Asymmetry matters: A genomic assessment of directional biases in gene flow between hybridizing spruces

Abstract

Assessing directional bias in interspecific gene flow might be important in determining the evolutionary trajectory of closely related species pairs. Using a set of 300 single nucleotide polymorphisms (SNPs) having variable propensity to cross species boundary, we evaluated the genomic extent and direction of interspecific gene flow in a progenitor‐derivative spruce species pair (black spruce and red spruce). A higher rate of gene flow was found from black spruce toward red spruce purebreds than vice versa. This asymmetry could reflect the historical gene flow between the two taxa at the time of species inception and during postglacial colonization. A clear asymmetry in introgression was depicted by a greater gene flow between red spruce and hybrids than between black spruce and hybrids. While backcrossing toward red spruce was invariably high across the genome, the actual species boundary is between hybrids and black spruce where gene flow is impeded at those genomic regions impermeable to introgression. Associations between hybrid index and climatic variables (total annual precipitation and mean annual temperature) were tested, as these might indicate a role for exogenous selection in maintaining the species boundary. While an apparent association was found between the hybrid index and precipitation, it collapsed when considered in light of the directional bias in interspecific gene flow. Hence, considering asymmetrical patterns of introgression allowed us to falsify an apparent role for exogenous selection. Although this was not formerly tested here, we suggest that this pattern could result from asymmetrical endogenous selection, a contention that deserves further investigations.

Discrepancies between genetic and ecological divergence patterns suggest a complex biogeographic history in a Neotropical genus

“…In summary, our study highlights an example of interspecific gene flow between ecologically divergent tree species, well‐fitting with the suggestion by Ellstrand (2014) that plant species form meta‐populations that exchange genes with variable, asymmetric rates. Given the relatively small number of neutral genetic markers used, we cannot make inferences about several important points, such as whether the amount of gene flow differs among genomic regions, or whether it involves regions of relevant adaptive value, which would be of great interest in the dissection of the relative weight of selection and gene flow on divergence patterns across the genome (in the Picea mariana / Picea rubens pair, for example, not introgressed or “impermeable” genomic regions coexist with highly introgressed, or “permeable”, ones (de Lafontaine & Bousquet, 2017)). Introgression is emerging as an important source of adaptation as proven by the large number of studies recently published (Suarez‐Gonzalez, Lexer, & Cronk Quentin, 2018, for a review).…”

“…All summary statistics were computed using Arlequin 3.5 (Excoffier & Lischer, 2010) and its companion ARLSUMSTAT. Calculations of posterior distributions of parameters were performed using the "abc" R package (Csilléry, François, & Blum, 2012) parameters are scaled to mutation rate (locus −1 generation −1 ), which is also estimated in the model. Absolute value should not be taken as strictly informative; ratios, differences, and comparisons are, on the contrary, entirely meaningful.…”

Mixing It Up: The Role of Hybridization in Forest Management and Conservation under Climate Change

“…Where reproductive barriers have evolved, the genomic signature of those barriers may result in regions of differentiation throughout the genome [79,80]. Identification of those regions, or candidate genes associated with those regions, are necessary for genetic conservation and inclusion into breeding programs, particularly if asymmetries have evolved [63,81]. Where genetic signatures of introgression are observed they may result from neutral introgression following contact or selection for different genetic regions in distinct genetic backgrounds [82].…”

A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies)

“…[10–13]), association mapping and ecological genomic studies (e.g. [6, 14–25]), the management of genetic diversity, and for traceability applications [15, 26–29]. One central feature of spruce gene SNPs is that they are informed markers, given the availability of high-confidence annotated spruce gene catalogs (e.g.…”