全基因组分析揭示凸颅鼢鼠属（哺乳纲，啮齿目，鼹形鼠科）的系统发育关系及对横断山脉一新种的描述

Tao Zhang; Meng-Long Lei; Hao Zhou; Zhong-Zheng Chen; Peng Shi

doi:10.24272/j.issn.2095-8137.2022.045

全基因组分析揭示凸颅鼢鼠属（哺乳纲，啮齿目，鼹形鼠科）的系统发育关系及对横断山脉一新种的描述

doi: 10.24272/j.issn.2095-8137.2022.045

张涛¹,
雷孟龙¹,
周豪^{2, 3},
陈中正^{1, 4, ,},
施鹏^{1, 5, 6, ,}

1.
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650204, 中国
2.
苏州大学药学院江苏省神经精神疾病重点实验室, 江苏苏州215123, 中国
3.
苏州大学与中国科学院昆明动物研究所人类疾病与药物开发动物模型联合实验室, 云南昆明650223, 中国
4.
安徽师范大学机构生态与环境学院皖江流域退化生态系统的恢复与重建省部共建协同创新中心, 安徽芜湖 241000, 中国
5.
中国科学院大学未来技术学院, 北京 100049, 中国
6.
中国科学院动物进化与遗传前沿交叉卓越创新中心, 云南昆明 650201, 中国

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出版历程
- 收稿日期: 2022-02-21
- 录用日期: 2022-03-17
- 网络出版日期: 2022-03-17
- 刊出日期: 2022-05-18

Phylogenetic relationships of the zokor genus Eospalax (Mammalia, Rodentia, Spalacidae) inferred from whole-genome analyses, with description of a new species endemic to Hengduan Mountains

Tao Zhang¹,
Meng-Long Lei¹,
Hao Zhou^{2, 3},
Zhong-Zheng Chen^{1, 4
, ,},
Peng Shi^{1, 5, 6
, ,}

1.
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650204, China
2.
Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
3.
Joint Laboratory of Animal Models for Human Diseases and Drug Development, Soochow University and Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
4.
Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui 241000, China
5.
School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
6.
Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China

Funds: This study was supported by the Second Tibetan Plateau Scientific Expedition and Research (STEP) Program (2019QZKK05010218, 2019QZKK05010110), National Natural Science Foundation of China (32100339, 31871277). P.S. was supported by the Yunling Scholar Project, Ten-Thousand Talents Plan of Yunnan Province. T.Z. was supported by the Youth Innovation Promotion Association, Chinese Academy of Sciences

