Convergent local adaptation to climate in distantly related conifers

Abstract

When confronted with an adaptive challenge, such as extreme temperature, closely related species frequently evolve similar phenotypes using the same genes. Although such repeated evolution is thought to be less likely in highly polygenic traits and distantly related species, this has not been tested at the genome scale. We performed a population genomic study of convergent local adaptation among two distantly related species, lodgepole pine and interior spruce. We identified a suite of 47 genes, enriched for duplicated genes, with variants associated with spatial variation in temperature or cold hardiness in both species, providing evidence of convergent local adaptation despite 140 million years of separate evolution. These results show that adaptation to climate can be genetically constrained, with certain key genes playing nonredundant roles.

Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir needles

“…5d), oxidoreductase and RNA-binding activity (Fig. 5e), and mitochondrial transcription termination factors implicated in adaptation to cold climates in conifers [68] (Fig. 5f).…”

The challenge of separating signatures of local adaptation from those of isolation by distance and colonization history: The case of two white pines

“…The redundancy of functions among recently duplicated genes in conifers could have offered the possibility for selection to act on paralogous genes in different species (Namroud et al., 2010). In distantly related P. glauca and Pinus contorta (divergence time ~140 MYA), an exome‐wide study detected 47 genes (~10–18% of top candidate genes) with convergent signatures of local adaptation to low temperatures (Yeaman et al., 2016). Paralogous genes in either species were more likely to show strong signatures of convergence than one‐to‐one orthologs.…”

“…Combining results across a number of different methods should be standard practice to detect strong candidate genes (De Mita et al., 2013; Lotterhos & Whitlock, 2014, 2015; de Villemereuil et al., 2014). The integration of phenotypic and genotypic information from populations growing in common‐garden experiments might be the most informative approach to discover loci important for local adaptation (Sork et al., 2013; Yeaman et al., 2016), and it could be used to validate candidate SNPs detected by F ST outlier or GEA methods (e.g., De Kort et al., 2014; Jaramillo‐Correa et al., 2015; Yoder et al., 2014). Another promising avenue would be taking advantage of the annual tree rings to establish relationships between annual growth and climatic variation in common‐garden experiments over a number of years.…”

“…Evidence of convergent evolution (Arendt & Reznick, 2008), or the repeated evolution of similar phenotypes from similar genetic mechanisms is increasing (Stern, 2013; Jones et al., 2012; Yeaman et al., 2016), but it is currently limited to a few taxa. Eastern white pine ( Pinus strobus , Figure 1) and western white pine ( P. monticola ) diverged <12 million years ago (Gernandt et al., 2008) and are well suited for studying local adaptation as both species are distributed latitudinally and longitudinally across a wide variety of climates in North America.…”

Population genomics of the eastern cottonwood (Populus deltoides)

“…The occurrence of convergent evolution was recently reported in conifers, where two distantly related species shared between ten and 18% of locally adapted genes (Yeaman et al., 2016). These findings indicate that sometimes adaptation to environmental factors occurs through mutations in the same genes in different species.…”