Diversification of plant species in arid Northwest China: species-level phylogeographical history of Lagochilus Bunge ex Bentham (Lamiaceae)

Demographic patterns of two related desert shrubs with overlapping distributions in response to past climate changes

Numerous studies have revealed that past geological events and climatic fluctuations had profoundly affected the genetic structure and demographic patterns of species. However, related species with overlapping ranges may have responded to such environmental changes in different ways. In this study, we compared the genetic structure and population dynamics of two typical desert shrubs with overlapping distributions in northern China, Nitraria tangutorum and Nitraria sphaerocarpa, based on chloroplast DNA (cpDNA) variations and species distribution models. We sequenced two cpDNA fragments (trnH-trnA and atpH-atpI) in 633 individuals sampled from 52 natural populations. Twenty-four chlorotypes, including eight rare chlorotypes, were identified, and a single dominant haplotype (H4) widely occurred in the entire geographical ranges of the two species. There were also a few distinctive chlorotypes fixed in different geographical regions. Population structure analyses suggested that the two species had significantly different levels of total genetic diversity and interpopulation differentiation, which was highly likely correlated with the special habitat preferences of the two species. A clear phylogeographic structure was identified to exist among populations of N. sphaerocarpa, but not exist for N. tangutorum. The neutral tests, together with the distribution of pairwise differences revealed that N. tangutorum experienced a sudden demographic expansion, and its expansion approximately occurred between 21 and 7 Kya before present, while a rapid range expansion was not identified for N. sphaerocarpa. The ecological niche modeling (ENM) analysis indicated that the potential ranges of two species apparently fluctuated during the past and present periods, with obvious contraction in the Last Glacial Maximum (LGM) and recolonization in the present, respectively, comparing to the Last Interglacial (LIG). These findings suggest that the two species extensively occurred in the Northwest of China before the Quaternary, and the current populations of them originated from a few separated glacial refugia following their habitat fragmentation in the Quarternary. Our results provide new insights on the impact of past geological and climatic fluctuations on the population dynamics of desert plants in northwestern China, and further enforce the hypothesis that there were several independent glacial refugia for these species during the Quaternary glaciations.

Genetic Structure and Population History of the Zaisan Toad-Headed Agama (Phrynocephalus melanurus) Inferred from Mitochondrial DNA

The agamid lizard Phrynocephalus melanurus is restricted to Northwest China (Dzungar Basin) and the adjacent Eastern Kazakhstan (Zaisan and Alakol basins). To elucidate the phylogeography of P. melanurus, we obtained the mitochondrial DNA COI segments of 175 sampled lizards from 44 localities across the whole distribution. Phylogenetic analyses revealed two main Clades comprising five geographically structured lineages (I, IIa, IIb1, IIb2, and IIb3) that fit an isolation-by-distance (IBD) model. The divergence from the most recent common ancestor was dated to ~1.87 million years ago (Ma). Demographic analyses demonstrated lineage-specific response to past climate change: stable population for Clade I, Subclade IIb1; past population expansion for IIb3 since 0.18 Ma, respectively. Bayesian phylogeographic diffusion analyses detected initial spreading at the Saur Mount vicinity, approximately 1.8 Ma. Historical species distribution model (SDM) projected expansion of the suitable habitat in the last interglacial and shift and contraction in the last glacial maximum and Holocene epochs. The SDM predicted a drastic reduction in suitable area throughout the range as a response to future climate change. Our findings suggest that the evolution of P. melanurus followed a parapatric divergence with subsequent dispersal and adaptation to cold and dry environments during the Quaternary. Overall, this work improves our understanding of the lineage diversification and population dynamics of P. melanurus, providing further insights into the evolutionary processes that occurred in Northwest China and adjacent Eastern Kazakhstan.

Conservation Priorities and Demographic History of Saussurea involucrata in the Tianshan Mountains and Altai Mountains

Rare and vulnerable endemic plants represent different evolutionary units that occur at different times, and protecting these species is a key issue in biological protection. Understanding the impact of the history of endangered plant populations on their genetic diversity helps to reveal evolutionary history and is crucial for guiding conservation efforts. Saussurea involucrata, a perennial alpine species mainly distributed in the Tianshan Mountains, is famous for its medicinal value but has become endangered due to over-exploitation. In the present study, we employed both nuclear and chloroplast DNA sequences to investigate the genetic distribution pattern and evolutionary history of S. involucrata. A total of 270 individuals covering nine S. involucrata populations were sampled for the amplification and sequencing of nrDNA Internal Transcribed Spacer (ITS) and chloroplast trnL-trnF, matK and ndhF-rpl32 sequences. Via calculation, we identified 7 nuclear and 12 plastid haplotypes. Among the nine populations, GL and BA were characterized by high haplotype diversity, whereas BG revealed the lowest haplotype diversity. Molecular dating estimations suggest that divergence among S. involucrata populations occurred around 0.75 Ma, coinciding with the uplift of Tianshan Mountains. Our results reveal that both isolation-by-distance (IBD) and isolation-by-resistance (IBR) have promoted genetic differentiation among populations of S. involucrata. The results from the ecological niche modeling analyses show a more suitable habitat for S. involucrata in the past than at present, indicating a historical distribution contraction of the species. This study provides new insight into understanding the genetic differentiation of S. involucrata, as well as the theoretical basis for conserving this species.

