Genetic diversity and population structure of Prunus mira (Koehne) from the Tibet plateau in China and recommended conservation strategies.
ABSTRACT: Prunus mira Koehne, an important economic fruit crop with high breeding and medicinal values, and an ancestral species of many cultivated peach species, has recently been declared an endangered species. However, basic information about genetic diversity, population structure, and morphological variation is still limited for this species. In this study, we sampled 420 P. mira individuals from 21 wild populations in the Tibet plateau to conduct a comprehensive analysis of genetic and morphological characteristics. The results of molecular analyses based on simple sequence repeat (SSR) markers indicated moderate genetic diversity and inbreeding (A = 3.8, Ae = 2.5, He = 0.52, Ho = 0.44, I = 0.95, FIS = 0.17) within P. mira populations. STRUCTURE, GENELAND, and phylogenetic analyses assigned the 21 populations to three genetic clusters that were moderately correlated with geographic altitudes, and this may have resulted from significantly different climatic and environmental factors at different altitudinal ranges. Significant isolation-by-distance was detected across the entire distribution of P. mira populations, but geographic altitude might have more significant effects on genetic structure than geographic distance in partial small-scale areas. Furthermore, clear genetic structure, high genetic differentiation, and restricted gene flow were detected between pairwise populations from different geographic groups, indicating that geographic barriers and genetic drift have significant effects on P. mira populations. Analyses of molecular variance based on the SSR markers indicated high variation (83.7% and 81.7%), whereas morphological analyses revealed low variation (1.30%-36.17%) within the populations. Large and heavy fruits were better adapted than light fruits and nutlets to poor climate and environmental conditions at high altitudes. Based on the results of molecular and morphological analyses, we classified the area into three conservation units and proposed several conservation strategies for wild P. mira populations in the Tibet plateau.
Project description:Qiu Ren, Jun-Xing Yang, and Xiao-Yong Chen (2018) Triplophysa stenura is an indigenous and widely distributed loach in the Qinghai-Tibet plateau and adjacent Three Parallel Rivers region of China. Morphological and phylogenetic analyses were performed in order to explore the genetic and morphological variation in T. stenura populations from different geographic regions and infer the divergence time and relationships between populations from the three rivers (Jinsha River, Nu River and Lancang River). Two mitochondrial genes (Cyt b, D-Loop) and 35 morphological characters were selected for genetic and morphological analyses, respectively. Phylogenetic and network analyses reveal that T. stenura is a single lineage with three well supported clades strictly corresponding to specific river systems. Divergence time analysis suggests that the divergence of T. stenura and formation of the Three Parallel Rivers are closely associated with the Kun-Huang Movement (1.1- 0.6 MYA), which lead to the uplift of the Qinghai-Tibet plateau. AMOVA reveals that there is moderate genetic differentiation among populations. Results from ANOVA suggest that several morphological characters show significant variation among populations and drainages. Descriptive morphological variation (e.g., color pattern) in different populations of T. stenura clarifies a set of characters that can be used to accurately identify members of this group in the future. We conclude that T. stenura has moderate population genetic structure and character variation in this study area and the divergence and evolution of T. stenura is associated with the uplift of the Qinghai-Tibet plateau.
Project description:Plant adaptation to high altitudes has long been a substantial focus of ecological and evolutionary research. However, the genetic mechanisms underlying such adaptation remain poorly understood. Here, we address this issue by sampling, genotyping, and comparing populations of Tibetan poplar, Populus szechuanica var. tibetica, distributed from low (~2,000 m) to high altitudes (~3,000 m) of Sejila Mountain on the Qinghai-Tibet Plateau. Population structure analyses allow clear classification of two groups according to their altitudinal distributions. However, in contrast to the genetic variation within each population, differences between the two populations only explain a small portion of the total genetic variation (3.64%). We identified asymmetrical gene flow from high- to low-altitude populations. Integrating population genomic and landscape genomic analyses, we detected two hotspot regions, one containing four genes associated with altitudinal variation, and the other containing ten genes associated with response to solar radiation. These genes participate in abiotic stress resistance and regulation of reproductive processes. Our results provide insight into the genetic mechanisms underlying high-altitude adaptation in Tibetan poplar.
