多基因位点系统发育揭示熊猴(<i>Macaca assamensis</i>)尼泊尔种群的独立物种地位及其对进化和保护的启示

Laxman Khanal; Mukesh Kumar Chalise; Peng-Fei Fan; Randall C. Kyes; Xue-Long Jiang

doi:10.24272/j.issn.2095-8137.2020.279

多基因位点系统发育揭示熊猴(Macaca assamensis)尼泊尔种群的独立物种地位及其对进化和保护的启示

doi: 10.24272/j.issn.2095-8137.2020.279

1.
Central Department of Zoology, Institute of Science and Technology, Tribhuvan University, Kathmandu 44613, Nepal
2.
中国科学院昆明动物研究所遗传资源与进化国家重点实验室，云南昆明 650223，中国
3.
Nepal Biodiversity Research Society (NEBORS), Lalitpur 23513, Nepal
4.
中山大学生命科学学院，广东广州 510275，中国
5.
Department of Psychology, Global Health, and Anthropology, Center for Global Field Study, and Washington National Primate Research Center, University of Washington, Seattle 98195, USA

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出版历程
- 收稿日期: 2020-09-26
- 录用日期: 2021-01-05
- 网络出版日期: 2021-01-06
- 刊出日期: 2021-01-18

Multilocus phylogeny suggests a distinct species status for the Nepal population of Assam macaques (Macaca assamensis): implications for evolution and conservation

1.
Central Department of Zoology, Institute of Science and Technology, Tribhuvan University, Kathmandu 44613, Nepal
2.
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China
3.
Nepal Biodiversity Research Society (NEBORS), Lalitpur 23513, Nepal
4.
School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
5.
Department of Psychology, Global Health, and Anthropology, Center for Global Field Study, and Washington National Primate Research Center, University of Washington, Seattle 98195, USA

Funds: This study was supported by the Chinese Academy of Sciences-World Academy of Sciences (CAS-TWAS) President’s PhD Fellowship Program to L.K., Second Tibetan Plateau Scientific Expedition and Research Program (2019QZKK0501), and National Key Research and Development Plan (#2017YFC0505202) China. R.C.K. was supported in part by the Office of Research Infrastructure Programs (ORIP) of the National Institutes of Health through Grant Number P51OD010425 to the WaNPRC. L.K. was supported by the Rufford Small Grants (17666-1) of Rufford Foundation, UK partly for fieldworks

More Information

Corresponding author: E-mail: lkhanal@cdztu.edu.np; jiangxl@mail.kiz.ac.cn

摘要

摘要: 长期以来，基于形态、行为和分子特征的猕猴属(Macaca)斯里兰卡猴种组(sinica group)系统发育关系一直饱受争议。熊猴(M. assamensis)尼泊尔种群生活在该物种分布范围的最西部，形态特征独特，但其系统发育关系仍未有相关研究。本研究利用多个线粒体和Y染色体基因位点检验熊猴尼泊尔种群与其他猕猴间的系统发育关系，估算其分化时间与遗传距离。结果显示，斯里兰卡猴种组分化为两个主要分支：第一个分支包括藏酋猴（M. thibetana）、斯里兰卡猴（M. sinica）和熊猴指名亚种(M. assamensis assamensis)，第二个分支包括帽猴（M. radiata）、喜马拉雅山脉东部和中部的白颊猕猴（M. leucogenys）、达旺猴（M. munzala）和熊猴尼泊尔种群。在第二分支当中，熊猴尼泊尔种群大约于1.9百万年前最先与该分支其他成员分开。研究结果揭示熊猴尼泊尔种群与东部的熊猴指名亚种显著分化，而与白颊猕猴和达旺猴更接近，说明熊猴尼泊尔种群可能是一个独立的物种。由于其系统发育关系特殊、分布区隔离且种群数量少，斯里兰卡猴种组尼泊尔种群亟需详细的分类修订并采取相应优先保护措施。
- 喜马拉雅山脉 /
- 猕猴 /
- 并系 /
- 斯里兰卡猴种组 /
- 分类
Abstract: Phylogenetic relationships within the sinica-group of macaques based on morphological, behavioral, and molecular characteristics have remained controversial. The Nepal population of Assam macaques (Macaca assamensis) (NPAM), the westernmost population of the species, is morphologically distinct but has never been used in phylogenetic analyses. Here, the phylogenetic relationship of NPAM with other congeners was tested using multiple mitochondrial and Y-chromosomal loci. The divergence times and evolutionary genetic distances among macaques were also estimated. Results revealed two major mitochondrial DNA clades of macaques under the sinica-group: the first clade included M. thibetana, M. sinica, and eastern subspecies of Assam macaque (M. assamensis assamensis); the second clade included M. radiata together with species from the eastern and central Himalaya, namely, M. leucogenys, M. munzala, and NPAM. Among the second-clade species, NPAM was the first to diverge from the other members of the clade around 1.9 million years ago. Our results revealed that NPAM is phylogenetically distinct from the eastern Assam macaques and closer to other species and hence may represent a separate species. Because of its phylogenetic distinctiveness, isolated distribution, and small population size, the Nepal population of sinica-group macaques warrants detailed taxonomic revision and high conservation priority.
- Himalaya /
- Macaques /
- Paraphyletic /
- sinica-group /
- Taxonomy