Phylogeography of the desert scorpion illuminates a route out of Central Asia

A comprehensive understanding of phylogeography requires the integration of knowledge across different organisms, ecosystems, and geographic regions. However, a critical knowledge gap exists in the arid biota of the vast Asian drylands. To narrow this gap, here we test an "out-of-Central Asia" hypothesis for the desert scorpion Mesobuthus mongolicus by combining Bayesian phylogeographic reconstruction and ecological niche modeling. Phylogenetic analyses of one mitochondrial and three nuclear loci and molecular dating revealed that M. mongolicus represents a coherent lineage that diverged from its most closely related lineage in Central Asia about 1.36 Ma and underwent radiation ever since. Bayesian phylogeographic reconstruction indicated that the ancestral population dispersed from Central Asia gradually eastward to the Gobi region via the Junggar Basin, suggesting that the Junggar Basin has severed as a corridor for Quaternary faunal exchange between Central Asia and East Asia. Two major dispersal events occurred probably during interglacial periods (around 0.8 and 0.4 Ma, respectively) when climatic conditions were analogous to present-day status, under which the scorpion achieved its maximum distributional range. M. mongolicus underwent demographic expansion during the Last Glacial Maximum, although the predicted distributional areas were smaller than those at present and during the Last Interglacial. Development of desert ecosystems in northwest China incurred by intensified aridification might have opened up empty habitats that sustained population expansion. Our results extend the spatiotemporal dimensions of trans-Eurasia faunal exchange and suggest that species' adaptation is an important determinant of their phylogeographic and demographic responses to climate changes.

Geography and past climate changes have shaped the evolution of a widespread lizard in arid Central Asia

The complex orogenic history and structure of Central Asia, coupled with Pleistocene glacial cycles have generated its stepwise aridification. Such events would have significantly influenced the evolution of many mid-latitude species in arid Central Asia (ACA). In this study, we employed two mitochondrial genes (CO1 and ND2) and genome-wide SNPs, coupled with ecological niche modeling, to investigate the lineage diversification and historical demography within a widespread lizard Phrynocepahlus helioscopus, and their associations with geography and past climate change. We obtained themtDNA dataset for 300 individuals from 96 localities within the known range of the lizard, among which 51 individuals from 27 localities were selected for generating the SNP dataset via genotyping-by-sequencing approach. Phylogenetic analyses of the concatenated mtDNA dataset revealed eight geographically correlated lineages that diverged by 4.21-10.41% for the CO1 gene, which were estimated to have coalesced ∼4.47 million years ago. However, we observed mito-nuclear discordance pattern regarding the population of Clade V (P. helioscopus sergeevi) from Tajikistan. Ancestral area estimations suggested that P. helioscopus originated from the Fergana Valley and then dispersed into the adjacent areas in ACA along with a history of multiple allopatric divergence processes, suggesting that Fergana may have been the cradle of diversification of P. helioscopus. The intensification of aridification across Central Asia during the Late Pliocene may have facilitated the rapid radiation of this arid-adapted lizard throughout this vast territory. Subsequently, the geological events (e.g., uplift of the Hissar-Alay, transgressions of the Caspian Sea) and geographic barriers (e.g., Amu Darya River, Zerarshan River) during the Pleistocene triggered the progressive diversification of P. helioscopus. Interestingly, Clade VIII (P. helioscopus varius) experienced rapid population growth coupled with range expansion while Clade IV (P. helioscopus cameranoi) underwent drastic population expansion associated with range contraction during the Last Glacial Maximum. In Clade IV, but not in Clade VIII, environmental turnover contributes more to mitochondrial genetic distinctiveness than geographic distance. Overall, the SNP dataset demonstrates that geographic distance plays a greater role than environmental distance. Both the mtDNA dataset and the SNP dataset suggest local-scale genetic differentiation in Clade IV and Clade VIII, revealing potential geographic barriers in the Ili River Valley and the Junggar Basin, respectively. Twenty-seven outlier SNPs associated with environmental factors (precipitation and temperature) were identified, which supports the signature of local adaptation to the arid desert environment. Finally, our finding suggests taxonomic implications, such as support for full species status for P. saidalievi (Clade II) and P. meridionalis (Clade I). Future analyses based on further evidence and increased taxon and geographic sampling should be carried out to corroborate our findings.

