Population genetic diversity and environmental adaptation of Tamarix hispida in the Tarim Basin, arid Northwestern China

Arid ecosystems, characterized by severe water scarcity, play a crucial role in preserving Earth's biodiversity and resources. The Tarim Basin in Northwestern China, a typical arid region isolated by the Tianshan Mountains and expansive deserts, provides a special study area for investigating how plant response and adaptation to such environments. Tamarix hispida, a species well adapted to saline-alkaline and drought conditions, dominates in the saline-alkali lands of the Tarim Basin. This study aims to examine the genetic diversity and environmental adaptation of T. hispida in the Tarim Basin. Genomic SNPs for a total of 160 individuals from 17 populations were generated using dd-RAD sequencing approach. Population genetic structure and genetic diversity were analyzed by methods including ADMIXTURE, PCA, and phylogenetic tree. Environmental association analysis (EAA) was performed using LFMM and RDA analyses. The results revealed two major genetic lineages with geographical substitution patterns from west to east, indicating significant gene flow and hybridization. Environmental factors such as Precipitation Seasonality (bio15) and Topsoil Sand Fraction (T_SAND) significantly shaped allele frequencies, supporting the species' genetic adaptability. Several genes associated with environmental adaptation were identified and annotated, highlighting physiological and metabolic processes crucial for survival in arid conditions. The study highlights the role of geographical isolation and environmental factors in shaping genetic structure and adaptive evolution. The identified adaptive genes related to stress tolerance emphasize the species' resilience and highlight the importance of specific physiological and metabolic pathways.

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.

Population genetic structure and evolutionary history of Psammochloa villosa (Trin.) Bor (Poaceae) revealed by AFLP marker

Psammochloa villosa is an ecologically important desert grass that occurs in the Inner Mongolian Plateau where it is frequently the dominant species and is involved in sand stabilization and wind breaking. We sought to generate a preliminary demographic framework for P. villosa to support the future studies of this species, its conservation, and sustainable utilization. To accomplish this, we characterized the genetic diversity and structure of 210 individuals from 43 natural populations of P. villosa using amplified fragment length polymorphism (AFLP) markers. We obtained 1,728 well-defined amplified bands from eight pairs of primers, of which 1,654 bands (95.7%) were polymorphic. Results obtained from the AFLPs suggested effective alleles among populations of 1.32, a Nei's standard genetic distance value of 0.206, a Shannon index of 0.332, a coefficient of gene differentiation (G ST) of 0.469, and a gene flow parameter (Nm) of 0.576. All these values indicate that there is abundant genetic diversity in P. villosa, but limited gene flow. An analysis of molecular variance (AMOVA) showed that genetic variation mainly exists within populations (64.2%), and we found that the most genetically similar populations were often not geographically adjacent. Thus, this suggests that the mechanisms of gene flow are surprisingly complex in this species and may occur over long distances. In addition, we predicted the distribution dynamics of P. villosa based on the spatial distribution modeling and found that its range has contracted continuously since the last interglacial period. We speculate that dry, cold climates have been critical in determining the geographic distribution of P. villosa during the Quaternary period. Our study provides new insights into the population genetics and evolutionary history of P. villosa in the Inner Mongolian Plateau and provides a resource that can be used to design in situ conservation actions and prioritize sustainable utilization.

Genetic structure and temporal environmental niche dynamics of sideoats grama [Bouteloua curtipendula (Michx.) Torr.] populations in Mexico

In the past years, several plant breeding programs have been done to select outstanding genotypes of sideoats grama (Bouteloua curtipendula) for restoration purposes. Such programs have been focused mainly on agronomic traits; however, little attention has been paid to the genetic structure and environmental adaptation of the selected genotypes. Thus, in this study we evaluated the genetic structure of 85 sideoats grama populations in Mexico. In addition, we modeled the past, present and future environmental niche of the genetic clusters of this species. Ninety sideoats grama populations were genetically analyzed through AFLP (Amplified Fragment Length Polymorphisms) markers. The environmental niche of the population clusters was modeled by using the maximum entropy method. The genetic analysis separated the populations into two genetically different clusters (p = 0.0003). The differentiation of these lineages can be partially explained by the paleoclimatic events experienced during the last interglacial and glacial maximums. Consequently, the genetic clusters have different environmental niche at the present time. Suitability areas for the distribution of Cluster I are mainly located in the central part of the country while the environmental niche of Cluster II is located in the semiarid region, close to the mountain range of the Sierra Madre Occidental. Thus, selection and restoration programs with sideoats grama must be carried out using local germplasm from each environmental niche. Given the environmental niche of both genetic clusters will suffer changes in the near and mid-century future, climate change must be considered for genotypes selection and restoration programs.