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Figure 1. Map of Nepal showing NPAM sampling locations

Inset shows distribution range of Assam macaques, adapted from IUCN Red List 2020 (Boonratana et al., 2020).

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Figure 2. ML gene tree of concatenated mtDNA (3 526 bp) among sinica-group macaques

Node values represent RAxML percentage bootstrap probability. Inset shows geographical distribution of sinica-group species; source: M. leucogenys (Fan et al., 2017); M. munzala (Biswas et al., 2011; Chakraborty et al., 2014; Sarania et al., 2017), M. a. assamensis (Minge et al., 2016; Zhou et al., 2011); NPAM (Khanal et al., 2018a, 2019).

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Figure 3. BI tree of concatenated mtDNA (3 526 bp) among macaques

Node numbers are Bayesian posterior probability values.

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Figure 4. BI tree of concatenated Y-chromosomal genes (2 967 bp)

Node numbers are Bayesian posterior probability values.

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Figure 5. Ultrametric tree showing divergence time estimates for macaques based on concatenated mtDNA sequences (3 526 bp) using BEAST

Blue bars indicate 95% highest posterior densities of divergence times and time scale below represents million years ago before present; nodal values represent Bayesian posterior probabilities.

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Table 1. Primer pairs and PCR conditions for amplification of studied loci

S.N.	Locus	Primer pairs (Forward/Reverse)		Ann. temp.	Length (bp)	References
S.N.	Locus	Name	Sequence (5′–3′)	Ann. temp.	Length (bp)	References
1.	cyt b	CYTF	AACCATCGTTGTACTTCAAC	56	1 140	Khanal et al., 2018a
1.	cyt b	CYTR	TCTGGTTTACAAGGCCAGTG	56	1 140	Khanal et al., 2018a
2	D-loop	LqqF	TCCTAGGGCAATCAGAAAGAAAG	58	1 090	Li & Zhang, 2004
2	D-loop	Saru5	GGCCAGGACCAAGCCTATTT	58	1 090	Hayasaka et al., 1991
3	16S rRNA	284F-EX	GGATTAGATACCCCACTATGCTTG	58	1 397	Tosi et al., 2003
3	16S rRNA	384R-EX	GCTACCTTTGCACRGTCAGGGTACCG	58	1 397	Tosi et al., 2003
4	TSPY1	TSPYA	AGCCAGGAAGGCCTTTTCTCG	60	2 203	Kim et al., 1996
	TSPY1	TSR1012	TGTCACCTGTGACGTTCACGA	60		Bunlungsup et al., 2016
	TSPY2	TSF566	AGGTCATTCATGGATGCAGAT	64		Bunlungsup et al., 2016
	TSPY2	TSR1676	CCACAGTTATAACCTGCTTTGC	64		Bunlungsup et al., 2016
	TSPY3	TSF1383	AATCCCCTGCAATACTACAGGAGG	64		Bunlungsup et al., 2016
	TSPY3	TSPY5R	CTGTGCATAAGACCATGCTGAG	64		Tosi et al., 2000
5	SRY	SW2	CTTGAGAATACATTGTCAGGG	56	764	Whitfield et al., 1993
5	SRY	SW3B	AGGTCTTTGTAGCCAATGTTACCCG	56	764	Whitfield et al., 1993

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Table 2. Estimates of evolutionary divergence over sequence pairs between sinica-group macaques using K2P model with cyt b sequences

Species	1	2	3	4	5	6	7
1. NPAM		0.01	0.013	0.016	0.012	0.016	0.016
2. M. munzala	0.039		0.013	0.018	0.012	0.017	0.017
3. M. leucogenys	0.069	0.073		0.016	0.013	0.016	0.016
4. M. assamensis	0.093	0.111	0.090		0.014	0.015	0.008
5. M. radiata	0.055	0.058	0.061	0.078		0.016	0.014
6. M. sinica	0.093	0.099	0.102	0.081	0.096		0.013
7. M. thibetana	0.090	0.102	0.087	0.026	0.075	0.067
Evolutionary distances (below diagonal) and standard error estimates (above diagonal).

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