[{"month":"11","project":[{"call_identifier":"H2020","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","grant_number":"704172","name":"Rate of Adaptation in Changing Environment"}],"oa_version":"Published Version","has_accepted_license":"1","publication":"Molecular Ecology Resources","language":[{"iso":"eng"}],"oa":1,"publication_identifier":{"issn":["1755-098X"],"eissn":["1755-0998"]},"type":"journal_article","date_published":"2022-11-01T00:00:00Z","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","file":[{"file_id":"12477","creator":"dernst","relation":"main_file","success":1,"access_level":"open_access","date_updated":"2023-02-02T08:11:23Z","file_name":"2022_MolecularEcologyRes_Szep.pdf","content_type":"application/pdf","date_created":"2023-02-02T08:11:23Z","file_size":6431779,"checksum":"3102e203e77b884bffffdbe8e548da88"}],"intvolume":"        22","title":"Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"NiBa"}],"date_created":"2022-07-24T22:01:43Z","publication_status":"published","issue":"8","author":[{"id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","first_name":"Eniko","last_name":"Szep","full_name":"Szep, Eniko"},{"id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","first_name":"Barbora","last_name":"Trubenova"},{"first_name":"Katalin","last_name":"Csilléry","full_name":"Csilléry, Katalin"}],"scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","_id":"11640","article_type":"original","publisher":"Wiley","file_date_updated":"2023-02-02T08:11:23Z","quality_controlled":"1","ec_funded":1,"page":"2941-2955","abstract":[{"text":"Spatially explicit population genetic models have long been developed, yet have rarely been used to test hypotheses about the spatial distribution of genetic diversity or the genetic divergence between populations. Here, we use spatially explicit coalescence simulations to explore the properties of the island and the two-dimensional stepping stone models under a wide range of scenarios with spatio-temporal variation in deme size. We avoid the simulation of genetic data, using the fact that under the studied models, summary statistics of genetic diversity and divergence can be approximated from coalescence times. We perform the simulations using gridCoal, a flexible spatial wrapper for the software msprime (Kelleher et al., 2016, Theoretical Population Biology, 95, 13) developed herein. In gridCoal, deme sizes can change arbitrarily across space and time, as well as migration rates between individual demes. We identify different factors that can cause a deviation from theoretical expectations, such as the simulation time in comparison to the effective deme size and the spatio-temporal autocorrelation across the grid. Our results highlight that FST, a measure of the strength of population structure, principally depends on recent demography, which makes it robust to temporal variation in deme size. In contrast, the amount of genetic diversity is dependent on the distant past when Ne is large, therefore longer run times are needed to estimate Ne than FST. Finally, we illustrate the use of gridCoal on a real-world example, the range expansion of silver fir (Abies alba Mill.) since the last glacial maximum, using different degrees of spatio-temporal variation in deme size.","lang":"eng"}],"day":"01","doi":"10.1111/1755-0998.13676","external_id":{"isi":["000825873600001"]},"isi":1,"citation":{"ista":"Szep E, Trubenova B, Csilléry K. 2022. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. Molecular Ecology Resources. 22(8), 2941–2955.","mla":"Szep, Eniko, et al. “Using GridCoal to Assess Whether Standard Population Genetic Theory Holds in the Presence of Spatio-Temporal Heterogeneity in Population Size.” <i>Molecular Ecology Resources</i>, vol. 22, no. 8, Wiley, 2022, pp. 2941–55, doi:<a href=\"https://doi.org/10.1111/1755-0998.13676\">10.1111/1755-0998.13676</a>.","short":"E. Szep, B. Trubenova, K. Csilléry, Molecular Ecology Resources 22 (2022) 2941–2955.","chicago":"Szep, Eniko, Barbora Trubenova, and Katalin Csilléry. “Using GridCoal to Assess Whether Standard Population Genetic Theory Holds in the Presence of Spatio-Temporal Heterogeneity in Population Size.” <i>Molecular Ecology Resources</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/1755-0998.13676\">https://doi.org/10.1111/1755-0998.13676</a>.","ieee":"E. Szep, B. Trubenova, and K. Csilléry, “Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size,” <i>Molecular Ecology Resources</i>, vol. 22, no. 8. Wiley, pp. 2941–2955, 2022.","apa":"Szep, E., Trubenova, B., &#38; Csilléry, K. (2022). Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.13676\">https://doi.org/10.1111/1755-0998.13676</a>","ama":"Szep E, Trubenova B, Csilléry K. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. <i>Molecular Ecology Resources</i>. 