Perennial herb diversity contributes more than annual herb diversity to multifunctionality in dryland ecosystems of North-western China

BACKGROUND

Considerable attention has been given to how different aspects of biodiversity sustain ecosystem functions. Herbs are a critical component of the plant community of dryland ecosystems, but the importance of different life form groups of herbs is often overlooked in experiments on biodiversity-ecosystem multifunctionality. Hence, little is known about how the multiple attributes of diversity of different life form groups of herbs affect changes to the multifunctionality of ecosystems.

METHODS

We investigated geographic patterns of herb diversity and ecosystem multifunctionality along a precipitation gradient of 2100 km in Northwest China, and assessed the taxonomic, phylogenetic and functional attributes of different life form groups of herbs on the multifunctionality.

RESULTS

We found that subordinate (richness effect) species of annual herbs and dominant (mass ratio effect) species of perennial herbs were crucial for driving multifunctionality. Most importantly, the multiple attributes (taxonomic, phylogenetic and functional) of herb diversity enhanced the multifunctionality. The functional diversity of herbs provided greater explanatory power than did taxonomic and phylogenetic diversity. In addition, the multiple attribute diversity of perennial herbs contributed more than annual herbs to multifunctionality.

CONCLUSIONS

Our findings provide insights into previously neglected mechanisms by which the diversity of different life form groups of herbs affect ecosystem multifunctionality. These results provide a comprehensive understanding of the relationship between biodiversity and multifunctionality, and will ultimately contribute to multifunctional conservation and restoration programs in dryland ecosystems.

Precipitation preferences alter the relative importance of herbaceous plant diversity for multifunctionality in the drylands of China

Background

Multiple components of biodiversity are excellent predictors of precipitation-induced changes in ecosystem function. However, the importance of differing scales (alpha versus beta) is usually overlooked in biodiversity–ecosystem multifunctionality studies. Consequently, little is known about how precipitation regulates the relationship between multifunctionality and multiple components of alpha and beta diversity.

Aims

We investigated geographic patterns of herbaceous plant diversity and ecosystem multifunctionality along a precipitation gradient spanning more than 2010 km in Northwest China.

Methods

We assessed the effects of herbaceous species, phylogenetic, and functional components at different scales on multifunctionality in drylands.

Results

The alpha diversity of species and functional beta diversity were key components explaining the variation in multifunctionality. As the main environmental factor, MAP (mean annual precipitation) affected multifunctionality by changing the mediating variables (i.e., species alpha and functional beta diversity). More importantly, a certain precipitation threshold was detected for the relationship of multifunctionality to species alpha and functional beta diversity. MAPs of approximately 158 mm and 140 mm modulated this relationship (shifting it from uncorrelated to significantly correlated).

Conclusions

Our findings provide insights into previously neglected mechanisms by which diversity in herbaceous layers at different scales affects ecosystem multifunctionality. It is highlighted that MAP regulates the relationship between diversity and multifunctionality in dryland ecosystems at different scales. Further, diversity may have substantial consequences for multifunctionality where MAP is higher. These empirical results provide a comprehensive understanding of the biodiversity–multifunctionality relationship in the context of precipitation, ultimately contributing to conservation and restoration programs for multifunctionality in drylands.

Regional fauna-flora biodiversity and conservation strategy in China

Evolutionary and historical development and current profiles are essential to generating a tangible conservation strategy. It is also critical to distinguish the regions with vigorous potential growth from those meeting evolutionary development bottlenecks and those whose development has been severely devastated. We used two sizeable national data repositories of terrestrial fauna and flora of China to approach the issues. The results indicate that the Southwest and Coastal regions have the most significant terrestrial faunal-floral biodiversity (TFFB). Thus, they should be prioritized in conservation for great potential promotions. Although there has been remarkable evolutionary development, the Central region has been severely devastated. A solution is to uphold a balanced association between social-economic development and TFFB sustainability. As for the Northeast and the western Northwest, there is no need to invest heavily in conservation measures. This study sheds light on exploring more practical conservation strategies regionally, nationally, and globally to achieve pragmatic goals.

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Terrestrial faunal-floral biodiversity (TFFB) in China

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Regional variation assessment of TFFB in China

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China’s regional disparity in human impact and evolutionary development

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Regionalized conservation strategies in China

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.

