Genetic structure of Himalayan marmot (Marmota himalayana) population alongside the Qinghai–Tibet Railway

In order to verify the effect of social behavior and geographical isolation on the genetic structure of the Himalayan marmot (Marmota himalayana) population, we examined the genetic diversity of Himalayan marmots alongside the Qinghai–Tibet Railway using microsatellite markers. Eight microsatellite loci were used to examine 120 animals of 4 populations: Ulan (U), Delhi (D), Tuotuohe (T) and Ando (A). The results show that: (1) Himalayan marmots alongside the Qinghai–Tibet Railway are highly genetically diversified. The allele number (Na), effective allele number (Ne), observed heterozygosity (Ho), Nei’s expected heterozygosity (He) and polymorphism information content (PIC) of the total Himalayan marmot population were 4.75, 3.0332, 0.6990, 0.6672, 0.6102, respectively. (2) Himalayan marmots may be able to avoid inbreeding by a mechanism that will prevent the genetic diversity reduction caused by their social lifestyle. Heterozygote excess was observed at most loci. The inbreeding coefficients within the subpopulation (F_IS), in the total population (F_IT), the differentiation index of population (F_ST), and the gene flow (Nm) were ?0.2265, ?0.0477, 0.1458, and 1.4646, respectively. (3) The genetic differentiation of the Himalayan marmot population was in accordance with Wright’s “isolation by distance” theory. The Mantel test indicates that the correlation between genetic distance and geographic distance was significant (P < 0.05, r = 0.698). (4) Each of the four geographical populations had moderate differentiation. Both geographic distance and isolation could affect the population genetic structure of the Himalayan marmot. The maximum gene flow (3.5915), the smallest genetic differentiation index (0.0651), the lowest genetic distance (0.0700) and the highest genetic identity (0.9526) were all between the Ulan population and Delhi populations. (5) The cluster analysis, based on Nei’s standard genetic distance, showed that the populations of Delhi and Ulan were first merged in a cluster, and then Tuotuohe population was merged in the clustering. The Ando population was the last element in the clustering.     

Genetic diversity and population structure of Lamiophlomis rotata (Lamiaceae), an endemic species of Qinghai–Tibet Plateau

Lamiophlomis rotata (Lamiaceae), a perennial medicinal herb, is endemic to the Qinghai–Tibet Plateau. A total of 188 individuals from eight natural populations of L. rotata in Qinghai–Tibet Plateau (four from Tibet, two from Yunnan, and two from Qinghai) were analyzed using intersimple sequence repeats (ISSR) and randomly amplified polymorphic DNA (RAPD) techniques. Our results revealed that the level of genetic variation in L. rotata was relatively high (P = 94.85%, I = 0.440 ± 0.220, H _T = 0.289 ± 0.028). Three genetic groups corresponding to the three geographic regions were detected, suggesting significant geographic structure. Our results suggest that the highly structured geographic pattern found in L. rotata might represent diverging evolutionary processes associated with the uplifting of the Qinghai–Tibet Plateau and Quaternary climatic oscillations. These findings imply that as many populations as possible should be preserved in situ for the conservation of this species. Given their genetic variability and peripheral distribution, Qinghai and Yunnan populations should be assigned priority for conservation. Optimal harvesting strategies, domestication and tissue culture of L. rotata should be developed as soon as possible to guarantee its sustainable use.     

Genetic diversity and structure of Lilium pumilum DC. in southeast of Qinghai–Tibet plateau

