Orostachys spinosa (Crassulaceae) origin and diversification: East Asia or South Siberian Mountains? Chloroplast DNA dat
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ORIGINAL ARTICLE
Orostachys spinosa (Crassulaceae) origin and diversification: East Asia or South Siberian Mountains? Chloroplast DNA data Arthur Yu. Nikulin1 · Vyacheslav Yu. Nikulin1 · Andrey A. Gontcharov1 Received: 20 December 2019 / Accepted: 3 September 2020 © Springer-Verlag GmbH Austria, part of Springer Nature 2020
Abstract Limited data are available on genetic structures of the herbaceous plant species populations inhabiting mountainous areas of Siberia and Northeastern Asian (Russian Far East). Although this area was not directly impacted by the extensive ice-sheets during the Quaternary, it experienced significant climatic fluctuations that influenced rich local flora. Orostachys spinosa (Crassulaceae) lacks any adaptations for long-distance dispersal, yet the species is characterized by an unusually wide range spanning from the Urals to the coast of the Pacific Ocean. We studied O. spinosa phylogeography and genetic diversity across its range sampling 203 individuals from 21 natural populations. Using sequences from three chloroplast DNA noncoding regions, we revealed 82 haplotypes and observed high level of population differentiation indicating presence of the phylogeographic structure (GST = 0.501 and NST = 0.822 (p GST usually indicates the presence of phylogeographic structure, that is, the more frequent occurrence of closely related haplotypes in the same area than less closely related haplotypes (Pons and Petit 1996). Analysis of molecular variance (AMOVA; Excoffier et al. 1992) was applied to evaluate the hierarchical partitioning
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of genetic variation among populations, groups and individuals using Arlequin v.3.11 (Excoffier et al. 2005). The significance of the results was tested using a nonparametric permutation procedure with 1000 permutations. Mismatch distribution analysis was used to test the hypothesis of demographic expansion of O. spinosa (Rogers and Harpending 1992). The observed number of differences between pairs of haplotypes was compared to the theoretical distribution using a sudden (stepwise) expansion model with the DnaSP5 v.5.10.1. A mismatch distribution test was performed for 16 populations of O. spinosa represented by ≥ 8 accessions each. To infer the divergence time between Orostachys lineages, we used the cpDNA data set to conduct a dating analysis with the BEAST software (Drummond et al. 2012). The analyses of the constancy of molecular evolution rate among lineages, estimation the divergence times and confidence intervals were according Zhang et al. (2014a) and Li et al. (2018). Chloroplast DNA substitution rates for most angiosperm species have been estimated to be in the range 1–3 × 10−9 substitutions per site per year (s/s/year) (Wolfe et al. 1987). As the fragments we used are non-coding regions of the cpDNA genome, we assumed an evolutionary rate of 1.52 × 10−9 s/s/year for the plastid dataset and 10 years were used as an approximation for g (Yamane et al. 2006; Li et al. 2018). We used GTR + G + I substitution model, lognormal
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