Effects of Water and Energy on Plant Diversity along the Aridity Gradient across Dryland in China

Plants need water and energy for their growth and reproduction. However, how water and energy availability influence dryland plant diversity along the aridity gradient in water-limited regions is still lacking. Hence, quantitative analyses were conducted to evaluate the relative importance of water and energy to dryland plant diversity based on 1039 quadrats across 184 sites in China's dryland. The results indicated that water availability and the water-energy interaction were pivotal to plant diversity in the entire dryland and consistent with the predictions of the water-energy dynamic hypothesis. The predominance of water limitation on dryland plant diversity showed a weak trend with decreasing aridity, while the effects of energy on plants were found to be significant in mesic regions. Moreover, the responses of different plant lifeforms to water and energy were found to vary along the aridity gradient. In conclusion, the study will enrich the limited knowledge about the effects of water and energy on plant diversity (overall plants and different lifeforms) in the dryland of China along the aridity gradient.

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.

Dispersal and genetic differentiation of Syntrichia caninervis populations across different desert regions in China

The moss Syntrichia caninervis is widely distributed in cool temperate and cold deserts where environmental pressures create a dependence on asexual reproduction (fragment reproduction). However, when compared to sporophyte-producing mosses, there is a lack of evidence to support the capacity of drought-tolerant mosses that predominantly fragment and produce protonema to disperse over long distances. We used 20 microsatellite loci to study genetic variation and structure in six populations (five natural populations and one population from a regeneration site) in three contrasting and widely separated regions of China. The genetic diversity and expected heterozygosity were lower in populations from the Tengger Desert than in populations from the other regions. Using PCoA, UPGMA and Structure analysis, the genetic grouping divided the three regions into three distinct groups. This may indicate that in regions where S. caninervis reproduces predominantly asexually, propagules are spread mainly by short-distance dispersal. The genetic diversity of the population from the regeneration site in the Tengger Desert was slightly higher than that of the nearby, naturally occurring population, and included some input from the Pamir Plateau almost 2,300 km to the west, suggesting long-distance dispersal of S. caninervis propagules across the region. Predominantly asexually reproducing populations of S. caninervis are mainly dependent on short-distance dispersal. Long-distance dispersal of S. caninervis propagules across the region is difficult. Establishment of populations with dominant asexual reproduction will eventually result in genetic differentiation.

Pleistocene climate change and phylogeographic structure of the Gymnocarpos przewalskii (Caryophyllaceae) in the northwest China: Evidence from plastid DNA, ITS sequences, and Microsatellite

Northwestern China has a wealth of endemic species, which has been hypothesized to be affected by the complex paleoclimatic and paleogeographic history during Quaternary. In this paper, we used Gymnocarpos przewalskii as a model to address the evolutionary history and current population genetic structure of species in northwestern China. We employed two chloroplast DNA fragments (rps16 and psbB-psbI), one nuclear DNA fragment (ITS), and simple sequence repeat (SSRs) to investigate the spatial genetic pattern of G. przewalskii. High genetic diversity (cpDNA: h S = 0.330, h T = 0.866; ITS: h S = 0.458, h T = 0.872) was identified in almost all populations, and most of the population have private haplotypes. Moreover, multimodal mismatch distributions were observed and estimates of Tajima's D and Fu's FS tests did not identify significantly departures from neutrality, indicating that recent expansion of G. przewalskii was rejected. Thus, we inferred that G. przewalskii survived generally in northwestern China during the Pleistocene. All data together support the genotypes of G. przewalskii into three groups, consistent with their respective geographical distributions in the western regions-Tarim Basin, the central regions-Hami Basin and Hexi Corridor, and the eastern regions-Alxa Desert and Wulate Prairie. Divergence among most lineages of G. przewalskii occurred in the Pleistocene, and the range of potential distributions is associated with glacial cycles. We concluded that climate oscillation during Pleistocene significantly affected the distribution of the species.