Project description:BACKGROUND:The Tibetan poplar (Populus szechuanica var. tibetica Schneid), which is distributed at altitudes of 2,000-4,500 m above sea level, is an ecologically important species of the Qinghai-Tibet Plateau and adjacent areas. However, the genetic adaptations responsible for its ability to cope with the harsh environment remain unknown. RESULTS:In this study, a total of 24 expressed sequence tag microsatellite (EST-SSR) markers were used to evaluate the genetic diversity and population structure of Tibetan poplars along an altitude gradient. The 172 individuals were of genotypes from low-, medium- and high-altitude populations, and 126 alleles were identified. The expected heterozygosity (HE) value ranged from 0.475 to 0.488 with the highest value found in low-altitude populations and the lowest in high-altitude populations. Genetic variation was low among populations, indicating a limited influence of altitude on microsatellite variation. Low genetic differentiation and high levels of gene flow were detected both between and within the populations along the altitude gradient. An analysis of molecular variance (AMOVA) showed that 6.38% of the total molecular variance was attributed to diversity between populations, while 93.62% variance was associated with differences within populations. There was no clear correlation between genetic variation and altitude, and a Mantel test between genetic distance and altitude resulted in a coefficient of association of r = 0.001, indicating virtually no correlation. CONCLUSION:Microsatellite genotyping results showing genetic diversity and low differentiation suggest that extensive gene flow may have counteracted local adaptations imposed by differences in altitude. The genetic analyses carried out in this study provide new insight for conservation and optimization of future arboriculture.
Project description:Long-lived tree species are genetically differentiated and locally adapted with respect to fitness-related traits, but the genetic basis of local adaptation remains largely unresolved. Recent advances in population genetics and landscape genomic analyses enable identification of putative adaptive loci and specific selective pressures acting on local adaptation. Here, we sampled 60 evergreen oak (Quercus aquifolioides) populations throughout the species' range and pool-sequenced 587 individuals at drought-stress candidate genes. We analyzed patterns of genetic diversity and differentiation for 381 single nucleotide polymorphisms (SNPs) from 65 candidate genes and eight microsatellites. Outlier loci were identified by genetic differentiation analysis and genome-environment associations. The response pattern of genetic variation to environmental gradient was assessed by linear isolation-by-distance/environment tests, redundancy analysis, and nonlinear methods. SNPs and microsatellites revealed two genetic lineages: Tibet and Hengduan Mountains-Western Sichuan Plateau (HDM-WSP), with reduced genetic diversity in Tibet lineage. More outlier loci were detected in HDM-WSP lineage than Tibet lineage. Among these, three SNPs in two genes responded to dry season precipitation in the HDM-WSP lineage but not in Tibet. By contrast, genetic variation in the Tibet lineage was related to geographic distance instead of the environment. Furthermore, risk of nonadaptedness (RONA) analyses suggested HDM-WSP lineage will have a better capacity to adapt in the predicted future climate compared with the Tibet lineage. We detected genetic imprints consistent with natural selection and molecular adaptation to drought on the Qinghai-Tibet Plateau (QTP) over a range of long-lived and widely distributed oak species in a changing environment. Our results suggest that different within-species adaptation processes occur in species occurring in heterogeneous environments.
