Exploitation of Key Regulatory Modules and Genes for High-Salt Adaptation in Schizothoracine by Weighted Gene Co-Expression Network Analysis

Schizothoracine fishes in saltwater lakes of the Tibetan Plateau are important models for studying the evolution and uplift of the Tibetan Plateau. Examining their adaptation to the high-salt environment is interesting. In this study, we first assembled the RNA-Seq data of each tissue of G. przewalskii, G. selincuoensis, and G. namensis from Qinghai Lake, Selincuo Lake, and Namtso Lake, respectively, obtained by the group previously. After obtaining reliable results, the adaptation of the gills, kidneys, and livers of the three species to the high-salinity environment was assessed by weighted gene co-expression network analysis (WGCNA). Using module eigengenes (ME), 21, 22, and 22 gene modules were identified for G. przewalskii, G. selincuoensis, and G. nemesis, respectively. Functional clustering analysis of genes in the significant association module identified several genes associated with osmolarity-regulated potential KEGG pathways in the gills of three species of Schizothoracine fish. Th17 cell differentiation pathway was up-regulated in the gills of all three species; histocompatibility class 2 II antigen and E alpha (h2-ea) were up-regulated genes in this pathway. Functional clustering analysis of genes in apparently related modules in the kidney unveiled several differential KEGG pathways. The pentose phosphate pathway was up-regulated in the three Schizothoracine fishes, and glucose-6-phosphate dehydrogenase (g6pd) was an up-regulated gene in this pathway. In the livers of the three Schizothorax species, the propanoate metabolism pathway was up-regulated, and succinate-CoA ligase GDP-forming subunit beta (suclg2) was an up-regulated gene in this pathway. The above analyses provide reference data for the adaptation of Schizothorax to high-salt environments and lay the foundation for future studies on the adaptive mechanism of Schizothorax in the plateau. These results partly fill the void in the knowledge gap in the survival adaptations of Schizothoracine fishes to highland saline lakes.

Genetic Diversity and Identification of Vaccinium Species Through Microsatellite Analysis

The Vaccinium genus contains about 500 species distributed worldwide but only a limited number of species have been studied for genetic diversity using molecular markers. In this study, a genetic analysis was conducted on three Vaccinium species (four cultivars of V. corymbosum, four wild populations of V. myrtillus, and two cultivars of V. ashei), for a total of 95 genotypes, using eight microsatellite (SSR) loci. A total of 57 alleles were detected. The number of alleles per locus ranged from 2 to 14, with an average of 7.25. Six unique alleles in V. corymbosum, four in V. ashei, and three in V. myrtillus were identified as being potential species markers. The dendrogram and principal coordinate analysis revealed a clear division of the three species into distinct groups, with each group further divided into sub-clusters based on the type of cultivars and population origin. The set of SSR primers used in this study demonstrated cross-species transferability, allowing their utilization in V. ashei and V. myrtillus, and can be used as a reliable tool for cultivar/population and species identification in blueberries.

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.

Diversification and historical demography of Haloxylon ammodendron in relation to Pleistocene climatic oscillations in northwestern China

The influence of aridification and climatic oscillations on the genetic diversity and evolutionary processes of organisms during the Quaternary in northwestern China is examined using Haloxylon ammodendron. Based on the variation of two cpDNA regions (trnS-trnG and trnV) and one nDNA sequence (ITS1-ITS4) in 420 individuals from 36 populations, the spatial genetic structure and demographic history of H. ammodendron in arid China is examined. Median-joining network and Bayesian inference trees enabled the identification of three diverged lineages within H. ammodendron from 24 different haplotypes and 16 ribotypes, distributed across western (Xinjiang), eastern (Gansu and Inner Mongolia) and southern (Qinghai) regions. AMOVA analysis demonstrated that more than 80% of observed genetic variation related to lineage split was based on cpDNA and nDNA variation. Allopatric divergence among the three groups was mainly triggered by geographical isolation due to Xingxingxia rock and uplift of the Qilian Mountains during the Quaternary. Local adaptive differentiation among western, eastern and southern groups occurred due to gene flow obstruction resulting from arid landscape fragmentation accompanied by local environmental heterogeneity of different geographical populations. The southern margin of the Junggar Basin and the Tengger Desert possibly served as two independent glacial refugia for H. ammodendron. The distribution of genetic variation, coupled with SDMs and LCP results, indicated that H. ammodendron probably moved northward along the Junggar Basin and westward along Tengger Desert at the end of the last glacial maximum; postglacial re-colonization was probably westward and southward along the Hexi Corridor.

