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Chen J, Wang S, Wang D, Chiu Y, Yang N, Lian X, Zhao Z, Wei Q. Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species. Front Genet 2024; 15:1302554. [PMID: 38425715 PMCID: PMC10902437 DOI: 10.3389/fgene.2024.1302554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Introduction: The Tibetan antelope (Pantholops hodgsonii) is a remarkable mammal thriving in the extreme Qinghai-Tibet Plateau conditions. Despite the availability of its genome sequence, limitations in the scaffold-level assembly have hindered a comprehensive understanding of its genomics. Moreover, comparative analyses with other Bovidae species are lacking, along with insights into genome rearrangements in the Tibetan antelope. Methods: Addressing these gaps, we present a multifaceted approach by refining the Tibetan Antelope genome through linkage disequilibrium analysis with data from 15 newly sequenced samples. Results: The scaffold N50 of the refined reference is 3.2 Mbp, surpassing the previous version by 1.15-fold. Our annotation analysis resulted in 50,750 genes, encompassing 29,324 novel genes not previously study. Comparative analyses reveal 182 unique rearrangements within the scaffolds, contributing to our understanding of evolutionary dynamics and species-specific adaptations. Furthermore, by conducting detailed genomic comparisons and reconstructing rearrangements, we have successfully pioneered the reconstruction of the X-chromosome in the Tibetan antelope. Discussion: This effort enhances our comprehension of the genomic landscape of this species.
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Affiliation(s)
- Jiarui Chen
- College of Eco‐Environmental Engineering, Qinghai University, Xining, Qinghai, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
| | - Shuwen Wang
- College of Eco‐Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Dong Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
- School of Geographical Science, Qinghai Normal University, Xining, Qinghai, China
| | - Yunkang Chiu
- Shenzhen Byoryn Technology Co., Ltd., Shenzhen, China
| | - Nan Yang
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xinming Lian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai, China
| | - Zicheng Zhao
- Shenzhen Byoryn Technology Co., Ltd., Shenzhen, China
| | - Qing Wei
- College of Eco‐Environmental Engineering, Qinghai University, Xining, Qinghai, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
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Li P, Zhang H, Yang D, Gong C, Wu D, Sun Y, Liu Y, Tang J, Hu H, Zhaxi Q, Xu W, Su L, Li Y, Wu X. Vigilance behaviour during the calving season in female Tibetan antelopes ( Pantholopshodgsonii). Biodivers Data J 2023; 11:e107957. [PMID: 37711367 PMCID: PMC10498271 DOI: 10.3897/bdj.11.e107957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/22/2023] [Indexed: 09/16/2023] Open
Abstract
Tibetan antelopes (Pantholopshodgsonii) migrate great distances to specific delivery and calving areas. In the current study, we investigated calving site selection and vigilance behaviour during delivery and nursing in migratory female Tibetan antelopes at Zonag Lake. According to observations and analysis, the females were distributed south of Zonag Lake, where vegetation was abundant. We determined their dates of migration (crossing the Qinghai-Tibet Highway observation site), showing a shift of one month during the period from June in 2008 to May 2021. Results also showed that 81.4% of females expressed high vigilance behaviour during calving and nursing compared to those without calves (7.1%). From delivery until calf standing, females were highly vigilant and spent considerable time scanning, with 96% of females showing vigilance behaviour. Females with calves (average 9.94 ± 0.62 s) spent more time on vigilance behaviour than females without calves (average 6.25 ± 1.38 s). Females with newborns spent the greatest amount of time being vigilant (average 51.63 ± 4.24 s). These results not only identify basic Tibetan antelope calving behaviour, but also provide scientific analysis and evidence for further ethological research on female Tibetan antelopes.
