A multiscale approach to detect selection in nonmodel tree species : Widespread adaptation despite population decline in Taxus baccata L
Mayol, Maria (Centre de Recerca Ecològica i d'Aplicacions Forestals)
Riba Rovira, Miquel (Centre de Recerca Ecològica i d'Aplicacions Forestals)
Cavers, Stephen (Centre for Ecology and Hydrology (Edinburg, Regne Unit))
Grivet, Delphine (University of Valladolid. Sustainable Forest Management Research Institute)
Vincenot, Lucie (Université de Normandie)
Cattonaro, Federica (Instituto di Genomica Applicata)
Vendramin, Giovanni G. (National Research Council)
González-Martínez, Santiago C. (Université de Bordeaux)

Date:	2020
Abstract:	Detecting the molecular basis of local adaptation and identifying selective drivers is still challenging in nonmodel species. The use of purely population genetic approaches is limited by some characteristics of genetic systems, such as pleiotropy and polygenic control, and parallel evidence from phenotypic-based experimental comparisons is required. In long-lived organisms, the detection of selective pressures might also be precluded by evolutionary lag times in response to the environment. Here, we used the English yew to showcase an example of a multiscale integrative approach in a nonmodel species with limited plant and genomic resources. We combined information from two independent sources, phenotypes in a common environment and genomic data in natural populations, to investigate the signature of selection. Growth differences among populations in a common environment, and phenological patterns of both shoot elongation and male strobili maturation, were associated with climate clines, providing evidence for local adaptation and guiding us in the selection of populations for genomic analyses. We used information on over 25,000 SNPs from c. 1,200 genes to infer the demographic history and to test for molecular signatures of selection at different levels: SNP, gene, and biological pathway. Our results confirmed an overall demographic history of population decline, but we also found evidence for putative local adaptation at the molecular level. We identified or confirmed several candidate genes for positive and negative selection in forest trees, including the pseudo-response regulator 7 (PRR7), an essential component of the circadian clock in plants. In addition, we successfully tested an approach to detect polygenic adaptation in biological pathways, allowing us to identify the flavonoid biosynthesis pathway as a candidate stress-response pathway that deserves further attention in other plants. Finally, our study contributes to the emerging view that explaining contemporary standing genetic variation requires considering adaptation to past climates, especially for long-lived trees.
Grants:	Ministerio de Economía y Competitividad CGL2011-30182-C02-01-02 Ministerio de Economía y Competitividad CGL2007-63107-BOS European Commission 676876
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Adaptation ; Demographic decline ; English yew (Taxus baccata) ; Environmental association ; Polygenic adaptation ; Single nucleotide polymorphism
Published in:	Evolutionary applications, Vol. 13, Issue 1 (January 2020) , p. 143-160, ISSN 1752-4571

DOI: 10.1111/eva.12838
PMID: 31892949

18 p, 1.9 MB

The record appears in these collections:
Research literature > UAB research groups literature > Research Centres and Groups (research output) > Experimental sciences > CREAF (Centre de Recerca Ecològica i d'Aplicacions Forestals)
Articles > Research articles
Articles > Published articles