1
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Joshi BD, Kumar V, De R, Sharma R, Bhattacharya A, Dolker S, Pal R, Kumar VP, Sathyakumar S, Adhikari BS, Habib B, Goyal SP. Mitochondrial cytochrome b indicates the presence of two paraphyletic diverged lineages of the blue sheep Pseudois nayaur across the Indian Himalaya: conservation implications. Mol Biol Rep 2022; 49:11177-11186. [PMID: 36097126 DOI: 10.1007/s11033-022-07832-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 06/30/2022] [Accepted: 07/29/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND Populations exhibit signatures of local adaptive traits due to spatial and environmental heterogeneity resulting in microevolution. The blue sheep is widely distributed across the high Asian mountains and are the snow leopard's principal prey species. These mountains differ in their evolutionary history due to differential glaciation and deglaciation periods, orography, and rainfall patterns, and such factors causes diversification in species. METHODS AND RESULTS Therefore, we assess the phylogeographic status of blue sheep using the mitochondrial cytochrome b gene (220 bp) across the Indian Himalayan region (IHR) and its relationship with other populations. Of the observed five haplotypes, two and three were from the western Himalayas (WH) and eastern Himalayas (EH) respectively. One of the haplotypes from WH was shared with the population of Pamir plateau, suggesting historical maternal connectivity between these areas. The phylogenetic analyses split the blue sheep into two paraphyletic clades, and western and eastern populations of IHR were within the Pamir and Tibetan plateau clades, respectively. We observed a relatively higher mean sequence divergence in the EH population than in the WH. CONCLUSION We propose five 'Evolutionary Significant Units' across the blue sheep distribution range based on observed variation in the species' ecological requirements, orography, climatic conditions, and maternal lineages, viz.; Western Himalaya-Pamir plateau (WHPP); Eastern Himalaya-Tibetan plateau (EHTP); Qilian mountains; Helan mountains and Hengduan mountains population. Despite the small sample size, population divergence was observed across the IHR, therefore, we suggest a transboundary, collaborative study on comparative morphology, anatomy, ecology, behaviour, and population genetics using harmonized different genetic markers for identifying the overall taxonomic status of the blue sheep across its range for planning effective conservation strategies.
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Affiliation(s)
- Bheem Dutt Joshi
- Wildlife Institute of India, 248001, Dehradun, Uttarakhand, India.,Zoological Survey of India, 700020, Kolkata, India.,ENPROTEC INDIA FOUNDATION, 222161, Lucknow, Uttar Pradesh, India
| | - Vinay Kumar
- Wildlife Institute of India, 248001, Dehradun, Uttarakhand, India
| | - Rahul De
- Wildlife Institute of India, 248001, Dehradun, Uttarakhand, India
| | - Reeta Sharma
- Wildlife Institute of India, 248001, Dehradun, Uttarakhand, India
| | | | | | - Ranjana Pal
- Wildlife Institute of India, 248001, Dehradun, Uttarakhand, India
| | | | | | | | - Bilal Habib
- Wildlife Institute of India, 248001, Dehradun, Uttarakhand, India.
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2
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Gao H, Li N, Huang Y, Qiao F, Li J, Li Z, Li Y, Wang Z, Teng L, Liu Z. Taxonomic status of Chinese blue sheep (Pseudois nayaur): new evidence of a distinct subspecies. Integr Zool 2020; 15:202-212. [PMID: 31773863 DOI: 10.1111/1749-4877.12422] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The blue sheep is an endemic species to the Qinghai-Tibet Plateau and surrounding regions. It has been regarded as having 2 subspecies: Pseudois nayaur nayaur and P. n. szechuanensis. However, such a classification remains controversial. Herein, we analyze 10 microsatellite loci and part of the mitochondrial control region for clarification in such taxonomic debates. We use samples from 168 individuals from 6 geographic populations covering almost all the distribution areas of the species in China to carry out comparisons. Phylogenetic trees derived from both the microsatellite and mitochondrial markers combined with the discriminant analysis of principal components (DAPC) and the STRUCTURE analysis reveal that the individuals in the Helan Mountains are well grouped with a distinct evolutionary lineage and are significantly different from the other populations of P. n. szechuanensis according to Fst values, implying that this isolated population should be categorized as a valid subspecies; namely, Pseudois nayaur alashanicus. The isolation-by-distance (IBD) analysis shows a significant positive relationship between genetic and geographical distances among the populations.