Lilium pumilum DC. is a valuable species not only for its showy flowers but also for its edible and medicinal values. As one of the distribution areas of L. pumilum, Qinghai–Tibet plateau has unique environmental features which have high impact on the evolution of the species. No population genetic studies have been done for L. pumilum so far. To provide the first reference data for evolutionary study and understanding the influence of eco-geographic factors on the distribution of genetic variation in L. pumilum, interspecific simple sequence repeat markers were used to investigate genetic diversity and population structure of 28 populations sampled from southeast of Qinghai–Tibet plateau. Fifteen selected primers generated a total of 147 polymorphic bands. The genetic diversity was low within populations (average He = 0.173), but higher at the species level (He = 0.392). A clear population structure and high level of genetic differentiation (F _ST = 0.518) were detected by unweighted pair group method for arithmetic averages, principle coordinate analysis and Bayesian clustering. All clustering approaches supported a division of the 28 populations into 4 major groups for which analysis of molecular variance confirmed a significant variation among groups (34.3 %). These population genetic parameters suggest limited gene flow among populations and evidence for isolation by distance (r = 0.272, P < 0.0001) was found in this study. Altitude, AMT and AMP explained 9.5, 11.5 and 14.0 % of the total variance among populations indicating that eco-geographic factors have a significant effect. Considering the low within-population genetic diversity, high differentiation among populations and the increasing anthropogenic pressure on the species, in situ conservation measures were recommended to preserve L. pumilum in Qinghai–Tibet plateau.     

Phylogeography of the Qinghai–Tibet Plateau endemic alpine herb Pomatosace filicula (Primulaceae)

In order to trace the response of alpine plants on the Qinghai–Tibet Plateau (QTP) to the Quaternary climate oscillations, the phylogeographic history of Pomatosace filicula Maxim. was investigated in the present study. Based on sequence variations of two maternally inherited plastid markers, matK and trnH-psbA, and the biparentally inherited nuclear ribosomal internal transcribed spacer (nrITS), we estimated the population genetic structure, lineage divergence timescale, and population dynamics of P. filicula. Seven plastid haplotypes and two nrITS genotypes were identified across the range-wide sampling of 200 individuals from 24 populations. Although AMOVA revealed a high level of differentiation among populations (F_ST = 0.560), no significant phylogeographic structure was detected (N_ST = 0.503, G_ST = 0.518, P > 0.05). Molecular dating suggested that the divergences between major plastid lineages and nrITS genotypes occurred during the early and middle Pleistocene, and the middle Pleistocene, respectively. This species most likely survived at multiple unglaciated sites on the QTP during the Last Glacial Maximum, with most of these sites located above 4000 m a.s.l. The species probably experienced range expansion at its distribution fringe, but demographic tests did not suggest significant population size changes. We proposed that pronounced effective gene flow (N_em = 0.393) and short generation time may have obscured the phylogeographic and demographic patterns of this species. Our findings will shed new light on the Quaternary evolutionary history of the alpine flora of the QTP.     

Patterns of grassland community composition and structure along an elevational gradient on the Qinghai–Tibet Plateau

青藏高原草地群落组成和结构的海拔梯度格局青藏高原高寒草地是维持区域生态安全的天然屏障,也在一定程度上造就了该区域较高的生物多样性。然而,我们对青藏高原高寒草地植物群落组成和结构的海拔分布格局及其自身维持机制仍知之甚少。本研究在青藏高原东北部沿公路形成的海拔梯度设置了39个实验样地(海拔跨度为2800–5100m),每个样地设5个调查样方进行群落调查,包括物种组成、高度、盖度,评估青藏高原高寒草地植物群落的α和β多样性的海拔梯度格局及其影响因素。研究结果发现草地群落高度随着海拔的增加而显著降低,而群落盖度变化却不显著。随着海拔的增加,植物物种丰富度(α多样性)显著增加,而群落变异性(β多样性)显著降低。约束聚类分析表明,随海拔增加草地群落结构逐渐发生变化,基于此,在这种变化过程中,我们监测到3个渐变的海拔间断点,分别在海拔3640、4252和4333 m处。结构方程模型(SEM)表明,降水增加和温度降低对α多样性有显著的正向作用,但植物群落α多样性的变化显著改变群落变异性。以上结果表明,青藏高原的群落组成和结构沿海拔梯度发生了从量变到质变的过程。     

Origin of Ostryopsis intermedia (Betulaceae) in the southeast Qinghai–Tibet Plateau through hybrid speciation