Phylogeographic structure of Heteroplexis (Asteraceae), an endangered endemic genus in the limestone karst regions of southern China

Though the karst regions in south and southwest China are plant diversity hotspots, our understanding of the phylogeography and evolutionary history of the plants there remains limited. The genus Heteroplexis (Asteraceae) is one of the typical representative plants isolated by karst habitat islands, and is also an endangered and endemic plant to China. In this study, species-level phylogeographic analysis of the genus Heteroplexis was conducted using restriction site-associated DNA sequencing (RADseq). The genetic structure showed a clear phylogeographic structure consistent with the current species boundaries in the H. microcephala, H. incana, H. vernonioides, H. sericophylla, and H. impressinervia. The significant global (R = 0.37, P < 0.01) and regional (R = 0.650.95, P < 0.05) isolation by distance (IBD) signals among species indicate strong geographic isolation in the karst mountains, which may result in chronically restricted gene flow and increased genetic drift and differentiation. Furthermore, the phylogeographic structure of Heteroplexis suggested a southward migration since the last glacial period. Demographic analysis revealed the karst mountains as a refuge for Heteroplexis species. Finally, both Treemix and ABBA-BABA statistic detected significant historical gene flow between species. Significant historical gene flow and long-term stability of effective population size (Ne) together explain the high genome-wide genetic diversity among species (π = 0.05370.0838). However, the recent collapse of Ne, widespread inbreeding within populations, and restricted contemporary gene flow suggest that Heteroplexis species are probably facing a high risk of genetic diversity loss. Our results help to understand the evolutionary history of karst plants and guide conservation.

Comparative evolutionary history of two closely related desert plant, Convolvulus tragacanthoide and Convolvulus gortschakovii (Convolvulaceae) from northwest China

Desert ecosystems are one of the most fragile ecosystems on Earth. The study of the effects of paleoclimatic and geological changes on genetic diversity, genetic structure, and species differentiation of desert plants is not only helpful in understanding the strategies of adaptation of plants to arid habitats, but can also provide reference for the protection and restoration of vegetation in desert ecosystem. Northwest China is an important part of arid regions in the northern hemisphere. Convolvulus tragacanthoides and Convolvulus gortschakovii are closely related and have similar morphology. Through our field investigation, we found that the annual precipitation of the two species distribution areas is significantly different. Thus, C. tragacanthoides and C. gortschakovii provide an ideal comparative template to investigate the evolutionary processes of closely related species, which have adapted to different niches in response to changes in paleogeography and paleoclimate in northwest China. In this study, we employed phylogeographical approaches (two cpDNA spacers: rpl14-rpl36 and trnT-trnY) and species distribution models to trace the demographic history of C. tragacanthoides and C. gortschakovii, two common subshrubs and small shrubs in northwest China. The results showed the following: (1) Populations of C. tragacanthoides in northwest China were divided into three groups: Tianshan Mountains-Ili Valley, west Yin Mountains-Helan Mountains-Qinglian Mountains, and Qinling Mountains-east Yin Mountains. There was a strong correlation between the distribution of haplotypes and the floristic subkingdom. The three groups corresponded to the Eurasian forest subkingdom, Asian desert flora subkingdom, and Sino-Japanese floristic regions, respectively. Thus, environmental differences among different flora may lead to the genetic differentiation of C. tragacanthoides in China. (2) The west Yin Mountains-Helan Mountains-Qinglian Mountains, and Qinling Mountains-east Yin Mountains were thought to form the ancestral distribution range of C. tragacanthoides. (3) C. tragacanthoides and C. gortschakovii adopted different strategies to cope with the Pleistocene glacial cycle. Convolvulus tragacanthoides contracted to the south during the glacial period and expanded to the north during the interglacial period; and there was no obvious north-south expansion or contraction of C. gortschakovii during the glacial cycle. (4) The interspecific variation of C. tragacanthoides and C. gortschakovii was related to the orogeny in northwest China caused by the uplift of the Tibetan Plateau during Miocene. (5) The 200 mm precipitation line formed the dividing line between the niches occupied by C. tragacanthoides and C. gortschakovii, respectively. In this study, from the perspective of precipitation, the impact of the formation of the summer monsoon limit line on species divergence and speciation is reported, which provides a new perspective for studying the response mechanism of species to the formation of the summer monsoon line, and also provides a clue for predicting how desert plants respond to future environmental changes.