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Affiliation(s)
- Peiwei Li
- Shaanxi Institute of Zoology, xi'an, ChinaShaanxi Institute of Zoologyxi'anChina
| | - Hongfeng Zhang
- Shaanxi Institute of Zoology, xi'an, ChinaShaanxi Institute of Zoologyxi'anChina
| | - Dongdong Yang
- Shaanxi Institute of Zoology, xi'an, ChinaShaanxi Institute of Zoologyxi'anChina
| | - Congran Gong
- Shaanxi Institute of Zoology, xi'an, ChinaShaanxi Institute of Zoologyxi'anChina
| | - Dong Wu
- Shaanxi Institute of Zoology, xi'an, ChinaShaanxi Institute of Zoologyxi'anChina
| | - Yuting Sun
- Shaanxi Institute of Zoology, xi'an, ChinaShaanxi Institute of Zoologyxi'anChina
| | - Yan Liu
- Shaanxi Institute of Zoology, xi'an, ChinaShaanxi Institute of Zoologyxi'anChina
| | - Junqing Tang
- School of Urban Planning and Design, Shenzhen Graduate School, Peking University, Shenzhen, ChinaSchool of Urban Planning and Design, Shenzhen Graduate School, Peking UniversityShenzhenChina
| | - Han Hu
- Shaanxi Institute of Zoology, xi'an, ChinaShaanxi Institute of Zoologyxi'anChina
| | - Qiupei Zhaxi
- Hoh Xil Nature Reserve service, Golmud, ChinaHoh Xil Nature Reserve serviceGolmudChina
| | - Wei Xu
- Three-River-Source National Park Service, Xining, ChinaThree-River-Source National Park ServiceXiningChina
| | - Lina Su
- Shaanxi Institute of Zoology, xi'an, ChinaShaanxi Institute of Zoologyxi'anChina
| | - Yinhu Li
- Shaanxi Institute of Zoology, xi'an, ChinaShaanxi Institute of Zoologyxi'anChina
| | - Xiaomin Wu
- Shaanxi Institute of Zoology, xi'an, ChinaShaanxi Institute of Zoologyxi'anChina
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Phylogeography of the Plateau Pika (Ochotona curzoniae) in Response to the Uplift of the Qinghai-Tibet Plateau. DIVERSITY 2023. [DOI: 10.3390/d15020307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The evolution and current distribution of species on the Qinghai-Tibet Plateau have been significantly impacted by historical occurrences, including the uplift of the plateau and the Quaternary climate upheaval. As a remnant species, the plateau pika (Ochotona curzoniae) is a great model for researching historical events. In this study, 302 samples from 42 sample sites were utilized to analyze the impact of historical events on the evolution and distribution pattern of plateau pikas. The genetic diversity, patterns of differentiation, and historical dynamics of the plateau pika were investigated using molecular markers that included four mitochondrial genes (COI, D-loop, Cytb, and 12S rRNA) and three nuclear genes (GHR, IRBP, and RAG1). The results showed that: (1) The genetic diversity of the plateau pika was high in the Tibetan Plateau (Hd = 0.9997, π = 0.01205), and the plateau pika evolved into five lineages that occupied different geographical areas, with lineage 1 (Group 1) in the south of the Yarlung Zangbo River, lineage 2 (Group 2) in the hinterland of the plateau, lineage 3 (Group 3) in the northeastern part of the plateau, lineage 4 (Group 4) in the Hengduan Mountains, and lineage 5 (Group 5) in the eastern part of the plateau. (2) The gene flow among the five lineages was low, and the differentiation level was high (Nm < 0.25; Fst > 0.25), indicating that the geographical barriers between the five lineages, such as the Yarlung Zangbo River, the Qaidam-Ghuong-Guide Basin, and the Lancang River, effectively promoted the population differentiation of the plateau pika. (3) The plateau pika first spread from the Hengduan Mountains to the entire Qinghai-Tibet Plateau and then conducted small-scale migration and dispersal in several refuges across the plateau in response to climate changes during the glacial and interglacial periods. (4) Except for Group 1 and Group 4, all the other populations exhibited a rapid expansion between 0.06 and 0.01 Mya, but the expansion was considerably delayed or halted by the effects of climate change during the last glacial maximum (0.02 Mya). Overall, the plateau pika on the Qinghai-Tibet Plateau exhibits high genetic diversity, and topographic obstacles, including mountains, valleys, and basins, created by the uplift of the plateau and climatic changes since the Quaternary period have played an important role in the differentiation and historical dynamics of the plateau pika population.