2022;22(8):2941-2955. doi:<a href=\"https://doi.org/10.1111/1755-0998.13676\">10.1111/1755-0998.13676</a>"},"year":"2022","date_updated":"2023-08-03T12:11:01Z","ddc":["570"],"volume":22,"acknowledgement":"ES was supported by an IST studentship provided by IST Austria. BT was funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Independent Fellowship (704172, RACE). This project received further funding awarded to KC from the Swiss National Science Foundation (SNSF CRSK-3_190288) and the Swiss Federal Research Institute WSL. We thank Nick Barton for many invaluable discussions and his comments on the thesis chapter and this manuscript. We thank Peter Ralph and Jerome Kelleher for useful discussions and Bisschop Gertjan for comments on this manuscript. We thank Fortunat Joos for providing us with the raw data from the LPX-Bern model for silver fir, and Willy Tinner for helpful insights about the demographic history of silver fir. We also thank the editor Alana Alexander for useful comments and advice on the manuscript. Open access funding provided by Eidgenossische Technische Hochschule Zurich."},{"oa":1,"type":"journal_article","date_published":"2019-07-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"content_type":"application/pdf","file_name":"2019_Evolution_TrubenovaBarbora.pdf","date_updated":"2020-07-14T12:47:34Z","checksum":"9831ca65def2d62498c7b08338b6d237","file_size":815416,"date_created":"2019-07-16T06:08:31Z","creator":"apreinsp","file_id":"6643","relation":"main_file","access_level":"open_access"}],"month":"07","project":[{"_id":"25AEDD42-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Rate of Adaptation in Changing Environment","grant_number":"704172"},{"call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"oa_version":"Published Version","has_accepted_license":"1","publication":"Evolution","language":[{"iso":"eng"}],"abstract":[{"text":"The environment changes constantly at various time scales and, in order to survive, species need to keep adapting. Whether these species succeed in avoiding extinction is a major evolutionary question. Using a multilocus evolutionary model of a mutation‐limited population adapting under strong selection, we investigate the effects of the frequency of environmental fluctuations on adaptation. Our results rely on an “adaptive‐walk” approximation and use mathematical methods from evolutionary computation theory to investigate the interplay between fluctuation frequency, the similarity of environments, and the number of loci contributing to adaptation. First, we assume a linear additive fitness function, but later generalize our results to include several types of epistasis. We show that frequent environmental changes prevent populations from reaching a fitness peak, but they may also prevent the large fitness loss that occurs after a single environmental change. Thus, the population can survive, although not thrive, in a wide range of conditions. Furthermore, we show that in a frequently changing environment, the similarity of threats that a population faces affects the level of adaptation that it is able to achieve. We check and supplement our analytical results with simulations.","lang":"eng"}],"day":"01","doi":"10.1111/evo.13784","external_id":{"isi":["000474031600001"]},"isi":1,"year":"2019","citation":{"short":"B. Trubenova, M. Krejca, P.K. Lehre, T. Kötzing, Evolution 73 (2019) 1356–1374.","mla":"Trubenova, Barbora, et al. “Surfing on the Seascape: Adaptation in a Changing Environment.” <i>Evolution</i>, vol. 73, no. 7, Wiley, 2019, pp. 1356–74, doi:<a href=\"https://doi.org/10.1111/evo.13784\">10.1111/evo.13784</a>.","ista":"Trubenova B, Krejca M, Lehre PK, Kötzing T. 2019. Surfing on the seascape: Adaptation in a changing environment. Evolution. 73(7), 1356–1374.","ama":"Trubenova B, Krejca M, Lehre PK, Kötzing T. Surfing on the seascape: Adaptation in a changing environment. <i>Evolution</i>. 2019;73(7):1356-1374. doi:<a href=\"https://doi.org/10.1111/evo.13784\">10.1111/evo.13784</a>","apa":"Trubenova, B., Krejca, M., Lehre, P. K., &#38; Kötzing, T. (2019). Surfing on the seascape: Adaptation in a changing environment. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.13784\">https://doi.org/10.1111/evo.13784</a>","ieee":"B. Trubenova, M. Krejca, P. K. Lehre, and T. Kötzing, “Surfing on the seascape: Adaptation in a changing environment,” <i>Evolution</i>, vol. 73, no. 7. Wiley, pp. 1356–1374, 2019.","chicago":"Trubenova, Barbora, Martin  Krejca, Per Kristian Lehre, and Timo Kötzing. “Surfing on the Seascape: Adaptation in a Changing Environment.” <i>Evolution</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/evo.13784\">https://doi.org/10.1111/evo.13784</a>."