More Information

Corresponding author: E-mail: zhongzheng112@126.com; ship@mail.kiz.ac.cn

摘要

摘要: 凸颅鼢鼠属（Eospalax）是一类严格地下生活的啮齿类动物，为中国特有属，主要分布于中国西部与北部的草原、高海拔草甸、森林和农田等生境。早在一个世纪前，研究者就已对凸颅鼢鼠属的6个物种进行了描述，但至今其分类学和系统发育关系仍存在争议。该研究对47个鼢鼠样本进行了高深度的全基因组测序，并构建了高可信度且稳健的系统发育关系。研究结果支持所有6个已命名物种的有效性。全基因组分析显示，凸颅鼢鼠属在上新世早期（约468万年前）首先分化为两个支系：一支栖息在青藏高原及其邻近的高海拔地区；另一支生活在黄土高原和秦岭大巴山脉低海拔地区。凸颅鼢鼠属最近的分化发生在高原鼢鼠（E. baileyi）和斯氏鼢鼠（E. smithii）之间以及在秦岭鼢鼠（E. rufescens）和罗氏鼢鼠（E. rothschildi）之间，时间为上新世晚期（分别约209和219万年前）。此外，我们还在远离鼢鼠所有已知分布地的横断山脉南部（四川省木里县）采集到了鼢鼠标本。形态学和分子水平的分析都强烈表明这些标本代表一新种，在此正式描述为木里鼢鼠 Eospalax muliensis sp. nov . 。木里鼢鼠属于高海拔支系，其在约422万年前，凸颅鼢鼠属属内第一次分化后不久，与其近缘物种发生划分。有意思的是，相比于凸颅鼢鼠属的其他物种，木里鼢鼠保留了更多假定的祖先型性状，提示凸颅鼢鼠属有可能起源于横断山脉。
- 鼢鼠 /
- 凸颅鼢鼠属 /
- 基因组系统发育分析 /
- 新物种 /
- 横断山脉
Abstract: Zokors in the genus Eospalax, which are endemic to northern and western China, are subterranean rodents that inhabit various niches, including grasslands, high-altitude meadows, forests, and farmlands. Six species in Eospalax were described a century ago but their taxonomy and phylogeny remain controversial. In this study, we performed high-depth whole-genome sequencing of 47 zokor samples, comprising all six previously described species. Genomic analyses revealed a reliable and robust phylogeny of Eospalax and supported the validity of the six named species. According to the inferred phylogenetic relationships, Eospalax first divergent into two clades in the early Pliocene (ca. 4.68 million years ago (Ma)), one inhabiting the high-altitude Qinghai-Xizang (Tibet) Plateau (QTP) and adjacent regions, and the another inhabiting the low-altitude Loess Plateau and Qinling-Daba Mountains. The most recent divergences occurred between E. baileyi and E. smithii and between E. rufescens and E. rothschildi in the late Pliocene (ca. 2.09 and 2.19 Ma, respectively). We also collected specimens of zokors in the southern Hengduan Mountains (Muli County, Sichuan Province), far from the known distributions of all other zokors. Morphological and molecular analyses strongly suggested that the specimens represent a new species, formally described here as Eospalax muliensis sp. nov . The new species belongs to the high-altitude clade and diverged from closely related species (ca. 4.22 Ma) shortly after the first divergence in Eospalax. Interestingly, Eospalax muliensis sp. nov . possesses more supposedly plesiomorphic characters, suggesting a possible origin of the genus in the Hengduan Mountains.
- Zokor /
- Eospalax /
- Phylogenomic analyses /
- New species /
- Hengduan Mountains

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Figure 1. Sampling of species in Eospalax

A: Geographic distribution of sampling sites. B: Image of typical Eospalax muliensis sp. nov. (upper panel) and aboveground mound (lower panel). Photo by Hao Zhou.

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Figure 2. Phylogenetic relationships among species of Eospalax

A: ML phylogenetic tree from whole-genome SNVs; 100 bootstraps were applied; scale bar represents level of similarity. B: Pairwise genetic distance among species in genera Myospalax and Eospalax. Genetic distances were calculated in over 50 000 windows (50 kb in size) across whole genome. Data are mean±SD.

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Figure 3. Alternative topologies and divergence times of genus Eospalax

Average weighting of ranked topologies in over 50 000 windows (50 kb in size) across whole genome (A). Three best topologies and their weighting are shown (B–D). Divergence times estimated using SNAPP based on whole-genome SNVs (E). Node numbers refer to divergence time, blue shadows represent 95% confidence intervals of divergent time. Red circle indicates node for split of Myospalax and Eospalax as a calibration point.

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Figure 4. Plot of principal components 1 and 2 from analysis of 21 craniodental measurements of Eospalax genus

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Figure 5. Dorsal, ventral, and lateral views of skull and mandible of Eospalax muliensis sp. nov. (KIZ 040324, holotype) (A), E. baileyi (DF 004) (B), E. cansus (LM 001) (C), E. fontanierii (FS 001) (D), E. rothschildi (ZB 001) (E), E. rufescens (FP 001) (F), and E. smithii (XZ 001) (G)

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Table 1. Previous and proposed classifications of Eospalax genus