Project description:BACKGROUND:Incarvillea sinensis is widely distributed from Southwest China to Northeast China and in the Russian Far East. The distribution of this species was thought to be influenced by the uplift of the Qinghai-Tibet Plateau and Quaternary glaciation. To reveal the imprints of geological events on the spatial genetic structure of Incarvillea sinensis, we examined two cpDNA segments ( trnH- psbA and trnS- trnfM) in 705 individuals from 47 localities. RESULTS:A total of 16 haplotypes was identified, and significant genetic differentiation was revealed (GST =0.843, NST?=?0.975, P?<?0.05). The survey detected two highly divergent cpDNA lineages connected by a deep gap with allopatric distributions: the southern lineage with higher genetic diversity and differentiation in the eastern Qinghai-Tibet Plateau, and the northern lineage in the region outside the Qinghai-Tibet Plateau. The divergence between these two lineages was estimated at 4.4 MYA. A correlation between the genetic and the geographic distances indicates that genetic drift was more influential than gene flow in the northern clade with lower diversity and divergence. However, a scenario of regional equilibrium between gene flow and drift was shown for the southern clade. The feature of spatial distribution of the genetic diversity of the southern lineage possibly indicated that allopatric fragmentation was dominant in the collections from the eastern Qinghai-Tibet Plateau. CONCLUSIONS:The results revealed that the uplift of the Qinghai-Tibet Plateau likely resulted in the significant divergence between the lineage in the eastern Qinghai-Tibet Plateau and the other one outside this area. The diverse niches in the eastern Qinghai-Tibet Plateau created a wide spectrum of habitats to accumulate and accommodate new mutations. The features of genetic diversity of populations outside the eastern Qinghai-Tibet Plateau seemed to reveal the imprints of extinction during the Glacial and the interglacial and postglacial recolonization. Our study is a typical case of the significance of the uplift of the Qinghai-Tibet Plateau and the Quaternary Glacial in spatial genetic structure of eastern Asian plants, and sheds new light on the evolution of biodiversity in the Qinghai-Tibet Plateau at the intraspecies level.
Project description:BACKGROUND: The Tibetan pig is one of domestic animals indigenous to the Qinghai-Tibet Plateau. Several geographically isolated pig populations are distributed throughout the Plateau. It remained an open question if these populations have experienced different demographic histories and have evolved independent adaptive loci for the harsh environment of the Plateau. To address these questions, we herein investigated ~ 40,000 genetic variants across the pig genome in a broad panel of 678 individuals from 5 Tibetan geographic populations and 34 lowland breeds. RESULTS: Using a series of population genetic analyses, we show that Tibetan pig populations have marked genetic differentiations. Tibetan pigs appear to be 3 independent populations corresponding to the Tibetan, Gansu and Sichuan & Yunnan locations. Each population is more genetically similar to its geographic neighbors than to any of the other Tibetan populations. By applying a locus-specific branch length test, we identified both population-specific and -shared candidate genes under selection in Tibetan pigs. These genes, such as PLA2G12A, RGCC, C9ORF3, GRIN2B, GRID1 and EPAS1, are involved in high-altitude physiology including angiogenesis, pulmonary hypertension, oxygen intake, defense response and erythropoiesis. A majority of these genes have not been implicated in previous studies of highlanders and high-altitude animals. CONCLUSION: Tibetan pig populations have experienced substantial genetic differentiation. Historically, Tibetan pigs likely had admixture with neighboring lowland breeds. During the long history of colonization in the Plateau, Tibetan pigs have developed a complex biological adaptation mechanism that could be different from that of Tibetans and other animals. Different Tibetan pig populations appear to have both distinct and convergent adaptive loci for the harsh environment of the Plateau.
Project description:Many species of high-altitude plateaus tend to be narrowly distributed along river valleys at lower elevations due to a limitation of suitable habitats. The eastern honeybee (Apis cerana) is such a species and this study explored the effects of long and narrow geographic distributions on honeybee populations. Genetic differentiation and diversity were assessed across populations of the southeastern Qinghai-Tibet Plateau. A total of 492 honeybee samples from eight sampling sites in four valleys were analyzed for the genetic differentiation and diversity of 31 microsatellite loci and mitochondrial tRNAleu-COII fragments. The following results were obtained: (1) Microsatellite genetic differentiation coefficients (F ST) ranged from 0.06 to 0.16, and mitochondrial F ST estimates ranged from 0.18 to 0.70 for different sampling sites in the same valley, indicating genetic differentiation. (2) Honeybees in adjacent valleys were also genetically differentiated. The F ST of microsatellites and mitochondria were 0.04-0.29 and 0.06-0.76, respectively. (3) Likely a result of small population sizes, the observed genetic diversity was low. The observed impedance of honeybee gene flow among valleys increased both genetic differentiation and population numbers in the Qinghai-Tibet Plateau. This study contributes significantly to the current understanding of the mechanism underlying population genetic differentiation and highlights the potential effects of utilizing genetic resources that are subject to the ecological conditions of the long and narrow geographic distributions of plateau-valley landforms.