},"date_updated":"2023-08-29T06:31:14Z","ddc":["576"],"volume":73,"acknowledgement":"The authors would like to thank to Tiago Paixao and Nick Barton for useful comments and advice.","intvolume":"        73","title":"Surfing on the seascape: Adaptation in a changing environment","department":[{"_id":"NiBa"}],"article_processing_charge":"Yes (via OA deal)","date_created":"2019-07-14T21:59:20Z","publication_status":"published","issue":"7","author":[{"id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","first_name":"Barbora","last_name":"Trubenova"},{"full_name":"Krejca, Martin ","last_name":"Krejca","first_name":"Martin "},{"last_name":"Lehre","first_name":"Per Kristian","full_name":"Lehre, Per Kristian"},{"full_name":"Kötzing, Timo","first_name":"Timo","last_name":"Kötzing"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","scopus_import":"1","_id":"6637","article_type":"original","publisher":"Wiley","file_date_updated":"2020-07-14T12:47:34Z","ec_funded":1,"quality_controlled":"1","page":"1356-1374"},{"has_accepted_license":"1","publication":"Ecology and Evolution","month":"09","project":[{"call_identifier":"H2020","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","name":"Rate of Adaptation in Changing Environment","grant_number":"704172"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"type":"journal_article","date_published":"2019-09-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["20457758"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","file":[{"checksum":"adcb70af4901977d95b8747eeee01bd7","file_size":2839636,"date_created":"2019-08-12T07:30:30Z","file_name":"2019_EcologyEvolution_Trubenova.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:40Z","relation":"main_file","access_level":"open_access","creator":"dernst","file_id":"6799"}],"issue":"17","author":[{"last_name":"Trubenova","first_name":"Barbora","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hager","first_name":"Reinmar","full_name":"Hager, Reinmar"}],"scopus_import":"1","_id":"6795","intvolume":"         9","title":"Green beards in the light of indirect genetic effects","date_created":"2019-08-11T21:59:24Z","department":[{"_id":"NiBa"}],"article_processing_charge":"No","publication_status":"published","file_date_updated":"2020-07-14T12:47:40Z","ec_funded":1,"quality_controlled":"1","page":"9597-9608","article_type":"original","publisher":"Wiley","external_id":{"isi":["000479973400001"]},"isi":1,"citation":{"ista":"Trubenova B, Hager R. 2019. Green beards in the light of indirect genetic effects. Ecology and Evolution. 9(17), 9597–9608.","short":"B. Trubenova, R. Hager, Ecology and Evolution 9 (2019) 9597–9608.","mla":"Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect Genetic Effects.” <i>Ecology and Evolution</i>, vol. 9, no. 17, Wiley, 2019, pp. 9597–608, doi:<a href=\"https://doi.org/10.1002/ece3.5484\">10.1002/ece3.5484</a>.","chicago":"Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect Genetic Effects.” <i>Ecology and Evolution</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/ece3.5484\">https://doi.org/10.1002/ece3.5484</a>.","ieee":"B. Trubenova and R. Hager, “Green beards in the light of indirect genetic effects,” <i>Ecology and Evolution</i>, vol. 9, no. 17. Wiley, pp. 9597–9608, 2019.","apa":"Trubenova, B., &#38; Hager, R. (2019). Green beards in the light of indirect genetic effects. <i>Ecology and Evolution</i>. Wiley. <a href=\"https://doi.org/10.1002/ece3.5484\">https://doi.org/10.1002/ece3.5484</a>","ama":"Trubenova B, Hager R. Green beards in the light of indirect genetic effects. <i>Ecology and Evolution</i>. 2019;9(17):9597-9608. doi:<a href=\"https://doi.org/10.1002/ece3.5484\">10.1002/ece3.5484</a>"},"year":"2019","date_updated":"2023-08-29T07:03:10Z","abstract":[{"text":"The green‐beard effect is one proposed mechanism predicted to underpin the evolu‐tion of altruistic behavior. It relies on the recognition and the selective help of altruists to each other in order to promote and sustain altruistic behavior. However, this mechanism has often been dismissed as unlikely or uncommon, as it is assumed that both the signaling trait and altruistic trait need to be encoded by the same gene or through tightly linked genes. Here, we use models of indirect genetic effects (IGEs) to find the minimum correlation between the signaling and altruistic trait required for the evolution of the latter. We show that this correlation threshold depends on the strength of the interaction (influence of the green beard on the expression of the altruistic trait), as well as the costs and benefits of the altruistic behavior. We further show that this correlation does not necessarily have to be high and support our analytical results by simulations.","lang":"eng"}],"day":"01","doi":"10.1002/ece3.5484","ddc":["576"],"volume":9}]