Abstract
Understanding the processes of divergence and speciation is an important task for evolutionary research, and climate oscillations play a pivotal role. We estimated the genetic structure and demographic history of two closely related species of Rhododendron, R. dauricum, and R. mucronulatum, distributed in northeastern China using 664,406 single nucleotide polymorphic loci of specific-locus amplified fragment sequencing (SLAF-seq) and 4 chloroplast DNA (cpDNA) fragments, sampling 376 individuals from 39 populations of these two species across their geographic distributions. The geographical distribution of cpDNA haplotypes revealed that R. dauricum and R. mucronulatum have different spatial genetic structures and haplotype diversity. Analysis of molecular variance (AMOVA) results showed that these two species have significant genetic differentiation and that the phylogeny demonstrates that these two species clustered a monophyletic group based on SLAF data, respectively, but not in cpDNA data. The evidence of significant gene flow was also detected from R. mucronulatum to R. dauricum. A deep divergence between the two species was observed and occurred during the early Oligocene. The niche models showed that the two species have different demographic histories. Thus, our results imply that geography and climate changes played important roles in the evolutionary process of R. dauricum and R. mucronulatum, and although there was an interspecific gene flow, the divergence was maintained by natural selection.
Highlights
Past climate oscillations and historical tectonism had a huge impact on the genetic structure and demographic histories of many species, even triggering divergence and speciation (Milne, 2006)
Later, considering the linkage disequilibrium (LD) between SNPs, we used the -r2 function in PLINK to quantify pairwise LD between all pairs of SNPs located within 1000 kb of each other, and the results showed that the LD of both species decayed rapidly (Supplementary Figure S1)
The analysis results of SLAF data showed that R. dauricum and R. mucronulatum have similar nucleotide diversity, but a higher level of species-wide nucleotide diversity was found in R. dauricum, consistent with a previous report (Jiang et al, 2016) and that of R. mucronulatum was zero in chloroplast DNA (cpDNA)
Summary
Past climate oscillations and historical tectonism had a huge impact on the genetic structure and demographic histories of many species, even triggering divergence and speciation (Milne, 2006). Species divergences are frequently driven by geographic isolation, environmental heterogeneity (ecological speciation) or a combination of both (Orr and Smith, 1998; Schluter, 2001; Nosil, 2012). Geographic isolation is generally considered an allopatric speciation, where gene flow among splitting populations is disrupted by physical barriers, and genetic divergence occurs between taxa by local adaptation, mutation, and genetic drift (Coyne and Orr, 2004). Under ecological speciation, divergence is driven by divergent natural selection between environments, giving rise to reproductive isolation between subsets of a single population by adaptation to different environments or ecological niches. When the homogenization of interspecific gene flow is weaker than the disproportionation of natural selection, species genetic differentiation may still be maintained (Rundell and Prince, 2009; Ribera et al, 2011)
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