":["2397-334X"]},"language":[{"iso":"eng"}],"page":"100-107","quality_controlled":"1","article_type":"original","publisher":"Springer Nature","author":[{"first_name":"Julia","last_name":"Reger","full_name":"Reger, Julia"},{"full_name":"Lind, Martin I.","first_name":"Martin I.","last_name":"Lind"},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","last_name":"Robinson"},{"last_name":"Beckerman","first_name":"Andrew P.","full_name":"Beckerman, Andrew P."}],"publication":"Nature Ecology & Evolution","_id":"7725","month":"11","title":"Predation drives local adaptation of phenotypic plasticity","intvolume":"         2","oa_version":"None","publication_status":"published","article_processing_charge":"No","date_created":"2020-04-30T10:46:02Z"}]