Spatial phylogenetics of the Chinese angiosperm flora provides insights into endemism and conservation

The flora of China is well known for its high diversity and endemism. Identifying centers of endemism and designating conservation priorities are essential goals for biodiversity studies. However, there is no comprehensive study from a rigorous phylogenetic perspective to understand patterns of diversity and endemism and to guide biodiversity conservation in China. We conducted a spatial phylogenetic analysis of the Chinese angiosperm flora at the generic level to identify centers of neo- and paleo-endemism. Our results indicate that: (i) the majority of grid cells in China with significantly high phylogenetic endemism (PE) were located in the mountainous regions; (ii) four of the nine centers of endemism recognized, located in northern and western China, were recognized for the first time; (iii) arid and semiarid regions in Northwest China were commonly linked to significant PE, consistent with other spatial phylogenetic studies worldwide; and (iv) six high-priority conservation gaps were detected by overlaying the boundaries of China's nature reserves on all significant PE cells. Overall, we conclude that the mountains of southern and northern China contain both paleo-endemics (ancient relictual lineages) and neo-endemics (recently diverged lineages). The areas we highlight as conservation priorities are important for broad-scale planning, especially in the context of evolutionary history preservation.

Phylogeography of Prunus armeniaca L. revealed by chloroplast DNA and nuclear ribosomal sequences

To clarify the phytogeography of Prunus armeniaca L., two chloroplast DNA fragments (trnL-trnF and ycf1) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to assess genetic variation across 12 P. armeniaca populations. The results of cpDNA and ITS sequence data analysis showed a high the level of genetic diversity (cpDNA: H_T = 0.499; ITS: H_T = 0.876) and a low level of genetic differentiation (cpDNA: F_ST = 0.1628; ITS: F_ST = 0.0297) in P. armeniaca. Analysis of molecular variance (AMOVA) revealed that most of the genetic variation in P. armeniaca occurred among individuals within populations. The value of interpopulation differentiation (N_ST) was significantly higher than the number of substitution types (G_ST), indicating genealogical structure in P. armeniaca. P. armeniaca shared genotypes with related species and may be associated with them through continuous and extensive gene flow. The haplotypes/genotypes of cultivated apricot populations in Xinjiang, North China, and foreign apricot populations were mixed with large numbers of haplotypes/genotypes of wild apricot populations from the Ili River Valley. The wild apricot populations in the Ili River Valley contained the ancestral haplotypes/genotypes with the highest genetic diversity and were located in an area considered a potential glacial refugium for P. armeniaca. Since population expansion occurred 16.53 kyr ago, the area has provided a suitable climate for the population and protected the genetic diversity of P. armeniaca.

The East Asian Winter Monsoon Acts as a Major Selective Factor in the Intraspecific Differentiation of Drought-Tolerant Nitraria tangutorum in Northwest China

The influence of Quaternary climate fluctuation on the geographical structure and genetic diversity of species distributed in the regions of the Qinghai–Tibet Plateau (QTP) has been well established. However, the underlying role of the East Asian monsoon system (EAMS) in shaping the genetic structure of the population and the demography of plants located in the arid northwest of China has not been explored. In the present study, Nitraria tangutorum, a drought-tolerant desert shrub that is distributed in the EAMS zone and has substantial ecological and economic value, was profiled to better understand the influence of EAMS evolution on its biogeographical patterns and demographic history. Thus, the phylogeographical structure and historical dynamics of this plant species were elucidated using its five chloroplast DNA (cpDNA) fragments. Hierarchical structure analysis revealed three distinct, divergent lineages: West, East-A, and East-B. The molecular dating was carried out using a Bayesian approach to estimate the time of intraspecies divergence. Notably, the eastern region, which included East-A and East-B lineages, was revealed to be the original center of distribution and was characterized by a high level of genetic diversity, with the intraspecific divergence time dated to be around 2.53 million years ago (Ma). These findings, combined with the data obtained by ecological niche modeling analysis, indicated that the East lineages have undergone population expansion and differentiation, which were closely correlated with the development of the EAMS, especially the East Asian winter monsoon (EAWM). The West lineage appears to have originated from the migration of N. tangutorum across the Hexi corridor at around 1.85 Ma, and subsequent colonization of the western region. These results suggest that the EAWM accelerated the population expansion of N. tangutorum and subsequent intraspecific differentiation. These findings collectively provide new information on the impact of the evolution of the EAMS on intraspecific diversification and population demography of drought-tolerant plant species in northwest China.