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Affiliation(s)
- Hui Gao
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Nannan Li
- Forestry Science and Technology Research Institute of Greater Hinggan in Inner Mongolia, Yakeshi, China
| | - Yongjie Huang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Fujie Qiao
- School of Life Sciences, Lvliang Univiersity, Lvliang, China
| | - Junle Li
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Zongzhi Li
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Yanxiang Li
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Zhenghuan Wang
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Liwei Teng
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China.,Key Laboratory of Conservation Biology, National Forestry and Grassland Administration, Harbin, China
| | - Zhensheng Liu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China.,Key Laboratory of Conservation Biology, National Forestry and Grassland Administration, Harbin, China
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3
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Sun G, Zhang H, Wei Q, Zhao C, Yang X, Wu X, Xia T, Liu G, Zhang L, Gao Y, Sha W, Li Y. Comparative Analyses of Fecal Microbiota in European Mouflon ( Ovis orientalis musimon) and Blue Sheep ( Pseudois nayaur) Living at Low or High Altitudes. Front Microbiol 2019; 10:1735. [PMID: 31417526 PMCID: PMC6682669 DOI: 10.3389/fmicb.2019.01735] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 07/15/2019] [Indexed: 12/30/2022] Open
Abstract
The gut microbiota is a complex and essential system organ that plays an integrative role in balancing key vital functions in the host. Knowledge of the impact of altitude on the gut microbiota of European mouflon (Ovis orientalis musimon) and blue sheep (Pseudois nayaur) is currently limited. In this study, we compared the characteristics of gut microbiota in 5 mouflon at low altitude (K group), 4 mouflon at high altitude (L group), 4 blue sheep at low altitude (M group), and 4 blue sheep at high altitude (N group). The V3–V4 region of the 16S rRNA gene was analyzed using high-throughput sequencing. Analyses based on the operational taxonomic units showed significant changes in the gut microbial communities between groups at different altitudes. At the phylum level, groups at the high altitudes had a higher relative abundance of Firmicutes and a lower relative abundance of Bacteroidetes than those at the low altitudes. A higher Firmicutes:Bacteroidetes ratio is beneficial to animals in terms of the gut microbiota-mediated energy harvest. The relative abundance of Proteobacteria was significantly higher in the gut microbiota of mouflon sheep at high altitudes. At the genus level, the Bacteroides:Prevotella ratio was significantly higher in the low-altitude group (than the high-altitude group) of mouflon sheep and the ratio was significantly higher in the high-altitude group (than the low-altitude group) in blue sheep. In addition, the Ruminococcaceae_UCG-005 related to cellulose and starch digestion was the predominant genus in blue sheep and the relative abundance of the genus was significant higher in the high-altitude group than the low-altitude group of blue sheep (P < 0.01). In conclusion, our results suggested that the gut microbiota of high-altitude groups of sheep had stronger abilities related to energy metabolism and the decomposition of substances, e.g., fiber and cellulose, and that such abilities are associated with high-altitude adaptation.
