Interacting stochastic and selective forces drive population and species divergence. Such interaction may generate contrasting clines between genetic and phenotypic factors, which can be related to either geographical or environmental variation depending on the predominant evolutionary force (which in its turn is partly determined by population size). Here, we investigated whether the morphological and genetic differentiation across a species complex in Abies in central Mexico fits isolation by distance (IBD) or isolation-by-adaptation (IBA) frameworks. This complex includes two species (A. religiosa and A. flinckii) with discernible morphological and environmental differences and dissimilar range sizes. After comparing variation at nuclear SSR loci and diagnostic morphological traits of needles with the climate variables contributing to ecological differentiation, we found that the widely distributed A. religiosa has more genetic diversity and is morphologically more heterogeneous than the geographically restricted A. flinckii. Morphological differentiation at three physiologically important traits (needle thickness, number of stomata rows and location of the resin duct) is significantly correlated with geography in A. flinckii (indicative of IBD), but is significantly associated with climate variation in A. religiosa (suggesting IBA). In agreement with quantitative genetics theory, PST (phenotypic differentiation)-G’ST (genetic differentiation) comparisons indicate contrasting contributions of putatively adaptive (A. religiosa) and stochastic (A. flinckii) factors to the morphological differentiation of species related to their population size. The integration of such quantitative genetic/evolutionary aspects may reinforce species descriptions and help in disentangling resilient taxonomic discordance.

Secondary contact of recently diverged species may have several outcomes, ranging from rampant hybridization to reinforced reproductive isolation. In plants, selfing tolerance and disjunct reproductive phenology may lead to reproductive isolation at contact zones. However, they may also evolve under both allopatric or parapatric frameworks and originate from adaptive and/or neutral forces. Inferring the historical demography of diverging taxa is thus a crucial step to identify factors that may have led to putative reproductive isolation. We explored various competing demographypotheses to account for the rapid divergence of a fir species complex (Abies flinckii–A. religiosa) distributed in “sky‐islands” across central Mexico (i.e., along the Trans‐Mexican Volcanic Belt; TMVB). Despite co‐occurring in two independent sympatric regions (west and centre), these taxa rarely interbreed because of disjunct reproductive phenologies. We genotyped 1147 single nucleotide polymorphisms, generated by GBS (genotyping by sequencing), across 23 populations, and compared multiple scenarios based on the geological history of the TMVB. The best‐fitting model revealed one of the most rapid and complete speciation cases for a conifer species‐pair, dating back to ~1.2 million years ago. Coupled with the lack of support for stepwise colonization, our coalescent inferences point to an early cessation of interspecific gene flow under parapatric speciation; ancestral gene flow during divergence was asymmetrical (mostly from western firs into A. religiosa) and exclusive to the most ancient (i.e., central) contact zone. Factors promoting rapid reproductive isolation should be explored in other slowly evolving species complexes as they may account for the large tropical and subtropical diversity.

Aim Estimating genetic diversity is key for understanging biogeographic and evolutionary processes. However, gathering genetic information is not feasible for all taxa or populations, particularly in the tropical regions. Identifying proxies for inferring such values has thus become essential. Here, we built on the niche centrality hypothesis (NCH; or central‐abundance hypothesis) and the nearly neutral theory of evolution (NNT) to identify some of such proxies using a montane tropical conifer species‐pair as model. The NCH predicts more genetic diversity under optimal ecological conditions, which should also allow for more efficient purifying selection, according to the NNT. Location The Transmexican Volcanic Belt, central Mexico. Taxa A fir species‐pair endemic to central Mexico, Abies flinckii and A.religiosa. Methods We estimated patterns of genetic diversity from nuclear SSRs (A, HE), and gene‐coding sequences (πS, πN), together with the efficacy of purifying selection, measured as πN/πS. After testing for niche overlap, we used several geographic and ecological proxies (i.e. longitude, latitude, elevation, estimated area and distance to the niche centroid in the present and in the LGM) to predict genetic diversity and πN/πS using general linear models. Results Populations at the west of the Trans Mexican Volcanic Belt (TVB) had lower genetic diversity than populations in the east of this mountain chain. Both species had significant niche overlap. The principal predictors for neutral genetic diversity (HE, A and πS) were longitude and latitude, followed by the current distance to the niche centroid; the efficiency of purifying selection was mostly accounted for by the current distance to the niche centroid (which was also correlated with elevation). No correlation was observed between genetic diversity or πN/πS and current population area. Main conclusions Historical and ecological factors have to be taken into account for explaining the amounts of genetic diversity in mountain tropical species. Following the NTT, populations closer to the niche centroid are more efficient at eliminating slightly deleterious mutations than marginal stands, independently of their size or geographic location (longitude). Expanding the central‐abundance theory within the scope of the NTT might help reconciling conflicting views concerning the extent of its empirical support.