Abstract
Efforts to detect loci under selection in plants have mostly focussed on single species. However, assuming that intraspecific divergence may lead to speciation, comparisons of genetic variation within and among recently diverged taxa can help to locate such genes. In this study, coalescent and outlier detection methods were used to assess nucleotide polymorphism and divergence at 79 nuclear gene fragments (1212 SNPs) in 16 populations (153 individuals) of the closely related, but phenotypically and ecologically distinct, pine taxa Pinus mugo, P. uliginosa and P. uncinata across their European distributions. Simultaneously, mitochondrial DNA markers, which are maternally inherited in pines and distributed by seeds at short geographic distance, were used to assess genetic relationships of the focal populations and taxa. The majority of nuclear loci showed homogenous patterns of variation between the taxa due to a high number of shared SNPs and haplotypes, similar levels of polymorphism, and low net divergence. However, against this common genetic background and an overall low population structure within taxa at mitochondrial markers, we identified several genes showing signatures of selection, accompanied by significant intra- and interspecific divergence. Our results indicate that loci involved in species divergence may be involved in intraspecific local adaptation.
Highlights
Identifying the molecular basis of evolution is a major challenge in biology
We looked at the patterns of genetic variation within and among the focal taxa in populations’ representative of their distribution range in Europe to search for patterns of divergence and local adaptation in a set of orthologous genomic regions
We found no fixed differences at any locus; the taxa shared 59–69% of SNPs, 46–56% of mtDNA haplotypes, showed low overall net divergence
Summary
Identifying the molecular basis of evolution is a major challenge in biology. Efforts to detect loci under selection in Communicated by F. Comparative genomic studies on model plant species have reached different conclusions regarding the rate and magnitude of genomic change that drives adaptation and speciation. Contrasting patterns of genomic divergence, including the size and location of regions under selection, were observed between dune and non-dune ecotypes of sunflower Helianthus petiolaris relative to H. annuus (Andrew and Rieseberg 2013). Scans of the patterns of polymorphism and divergence identified genomic regions enriched for genes involved in ion transport and metal detoxification in adaptively differentiated Arabidopsis lyrata
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