Haploblocks contribute to parallel climate adaptation following global invasion of a cosmopolitan plant
2025
Battlay, Paul | Hendrickson, Brandon, T. | Mendez-Reneau, Jonas, I. | Santangelo, James, G. | Albano, Lucas, J. | Wilson, J. N. | Caizergues, Aude, E. | King, Nevada | Puentes, Adriana | Tudoran, Amelia | Violle, Cyrille | Vasseur, François | Patterson, Courtney, M. | Foster, Michael | Stamps, Caitlyn | Innes, Simon, G. | Allio, Rémi | Angeoletto, Fabio | Anstett, Daniel, N. | Anstett, Julia | Bucharova, Anna | Comerford, Mattheau, S. | David, Santiago | Falahati-Anbaran, Mohsen | Godsoe, William | González-Lagos, César | Gundel, Pedro, E. | Hood, Glen Ray | Lampei, Christian | Lara, Carlos | Lázaro-Lobo, Adrián | Silva Leandro, Deleon | Merritt, Thomas, J. S. | Mitchell, Nora | Mohammadi Bazargani, Mitra | Moles, Angela | Murúa, Maureen | Paule, Juraj | Pfeiffer, Vera | Raeymaekers, Joost, A. M. | Rennison, Diana, J. | Rios, Rodrigo, S. | Rowntree, Jennifer, K. | Schneider, Adam, C. | Whitney, Kaitlin Stack | Tamburrino, Ítalo | Vanwallendael, Acer | Kim, Paul, Y. | Ness, Rob W. | Johnson, Marc T.J. | Hodgins, Kathryn A. | Kooyers, Nicholas, J. | Monash University [Melbourne] | University of Louisiana | University of California [Berkeley] (UC Berkeley) ; University of California (UC) | University of Toronto at Mississauga | Swedish University of Agricultural Sciences = Sveriges lantbruksuniversitet (SLU) | Centre d’Ecologie Fonctionnelle et Evolutive (CEFE) ; École Pratique des Hautes Études (EPHE) ; Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [Occitanie])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier ; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM)-Université de Montpellier Paul-Valéry (UMPV) | Grambling State University | Centre de Biologie pour la Gestion des Populations (UMR CBGP) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [Occitanie])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier ; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM) | Universidade Federal de Rondonópolis | Michigan State University [East Lansing] ; Michigan State University System | Cornell University [Ithaca] (CU) | University of British Columbia [Canada] (UBC) | Philipps Universität Marburg = Philipps University of Marburg | University of Massachusetts [Boston] (UMass Boston) ; University of Massachusetts System (UMASS) | NTNU University Museum [Trondheim] ; Norwegian University of Science and Technology [Trondheim] (NTNU) ; Norwegian University of Science and Technology (NTNU)-Norwegian University of Science and Technology (NTNU) | Lincoln University [Nouvelle-Zélande] | Universidad Adolfo Ibáñez = University Adolfo Ibañez [Santiago] | Universidad de Talca | Universidad de Buenos Aires [Buenos Aires] (UBA) | Wayne State University [Detroit] | Universidad Católica de la Santísima Concepción (UCSC) | Instituto Mixto de Investigación en Biodiversidad (IMIB) | Universidade Federal de Mato Grosso (UFMT) | Laurentian University | University of Wisconsin–Eau Claire (UWEC) | University of New South Wales [Sydney] (UNSW) | Universidad Mayor [Santiago de Chile] | Freie Universität Berlin = Free University of Berlin | Washington State University (WSU) | Nord University [Bodø] | University of California (UC) | Universidad de La Serena (USERENA) | Plymouth University | University of Wisconsin-La Crosse (UW-La Crosse) | Rochester Institute of Technology (RIT) | Universidad de Chile = University of Chile [Santiago] (UCHILE) | North Carolina State University [Raleigh] (NC State) ; University of North Carolina System (UNC) | Funding was provided by an NSERC CGS Doctoral Award to L.J.A.; NSF grants OIA-1920858 and DBI-2244712 to N.J.K.; CNRS-University of Toronto PhD Student Travel Grant to M.T.J.J. and C.V.; NSERC Discovery Grant (RGPIN-2016-06063), Canada Research Chair (950-231981), NSERC Steacie Fellowship (544292) and NSERC RTI Grant (EQPEQ 423691) to M.T.J.J.; and ARC (DP220102362) and HFSP (RGP0001) grants to K.A.H. | Global Urban Evolution Network | Louisiana Optical Network
This work would not have been possible without white clover collections by 287 fellow scientists in the Global Urban Evolution Network. Support for field work was provided by A. Daugereaux, the UL-Ecology Center and numerous field and laboratory assistants in each common garden. The Louisiana Optical Network Infrastructure provided computational support. The use of genetic data originating from Ecuador was approved by the Ecuadorian Ministerio del Ambiente (access permit MAE-DNB-2018-0106 and transfer permit ATM-CM-2018-0106-001-2019).Data availability: Low-coverage whole-genome sequences for accessions used in population genomics analyses can be found as fastq files in the NCBI SRA database (Bioprojects: PRJNA1081485, PRJNA1179961). Metadata and fitness data from the four-way common garden study can be found on Dryad101 and associated low-coverage whole-genome sequences are in the NCBI SRA database (Biooproject: PRJNA1098360). Raw fastq files from RNA-seq expression experiment can be found in the NCBI SRA database (Bioproject: PRJNA1131002). Source data are provided with this paper.
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Mostrar más [+] Menos [-]Inglés. The role of rapid adaptation during species invasions has historically been minimized with the assumption that introductions consist of few colonists and limited genetic diversity. While overwhelming evidence suggests that rapid adaptation is more prevalent than originally assumed, the demographic and adaptive processes underlying successful invasions remain unresolved. Here we leverage a large whole-genome sequence dataset to investigate the relative roles of colonization history and adaptation during the worldwide invasion of the forage crop, Trifolium repens (Fabaceae). We show that introduced populations encompass high levels of genetic variation with little evidence of bottlenecks. Independent colonization histories on different continents are evident from genome-wide population structure. Five haploblocks—large haplotypes with limited recombination—on three chromosomes exist as standing genetic variation within the native and introduced ranges and exhibit strong signatures of parallel climate-associated adaptation across continents. Field experiments in the native and introduced ranges demonstrate that three of the haploblocks strongly affect fitness and exhibit patterns of selection consistent with local adaptation across each range. Our results provide strong evidence that large-effect structural variants contribute substantially to rapid and parallel adaptation of an introduced species throughout the world.
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