It remains unknown how Ostryopsis intermedia B. Tian & J. Q. Liu (Betulaceae) originated in the SE Qinghai–Tibet Plateau (QTP). We examined sequence variations of two maternally inherited chloroplast (cp) DNA fragments and amplified fragment length polymorphisms (AFLP) of 32 populations for this species and two congeners, O. davidiana Decne. and O. nobilis Balf. f. W. W. Sm., distributed in northern China and the SE QTP. Each of the two distinct cpDNA haplotype groups was fixed by O. davidiana or O. intermedia, respectively, whereas both were found in O. nobilis. All analyses of AFLP suggested that O. intermedia is more closely related to O. davidiana than to O. nobilis and Bayesian clustering analysis (K = 2) further suggested that the genomic composition of O. intermedia showed a slightly mosaic origin from the other two species, although mostly from O. davidiana. Analyses of AFLP indicated the highest nuclear genetic diversity for O. davidiana and lowest forO. intermedia. The origin of O. intermedia through hybrid speciation due to southward migration of O. davidiana and the following hybridization with O. nobilis may provide the most reasonable explanation for the inconsistency between phylogenetic relationships of three species and degrees of genetic diversity from cpDNA sequences or AFLP datasets. Ostryopsis intermedia may represent one more diploid hybrid species found in the QTP, although further strong tests are needed based on additional data.     

Phylogeography of an alpine aquatic herb Ranunculus bungei (Ranunculaceae) on the Qinghai–Tibet Plateau

Many phylogeographic studies of terrestrial plant species on the Qinghai–Tibet Plateau (QTP) have been carried out to elucidate the range shifts in response to climatic oscillations in the Quaternary. However, patterns of range shifts for aquatic plants following the climate change on the QTP are poorly understood. Here, we studied the historical range shifts of the aquatic herb Ranunculus bungei Steud. on the QTP using four chloroplast (cpDNA) non-coding spacers. We revealed low within-population genetic diversity (H_S = 0.052) and high interpopulation genetic differentiation (G_ST = 0.914; N_ST = 0.954). But the high population differentiation was not coupled with a distinct phylogeographic structure (N_ST > G_ST, P > 0.05). Phylogenetic analyses revealed two main cpDNA haplotype lineages and the split between these two lineages can be dated back to the late Tertiary (3.84–11.90 Ma). Two independent range expansions within the two intraspecific lineages at approximately 0.15–0.46 and 0.17–0.50 Ma were revealed. Our results suggested that R. bungei survived the Last Glacial Maximum and/or previous glacial periods on the QTP. Colonization or recolonization during the repeated range expansions may have replaced the early haplotypes and the pre-existing genetic structure and could explain the non-significant phylogeographical structure.     

Survival and reproduction of plant species in the Qinghai–Tibet Plateau

The Qinghai–Tibet Plateau (QTP) is the highest and largest plateau in the world. It covers correspondingly wide geological, topographical, and climatic gradients, and thus hosts greater biodiversity than surrounding lowlands and other high elevation regions. Due to its extreme environmental and biological diversity, the QTP is an ideal region for studying adaptations of plant species under harsh environmental conditions at multiple evolutionary levels. Many recent ecological studies have revealed functions of distinctive morphological features of various plants in the region that improve their reproductive success. Examples include large and showy bracts, hairy inflorescences, and drooping flowers. Numerous other investigations have examined QTP plants' sexual systems, patterns of biomass allocations, and biotic interactions. This paper summarizes recent advances in understanding of morphological adaptations, plant–plant interactions, plant–pollinator interactions, floral color patterns, pollination adaptations, and resource allocation patterns of alpine plants of the QTP. The overall aim is to synthesize current knowledge of the general mechanisms of plant survival and reproduction in this fascinating region.     