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 Biodiversity Conservation of a Relict and Medicinal Subshrub Capparis spinosa in Arid Central Asia

As a Tertiary Tethyan relict, Capparis spinosa is a typical wind-preventing and sand-fixing deciduous subshrub in arid central Asia. Due to its medicinal and energy value, this species is at risk of potential threat from human overexploitation, habitat destruction and resource depletion. In this study, our purpose was to evaluate the conservation strategies of C. spinosa according to its genetic structure characteristics and genetic diversity pattern among 37 natural distributional populations. Based on genomic SNP data generated from dd-RAD sequencing, genetic diversity analysis, principal component analysis, maximum likelihood phylogenetic trees and ADMIXTURE clustering, the significant population structure and differentiation were explored. The results showed the following: (1) Six distinct lineages were identified corresponding to geographic locations, and various levels of genetic diversity existed among the lineages for the natural habitat heterogeneity or human interferences; (2) The lineage divergences were influenced by isolation by distances, vicariance and restricted gene flow under complex topographic and climatic conditions. Finally, for the preservation of the genetic integrity of C. spinosa, we suggest that conservation units should be established corresponding to different geographic groups, and that attention should be paid to isolated and peripheral populations that are experiencing biodiversity loss. Simultaneously, monitoring and reducing anthropogenic disturbances in addition to rationally and sustainably utilizing wild resources would be beneficial to guarantee population resilience and evolutionary potential of this xerophyte in response to future environmental changes.

Otolith Microchemistry and Demographic History Provide New Insight into the Migratory Behavior and Heterogeneous Genetic Divergence of Coilia grayii in the Pearl River

Coilia grayii is the anadromous form of anchovy that is distributed in the East and South China Seas. It is a common fish species in the estuarine area of the Pearl River. Nevertheless, freshwater populations appear upstream in the Pearl River, but the migratory pathway has been mostly impeded by dam construction. Behavioral differences and constrained habitat within tributaries are suspected of promoting genetic divergence in these populations. In this study, we investigated the migratory behavior and genetic divergence of six populations of C. grayii fragmented by dams based on the otolith strontium/calcium (Sr/Ca) ratio, mitochondrial DNA, and microsatellite genotyping. All populations were in freshwater with low Sr/Ca ratios, except the estuarine population (Humen population) hatched in brackish water. Reduced nucleotide diversity corresponding to distance was observed. Populations from distant hydrological regions exhibited a decline in genetic diversity and a significant difference with the remaining populations after fitting the isolation by distance model. Pairwise fixation indices confirmed these results and moderate and significant differentiation was found between Hengxian site and downstream sites. Furthermore, STRUCTURE analyses revealed that all separated populations exhibited an admixed phylogenetic pattern except for individuals from the Hengxian locality. The upstream sites showed significantly increased resistance to gene flow from the estuarine population because of isolation by the dam. The results of the neutrality test and Bayesian skyline plots demonstrated complex demography—individuals’ experienced historical expansion and partial upper-dam populations had recently undergone a colonization, forming a new genetic structure. Accordingly, this study demonstrates differences in the migration pattern and genetic differentiation of C. grayii as a consequence of demographic history and current processes (habitat fragmentation and colonization).

Spatial Genetic Structure of Prunus mongolica in Arid Northwestern China Based on RAD Sequencing Data

The extensive range of sand deserts, gravel deserts, and recent human activities have shaped habitat fragmentation of relict and endangered plants in arid northwestern China. Prunus mongolica is a relict and endangered shrub that is mainly distributed in the study area. In the present study, population genomics was integrated with a species distribution model (SDM) to investigate the spatial genetic diversity and structure of P. mongolica populations in response to habitat fragmentation and create a proposal for the conservation of this endangered species. The results showed that the northern marginal populations were the first isolated from other populations. The SDM suggested that these marginal populations had low levels of habitat suitability during the glacial period. They could not obtain migration corridors, and thus possessed low levels of gene flow connection with other populations. Additionally, several populations underwent secondarily geographical isolation from other central populations, which preserved particular genetic lineages. Genetic diversity was higher in southern populations than in northern ones. It was concluded that long-term geographical isolation after historical habitat fragmentation promoted the divergence of marginal populations and refugial populations along mountains from other populations. The southern populations could have persisted in their distribution ranges and harbored higher levels of genetic diversity than the northern populations, whose distribution ranges fluctuated in response to paleoclimatic changes. We propose that the marginal populations of P. mongolica should be well considered in conservation management.