Molecular signatures of divergence and selection in closely related pine taxa

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. Electronic supplementary material The online version of this article (10.1007/s11295-018-1296-3) contains supplementary material, which is available to authorized users.

Development of a single nucleotide polymorphism array for population genomic studies in four European pine species

“…shared SNPs among the species, as found in comparative transcriptome sequencing (Wachowiak et al, 2015) and candidate gene studies (Wachowiak, Zaborowska, et al, 2018), confirms their close Under multivariate analysis, three major clusters were identified (with similar resolution when including all available SNPs or only a subset of common polymorphic SNPs), which corresponded to P. sylvestris, P. uncinata and P. mugo/ P. uliginosa. The position of the P. uliginosa samples, between P. sylvestris and P. mugo but more proximate to the latter, has been observed in previous studies (Wachowiak, Żukowska, Wójkiewicz, Cavers, & Litkowiec, 2016).…”

Pre-colonial Amerindian legacies in forest composition of southern Brazil

“…Amerindians transplanted cassava, beans, maize, and genipap from the Amazon to southern Brazil as part of a cyclic agroforestry production system [62]. The Southern-Jê were probably responsible for Araucaria forest expansion over grasslands [27,34,35]. Pre-colonial Southern-Jê and Guarani archaeology reveals evidence of agriculture [30,62,63] and pottery production [30,[62][63][64], and both these activities require fire.…”

“…Around 3000 years ago, forest expansion over grasslands intensified [32,33], coinciding with the arrival of the Southern-Jê people in southern Brazil [25,26]. Together with climate changes, humans may have acted as a complementary driver of forest expansion due to transportation of seeds [27,28,34,35], and maintained grasslands using fire [32,33,36]. Recent research has shown that human action was essential for these forests to reach their maximum distribution [34,35].…”

“…Together with climate changes, humans may have acted as a complementary driver of forest expansion due to transportation of seeds [27,28,34,35], and maintained grasslands using fire [32,33,36]. Recent research has shown that human action was essential for these forests to reach their maximum distribution [34,35]. There are many evidence of the long-term use of A. angustifolia by past Amerindian societies also suggests they promoted the population expansion of this species, which is the dominant species of Araucaria moist forests in southern Brazil [37].…”

cis dominantly explains regulatory divergence between two indica rice genotypes; drought further enhances regulatory differences

“…Reports showed that natural selection reduces the level of variability of local genomic regions leaving molecular patterns of selection such as increased genetic divergence around adaptive loci (Nielsen et al 2005;Verta and Jones, 2019;Wachowiak et al 2018). We further tested this hypothesis by co-localizing cis-diverging genes to drought-yield QTL marker regions (shown below; also see Ereful et al 2016).…”