Genetic structure of an isolated group of the indigenous population of northern Siberia, the Nganasans (Tavginians) of Ta?mir

Demographic data of genetic interest were studied in presently living population in comparison with preseding generations of Nganasans. Decrease of sex ratio in the whole population has been revealed along with the reduction of reproductive and, possibly, effective size. The number and variance of livebirths per female were 7.29 and 9.86 respectively. Crow' index of the opportunity for selection (I) and its components (Im and If) were estimated. I was found to be 1.17, whereas Im and If--1.56 and 0.18 respectively. Linear pattern of settling in the past as well as the type of migration between adjoining subpopulations depended on culture and economy of arctic reindeer hunters as well as landscape character.     

Plant diversity and ecology on the Qinghai–Tibet Plateau

The Qinghai–Tibet Plateau (QTP) comprises a platform (sometimes called the Qinghai–Tibet Plateau sensu stricto), the Himalayas, and Hengduan Mountains (Liang et al.,2018; Mao et al.,2021). The latter two parts and adjacent highlands are also called the Pan-Himalaya. Numerous plants are distributed there with many endemic species, probably because of the high diverse landscapes created by continuous geological and climatic activities (Favre et al.,2015; Mao et al.,2021). As the well known biodiversity hotspot of the alpine plants in the world (Sun et al.,2017), many studies have been conducted on evolutionary origin and ecological adaptation of those species occurring in the QTP (e.g., Wen et al.,2014, 2019; Zhang et al.,2019). In the present special issue, we collected 15 related papers on this topic. Among them, two are invited reviews. Mao et al. (2021) provide a comprehensive review of evolutionary origin of species diversity on the QTP. Especially, they outlined major disputes and likely causes in this research topic, including circumscribing and naming the QTP, the QTP uplifts, dating of molecular phylogenetic trees, non-causal correlations between QTP uplifts and species diversification and the unified ice sheet. The authors also summarized genomic advancements related to high-altitude adaptation of both plants and animals. Tong et al. (2021) reviewed the reproductive strategies of animal-pollinated alpine plants on the QTP, involving pollination system, pollen limitation, self-pollination, and sexual system. In this region, 95.4% of animal-pollinated plants are pollinated by insects (i.e., bees, moths, butterflies, and flies) with only 4% by vertebrates (i.e., bats and birds). Self-pollination through self-compatibility shift from outcrossing has become an effective reproductive strategy to overcome pollen limitation in alpine plants. The other 13 research papers aimed to address origin and adaptation of alpine flora involving three major lines of evidence: genomics, ecology, and paleobotany. We hope that the collection of these papers will increase our understanding of the origin, speciation, and adaptation of alpine species on the QTP.     

Genetic variation and population structure of “Zangli” pear landraces in Tibet revealed by SSR markers

Pear (Pyrus L.) is one of the most important fruits in temperate regions. Even in the mountainous border region of Tibet, Sichuan, and Yunnan Provinces (China), a variety of highly adapted pear landraces were discovered in Tibetan Autonomous Prefecture and were named “Zangli pears.” Here, we analyzed genetic diversity of 29 genotypes of Zangli distributed in Tibetan Region, together with 30 genotypes of sand pear (P. pyrifolia) in border regions, and 8 genotypes of P. ussuriensis as out groups, using simple sequence repeats (SSR) markers. Twenty-eight SSR markers displayed high polymorphism with a total of 202 alleles. Cluster analysis revealed a close genetic relationship between Zangli and sand pears, while population structure analysis revealed that gene flow between the western and eastern side of the Jin-sha River was restricted by geographic isolation. Diversity statistics for five geographic groups implied a migration event from Sichuan and Yunnan Provinces to the border region of western Sichuan, eastern Tibet, and northwestern Yunnan Provinces. Six specific genetic alleles in Zangli pear landraces might be related to their adaption to severe environmental conditions.     