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Affiliation(s)
- Guolei Sun
- College of Life Science, Qufu Normal University, Qufu, China
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, Qufu, China
| | - Qinguo Wei
- College of Life Science, Qufu Normal University, Qufu, China
| | - Chao Zhao
- College of Life Science, Qufu Normal University, Qufu, China
| | - Xiufeng Yang
- College of Life Science, Qufu Normal University, Qufu, China
| | - Xiaoyang Wu
- College of Life Science, Qufu Normal University, Qufu, China
| | - Tian Xia
- College of Life Science, Qufu Normal University, Qufu, China
| | - Guangshuai Liu
- College of Life Science, Qufu Normal University, Qufu, China
| | - Lei Zhang
- College of Life Science, Qufu Normal University, Qufu, China
| | | | - Weilai Sha
- College of Life Science, Qufu Normal University, Qufu, China
| | - Ying Li
- Wild World Jinan, Jinan, China
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4
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Dong M, Xu H, Li D, Xie M, Wu J, Wen A, Wang Q, Zhu G, Ni Q, Zhang M, Yao Y. Complete mitochondrial genome of a dwarf blue sheep ( Pseudois schaeferi) and its phylogenetic analysis. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1607584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Mengmeng Dong
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Diyan Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Meng Xie
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Jiayun Wu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Anxiang Wen
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Qin Wang
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Guangxiang Zhu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Qingyong Ni
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Ya’an, China
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5
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Dong M, Xu H, Li D, Xie M, Wu J, Wen A, Wang Q, Zhu G, Ni Q, Zhang M, Yao Y. The complete mitochondrial genome of a blue sheep ( Pseudois nayaur szechuanensis) from Gongga mountains of Sichuan, China. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1536469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Mengmeng Dong
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Diyan Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Meng Xie
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Jiayun Wu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Anxiang Wen
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Qin Wang
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Guangxiang Zhu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Qingyong Ni
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Ya’an, China
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6
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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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7
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Tan S, Wang Z, Jiang L, Peng R, Zhang T, Peng Q, Zou F. Molecular phylogeny and phylogeography of genus Pseudois (Bovidae, Cetartiodactyla): New insights into the contrasting phylogeographic structure. Ecol Evol 2017; 7:7047-7057. [PMID: 28904782 PMCID: PMC5587526 DOI: 10.1002/ece3.3269] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 06/09/2017] [Accepted: 06/12/2017] [Indexed: 11/29/2022] Open
Abstract
Blue sheep, Pseudois nayaur, is endemic to the Tibetan Plateau and the surrounding mountains, which are the highest‐elevation areas in the world. Classical morphological taxonomy suggests that there are two subspecies in genus Pseudois (Bovidae, Artiodactyla), namely Pseudois nayaur nayaur and Pseudois nayaur szechuanensis. However, the validity and geographic characteristics of these subspecies have never been carefully discussed and analyzed. This may be partially because previous studies have mainly focused on the vague taxonomic status of Pseudois schaeferi (dwarf blue sheep). Thus, there is an urgent need to investigate the evolutionary relationship and taxonomy system of this genus. This study enriches a previous dataset by providing a large number of new samples, based on a total of 225 samples covering almost the entire distribution of blue sheep. Molecular data from cytochrome b and the mitochondrial control region sequences were used to reconstruct the phylogeny of this species. The phylogenetic inferences show that vicariance plays an important role in diversification within this genus. In terms of molecular dating results and biogeographic analyses, the striking biogeographic pattern coincides significantly with major geophysical events. Although the results raise doubt about the present recognized distribution range of blue sheep, they have corroborated the validity of the identified subspecies in genus Pseudois. Meanwhile, these results demonstrate that the two geographically distinct populations, the Helan Mountains and Pamir Plateau populations, have been significantly differentiated from the identified subspecies, a finding that challenges the conventional taxonomy of blue sheep.
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Affiliation(s)
- Shuai Tan
- Sichuan Key Laboratory of Conservation Biology on Endangered WildlifeKey Laboratory of Bio‐resources and Eco‐environment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
| | - Zhihong Wang
- Sichuan Key Laboratory of Conservation Biology on Endangered WildlifeKey Laboratory of Bio‐resources and Eco‐environment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
| | - Lichun Jiang
- Sichuan Key Laboratory of Conservation Biology on Endangered WildlifeKey Laboratory of Bio‐resources and Eco‐environment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
| | - Rui Peng
- Sichuan Key Laboratory of Conservation Biology on Endangered WildlifeKey Laboratory of Bio‐resources and Eco‐environment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
| | - Tao Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered WildlifeKey Laboratory of Bio‐resources and Eco‐environment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
| | - Quekun Peng
- Sichuan Key Laboratory of Conservation Biology on Endangered WildlifeKey Laboratory of Bio‐resources and Eco‐environment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
- Department of Biomedical ScienceChengdu Medical CollegeChengduSichuanChina
| | - Fangdong Zou
- Sichuan Key Laboratory of Conservation Biology on Endangered WildlifeKey Laboratory of Bio‐resources and Eco‐environment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
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8
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Development and characterization of nine polymorphic microsatellite markers for the blue sheep (Pseudois nayaur). CONSERV GENET RESOUR 2015. [DOI: 10.1007/s12686-014-0327-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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9
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Jiang LC, Tan S, Peng R, Zou FD. The complete mitochondrial genome sequence of the blue sheep, Pseudois nayaur nayaur (Cetartiodactyla: Caprinae). MITOCHONDRIAL DNA 2014; 26:867-8. [PMID: 24409917 DOI: 10.3109/19401736.2013.861434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The blue sheep (Pseudois nayaur nayaur) belongs to the subfamily Caprinae, and is distributed in the Qinghai-Tibet Plateau and peripheral mountains of China. In this study, the complete mitochondrial genome of P. n. nayaur was sequenced. It was determined to be of 16,700 bases. The nucleotide sequence data of 12 heavy-strand protein-coding genes of P. n. nayaur and other 29 caprine species were used for phylogenetic analysis. Phylogenetic trees were reconstructed by Bayesian and maximum likelihood methods, and it suggested that P. n. nayaur was the sister group of P. schaeferi and P. nayaur, and also indicated a close relationship of genus Pseudois with genus Capra.