Project description:Pleistocene climatic oscillations have greatly influenced the evolutionary history and distribution pattern of most extant species. However, their effects on species on the Qinghai-Tibet Plateau (QTP) are not well understood. To investigate the effects of past climatic shifts, particularly the Last Glacial Maximum (LGM), on plateau fish, we analysed the phylogeographic structure and demographic history of five closely related taxa of the subfamily Schizothoracinae, a representative endemic taxon of the QTP, from nine endorheic lakes on the central QTP and three peripheral exorheic rivers using the mitochondrial control region (D-loop) sequence and 12 microsatellite (SSR) markers. Phylogram from D-loop haplotypes revealed two well-supported lineages (North and South) separated by the Tanggula Mountains. The results from the D-loop and SSR revealed that endorheic populations possess high genetic diversity and a unique genetic structure. The most recent demographic expansion occurred post-LGM for most endorheic populations and in the last interglacial period for Siling Co and all exorheic populations. Phylogeographic structure, together with species distribution modelling, supports the scenario of multiple glacial refugia on the QTP during the LGM and suggests that Siling Co (4540?m asl) is a cryptic glacial microrefugia for plateau fish, which would be the highest glacial microrefugia known.
Project description:BACKGROUND: Environmental stress can accelerate the evolutionary rate of specific stress-response proteins and create new functions specialized for different environments, enhancing an organism's fitness to stressful environments. Pikas (order Lagomorpha), endemic, non-hibernating mammals in the modern Holarctic Region, live in cold regions at either high altitudes or high latitudes and have a maximum distribution of species diversification confined to the Qinghai-Tibet Plateau. Variations in energy metabolism are remarkable for them living in cold environments. Leptin, an adipocyte-derived hormone, plays important roles in energy homeostasis. METHODOLOGY/PRINCIPAL FINDINGS: To examine the extent of leptin variations within the Ochotona family, we cloned the entire coding sequence of pika leptin from 6 species in two regions (Qinghai-Tibet Plateau and Inner Mongolia steppe in China) and the leptin sequences of plateau pikas (O. curzonia) from different altitudes on Qinghai-Tibet Plateau. We carried out both DNA and amino acid sequence analyses in molecular evolution and compared modeled spatial structures. Our results show that positive selection (PS) acts on pika leptin, while nine PS sites located within the functionally significant segment 85-119 of leptin and one unique motif appeared only in pika lineages-the ATP synthase alpha and beta subunit signature site. To reveal the environmental factors affecting sequence evolution of pika leptin, relative rate test was performed in pikas from different altitudes. Stepwise multiple regression shows that temperature is significantly and negatively correlated with the rates of non-synonymous substitution (Ka) and amino acid substitution (Aa), whereas altitude does not significantly affect synonymous substitution (Ks), Ka and Aa. CONCLUSIONS/SIGNIFICANCE: Our findings support the viewpoint that adaptive evolution may occur in pika leptin, which may play important roles in pikas' ecological adaptation to extreme environmental stress. We speculate that cold, and probably not hypoxia, may be the primary environmental factor for driving adaptive evolution of pika leptin.
Project description:Background:Animals inhabiting high altitudes consistently show slow life-histories. The pace-of-life syndrome (POLS) hypothesis posits behavioural, physiological and/or morphological traits that mediate the trade-off between current and future reproduction or survival, which have coevolved along a slow-fast life history continuum. Previous studies have shown that the life histories of plateau pikas varied across altitude, high-altitude individuals showed slow pace of life which were characterized by few litters per year with small litter sizes. Thus, we hypothesized that pikas populations at higher altitudes would also express personalities characteristic associated with slow life history, such as high sociability, low activity or aggressiveness. We tested this hypothesis by comparing the activity and docility of three plateau pika (Ochotona curzoniae) populations distributed along an altitudinal gradient of the Tibetan Plateau. We predicted that high-altitude pika would be more docile and less active. Results:The behaviour of 556 pikas, from which 120 individuals were measured at least twice, was quantified. We observed that plateau pikas at high altitudes were less active and more docile than pika at lower altitudes. Activity and docility were significantly and negatively correlated in populations from high altitudes but not in populations from low altitudes. Conclusions:Our results support the POLS hypothesis, highlight the existence of personality variation among populations distributed along an altitudinal gradient and emphasise the importance of environmental selection on personality divergence.