High rate of adaptive evolution in two widespread European pines

Abstract

Comparing related organisms with differing ecological requirements and evolutionary histories can shed light on the mechanisms and drivers underlying genetic adaptation. Here, by examining a common set of hundreds of loci, we compare patterns of nucleotide diversity and molecular adaptation of two European conifers (Scots pine and maritime pine) living in contrasted environments and characterized by distinct population genetic structure (low and clinal in Scots pine, high and ecotypic in maritime pine) and demographic histories. We found higher nucleotide diversity in Scots pine than in maritime pine, whereas rates of new adaptive substitutions (ω ), as estimated from the distribution of fitness effects, were similar across species and among the highest found in plants. Sample size and population genetic structure did not appear to have resulted in significant bias in estimates of ω . Moreover, population contraction-expansion dynamics for each species did not affect differentially the rate of adaptive substitution in these two pines. Several methodological and biological factors may underlie the unusually high rate of adaptive evolution of Scots pine and maritime pine. By providing two new case studies with contrasting evolutionary histories, we contribute to disentangling the multiple factors potentially affecting adaptive evolution in natural plant populations.

Genomics of clinal local adaptation inPinus sylvestrisunder continuous environmental and spatial genetic setting

“…The neutral nucleotide diversity around 0.004 per bp found in this study is similar to what has been observed in previous studies of this species (Kujala & Savolainen, 2012) and in several other conifers (Eckert et al, 2013) (Brown, Gill, Kuntz, Langley, & Neale, 2004) (Grivet et al, 2017). Given the mostly continuous distribution of wind-pollinated P. sylvestris and the previous findings of near-absent population structure, only very negligible differences between populations were anticipated, with the exceptions of geographically isolated populations (Kujala & Savolainen, 2012;Pyhäjärvi et al, 2007;Wachowiak, Balk, & Savolainen, 2009).…”

Utilization of tissue ploidy level variation inde novotranscriptome assembly ofPinus sylvestris

“…Overall, the H e per nucleotide for the assembled transcriptomes we assessed was lower than expected based on previous studies (Grivet et al, 2017), ranging from 1.2 x 10 -4 to 8.3 x 10 -4 (Table 2), an order of magnitude lower than previously reported in P. sylvestris ((Pyhäjärvi et al, 2011). The minimum required read depth and missing data threshold we applied to our data set were relatively lenient, which has probably increased the number of callable sites relative to variant calls.…”

“…We generated three vcf files per reference transcriptome according to the ploidy of the tissues: one vcf for the ME (haploid), one for the EM (diploid), and one combining NE+PH+VB (Tajima, 1989) per nucleotide was calculated for each transcript individually. Given that the expected value of π is equal to θ (=4N e μ ), we contrasted our observations to earlier, independent θ estimates for P. sylvestris (Grivet et al, 2017;Kujala & Savolainen, 2012;Pyhäjärvi et al, 2007;Pyhäjärvi, Kujala, & Savolainen, 2011…”

“…Number of input proteins used per reference species and the number of orthologs identified in P. sylvestris with the OGA approach. Grivet et al, 2017, assuming that one-third of coding sites are nonsynonymous and two-third are synonymous.…”

The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation

“…However, given increasing and recent evidence of pervasive effects of different types of selection across genic regions with HT data (e.g. Zhang Grivet et al 2017). Since Q. robur is the most pioneering species, it has likely been submitted to very strong environmental pressures at the time of stand establishment.…”