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Affiliation(s)
- Li-Chun Jiang
- a Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Key Laboratory of Bio-resources and Eco-environment (Ministry of Education) , College of Life Sciences, Sichuan University , Chengdu , Sichuan , P.R. China and.,b Key Laboratory for Molecular Biology and Biopharmaceutics , School of Life Science and Technology, Mianyang Normal University , Mianyang , Sichuan , P.R. China
| | - Shuai Tan
- a Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Key Laboratory of Bio-resources and Eco-environment (Ministry of Education) , College of Life Sciences, Sichuan University , Chengdu , Sichuan , P.R. China and
| | - Rui Peng
- a Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Key Laboratory of Bio-resources and Eco-environment (Ministry of Education) , College of Life Sciences, Sichuan University , Chengdu , Sichuan , P.R. China and
| | - Fang-Dong Zou
- a Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Key Laboratory of Bio-resources and Eco-environment (Ministry of Education) , College of Life Sciences, Sichuan University , Chengdu , Sichuan , P.R. China and
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10
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Jiang LC, Gou LK, Zhang X, Zhao QM, Tan S, Peng R, Wei YQ, Zou FD. Complete mitochondrial genome of a new subspecies of the blue sheep, Pseudois nayaur (Cetartiodactyla: Caprinae) from Helan Mountain in China. MITOCHONDRIAL DNA 2014; 26:797-8. [PMID: 24409913 DOI: 10.3109/19401736.2013.855759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The population of blue sheep, Pseudois nayaur, from Helan Mountain in China is considered as a new subspecies. We first determined and annotated its complete mitochondrial genome. The mitogenome is 16,795 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a control region. As in other mammals, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes, which are encoded on the light strand. Its overall base composition is A: 33.2%, T: 26.6%, C: 26.8% and G: 13.3%. The complete mitogenome of the new subspecies of P. nayaur could provide an important data to further explore the taxonomic status of the subspecies.
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Affiliation(s)
- Li-Chun Jiang
- a Key Laboratory for Ecosystem Models and Application of The State Ethnic Affairs Commission , School of Biological Science and Engineering, Beifang University of Nationalities , Yinchuan , Ningxia , PR China .,b Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Key Laboratory of Bio-resources and Eco-environment (Ministry of Education) , College of Life Sciences, Sichuan University , Chengdu , Sichuan , PR China , and.,c Key Laboratory for Molecular Biology and Biopharmaceutics , School of Life Science and Technology, Mianyang Normal University , Mianyang , Sichuan , PR China
| | - Liang-Ke Gou
- b Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Key Laboratory of Bio-resources and Eco-environment (Ministry of Education) , College of Life Sciences, Sichuan University , Chengdu , Sichuan , PR China , and
| | - Xin Zhang
- a Key Laboratory for Ecosystem Models and Application of The State Ethnic Affairs Commission , School of Biological Science and Engineering, Beifang University of Nationalities , Yinchuan , Ningxia , PR China
| | - Qing-Mei Zhao
- a Key Laboratory for Ecosystem Models and Application of The State Ethnic Affairs Commission , School of Biological Science and Engineering, Beifang University of Nationalities , Yinchuan , Ningxia , PR China
| | - Shuai Tan
- b Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Key Laboratory of Bio-resources and Eco-environment (Ministry of Education) , College of Life Sciences, Sichuan University , Chengdu , Sichuan , PR China , and
| | - Rui Peng
- b Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Key Laboratory of Bio-resources and Eco-environment (Ministry of Education) , College of Life Sciences, Sichuan University , Chengdu , Sichuan , PR China , and
| | - Yu-Qing Wei
- a Key Laboratory for Ecosystem Models and Application of The State Ethnic Affairs Commission , School of Biological Science and Engineering, Beifang University of Nationalities , Yinchuan , Ningxia , PR China
| | - Fang-Dong Zou