Phylogeography and conservation genetics of the endangered Tugarinovia mongolica (Asteraceae) from Inner Mongolia, Northwest China

Tugarinovia (Family Asteraceae) is a monotypic genus. It’s sole species, Tugarinovia mongolica Iljin, is distributed in the northern part of Inner Mongolia, with one additional variety, Tugarinovia mongolica var ovatifolia, which is distributed in the southern part of Inner Mongolia. The species has a limited geographical range and declining populations. To understand the phylogeographic structure of T. mongolica, we sequenced two chloroplast DNA regions (psbA-trnH and psbK-psbI) from 219 individuals of 16 populations, and investigated the genetic variation and phylogeographic patterns of T. mongolica. The results identified a total of 17 (H1-H17) chloroplast haplotypes. There were no haplotypes shared between the northern (T. mongolica) and southern groups (T. mongolica var. ovatifolia), and they formed two distinct lineages. The regional split was also supported by AMOVA and BEAST analyses. AMOVA showed the main variation that occurred between the two geographic groups. The time of divergence of the two groups can be dated to the early Pleistocene epoch, when climate fluctuations most likely resulted in the allopatric divergence of T. mongolica. The formation of the desert blocked genetic flow and enhanced the divergence of the northern and southern groups. Our results indicate that the genetic differences between T. mongolica and T. mongolica var. ovatifolia are consistent with previously proposed morphological differences. We speculate that the dry, cold climate and the expansion of the desert during the Quaternary resulted in the currently observed distribution of extant populations of T. mongolica. In the northern group, the populations Chuanjinsumu, Wuliji and Yingen displayed the highest genetic diversity and should be given priority protection. The southern group showed a higher genetic drift (F_ST = 1, G_ST = 1), and the inbreeding load (H_S = 0) required protection for each population. Our results propose that the protection of T. mongolica should be implemented through in situ and ex situ conservation practices to increase the effective population size and genetic diversity.

Intraspecific divergences and phylogeography of Panzerina lanata (Lamiaceae) in northwest China

Climatic fluctuations during the Quaternary significantly affect many species in their intraspecific divergence and population structure across northwest China. In order to investigate the impact of climate change on herbaceous plants, we studied Panzerina lanata (Lamiaceae), a widely distributed species. Sequences of two chloroplast DNA (cpDNA) intergenic spacers (trnH-psbA and rpoB-trnC) and a nuclear ribosomal region (nrDNA, ITS) were generated from 27 populations of Panzerina lanata and resulted in the identification of seven chloroplast haplotypes and thirty-two nuclear haplotypes. We applied AMOVA, neutrality test and mismatch distribution analysis to estimate genetic differentiation and demographic characteristics. The divergence times of the seven cpDNA haplotypes were estimated using BEAST. Our results revealed high levels of genetic diversity (cpDNA: Hcp = 0.6691, H _T = 0.673; nrDNA: Hnr = 0.5668, H _T = 0.577). High level of genetic differentiation (G _ST = 0.950) among populations was observed in the cpDNA sequences, while the genetic differentiation values (G _ST = 0.348) were low in nuclear sequences. AMOVA results revealed major genetic variation among the three groups: northern, central, and eastern group. However, the genetic differentiation in ITS data was not found. The species distribution modeling and demographic analysis indicated that P. lanata had not experienced recent range expansion. The occurrence of divergence between seven cpDNA haplotypes, probably during Pleistocene, coincides with aridification and expansion of the desert across northwest China that resulted in species diversification and habitat fragmentation. In addition, we discovered that the deserts and the Helan Mountains acted as effective geographic barriers that promoting the intraspecific diversity of P. lanata.

Insight into Central Asian flora from the Cenozoic Tianshan montane origin and radiation of Lagochilus (Lamiaceae)

The Tianshan Mountains play a significant role in the Central Asian flora and vegetation. Lagochilus has a distribution concentration in Tianshan Mountains and Central Asia. To investigate generic spatiotemporal evolution, we sampled most Lagochilus species and sequenced six cpDNA locations (rps16, psbA-trnH, matK, trnL-trnF, psbB-psbH, psbK-psbI). We employed BEAST Bayesian inference for dating, and S-DIVA, DEC, and BBM for ancestral area/biome reconstruction. Our results clearly show that the Tianshan Mountains, especially the western Ili-Kirghizia Tianshan, as well as Sunggar and Kaschgar, was the ancestral area. Ancestral biome was mainly in the montane steppe zone of valley and slope at altitudes of 1700–2700 m, and the montane desert zone of foothill and front-hill at 1000–1700 m. Here two sections Inermes and Lagochilus of the genus displayed “uphill” and “downhill” speciation process during middle and later Miocene. The origin and diversification of the genus were explained as coupled with the rapid uplift of the Tianshan Mountains starting in late Oligocene and early Miocene ca. 23.66~19.33 Ma, as well as with uplift of the Qinghai-Tibetan Plateau (QTP) and Central Asian aridification.

