Chloroplast phylogeography and evolution of highly polymorphic microsatellites in lodgepole pine (Pinus contorta)

Abstract

We employed a novel set of six highly polymophic chloroplastic simple sequence repeat (cpSSR) loci to investigate the phylogeography of lodgepole pine ( Pinus contorta Dougl. Ex. Loud.), and to examine aspects of the evolutionary process operating on these repetitive DNA sequences. Chloroplast haplotypes of 500 trees, sampled throughout the range of lodgepole pine, were determined. We found a marked association of genetic distance with physical distance within the scale of 0 to 1,000 km, but no association beyond that range. Likewise, geographic clustering was observed only among recent clades in a dendrogram. These phylogeographic patterns are consistant with a rapid rangewide expansion ("big-bang") followed by recent, local population differentiation ("galaxy formation"). In support of this expansion, coalescent simulations of the genealogical process gave a long-term effective population size in the low thousands, and a time to common ancestry of about 1,500 generations (12,000 years), consistent with a post-Pleistocene population expansion as documented by previous pollen-sediment analyses. Two lines of evidence (mapping mutational events onto a phylogeny, and evaluation of observed versus expected gene diversity) suggest that five of the cpSSR loci evolve primarily by a stepwise model of evolution of single repeat changes (but with a small proportion of changes involving two or more repeats), and the coalescent simulations point to a mutation rate of about 10(-3).

Diversity of microsatellite markers in the populations of Picea asperata originating from the mountains of China

“…This suggests that genetic variation at the microsatellite loci investigated in this study better fits the two-phase mutation model (TMP) [19] than the stepwise mutation model (SMM) [20]. This finding is consistent with the observations reported in wheat by Huang et al [21] and in lodgepole pine by Marshall et al [22]. Additionally, 5.0% of the alleles differed from each other by a single basepair, which indicates that some of the size differences at the SSR loci are the results of insertiondeletion events in the flanking regions instead of repeat number increases or decreases in the nucleotide repeat regions, as sometimes reported also in other plant taxa [23,24].…”

Molecular phylogeny of wild Hops, Humulus lupulus L.

“…Scots pine (Pinus sylvestris) is distributed from Scotland to east Siberia, and the current population structure in Europe was formed 7000-900 years ago (Dvornyk et al, 2002). In North America, lodgepole pine (Pinus contorta) expanded into a range of 2200 km over 12 000 years (Marshall et al, 2002). The distribution of European hop haplotypes found in our study covers a range of 7000 km, calculated as the distance between Portugal and the Altai region.…”

Genomics of Origin, Domestication and Evolution of Phaseolus vulgaris

“…This is clear evidence of the crucial role of marker mutation rates for describing the diversity of plant populations (Thuillet et al 2005). In particular, the loss of diversity detected with cpSSRs is intermediate between the SSRs and AFLPs, as is their mutation rate (Provan et al 1999;Marshall et al 2002). Indeed, as showed in several studies (Glémin andBataillon 2009, Rossi et al 2009;Nanni et al 2011;Bitocchi et al 2012Bitocchi et al , 2013Desiderio et al 2013), in populations that have experienced a bottleneck, the differences in loss of diversity estimates using different markers are related to their different mutation rates: in markers characterized by high mutation rates, such as SSRs, the recovery of the diversity lost after a bottleneck is faster than for markers with lower mutation rates, such as sequence data.…”