- b Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Key Laboratory of Bio-resources and Eco-environment (Ministry of Education) , College of Life Sciences, Sichuan University , Chengdu , Sichuan , PR China , and
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11
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Gu L, Liu Y, Que P, Zhang Z. Quaternary climate and environmental changes have shaped genetic differentiation in a Chinese pheasant endemic to the eastern margin of the Qinghai-Tibetan Plateau. Mol Phylogenet Evol 2013; 67:129-39. [DOI: 10.1016/j.ympev.2012.12.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Revised: 12/13/2012] [Accepted: 12/15/2012] [Indexed: 10/27/2022]
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12
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Cai X, Yu S, Mipam T, Zhang X, Yue B. Phylogenetic lineages of Monopterus albus
(Synbranchiformes: Synbranchidae) in China inferred from mitochondrial control region. J ZOOL SYST EVOL RES 2012. [DOI: 10.1111/jzs.12004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xin Cai
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife; College of Life Sciences; Sichuan University; Chengdu China
- School of Life Science and Engineering; Southwest University of Science and Technology; Mianyang China
| | - Shumin Yu
- College of Veterinary Medicine; Sichuan Agricultural University; Ya'an China
| | - Tserangdonko Mipam
- College of Life Science and Technology; Southwest University for Nationalities; Chengdu China
| | - Xiuyue Zhang
- Department of Agronomy; Dezhou University; Dezhou China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife; College of Life Sciences; Sichuan University; Chengdu China
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13
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Molecular evidence for the subspecific differentiation of blue sheep (Pseudois nayaur) and polyphyletic origin of dwarf blue sheep (Pseudois schaeferi). Genetica 2012; 140:159-67. [DOI: 10.1007/s10709-012-9667-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 07/11/2012] [Indexed: 10/28/2022]
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14
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Mitogenomic analysis of the genus Pseudois: evidence of adaptive evolution of morphological variation in the ATP synthase genes. Mitochondrion 2012; 12:500-5. [PMID: 22820118 DOI: 10.1016/j.mito.2012.07.107] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 06/21/2012] [Accepted: 07/10/2012] [Indexed: 12/22/2022]
Abstract
The genus Pseudois includes two variable taxa, blue sheep (Pseudois nayaur) and dwarf blue sheep (Pseudois schaeferi), that exhibit notable geographic variation in morphology and ecological niche, suggesting the potential for significant adaptive differentiation between these two goats. Blue sheep are broadly distributed in the Tibetan Plateau and peripheral mountains through Central Asia, while dwarf blue sheep are only found in the gorges of the upper Yangtze River (Jinsha River) near Batang county, Sichuan province and adjacent mountains. Although they are all adapted to high altitude environments, endangered dwarf blue sheep show unique morphological variation and niche shifts compared to blue sheep. Mitochondria play important roles in oxygen usage and energy metabolism. The energetically demanding lifestyles of these high altitude species may have altered the selective regimes on mitochondrial genes encoding proteins related to cellular respiration. Here, we compared the sequences of 13 protein-coding genes in the mitochondrial genome of dwarf blue sheep with those of blue sheep to understand the genetic basis of morphological variation. Using neighbor-joining, maximum-likelihood and Bayesian approaches, we estimated rates of synonymous (d(S)) and nonsynonymous (d(N)) substitutions. Independent analyses showed that no ω ratio was larger than 1, suggesting that all mitochondrial 13 genes were under the purifying selection. Surprisingly, we found that the ω ratio (d(N)/d(S)) of the ATP synthase complex (ATP6 and ATP8) in blue sheep is sixteen times that of dwarf blue sheep (0.340 compared to 0.021). This result was confirmed by a separate analysis of ATP synthase genes from two additional P. schaeferi individuals and two P. nayaur individuals. We hypothesize that the large body size and diverse feeding styles are factors influencing the nonsynonymous substitutions in the ATP synthase complex of blue sheep.
