Admixture and selection patterns across the European distribution of Scots pine, Pinus sylvestris (Pinaceae)

Abstract

We analysed data on nucleotide polymorphism at 78 nuclear genes to search for signatures of divergence and selection in populations from across the distribution of Pinus sylvestris in Europe. Data on variation at a large set of maternally inherited mitochondrial DNA markers were also analysed. Most nuclear loci showed homogeneous patterns of variation across populations from Spain, Central Europe, Nordic countries and Scotland. Mitochondrial markers did not reveal strong population structure but suggested admixture of samples carrying different mitochondrial lineages in certain parts of the distribution. At nuclear DNA loci, we found high nucleotide polymorphism, generally low population differentiation and weak signals of isolation by distance. Together with the mitochondrial DNA results, these patterns seem most likely to be associated with a process of colonization from multiple sources and efficient gene flow. The results are in line with demographic inference indicating establishment of Central European and Nordic populations before the Last Glacial Maximum and admixture of colonization fronts from mainland Europe in Scottish populations. Coalescent and outlier detection methods identified several genes showing molecular signatures of selection especially in response to temperature variation in ecologically and phenotypically divergent populations. The study provides a large set of markers for analysis of genetic diversity in populations of P. sylvestris, including candidate genes that are implicated in local adaptation and population divergence.

Scots pine – panmixia and the elusive signal of genetic adaptation

“…The low genetic differentiation in Scots pine is, to our knowledge, unique for a species with comparable distribution ranges. A global F ST of 0.048 across its continental distribution uncovered in this study is in agreement with previous results that estimated a F ST of 0.02 on average for the western part of Europe (Pyhäjärvi et al ., 2020; Tyrmi et al ., 2020; Wachowiak et al ., 2022a; Milesi et al ., 2023). We confirm the genetic proximity of the Scottish populations to the mainland ones (Wachowiak et al ., 2011, 2022a), and the presence of genetically distinct populations in Turkey and the Carpathian Mountains detected at high K values (Naydenov et al ., 2007; Dering et al ., 2017; Tóth et al ., 2017b).…”

Scots pine – panmixia and the elusive signal of genetic adaptation

“…The low genetic differentiation in Scots pine is, to our knowledge, unique for a species with comparable distribution ranges. A global F ST of 0.048 across its continental distribution uncovered in this study is in agreement with previous results that estimated a F ST of 0.02 on average for the western part of Europe (Pyhäjärvi et al ., 2020; Tyrmi et al ., 2020; Wachowiak et al ., 2022a; Milesi et al ., 2023). We confirm the genetic proximity of the Scottish populations to the mainland ones (Wachowiak et al ., 2011; Wachowiak et al ., 2022a), and the presence of genetically distinct populations in Turkey and the Carpathian Mountains detected at high K values (Naydenov et al ., 2007; Dering et al ., 2017; Tóth et al ., 2017b).…”

“…A global F ST of 0.048 across its continental distribution uncovered in this study is in agreement with previous results that estimated a F ST of 0.02 on average for the western part of Europe (Pyhäjärvi et al ., 2020; Tyrmi et al ., 2020; Wachowiak et al ., 2022a; Milesi et al ., 2023). We confirm the genetic proximity of the Scottish populations to the mainland ones (Wachowiak et al ., 2011; Wachowiak et al ., 2022a), and the presence of genetically distinct populations in Turkey and the Carpathian Mountains detected at high K values (Naydenov et al ., 2007; Dering et al ., 2017; Tóth et al ., 2017b). The uniqueness of these populations, and in general the differentiation between European populations, are more visible at the maternally inherited mitochondrial DNA markers due to the more limited dispersal ability of seeds (Tóth et al ., 2017a).…”

Evolutionary targets of gene expression divergence in a complex of closely related pine species

“…Two were annotated as caffeoyl CoA O‐methyltransferase ( CCoAOMT ) and catechol‐O‐methyltransferase ( COMT ), and the third was also grouped with COMT ‐like sequences or type II OMTs from the genus Pinus . The best‐recognized function of CCoAOMT is its role in lignin synthesis, and interestingly the patterns of nucleotide polymorphism at the gene showed signatures of natural selection in Pinus taeda and P. sylvestris (González‐Martínez et al, 2006; Wachowiak et al, 2022). Finding the COMT gene was unexpected, since to our knowledge, such sequences have not been noted earlier in Scots pine, despite extensive research related to the wood production process in this species (Paasela et al, 2017; Lim et al, 2021), so we did not expect COMT expression in its close relatives.…”