Hymenobacter tibetensis sp. nov., a UV-resistant bacterium isolated from Qinghai–Tibet plateau

A brick-red-pigmented strain (XTM003^T) isolated from the Qinghai–Tibet plateau was investigated using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequence indicated that the organism belonged to the genus Hymenobacter. The predominant menaquinone was MK7. The major fatty acids included iso-15:0, 16:1w5c and summed feature 3 (C_{16: 1}ω7c and/or C_{16: 1}ω6c). The G+C content of the DNA was 55.8%. In addition, DNA–DNA hybridization studies demonstrated that strain XTM003^T had a relatedness value of 50.7% with the phylogenetically most closely related species Hymenobacter norwichensis DSM 15439^T. Based on the results of phenotypic characteristics and DNA–DNA hybridization studies, strain XTM003^T is considered to represent a novel species, for which the name Hymenobacter tibetensis sp. nov. is proposed. The type strain is XTM003^T (=CCTCC AB 207089^T=NRRL B-51271^T).     

Evolutionary history and underlying adaptation of alpine plants on the Qinghai–Tibet Plateau

As the highest and largest plateau in the world, the Qinghai–Tibet Plateau, with its numerous endemic species, is one of the important alpine biodiversity hotspots. Only recently have the evolutionary histories and underlying adaptations of these alpine plants become clear, through research mostly based on testable experiments and analyses. In this issue, we collected a total of 13 papers related to such aims. In addition, we selected a few published papers to highlight the major findings in the recent past. We also outlined the outlook and direction of future research.     

Phylogeny of the Rhizobium–Allorhizobium–Agrobacterium clade supports the delineation of Neorhizobium gen. nov.

The genera Agrobacterium, Allorhizobium, and Rhizobium belong to the family Rhizobiaceae. However, the placement of a phytopathogenic group of bacteria, the genus Agrobacterium, among the nitrogen-fixing bacteria and the unclear position of Rhizobium galegae have caused controversy in previous taxonomic studies. To resolve uncertainties in the taxonomy and nomenclature within this family, the phylogenetic relationships of generic members of Rhizobiaceae were studied, but with particular emphasis on the taxa included in Agrobacterium and the “R. galegae complex” (R. galegae and related taxa), using multilocus sequence analysis (MLSA) of six protein-coding housekeeping genes among 114 rhizobial and agrobacterial taxa. The results showed that R. galegae, R. vignae, R. huautlense, and R. alkalisoli formed a separate clade that clearly represented a new genus, for which the name Neorhizobium is proposed. Agrobacterium was shown to represent a separate cluster of mainly pathogenic taxa of the family Rhizobiaceae. A. vitis grouped with Allorhizobium, distinct from Agrobacterium, and should be reclassified as Allorhizobium vitis, whereas Rhizobium rhizogenes was considered to be the proper name for former Agrobacterium rhizogenes. This phylogenetic study further indicated that the taxonomic status of several taxa could be resolved by the creation of more novel genera.     

Diversity and distribution of alkaliphilic psychrotolerant bacteria in the Qinghai–Tibet Plateau permafrost region

The Qinghai–Tibet Plateau represents a unique permafrost environment, being a result of high elevation caused by land uplift. And the urgency was that plateau permafrost was degrading rapidly under the current predicted climatic warming scenarios. Hence, the permafrost there was sampled to recover alkaliphilic bacteria populations. The viable bacteria on modified PYGV agar were varied between 10² and 10⁵ CFU/g of dry soil. Forty-eight strains were gained from 18 samples. Through amplified ribosomal DNA restriction analysis (ARDRA) and phylogenetic analyses, these isolates fell into three categories: high G + C gram positive bacteria (82.3%), low G + C gram positive bacteria (7.2%), and gram negative α-proteobacteria (10.5%). The strains could grow at pH values ranging from 6.5 to 10.5 with optimum pH in the range of 9–9.5. Their growth temperatures were below 37°C and the optima ranging from 10 to 15°C. All strains grew well when NaCl concentration was below 15%. These results indicate that there are populations of nonhalophilic alkaliphilic psychrotolerant bacteria within the permafrost of the Qinhai-Tibet plateau. The abilities of many of the strains to produce extracellular protease, amylase and cellulase suggest that they might be of potential value for biotechnological exploitation.     