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Fan Z, Liu S, Liu Y, Zhang X, Yue B. How Quaternary geologic and climatic events in the southeastern margin of the Tibetan Plateau influence the genetic structure of small mammals: inferences from phylogeography of two rodents, Neodon irene and Apodemus latronum. Genetica 2011; 139:339-51. [DOI: 10.1007/s10709-011-9553-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 01/19/2011] [Indexed: 10/18/2022]
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Chen S, Costa V, Beja-Pereira A. Evolutionary patterns of two major reproduction candidate genes (Zp2 and Zp3) reveal no contribution to reproductive isolation between bovine species. BMC Evol Biol 2011; 11:24. [PMID: 21266067 PMCID: PMC3037879 DOI: 10.1186/1471-2148-11-24] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 01/25/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND It has been established that mammalian egg zona pellucida (ZP) glycoproteins are responsible for species-restricted binding of sperm to unfertilized eggs, inducing the sperm acrosome reaction, and preventing polyspermy. In mammals, ZP apparently represents a barrier to heterospecific fertilization and thus probably contributes to reproductive isolation between species. The evolutionary relationships between some members of the tribe Bovini are complex and highly debatable, particularly, those involving Bos and Bison species for which interspecific hybridization is extensively documented. Because reproductive isolation is known to be a major precursor of species divergence, testing evolutionary patterns of ZP glycoproteins may shed some light into the speciation process of these species. To this end, we have examined intraspecific and interspecific genetic variation of two ZP genes (Zp2 and Zp3) for seven representative species (111 individuals) from the Bovini tribe, including five species from Bos and Bison, and two species each from genera Bubalus and Syncerus. RESULTS A pattern of low levels of intraspecific polymorphism and interspecific divergence was detected for the two sequenced fragments each for Zp2 and Zp3. At intraspecific level, none of neutrality tests detected deviations from neutral equilibrium expectations for the two genes. Several haplotypes in both genes were shared by multiple species from Bos and Bison. CONCLUSIONS Here we argue that neither ancestral polymorphism nor introgressive hybridization alone can fully account for haplotype sharing among species from Bos and Bison, and that both scenarios have contributed to such a pattern of haplotype sharing observed here. Additionally, codon-based tests revealed strong evidence for purifying selection in the Zp3 coding haplotype sequences and weak evidence for purifying selection in the Zp2 coding haplotype sequences. Contrary to a general genetic pattern that genes or genomic regions contributing to reproductive isolation between species often evolve rapidly and show little or no gene flow between species, these results demonstrate that, particularly, those sequenced exons of the Zp2 and the Zp3 did not show any contribution to reproductive isolation between the bovine species studied here.
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Affiliation(s)
- Shanyuan Chen
- Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
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Xu S, Ren W, Zhou X, Zhou K, Yang G. Sequence polymorphism and geographical variation at a positively selected MHC-DRB gene in the finless porpoise (Neophocaena phocaenoides): implication for recent differentiation of the Yangtze finless porpoise? J Mol Evol 2010; 71:6-22. [PMID: 20563867 DOI: 10.1007/s00239-010-9357-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2009] [Accepted: 06/01/2010] [Indexed: 01/03/2023]
Abstract
Sequence polymorphism at the MHC class II DRB locus was investigated in three finless porpoise (Neophocaena phocaenoides) populations in Chinese waters. Intragenic recombination and strong positive selection were the main forces in generating sequence diversity in the DRB gene. MHC sequence diversity changed significantly along the study period. Significant decrease in heterozygosity and lost alleles have been detected in the Yangtze River population and South China Sea population since 1990. Furthermore, there is a trend of increasing population differentiation over time. Especially, the genetic differentiation between the Yangtze River population and the Yellow Sea population was very low prior to 1990 (F (ST) = 0.036, P = 0.009), but became very significant after 1990 (F (ST) = 0.134, P < 0.001), suggesting a recent augmentation of genetic differentiation between both populations probably in a relatively short-term period. Porpoises from the Yangtze River displayed divergent frequencies of shared and private alleles from those displayed by two marine populations, which suggest that the former riverine population has been under a different selection regime (characteristic of a fresh water environment) than that of its marine counterparts.
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Affiliation(s)
- Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210046, China
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Shafer AB, Hall JC. Placing the mountain goat: A total evidence approach to testing alternative hypotheses. Mol Phylogenet Evol 2010; 55:18-25. [DOI: 10.1016/j.ympev.2010.01.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Revised: 12/01/2009] [Accepted: 01/15/2010] [Indexed: 12/24/2022]
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