Long-Distance Dispersal after the Last Glacial Maximum (LGM) Led to the Disjunctive Distribution of Pedicularis kansuensis (Orobanchaceae) between the Qinghai-Tibetan Plateau and Tianshan Region

Quaternary climate fluctuations have profoundly affected the current distribution patterns and genetic structures of many plant and animal species in the Qinghai-Tibetan Plateau (QTP) and adjacent mountain ranges, e.g. Tianshan (TSR), Altay, etc. In this greater area disjunct distributions are prominent but have nevertheless received little attention with respect to the historical processes involved. Here, we focus on Pedicularis kansuensis to test whether the current QTP and TSR disjunction is the result of a recent Holocene range expansion involving dispersal across arid land bridge(s) or a Pleistocene range fragmentation involving persistence in refugia. Two chloroplast DNA spacers were sequenced for 319 individuals from 34 populations covering the entire distribution range of this species in China. We found a total of 17 haplotypes of which all occurred in the QTP, and only five in the TSR. Overall genetic diversity was high (H_T = 0.882, H_S = 0.559) and higher in the QTP than in the TSR. Genetic differentiation among regions and populations was relatively low (G_ST = 0.366) and little evidence for a phylogeographic pattern emerged. The divergence times for the four main lineages could be dated to the early Pleistocene. Surprisingly, the two ubiquitous haplotypes diverged just before or around the Last Glacial Maximum (LGM) and were found in different phylogenetic lineages. The Species Distribution Model suggested a disappearance of P. kansuensis from the TSR during the LGM in contrast to a relatively constant potential distribution in the QTP. We conclude that P. kansuensis colonized the TSR after the LGM. The improbable long-distance dispersal by wind or water across arid land seed flow may well have had birds or men as vector.

Phylogeographic History of Atraphaxis Plants in Arid Northern China and the Origin of A. bracteata in the Loess Plateau

In China, species of Atraphaxis (Polygonaceae) primarily inhabit arid zones across temperate steppe and desert regions. The complex geologic history (e.g., expansion of deserts) and extreme climate shifts of the region appear to have played an important role in shaping the phylogeography of Atraphaxis. The present study focuses on species-level phylogeographic patterns of Atraphaxis in China, with the goal of determining the impact of past environmental changes, in northern China, on the evolutionary history of the genus. Five hundred and sixty-four individuals distributed among 71 populations of 11 species of Atraphaxis from across the geographic range of the genus were studied using sequence data from two plastid spacers, psbK-psbI and psbB-psbH. The results demonstrate that most chloroplast haplotypes are species-specific, except for some present among widespread species. The phylogeny of Atraphaxis was well structured, and molecular dating analyses suggest that the main divergence events occurred during the late Pliocene and Pleistocene (5.73–0.03 million years ago). The statistical dispersal-vicariance analysis (S-DIVA) results provide evidence that phylogeographic patterns for the genus were characterized by both vicariance events and regional dispersal. The presented data suggest that the rapid expansion of deserts and climatic changes in northern China during the late Pliocene and Pleistocene have driven the diversification and spread of Atraphaxis in the region. The expansion of the Tengger Desert provided appropriate conditions for the origin of A. bracteata. Additionally, a contact zone in the north of the Hexi Corridor was identified as having played a significant role as a migratory route for species in adjacent areas.

Phylogeography of Diptychus maculatus (Cyprinidae) endemic to the northern margin of the QTP and Tien Shan region

Background

Phylogeography and historical demography of the cyprinid fish Diptychus maculatus (subfamily Schizothoracinae) are evaluated across three river systems in the Northern Qinghai-Tibetan Plateau (QTP) and Tien Shan range: the Indus River, Tarim River and Ili River.

Results

Results from both mtDNA (16S rRNA, Cyt b and D-loop) and nucDNA (RAG-2) resolved four reciprocally monophyletic clades, representing populations from Indus River, South Tarim River, North Tarim River and Ili River, respectively. The divergence times was estimated to be 1.5–2.5 Mya. It is consistent with the hypothesis that the split of four clades is the consequence of vicariance resulting from both the intensive uplift of QTP and Tien Shan as well as the resultant expansion of the Taklimakan Desert. Several lines of evidences indicate dynamic demographic histories for the populations, with late Pleistocene and Holocene population bottlenecks and expansions except the Indus River.

Conclusions

Our results clearly depicted the phylogenetic relationship of D. maculatus from Indus River, Tarim River and Ili River. The analyses implicated the relationship among the distribution of D. maculatus, paleo-drainages and geographic events, and implied the existence of the South Tarim River in history.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0756-3) contains supplementary material, which is available to authorized users.

