{"doi":"10.1073/pnas.1719998115","title":"Combining population genomics and fitness QTLs to identify the genetics of local adaptation in\n                    <i>Arabidopsis thaliana</i>","abstract":"<jats:title>Significance</jats:title>\n                  <jats:p>\n                    Local adaptation can occur due to individual genetic variants that increase the fitness of individuals in their home environments but decrease fitness in other environments [genetic trade-offs (GTs)] or genetic variants that increase fitness in one environment but have no effect in other environments [conditional neutrality (CN)]. Here, we show that GT quantitative trait loci (QTLs) for fitness between Italian and Swedish\n                    <jats:italic>Arabidopsis thaliana</jats:italic>\n                    exhibit strong population genomic signatures of local adaptation, including elevated levels of allele frequency differentiation, correlations to climatic variables, and recent sweeps. Highly divergent genes between Italy and Sweden populations show evidence of more recent selection in Sweden than Italy, and the biological annotations of these genes suggest interesting mechanisms underlying local adaptation.\n                  </jats:p>","journal":"Proceedings of the National Academy of Sciences","year":2018,"id":670801,"datarank":2.020951726726707,"base_score":4.204692619390966,"endowment":4.204692619390966,"self_citation_contribution":0.6307038929086449,"citation_network_contribution":1.3902478338180622,"self_endowment_contribution":0.6307038929086449,"citer_contribution":1.3902478338180622,"corpus_percentile":null,"corpus_rank":null,"citation_count":66,"citer_count":54,"citers_with_citation_signal":48,"citers_with_endowment":48,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1752308,"name":"Brook T. Moyers","orcid":null,"position":1,"is_corresponding":false},{"id":1752310,"name":"Lua Lopez","orcid":null,"position":2,"is_corresponding":false},{"id":491896,"name":"Jesse R. Lasky","orcid":"0000-0001-7688-5296","position":3,"is_corresponding":false},{"id":839724,"name":"J. Grey Monroe","orcid":"0000-0002-4025-5572","position":4,"is_corresponding":false},{"id":1752313,"name":"Jack L. Mullen","orcid":null,"position":5,"is_corresponding":false},{"id":127491,"name":"Christopher G. Oakley","orcid":"0000-0002-8082-5621","position":6,"is_corresponding":false},{"id":1752316,"name":"Junjiang Lin","orcid":null,"position":7,"is_corresponding":false},{"id":167383,"name":"Jon Ågren","orcid":null,"position":8,"is_corresponding":false},{"id":237916,"name":"Daniel R. Schrider","orcid":"0000-0001-5249-4151","position":9,"is_corresponding":false},{"id":20049,"name":"Andrew D. Kern","orcid":"0000-0003-4381-4680","position":10,"is_corresponding":false},{"id":62599,"name":"John K. McKay","orcid":null,"position":11,"is_corresponding":false},{"id":83862,"name":"Nicholas Price","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Combining population genomics and fitness QTLs to identify the genetics of local adaptation in <i>Arabidopsis thaliana</i>.","abstract":"Evidence for adaptation to different climates in the model species <i>Arabidopsis thaliana</i> is seen in reciprocal transplant experiments, but the genetic basis of this adaptation remains poorly understood. Field-based quantitative trait locus (QTL) studies provide direct but low-resolution evidence for the genetic basis of local adaptation. Using high-resolution population genomic approaches, we examine local adaptation along previously identified genetic trade-off (GT) and conditionally neutral (CN) QTLs for fitness between locally adapted Italian and Swedish <i>A. thaliana</i> populations [Ågren J, et al. (2013) <i>Proc Natl Acad Sci USA</i> 110:21077-21082]. We find that genomic regions enriched in high <i>F</i><sub><i>ST</i></sub> SNPs colocalize with GT QTL peaks. Many of these high <i>F</i><sub><i>ST</i></sub> regions also colocalize with regions enriched for SNPs significantly correlated to climate in Eurasia and evidence of recent selective sweeps in Sweden. Examining unfolded site frequency spectra across genes containing high <i>F</i><sub><i>ST</i></sub> SNPs suggests GTs may be due to more recent adaptation in Sweden than Italy. Finally, we collapse a list of thousands of genes spanning GT QTLs to 42 genes that likely underlie the observed GTs and explore potential biological processes driving these trade-offs, from protein phosphorylation, to seed dormancy and longevity. Our analyses link population genomic analyses and field-based QTL studies of local adaptation, and emphasize that GTs play an important role in the process of local adaptation.","is_dataset_classified":null,"base_score":0.0,"endowment":0.0,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"29686078","pmcid":"PMC5948977","openalex_id":null,"authors":[],"funders":[{"funder_name":"National Science Foundation","grant_id":"1523752","title":"NSF Postdoctoral Fellowship in Biology FY 2015"},{"funder_name":"HHS | National Institutes of Health","grant_id":"R01GM078204","title":null},{"funder_name":"National Science Foundation","grant_id":"1022202","title":"Collaborative Research (Arabidopsis 2010): Ecological Genomics of Adaptation to the Environment"},{"funder_name":"NIGMS NIH HHS","grant_id":"R01 GM117241","title":null},{"funder_name":"National Science Foundation","grant_id":"1556262","title":"Evolutionary genetics of adaptation in natural populations of Arabidopsis thaliana"},{"funder_name":"National Institutes of Health","grant_id":"5R01GM078204-02","title":"The Population Genetics of Divergence"}],"total_grants":6,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[],"oa_status":"bronze","license":"CC BY NC ND","oa_locations":[{"url":"https://www.pnas.org/content/pnas/115/19/5028.full.pdf","host_type":"publisher"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5948977","host_type":"repository"},{"url":"http://urn.kb.se/resolve?urn=urn:nbn:se:kau:diva-80819","host_type":"repository"},{"url":"http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-356386","host_type":"repository"},{"url":"https://escholarship.org/uc/item/7357q6sx","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC5948977","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC5948977?pdf=render","host_type":"Europe_PMC"},{"url":"https://doi.org/10.1073/pnas.1719998115","host_type":""},{"url":"https://pubmed.ncbi.nlm.nih.gov/29686078","host_type":""},{"url":"http://dx.doi.org/10.1073/pnas.1719998115","host_type":""},{"url":"https://dx.doi.org/10.1073/pnas.1719998115","host_type":""},{"url":"https://escholarship.org/content/qt7357q6sx/qt7357q6sx.pdf","host_type":""},{"url":"https://doi.org/https://doi.org/10.1073/pnas.1719998115","host_type":""}],"fields_of_study":["0301 basic medicine","03 medical and health sciences","0303 health sciences"],"mesh_terms":["Arabidopsis","Adaptation, Physiological","Polymorphism, Single Nucleotide","Genome, Plant","Quantitative Trait Loci","Italy","Sweden"],"keywords":["Ecotype","Divergent selection","Fst","Tradeoff","Selective Sweep","570","Physiological","Quantitative Trait Loci","Arabidopsis","Polymorphism, Single Nucleotide","Genetics","Adaptation","Polymorphism","580","Ekologi","Sweden","Genome","Ecology","Human Genome","Genetics and Genomics","Genetik och genomik","Plant","Single Nucleotide","Biological Sciences","Adaptation, Physiological","Climate Action","Italy","Genome, Plant","Biotechnology"],"sdg_mappings":[{"sdg_number":10,"sdg_label":"10. No inequality"},{"sdg_number":13,"sdg_label":"13. Climate action"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-15T23:56:05.899891Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}