High uncertainties detected in the wetlands distribution of the Qinghai–Tibet Plateau based on multisource data

Landscape and Ecological Engineering - Twenty wetland-related data products (including remote sensing datasets, compilation datasets and model simulation datasets) were collected to evaluate the...     

Phylogenomics and rapid diversification of the genus Eutrema on the Qinghai–Tibet Plateau and adjacent regions

Both geographic isolation and polyploidization are assumed to play an important role in driving species diversification. However, this is rarely illustrated through phylogenomic analyses. The genus Eutrema (Brassicaceae), which also includes the salt-resistant species, are distributed mainly in Asia with extensive species diversification in the Qinghai–Tibet Plateau (QTP) and adjacent regions. In this study, we revealed almost fully resolved backbone relationships of the genus with genome re-sequencing data for genomes of 168 individuals from 28 species. Phylogenetic analyses of both plastomes and single-copy nuclear genes from the whole genome recovered six well-supported clades with almost consistent relationships. The first two clades are mainly distributed in central China and central Asia, while the other four in the QTP and adjacent regions. All of them diversified within 12 million years. Within each clade, we recovered numerous conflicts in the interspecific relationships between nuclear and plastome phylogenies, likely suggesting hybridization and incomplete lineage sorting during species diversification. Our estimation of genome size and comparison of the number of the single-copy nuclear genes demonstrated frequent occurrences of polyploids in the genus. Except for an establishment of the backbone phylogeny, our phylogenomic analyses suggest that in addition to strong geographic isolation, polyploidization may have played an important role in species diversification of this genus.     

Genetic diversity and population structure of North America’s rarest heron, the reddish egret (Egretta rufescens)

The global distribution of the reddish egret is characterized by disjunct colonies occurring from the Pacific side of Northwest Mexico to the Caribbean. We examined distantly isolated colonies of reddish egret to determine global population genetic structure. We used seven polymorphic microsatellites to accomplish five goals: (1) to assess range wide population differentiation among reddish egret (Egretta rufescens) populations, (2) identify extent of gene flow, (3) determine any historical occurrence of bottlenecks, (4) assess genetic differentiation between color morphs, (5) clarify subspecies status of E. r. dickeyi, a completely dark morph population located in and around the Baja California peninsula, Mexico. Genetic differentiation was dramatic (global Fst = 0.161) throughout the reddish egrets range extending from Baja California, Mexico to Great Inagua, Bahamas. Differentiation occurred among three distinct regions (Fst = 0.238) but not among colonies/islands within regions suggesting regional philopatry. Genetic diversity (alleles per locus, and heterozygosity) in Baja California Sur, Mexico and Great Inagua, Bahamas populations is lower than in the Texas/Mexico population due to minimal dispersal between regions and smaller population sizes. Dark and white color morphs when present within the same region showed no differentiation. Patterns of recent population bottlenecks are not evident in each of the three regional populations. With evidence of limited gene flow in addition to low genetic diversity and prospects of habitat loss we recommend that reddish egrets be managed as three distinct or evolutionary significant units.     

Hunter–Gatherer population structure and the evolution of contingent cooperation

Unlike other vertebrates, humans cooperate in large groups with unrelated individuals. Many authors have argued that the evolution of such cooperation has resulted from reciprocity and other forms of contingent cooperation. This argument is not well supported by existing theory. The theory of contingent cooperation in pairs is well developed: reciprocating strategies are stable when common, and can increase when rare as long as population structure leads to modest levels of relatedness. In larger groups, however, it is not clear whether contingent cooperation can increase when rare. Existing work suggests that contingent strategies cannot increase unless relatedness is high, but depends on unrealistic assumptions about the effects of population structure. Here we develop and analyze a model incorporating a two level population structure that captures important features of human hunter–gatherer societies. This model suggests that previous work underestimates the range of conditions under which contingent cooperation can evolve, but also predicts that cooperation will not evolve unless (1) social groups are small, and (2) the relatedness within ethnolinguistic groups is at the high end of the range of empirical estimates.