Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci

Abstract

Nucleotide variation at 12-16 nuclear loci was studied in three spruce species from the Qinghai-Tibetan Plateau (QTP), Picea likiangensis, P. wilsonii, and P. purpurea, and one species from the Tian Shan mountain range, P. schrenkiana. Silent nucleotide diversity was limited in P. schrenkiana and high in the three species from the QTP, with values higher than in boreal spruce species, despite their much more restricted distributions compared with that of the boreal species. In contrast to European boreal species that have experienced severe bottlenecks in the past, coalescent-based analysis suggests that DNA polymorphism in the species from the QTP and adjacent areas is compatible with the standard neutral model (P. likiangensis, P. wilsonii, and P. schrenkiana) or with population growth (P. purpurea). In order to test if P. purpurea is a diploid hybrid of P. likiangensis and P. wilsonii, we used a combination of approaches, including model-based inference of population structure, isolation-with-migration models, and recent theoretical results on the effect of introgression on the geographic distribution of diversity. In contrast to the three other species, each of which was predominantly assigned to a single cluster in the Structure analysis, P. purpurea individuals were scattered over the three main clusters and not, as we had expected, confined to the P. likiangensis and P. wilsonii clusters. Furthermore, the contribution of P. schrenkiana was by far the largest one. In agreement with this, the divergence between P. purpurea and P. schrenkiana was lower than the divergence of either P. likiangensis or P. wilsonii from P. schrenkiana. These results, together with previous ones showing that P. purpurea and P. wilsonii share the same haplotypes at both chloroplast and mitochondrial markers, suggest that P. purpurea has a complex origin, possibly involving additional species.

The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers

“…menziesii (Eckert et al, 2009a;Wei et al, 2011). In a recent study reporting the sequencing of 14-16 genes in 3 Picea species from the Qinghai-Tibetan plateau (Li et al, 2010), mean r 2 values were also higher than those estimated for P. glauca or P. abies (Table 4). The authors suggested that pooling data from different species might have inflated r 2 , given that recombination rates were admittedly high (Li et al, 2010).…”

“…Thus, structure in the data set might not be the only contributing factor to the higher average r 2 value observed in genes from these Asian spruce taxa. Although they might have been less affected by glaciations than boreal spruces (Li et al, 2010), the restricted distribution of some of these species might also be indicative of smaller historical population size, potentially leading to increased LD. Further studies are required, whether of empirical or simulation nature, to investigate the sensitivity of LD estimates to these factors.…”

“…Moreover, recombination rates observed in conifer genomes are different from those of other plant species: they are significantly lower in conifer trees (gymnosperms) than in angiosperm species, both at the genome and at the gene levels (Jaramillo-Correa et al, 2010). Studies of small gene sets have shown low-to-moderate levels of nucleotide diversity and LD decaying within gene limits in several conifer species (Brown et al, 2004;Neale and Savolainen, 2004;Pot et al, 2005;Heuertz et al, 2006;González-Martínez et al, 2006b;Pyhäjärvi et al, 2007;Wachowiak et al, 2009;Li et al, 2010;Namroud et al, 2010). Higher LD was found in Douglas fir genes with a half-decay of LD over 1 kb, on average (Eckert et al, 2009a).…”

Genetic divergence, range expansion and possible homoploid hybrid speciation among pine species in Northeast China

“…This independent inheritance of two cytoplasmic genomes provides the opportunity for tracing paternal and maternal genetic changes within a single species because of different rates of gene flow and for discriminating female and male parents of hybrids (Ennos, 1994;Liston et al, 2007;Wachowiak and Prus-G"owacki, 2008). In addition, the analysis of multiple nuclear loci can be used to examine interspecific divergence and clarify parental origins of putative hybrid species (for example, Ma et al, 2006;Li et al, 2010). Thus, here we use sequences from cpDNA, mtDNA and eight nuclear genes to address the following specific questions.…”

Phylogeography of Rosa soulieana (Rosaceae) in the Hengduan Mountains: refugia and ‘melting’ pots in the Quaternary climate oscillations

“…According to the second view, high species richness in these regions is a consequence of rapid adaptive radiation due to diverse and complex topography, especially for most of the species-rich genera (e.g., Cupressus spp., Xu et al 2010; Rheum spp., Sun et al 2012; Primula spp., Zhang et al 2013;reviewed in Liu et al 2014), or resulted from limited gene flow caused by repeated bottlenecks in the Quaternary, as exampled by Picea spp. (Li et al 2010), Tsuga dumosa (Cun and Wang 2010), Aconitum gymnandrum (Wang et al 2009). Third, high intra-specific and interspecific diversity can be a result of topographic changes due to river recaptures, e.g., Terminalia franchetii , Salweenia spp.…”