Phylogeography of Libanotis buchtormensis (Umbelliferae) in Disjunct Populations along the Deserts in Northwest China

In Northwest China, aridification and desert expansion play significant roles in promoting desert plant diversification and speciation. However, to date, little is known about the effects of the desert barrier on the population structure of montane, non-desert species in the area. In this study, we sequenced chloroplast DNA regions (trnL–trnF and trnS–trnG) and a nuclear gene (rpb2) to investigate the population differentiation and phylogeographical history of Libanotis buchtormensis, a perennial montane species possessing a disjunct distribution at the periphery of the central desert. In total, 23 chloroplast haplotypes and 24 nuclear haplotypes were recovered from the 21 natural populations and six hebarium specimens. Phylogenetic analysis based on the combined plastid and nuclear dataset revealed two distinct lineages of L. buchtormensis, which inhabit the disjunct areas on both sides of the desert zone. The molecular dating analysis indicated that the divergence between the southeastern and the northwestern populations occurred in the middle Pleistocene, concomitantly with the desert expansion. The geographical vicariance likely contributed to the present disjunct distribution of L. buchtormensis across the deserts in Northwest China. Populations in the southeastern region may have migrated from the northwestern region, and seem to be a peripheral distribution of L. buchtormensis.

Phylogeographic Structure of a Tethyan Relict Capparis spinosa (Capparaceae) Traces Pleistocene Geologic and Climatic Changes in the Western Himalayas, Tianshan Mountains, and Adjacent Desert Regions

Complex geological movements more or less affected or changed floristic structures, while the alternation of glacials and interglacials is presumed to have further shaped the present discontinuous genetic pattern of temperate plants. Here we consider Capparis spinosa, a xeromorphic Tethyan relict, to discuss its divergence pattern and explore how it responded in a stepwise fashion to Pleistocene geologic and climatic changes. 267 individuals from 31 populations were sampled and 24 haplotypes were identified, based on three cpDNA fragments (trnL-trnF, rps12-rpl20, and ndhF). SAMOVA clustered the 31 populations into 5 major clades. AMOVA suggests that gene flow between them might be restricted by vicariance. Molecular clock dating indicates that intraspecific divergence began in early Pleistocene, consistent with a time of intense uplift of the Himalaya and Tianshan Mountains, and intensified in mid-Pleistocene. Species distribution modeling suggests range reduction in the high mountains during the Last Glacial Maximum (LGM) as a result of cold climates when glacier advanced, while gorges at midelevations in Tianshan appear to have served as refugia. Populations of low-altitude desert regions, on the other hand, probably experienced only marginal impacts from glaciation, according to the high levels of genetic diversity.

Continental Refugium in the Mongolian Plateau during Quaternary Glacial Oscillations: Phylogeography and Niche Modelling of the Endemic Desert Hamster, Phodopus roborovskii

The Mongolian Plateau (MP), which is situated in the interior of Asia and possesses a typical continental climate, experienced harsh climatic conditions during the Quaternary glacial fluctuations. Although these events likely had huge impacts on the local animal populations, the current effects have hardly been explored. To investigate whether the MP supported a refugium along an oceanic-continental gradient (ROCG), and whether this refugium was glacial or interglacial, we investigated the demographic and phylogeographic history of an endemic mammal species, the desert hamster Phodopus roborovskii. We reconstructed the demographic variation, the phylogeographic diffusion, and modelled the potential habitat during historical periods. The genetic diversity in the MP was the highest among all the localities, and the MP was a suitable habitat throughout the modelled historical periods. A phylogeographic diffusion analysis emphasized the importance of the MP as the centre of origin, preservation and spread for P. roborovskii. The homogeneous landscape provided the opportunity for a wide gene flow, which resulted in low resolution of the phylogenetic relationships. Moreover, P. roborovskii was favoured by the interglacial condition, with both its demographical and geographical ranges expanded within the interglacial periods. The range variation from the Last Glacial Maximum to the current condition reflects a distinct longitudinal shift, while both ranges largely contracted from that of the Last Interglacial. Our results support that the MP served as a refugium and spread centre for P. roborovskii during the Quaternary climate fluctuations. The interglacial expansion and the longitudinal shifts highlighted the important effects of precipitations on the distribution range of species adapted to arid and semi-arid during glacial oscillations.

The role of East Asian monsoon system in shaping population divergence and dynamics of a constructive desert shrub Reaumuria soongarica

Both of the uplift of Qinghai-Tibet Plateau (QTP) and the development of East Asian monsoon system (EAMS) could have comprehensively impacted the formation and evolution of Arid Central Asia (ACA). To understand how desert plants endemic to ACA responded to these two factors, we profiled the historical population dynamics and distribution range shift of a constructive desert shrub Reaumuria soongarica (Tamaricaceae) based on species wide investigation of sequence variation of chloroplast DNA and nuclear ribosomal ITS. Phylogenetic analysis uncovered a deep divergence occurring at ca. 2.96 Mya between the western and eastern lineages of R. soongarica, and ecological niche modeling analysis strongly supported that the monsoonal climate could have fragmented its habitats in both glacial and interglacial periods and impelled its intraspecific divergence. Additionally, the population from the east monsoonal zone expanded rapidly, suggesting that the local monsoonal climate significantly impacted its population dynamics. The isolation by distance tests supported strong maternal gene flow along the direction of the East Asian winter monsoon, whose intensification induced the genetic admixture along the latitudinal populations of R. soongarica. Our results presented a new case that the development of EAMS had prominently impacted the intraspecific divergence and population dynamics of this desert plant.

