Genome‐wide admixture and ecological niche modelling reveal the maintenance of species boundaries despite long history of interspecific gene flow

Abstract

The maintenance of species boundaries despite interspecific gene flow has been a continuous source of interest in evolutionary biology. Many hybridizing species have porous genomes with regions impermeable to introgression, conferring reproductive barriers between species. We used ecological niche modelling to study the glacial and postglacial recolonization patterns between the widely hybridizing spruce species Picea glauca and P. engelmannii in western North America. Genome-wide estimates of admixture based on a panel of 311 candidate gene single nucleotide polymorphisms (SNP) from 290 genes were used to assess levels of admixture and introgression and to identify loci putatively involved in adaptive differences or reproductive barriers between species. Our palaeoclimatic modelling suggests that these two closely related species have a long history of hybridization and introgression, dating to at least 21 000 years ago, yet species integrity is maintained by a combination of strong environmental selection and reduced current interspecific gene flow. Twenty loci showed evidence of divergent selection, including six loci that were both Fst outliers and associated with climatic gradients, and fourteen loci that were either outliers or showed associations with climate. These included genes responsible for carbohydrate metabolism, signal transduction and transcription factors.

Molecular Proxies for Climate Maladaptation in a Long-Lived Tree (Pinus pinasterAiton, Pinaceae)

“…Model convergence was assured by performing three independent runs of 100,000 iterations and a burn-in of 10,000 chains with random seeds. Statistical support was assessed by Spearman's rank correlation (r) tests for those associations exhibiting unusually high BF (Eckert et al 2010b;De La Torre et al 2014). This was complemented by comparing these unusually high BFs to those observed for…”

The Neotoma Paleoecology Database, a multiproxy, international, community-curated data resource

“…Networks of paleoecological records, therefore, provide fundamental scientific infrastructure for understanding the responses of species to large and abrupt environmental changes, the mechanisms that promote resilience, and the interplay between climatic and biotic interactions (Dawson et al, 2011;Blois et al, 2013;Moritz and Agudo, 2013;Jackson and Blois, 2015). Examples include the processes controlling contemporary and past patterns of community, species, and genetic diversity (Fritz et al, 2013;Blarquez et al, 2014;De La Torre et al, 2014;Gutiérrez-García et al, 2014;Sandom et al, 2014;Cinget et al, 2015;Jezkova et al, 2015); identification of species refugia (Bennett and Provan, 2008;Gavin et al, 2014;Vickers and Buckland, 2015); rates of species expansion (Ordonez and Williams, 2013;Giesecke et al, 2017); the reshuffling of species into no-analog communities during climate change (Graham et al, 1996;Radeloff et al, 2015;Finsinger et al, 2017); the timing and patterns of abrupt ecological and climate change (Shuman et al, 2009;Seddon et al, 2015); quantification of the time lags between abrupt climate change and local ecological response (Ammann et al, 2013;Birks, 2015); and the timing, causes, and consequences of late Quaternary megafaunal extinctions (Lorenzen et al, 2011;Doughty et al, 2013;Emery-Wetherell et al, 2017).…”

Ecological and association genetics in two Mediterranean pine species

“…Model convergence was assured by performing three independent runs of 100,000 iterations and a burn-in of 10,000 chains with random seeds. Statistical support was assessed by Spearman's rank correlation (r) tests for those associations exhibiting unusually high BF (Eckert et al 2010b;De La Torre et al 2014). This was complemented by comparing these unusually high BFs to those observed for SNPs that did not show any associations with the environment in any of the two previous methods (mlr and LFMM; see Figure S1).…”

“…Molecular marker information gained from genotyping is the other fundamental source of data for the study of the genetic basis of evolutionary processes and adaptation. Conifers have large and complex genomes (>20 Gbp) characterized by a large nuclear volume and rDNA repeat units, the proliferation of repetitive sequences from transposable elements and perhaps larger genes and abundant pseudogenes (Ahuja and Neale 2005;De La Torre et al 2014). Pines are known to have very slow chromosomal evolution and all species feature 12 pairs of morphologically similar chromosomes (Guevara et al 2005).…”