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Fei J, Liu M, Zhang S, Chen X, Zhang S. Technical note: A protein analysis-based method for identifying shahtoosh. Forensic Sci Int 2022; 336:111341. [DOI: 10.1016/j.forsciint.2022.111341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 12/15/2021] [Accepted: 05/06/2022] [Indexed: 11/04/2022]
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Joshi B, Lyngdoh S, Singh SK, Sharma R, Kumar V, Tiwari VP, Dar SA, Maheswari A, Pal R, Bashir T, Reshamwala HS, Shrotriya S, Sathyakumar S, Habib B, Kvist L, Goyal SP. Revisiting the Woolly wolf (Canis lupus chanco) phylogeny in Himalaya: Addressing taxonomy, spatial extent and distribution of an ancient lineage in Asia. PLoS One 2020; 15:e0231621. [PMID: 32298359 PMCID: PMC7162449 DOI: 10.1371/journal.pone.0231621] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 03/27/2020] [Indexed: 11/23/2022] Open
Abstract
Of the sub-species of Holarctic wolf, the Woolly wolf (Canis lupus chanco) is uniquely adapted to atmospheric hypoxia and widely distributed across the Himalaya, Qinghai Tibetan Plateau (QTP) and Mongolia. Taxonomic ambiguity still exists for this sub-species because of complex evolutionary history anduse of limited wild samples across its range in Himalaya. We document for the first time population genetic structure and taxonomic affinity of the wolves across western and eastern Himalayan regions from samples collected from the wild (n = 19) using mitochondrial control region (225bp). We found two haplotypes in our data, one widely distributed in the Himalaya that was shared with QTP and the other confined to Himachal Pradesh and Uttarakhand in the western Himalaya, India. After combining our data withpublished sequences (n = 83), we observed 15 haplotypes. Some of these were shared among different locations from India to QTP and a few were private to geographic locations. A phylogenetic tree indicated that Woolly wolves from India, Nepal, QTP and Mongolia are basal to other wolves with shallow divergence (K2P; 0.000-0.044) and high bootstrap values. Demographic analyses based on mismatch distribution and Bayesian skyline plots (BSP) suggested a stable population over a long time (~million years) with signs of recent declines. Regional dominance of private haplotypes across its distribution range may indicate allopatric divergence. This may be due to differences in habitat characteristics, availability of different wild prey species and differential deglaciation within the range of the Woolly wolf during historic time. Presence of basal and shallow divergence within-clade along with unique ecological requirements and adaptation to hypoxia, the Woolly wolf of Himalaya, QTP, and Mongolian regions may be considered as a distinct an Evolutionary Significant Unit (ESU). Identifying management units (MUs) is needed within its distribution range using harmonized multiple genetic data for effective conservation planning.
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Affiliation(s)
| | | | | | - Reeta Sharma
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | - Vinay Kumar
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | | | - S. A. Dar
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | | | - Ranjana Pal
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | - Tawqir Bashir
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | | | | | - S. Sathyakumar
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | - Bilal Habib
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | - Laura Kvist
- Department of Biology, University of Oulu, Oulu, Finland
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Kabbara S, Hérivaux A, Dugé de Bernonville T, Courdavault V, Clastre M, Gastebois A, Osman M, Hamze M, Cock JM, Schaap P, Papon N. Diversity and Evolution of Sensor Histidine Kinases in Eukaryotes. Genome Biol Evol 2019; 11:86-108. [PMID: 30252070 PMCID: PMC6324907 DOI: 10.1093/gbe/evy213] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2018] [Indexed: 12/20/2022] Open
Abstract
Histidine kinases (HKs) are primary sensor proteins that act in cell signaling pathways generically referred to as "two-component systems" (TCSs). TCSs are among the most widely distributed transduction systems used by both prokaryotic and eukaryotic organisms to detect and respond to a broad range of environmental cues. The structure and distribution of HK proteins are now well documented in prokaryotes, but information is still fragmentary for eukaryotes. Here, we have taken advantage of recent genomic resources to explore the structural diversity and the phylogenetic distribution of HKs in the prominent eukaryotic supergroups. Searches of the genomes of 67 eukaryotic species spread evenly throughout the phylogenetic tree of life identified 748 predicted HK proteins. Independent phylogenetic analyses of predicted HK proteins were carried out for each of the major eukaryotic supergroups. This allowed most of the compiled sequences to be categorized into previously described HK groups. Beyond the phylogenetic analysis of eukaryotic HKs, this study revealed some interesting findings: 1) characterization of some previously undescribed eukaryotic HK groups with predicted functions putatively related to physiological traits; 2) discovery of HK groups that were previously believed to be restricted to a single kingdom in additional supergroups, and 3) indications that some evolutionary paths have led to the appearance, transfer, duplication, and loss of HK genes in some phylogenetic lineages. This study provides an unprecedented overview of the structure and distribution of HKs in the Eukaryota and represents a first step toward deciphering the evolution of TCS signaling in living organisms.