Phylogeographical structure inferred from cpDNA sequence variation of Zygophyllum xanthoxylon across north-west China

Zygophyllum xanthoxylon, a desert species, displaying a broad east-west continuous distribution pattern in arid Northwestern China, can be considered as a model species to investigate the biogeographical history of this region. We sequenced two chloroplast DNA spacers (psbK-psbI and rpl32-trnL) in 226 individuals from 31 populations to explore the phylogeographical structure. Median-joining network was constructed and analysis of AMOVA, SMOVA, neutrality tests and distribution analysis were used to examine genetic structure and potential range expansion. Using species distribution modeling, the geographical distribution of Z. xanthoxylon was modeled during the present and at the Last Glacial Maximum (LGM). Among 26 haplotypes, one was widely distributed, but most was restricted to either the eastern or western region. The populations with the highest levels of haplotype diversity were found in the Tianshan Mountains and its surroundings in the west, and the Helan Mountains and Alxa Plateau in the east. AMOVA and SAMOVA showed that over all populations, the species lacks phylogeographical structure, which is speculated to be the result of its specific biology. Neutrality tests and mismatch distribution analysis support past range expansions of the species. Comparing the current distribution to those cold and dry conditions in LGM, Z. xanthoxylon had a shrunken and more fragmented range during LGM. Based on the evidences from phylogeographical patterns, distribution of genetic variability, and paleodistribution modeling, Z. xanthoxylon is speculated most likely to have originated from the east and migrated westward via the Hexi Corridor.

Phylogeography of the arid shrub Atraphaxis frutescens (Polygonaceae) in northwestern China: evidence from cpDNA sequences

Climatic fluctuations during the Pleistocene are usually considered as a significant factor in shaping intraspecific genetic variation and influencing demographic histories. To well-understand these processes in desert northwest China, we selected arid adapted Atraphaxis frutescens as the study species. Two cpDNA regions (psbK-psbI, psbB-psbH) were sequenced in 272 individuals from 33 natural populations across the range of this shrub, and 10 haplotypes were identified. It was found to contain high levels of total gene diversity (H T = 0.858), and low levels of within-population diversity (H S = 0.092). Analysis of molecular variance (AMOVA) indicates that genetic differentiation primarily occurs among groups of populations. Based on BEAST (Bayesian Evolutionary Analysis Sampling Trees) analysis, we suggest that intraspecific differentiation of the species, resulting from isolated populations, accompanied enhanced desertification during the middle and late Pleistocene. The expansion of the Gurbantunggut and Kumtag deserts in this area appears to have triggered divergence among populations of the western, central, and eastern portions of the region and shaped genetic differentiation among them. Two possible independent glacial refugia were predicted, the Ili Valley and the northern Junggar Basin. Extensive development of arid habitats (desert margin and arid piedmont grassland) coupled with a more equable climate because the early Holocene are factors likely to have generated recent expansion of A. frutescens.

Molecular phylogeography and population genetic structure of O. longilobus and O. taihangensis (Opisthopappus) on the Taihang mountains

Historic events such as the uplift of mountains and climatic oscillations in the Quaternary periods greatly affected the evolution and modern distribution of the flora. We sequenced the trnL–trnF, ndhJ-trnL and ITS from populations throughout the known distributions of O. longilobus and O. taihangensis to understand the evolutionary history and the divergence related to the past shifts of habitats in the Taihang Mountains regions. The results showed high genetic diversity and pronounced genetic differentiation among the populations of the two species with a significant phylogeographical pattern (N_ST>G_ST, P<0.05), which imply restricted gene flow among the populations and significant geographical or environmental isolation. Ten chloroplast DNA (cpDNA) and eighteen nucleus ribosome DNA (nrDNA) haplotypes were identified and clustered into two lineages. Two corresponding refuge areas were revealed across the entire distribution ranges of O. longilobus and at least three refuge areas for O. taihangensis. O. longilobus underwent an evolutionary historical process of long-distance dispersal and colonization, whereas O. taihangensis underwent a population expansion before the main uplift of Taihang Mountains. The differentiation time between O. longilobus and O. taihangensis is estimated to have occurred at the early Pleistocene. Physiographic complexity and paleovegetation transition of Taihang Mountains mainly shaped the specific formation and effected the present distribution of these two species. The results therefore support the inference that Quaternary refugial isolation promoted allopatric speciation in Taihang Mountains. This may help to explain the existence of high diversity and endemism of plant species in central/northern China.