Genetic Structure and Eco-Geographical Differentiation of Wild Sheep Fescue (Festuca ovina L.) in Xinjiang, Northwest China

Glaciation and mountain orogeny have generated new ecologic opportunities for plants, favoring an increase in the speciation rate. Moreover, they also act as corridors or barriers for plant lineages and populations. High genetic diversity ensures that species are able to survive and adapt. Gene flow is one of the most important determinants of the genetic diversity and structure of out-crossed species, and it is easily affected by biotic and abiotic factors. The aim of this study was to characterize the genetic diversity and structure of an alpine species, Festuca ovina L., in Xinjiang, China. A total of 100 individuals from 10 populations were analyzed using six amplified fragment length polymorphism (AFLP) primer pairs. A total of 583 clear bands were generated, of which 392 were polymorphic; thus, the percentage of polymorphic bands (PPB) was 67.24%. The total and average genetic diversities were 0.2722 and 0.2006 (0.1686-0.2225), respectively. The unweighted group method with arithmetic mean (UPGMA) tree, principal coordinates analysis (PCoA) and Structure analyses revealed that these populations or individuals could be clustered into two groups. The analysis of molecular variance analysis (AMOVA) suggested that most of the genetic variance existed within a population, and the genetic differentiation (Fst) among populations was 20.71%. The Shannon differentiation coefficient (G'st) among populations was 0.2350. Limited gene flow (Nm = 0.9571) was detected across all sampling sites. The Fst and Nm presented at different levels under the genetic barriers due to fragmentation. The population genetic diversity was significant relative to environmental factors such as temperature, altitude and precipitation.

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.

Evolutionary History of a Desert Shrub Ephedra przewalskii (Ephedraceae): Allopatric Divergence and Range Shifts in Northwestern China

Based on two chloroplast DNA sequences, psbA-trnH and trnT-trnF, phylogeographical patterns of a desert shrub, Ephedra przewalskii, were examined across most of its geographic range in northwestern China. A total of sixteen haplotypes were detected. There was a common haplotype in each basin, that was haplotype A in Tarim Basin, haplotype G in Junggar Basin, and haplotype M in Qaidam Basin. Genetic variance mainly occurred among populations, geographic regions, and eleven geographic groups subdivided by SAMOVA analysis. E. przewalskii likely had a smaller and more fragmented geographic range during the Last Glacial Maximum, which was determined based on ecological niche modelling. Three groups of E. przewalskii populations were detected to have experience range expansion, and this was based on significant values of Fu’s F_S, Tajima’s D, and unimodel mismatch distributions. The cold and dry climate during the glacial period of the Quaternary is postulated to have been a driver for significant genetic isolation and divergence among populations or groups in E. przewalskii, whereas the warmer and wetter climate during the interglacial period is speculated to have provided favourable conditions for range expansion of the species.

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.

Refugia persistence of Qinghai-Tibetan plateau by the cold-tolerant bird Tetraogallus tibetanus (Galliformes: Phasianidae)

Most of the temperate species are expected to have moved to lower altitudes during the glacial periods of the Quaternary. Here we tested this hypothesis in a cold-tolerant avian species Tibetan snowcock (Tetraogallus tibetanus) using two segments of mitochondrial gene (a 705bp Cytochrome-b; abbrev. Cyt-b and an 854 bp Control Region; abbrev. CR) and eight microsatellite loci by characterizing population differentiation and gene flow across its range. Combined (Cyt-b + CR) datasets detected several partially lineages with poor support. Microsatellite data, however, identified two distinct lineages congruent with the geographically separated western and central regions of Qinghai-Tibetan Plateau (QTP). The phylogeographic patterns that we observed might be explained by a combination of vicariance events that led to local isolation of T. tibetanus during warm periods and range expansions and population intermixing during cold periods. The results of this study add to our knowledge of population differentiation and connectivity in high altitude mountain ecosystems.

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.