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Affiliation(s)
- Samar Kabbara
- Groupe d’Etude des Interactions Hôte-Pathogène, GEIHP, EA3142, Université d’Angers, SFR 4208 ICAT, France
| | - Anaïs Hérivaux
- Groupe d’Etude des Interactions Hôte-Pathogène, GEIHP, EA3142, Université d’Angers, SFR 4208 ICAT, France
| | | | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université François Rabelais de Tours, France
| | - Marc Clastre
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université François Rabelais de Tours, France
| | - Amandine Gastebois
- Groupe d’Etude des Interactions Hôte-Pathogène, GEIHP, EA3142, Université d’Angers, SFR 4208 ICAT, France
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - J Mark Cock
- Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, UPMC Université Paris 06, CNRS, Roscoff, France
| | - Pauline Schaap
- School of Life Sciences, University of Dundee, United Kingdom
| | - Nicolas Papon
- Groupe d’Etude des Interactions Hôte-Pathogène, GEIHP, EA3142, Université d’Angers, SFR 4208 ICAT, France
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Chen J, Lin G, Qin W, Yan J, Zhang T, Su J. The roles of calving migration and climate change in the formation of the weak genetic structure in the Tibetan antelope (Pantholops hodgsonii). Integr Zool 2018; 14:248-258. [PMID: 29851262 DOI: 10.1111/1749-4877.12334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Geographical barriers and distance can reduce gene exchange among animals, resulting in genetic divergence of geographically isolated populations. The Tibetan antelope (Pantholops hodgsonii) has a geographical range of approximately 1600 km across the Qinghai-Tibet Plateau, which comprises a series of tall mountains and big rivers. However, previous studies indicate that there is little genetic differentiation among their geographically delineated populations. To better understand the genetic structure of P. hodgsonii populations, we collected 145 samples from the 3 major calving regions, taking into consideration their various calving grounds and migration routes. We used a combination of mitochondrial sequences (Cyt b, ATPase, D-loop and COX I) to investigate the genetic structure and the evolutionary divergence of the populations. Significant, albeit weak, genetic differentiation was detected among the 3 geographical populations. Analysis of the genetic divergence process revealed that the animals gradually entered a period of rapid genetic differentiation approximately 60 000 years ago. The calving migration of P. hodgsonii cannot be the main cause of their weak genetic structure because this cannot fully homogenize the genetic pool. Instead, the geological and climatic events as well as the coupling vegetation succession process during this period have been suggested to greatly contribute to the genetic structure and the expansion of genetic diversity.
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Affiliation(s)
- Jiarui Chen
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Gonghua Lin
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
| | - Wen Qin
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jingyan Yan
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Tongzuo Zhang
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
| | - Jianping Su
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
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Joshi BD, Matura R, M A P, De R, Pandav B, Sharma V, Nigam P, Goyal SP. Palghat gap reveals presence of two diverged populations of Nilgiri tahr ( Nilgiritragus hylocrius) in Western Ghats, India. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:245-249. [PMID: 33474132 PMCID: PMC7800121 DOI: 10.1080/23802359.2018.1436990] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genetic analysis is an important tool in understanding population structure, genetic diversity, and phylogenetics of endangered species likely to be affected by microevolution and anthropogenic factors. Western Ghats landscape is one of the identified biodiversity hotspots in India, and micro-evolutionary processes are observed in this landscape due to the presence of the gaps in the mountain ranges. Nilgiri tahr is endemic to and distributed in this landscape while very little is known about genetic characteristics, population structure and impact of these gaps on the species. In the present study, two different populations of Nilgiri tahr from the north (NPG) and south (SPG) of Palghat gap (PG) were studied using the cytochrome b gene (Cyt b; 310 bp) of mtDNA genome in the Western Ghats, India. Two variable sites were observed in the Cyt b fragment while the mean pairwise genetic distance between these two populations was 0.007. All the samples phylogenetically clustered in either north or south of PG. The presence of shallow divergence indicates the presence of suitable habitat in past which may have facilitated movement between NPG and SPG. A subsequent change in Paleo-climatic conditions and gradual formation of PG may have resulted in population diversification during the Pleistocene. Besides, Forensically Informative Nucleotide Sequence (FINS) observed would help in geo-assigning any individual from NPG or SPG to understand the likely influences on population demography due to poaching.
