Spatial genetic structure of forest and xerophytic plant species in arid Eastern Central Asia: insights from comparative phylogeography and ecological niche modelling

Phylogeography and Population Genetics Analyses Reveal Evolutionary History of the Desert Resource Plant Lycium ruthenicum (Solanaceae)

Climactic oscillations during the Quaternary played a significant role in the formation of genetic diversity and historical demography of numerous plant species in northwestern China. In this study, we used 11 simple sequence repeats derived from expressed sequence tag (EST-SSR), two chloroplast DNA (cpDNA) fragments, and ecological niche modeling (ENM) to investigate the population structure and the phylogeographic history of Lycium ruthenicum, a plant species adapted to the climate in northwestern China. We identified 20 chloroplast haplotypes of which two were dominant and widely distributed in almost all populations. The species has high haplotype diversity and low nucleotide diversity based on the cpDNA data. The EST-SSR results showed a high percentage of total genetic variation within populations. Both the cpDNA and EST-SSR results indicated no significant differentiation among populations. By combining the evidence from ENM and demographic analysis, we confirmed that both the last interglacial (LIG) and late-glacial maximum (LGM) climatic fluctuations, aridification might have substantially narrowed the distribution range of this desert species, the southern parts of the Junggar Basin, the Tarim Basin, and the eastern Pamir Plateau were the potential glacial refugia for L. ruthenicum during the late middle Pleistocene to late Pleistocene Period. During the early Holocene, the warm, and humid climate promoted its demographic expansion in northwestern China. This work may provide new insights into the mechanism of formation of plant diversity in this arid region.

Phylogeography of Amygdalus mongolica in relation to Quaternary climatic aridification and oscillations in northwestern China

Quaternary period geological events and climatic oscillations significantly affect the geographic structure and genetic diversity of species distribution in arid northwestern China. Amygdalus mongolica is a relict and endangered shrub that occurs primarily in arid areas of northwestern China. Based on variation patterns present at three cpDNA regions (psbK-psbI, trnL-trnF and trnV) and in one nDNA sequence (ITS1-ITS4) in 174 individuals representing 15 populations, the spatial genetic structure and demographic history of A. mongolica was examined across its entire geographic range. The 17 different haplotypes and 10 ribotypes showed two lineages, distributed across the Western (Mazong Mountains, Hexi Corridor, and Alxa Left Banner) and Eastern regions (Urad Houqi, Yinshan Mountains, Urad Zhongqi, and Daqing Mountains) according to the median-joining network and the BI (Bayesian inference) and ML (Maximum likelihood) trees. AMOVA analysis demonstrated that over 65% of the observed genetic variation was related to this lineage split. The expansions of the Ulanbuhe and Tengger deserts and the eastward extension of the Yinshan Mountains since the Quaternary period likely interrupted gene flow and triggered the observed divergence in the two allopatric regions; arid landscape fragmentation accompanied by local environmental heterogeneity further increased local adaptive differentiation between the Western and Eastern groups. Based on the evidence from phylogeographical patterns and the distribution of genetic variation, A. mongolica distributed in the eastern and western regions are speculated to have experienced eastward migration along the southern slopes of the Lang Mountains and westward migration along the margins of the Ulanbuhe and Tengger deserts to the Hexi Corridor, respectively. For setting a conservation management plan, it is recommended that the south slopes of the Lang Mountains and northern Helan Mountains be identified as the two primary conservation areas, as they have high genetic variation and habitats that are more suitable.

Genomic Phylogeography of Gymnocarpos przewalskii (Caryophyllaceae): Insights into Habitat Fragmentation in Arid Northwestern China

Extensive range of deserts and gobis (rocks) had promoted habitat fragmentation of species in arid northwestern China. Distribution of endangered Gymnocarpos przewalskii Maxim. covers most of gobis (rocks) and desert terrain across arid regions of northwestern China. In the present study, we had employed genomic phylogeographical analysis to investigate population structure of G. przewalskii and test the effect of environmental conditions on spatial pattern of genetic diversity. Results showed four groups were identified from east to west: Edge of the Alxa Desert, Hexi Corridor, Hami Basin, and North edge of the Tarim Basin. Genetic diversity was at an equal level among four groups. General linear model (GLM) analysis showed spatial pattern of genetic diversity was significant correlated with three habitat variables including habitat suitability at present (Npre) and last glacial maximum (LGM) (NLGM) periods, and locality habitat stability (NStab). It concluded that habitat fragmentation had triggered lineage divergences of G. przewalskii in response to long-term aridification. Genome-wide single nucleotide polymorphisms (SNPs) could increase the ability of clarifying population structures in comparison with traditional molecular markers. Spatial pattern of genetic diversity was determined by fragmented habitats with high habitat suitability (Npre and NLGM) and stability (NStab). At last, we propose to establish four conservation units which are in consistent with the population grouping to maintain the genetic integrity of this endangered species.

Spatial Patterns of Species Diversity and Phylogenetic Structure of Plant Communities in the Tianshan Mountains, Arid Central Asia

The Tianshan Mountains, located in arid Central Asia, have a humid climate and are biodiversity hotspots. Here, we aimed to clarify whether the pattern of species diversity and the phylogenetic structure of plant communities is affected by environmental variables and glacial refugia. In this study, plant community assemblies of 17 research sites with a total of 35 sample plots were investigated at the grassland/woodland boundaries on the Tianshan Mountains. Community phylogeny of these plant communities was constructed based on two plant DNA barcode regions. The indices of phylogenetic diversity and phylogenetic community structure were calculated for these sample plots. We first estimated the correlation coefficients between species richness (SR) and environmental variables as well as the presence of glacial refugia. We then mapped the significant values of indices of community phylogeny (PD, RPD, NRI, and NTI) to investigate the correlation between community phylogeny and environmental structure or macrozones in the study area. The results showed that a significantly higher value of SR was obtained for the refugial groups than for the colonizing groups (P < 0.05); presence of refugia and environmental variables were highly correlated to the pattern of variation in SR. Indices of community phylogeny were not significantly different between refugial and colonizing regions. Comparison with the humid western part showed that plant communities in the arid eastern part of the Tianshan Mountains tended to display more significant phylogenetic overdispersion. The variation tendency of the PhyloSor index showed that the increase in macro-geographical and environmental distance did not influence obvious phylogenetic dissimilarities between different sample plots. In conclusion, glacial refugia and environmental factors profoundly influenced the pattern of SR, but community phylogenetic structure was not affected by glacial refugia among different plant communities on the Tianshan Mountains. This pattern of community phylogenetic structure could have resulted from shared ancestry and species pool among these sample plots.