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Affiliation(s)
| | - Rakesh Matura
- Wildlife Institute of India, Dehradun, Uttakrakhand, India
| | - Predit M A
- Wildlife Institute of India, Dehradun, Uttakrakhand, India
| | - Rahul De
- Wildlife Institute of India, Dehradun, Uttakrakhand, India
| | - Bivash Pandav
- Wildlife Institute of India, Dehradun, Uttakrakhand, India
| | - Vipin Sharma
- Wildlife Institute of India, Dehradun, Uttakrakhand, India
| | - Parag Nigam
- Wildlife Institute of India, Dehradun, Uttakrakhand, India
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Ahmad K, Kumar VP, Joshi BD, Raza M, Nigam P, Khan AA, Goyal SP. Genetic diversity of the Tibetan antelope (Pantholops hodgsonii) population of Ladakh, India, its relationship with other populations and conservation implications. BMC Res Notes 2016; 9:477. [PMID: 27769305 PMCID: PMC5073904 DOI: 10.1186/s13104-016-2271-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 10/08/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Tibetan antelope (Pantholops hodgsonii), or chiru, is an endangered antelope, distributed in China [Xinjiang, Xizang, Qinghai, Zhuolaihu Lake (Breeding habitat)], and India (Aksai Chin and Ladakh). There is a global demand for the species prized wool, which is used in weaving shahtoosh shawls. Over the years, the population of the Tibetan antelope has drastically declined from more than a million to a few thousand individuals, mainly due to poaching. Field studies undertaken in Ladakh, India also indicated winter migration of the population to Tibet. Migration between winter and calving habitats is well established to be female-biased across the Qinghai Tibetan Plateau (QTP). For effective conservation planning, genetic characterization is considered the best way to understand the likely impact of threats for ensuring the long-term viability of the population. In this regard, genetic characteristics of all Chinese populations are well-studied using mitochondrial and microsatellite markers, but information is lacking for the Indian population. Therefore, using the control region marker, we document for the first time the genetic variation of the Indian population of the Tibetan antelope, the extent of migration and its relationships with other populations of China. RESULTS The partial fragment of control region (259 bp) marker was successfully amplified in 30 Tibetan antelope samples that were collected from the Chang Chenmo Valley in eastern Ladakh, India. We also retrieved control region sequences (n = 88) available in the public domain from GenBank of different Chinese populations. Low levels of nucleotide (π; 0.004) and haplotype (hd; 0.543) diversity were observed in the Indian population when compared to Chinese populations (π = 0.01357-0.02048 and hd = 0.889-0.986). Commonly used indices (Tajima's D and Fu's Fs) were analyzed for inferring the demographic history of the Indian populations, and all values were negative indicating population expansion or demographic equilibrium, though nonsignificant. We observed five haplotypes in the Indian population, and these were not reported in previously studied populations of QTP. Bayesian-based phylogenetic analysis indicates the presence of four clades, however, the posterior probability support for three of these clades is weak (<0.5). Of these, the Indian population formed a distinct clade, whereas the Chinese populations exhibited shared haplotypes, and no geographic structure was observed. Median-joining network analysis was conducted for 46 haplotypes in the overall population, except the samples from India which showed a star-like topology. The Indian population is separated by one median vector from the Chinese population. CONCLUSIONS The present study revealed the presence of different sub-clades in the Bayesian phylogenetic tree and five new haplotypes only in the Indian population or sampling location. Furthermore, in the phylogenetic tree, Indian haplotypes of Tibetan antelopes were clustered with the haplotype reported in the Chinese population of the Xinjiang region. Median-joining network analysis showed shared haplotypes pattern in all populations of QTP except the samples from India which showed new haplotypes. Given the presence of low nucleotide and haplotype diversity in eastern Ladakh populations and limited information available for populations of the western side in its range, we suggest to include genetic studies of Tibetan antelope populations around Aksai Chin (Fig. 1) under the proposed transboundary agenda between India and China and assess relationships with other populations. Such understanding would enable the planning of conservation strategies for ensuring long-term survival of westernmost populations in its range, and if required, it would establish connectivity with the other populations.
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Affiliation(s)
- Khursheed Ahmad
- Centre for Mountain Wildlife Sciences, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, Jammu and Kashmir 190006 India
| | - Ved P. Kumar
- Wildlife Forensic and Conservation Genetics Cell, Wildlife Institute of India, Post Box #18, Chandrabani, Dehradun, Uttarakhand 248001 India
| | - Bheem Dutt Joshi
- Wildlife Forensic and Conservation Genetics Cell, Wildlife Institute of India, Post Box #18, Chandrabani, Dehradun, Uttarakhand 248001 India
| | - Mohamed Raza
- Centre for Mountain Wildlife Sciences, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, Jammu and Kashmir 190006 India
| | - Parag Nigam
- Wildlife Health Managment, Wildlife Institute of India, Post Box #18, Chandrabani, Dehradun, Uttarakhand 248001 India
| | - Anzara Anjum Khan
- Centre for Mountain Wildlife Sciences, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, Jammu and Kashmir 190006 India
| | - Surendra P. Goyal
- Wildlife Forensic and Conservation Genetics Cell, Wildlife Institute of India, Post Box #18, Chandrabani, Dehradun, Uttarakhand 248001 India
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Liu W, Zhao Y, You J, Qi D, Zhou Y, Chen J, Song Z. Morphological and Genetic Variation along a North-to-South Transect in Stipa purpurea, a Dominant Grass on the Qinghai-Tibetan Plateau: Implications for Response to Climate Change. PLoS One 2016; 11:e0161972. [PMID: 27580056 PMCID: PMC5006974 DOI: 10.1371/journal.pone.0161972] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/15/2016] [Indexed: 02/06/2023] Open
Abstract
Estimating the potential of species to cope with rapid environmental climatic modifications is of vital importance for determining their future viability and conservation. The variation between existing populations along a climatic gradient may predict how a species will respond to future climate change. Stipa purpurea is a dominant grass species in the alpine steppe and meadow of the Qinghai-Tibetan Plateau (QTP). Ecological niche modelling was applied to S. purpurea, and its distribution was found to be most strongly correlated with the annual precipitation and the mean temperature of the warmest quarter. We established a north-to-south transect over 2000 km long on the QTP reflecting the gradients of temperature and precipitation, and then we estimated the morphological by sampling fruited tussocks and genetic divergence by using 11 microsatellite markers between 20 populations along the transect. Reproductive traits (the number of seeds and reproductive shoots), the reproductive-vegetative growth ratio and the length of roots in the S. purpurea populations varied significantly with climate variables. S. purpurea has high genetic diversity (He = 0.585), a large effective population size (Ne >1,000), and a considerable level of gene flow between populations. The S. purpurea populations have a mosaic genetic structure: some distant populations (over 1000 km apart) clustered genetically, whereas closer populations (< 100 km apart) had diverged significantly, suggesting local adaptation. Asymmetrical long-distance inter-population gene flow occurs along the sampling transect and might be mediated by seed dispersal via migratory herbivores, such as the chiru (Pantholops hodgsonii). These findings suggest that population performance variation and gene flow both facilitate the response of S. purpurea to climate change.
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Affiliation(s)
- Wensheng Liu
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
- College of Environment Science and Engineering, Southwest Forestry University, Kunming, China
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, China
| | - Yao Zhao
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Jianling You
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Danhui Qi
- College of Environment Science and Engineering, Southwest Forestry University, Kunming, China
| | - Yin Zhou
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Jiakuan Chen
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Zhiping Song
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
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Okada A, Ito TY, Buuveibaatar B, Lhagvasuren B, Tsunekawa A. Genetic structure in Mongolian gazelles based on mitochondrial and microsatellite markers. Mamm Biol 2015. [DOI: 10.1016/j.mambio.2015.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Hu J, Jiang Z, Chen J, Qiao H. Niche divergence accelerates evolution in Asian endemic Procapra gazelles. Sci Rep 2015; 5:10069. [PMID: 25951051 PMCID: PMC4423425 DOI: 10.1038/srep10069] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 02/23/2015] [Indexed: 12/01/2022] Open
Abstract
Ecological niche divergence and adaptation to new environments are thought to play important roles in driving speciation. Whether recently evolved species show evidence for niche divergence or conservation is vital towards understanding the role of ecology in the process of speciation. The genus Procapra is an ancient, monophyletic lineage endemic to Asia that contains three extant species (P. gutturosa, P. przewalskii and P. picticaudata). These species mainly inhabit the Qinghai-Tibetan and Mongolian Plateaus, and today have primarily allopatric distributions. We applied a series of geographic information system-based analyses to test for environmental variation and niche divergence among these three species. We found substantial evidence for niche divergence in species' bioclimatic preferences, which supports the hypothesis that niche divergence accelerates diversification in Procapra. Our results provide important insight into the evolutionary history of ungulates in Asia and help to elucidate how environmental changes accelerate lineage diversification.
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Affiliation(s)
- Junhua Hu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhigang Jiang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Chen
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Huijie Qiao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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Bei Y, Chen W, Sun B, Li J, Lai J, Meng S. Population structure of the endangered Hume's pheasant (Syrmaticus humiae) inferred from a partial sequence of the mitochondrial DNA control region. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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