Allen (1940)	Fan & Shi (1982)	Song (1986)	Li & Chen (1989)	Jiang et al (2017)	Wei et al (2021)	Present study
fontanierii	fontanierii	fontanierii	fontanierii	fontanierii	fontanierii	fontanierii
(fontanierii)	cansus	cansus	(fontanierii)	rothschildi	cansus	cansus
(cansus)	(cansus)	rothschildi	(baileyi)	rufescens	baileyi	baileyi
(baileyi)	(rufescens)	rufescens	(cansus)	smithii	rothschildi	smithii
rothschildi	rothschildi	(rufescens)	(rufescens)	cansus	rufescens	rothschildi
smithii	smithii	(baileyi)	rothschildi		smithii	(rothschildi^*)
	baileyi		(rothschildi)			(hubeiensis^*)
			(hubeiensis)			rufescens
			smithii			muliensis
Recognized species (subspecies) are presented, but not synonyms. ^*: These two subspecies were not verified in present study but followed Li & Chen (1989).

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Table 2. Body weight and external and cranial measurements (mm) (mean±SD and ranges) of Eospalax specimens (n) examined in this study

Variable	Eospalax muliensis	E. baileyi	E. cansus	E. fontanierii	E. rothschildi	E. rufescens	E. smithii
	n=14	n=34	n=5	n=1	n=2	n=2^*	n=4
BW	155.64±43.78 118.24–280.22; 12	248.44±73.20 133.63–384.33; 34	N/A	N/A	N/A	N/A	N/A
HB	168.92±14.64 145.00–204.00; 12	191.47±16.03 160.00–220.00; 34	N/A	N/A	N/A	N/A	N/A
TL	52.86±8.82 45.00–70.00; 7	N/A	N/A	N/A	N/A	N/A	N/A
HF	28.00±2.08 25.00–32.00; 7	N/A	N/A	N/A	N/A	N/A	N/A
GLS	40.52±1.83 38.01–45.52; 14	44.43±2.46 40.57–50.18; 32	44.38±3.07 41.45–49.05; 5	50.94	41.83±3.17 39.58–44.07; 2	40.60±4.10 37.70–43.50; 2	48.22±1.88 45.56–49.63; 4
CBL	38.15±1.90 35.55–43.34; 13	42.46±2.53 37.84–48.67; 32	42.17±3.32 39.33–47.09; 5	49.36	39.62±2.26 38.02–41.21; 2	37.82±4.38 34.72–40.91; 2	45.81±1.79 43.43–47.30; 4
BL	35.87±1.83 33.30–40.76; 13	40.14±2.59 35.55–46.44; 32	39.88±3.15 37.26–44.62; 5	46.29	37.58±2.31 35.95–39.21; 2	35.85±4.71 32.52–39.18; 2	43.20±1.86 40.78–44.86; 4
PL	27.02±1.21 25.60–30.39; 14	30.63±1.83 26.62–34.73; 32	30.74±2.32 28.72–34.18; 5	35.93	31.33±2.29 29.71–32.95; 2	26.84±2.49 25.08–28.60; 2	33.07±1.87 30.46–34.59; 4
ZMW	26.25±1.75 23.57–30.60; 14	30.83±2.91 25.75–36.58; 32	29.51±3.21 26.90–33.78; 5	37.01	29.06±3.73 26.42–31.70; 2	27.52±4.51 24.33–30.71; 2	34.76±2.93 30.47–36.88; 4
IOB	7.11±0.32 6.61–7.64; 14	7.80±0.37 6.95–8.37; 32	7.34±0.36 7.01–7.91; 5	8.53	7.81±0.33 7.57–8.04; 2	7.03±0.48 6.69–7.37; 2	8.04±0.27 7.69–8.33; 4
FIB	6.24±0.23 5.80–6.72; 14	8.67±0.76 7.32–10.28; 32	7.73±0.57 7.22–8.35; 5	8.62	7.60±1.03 6.87–8.33; 2	7.10±0.59 6.68–7.52; 2	9.07±0.79 8.04–9.75; 4
RSW	8.99±0.50 8.32–10.31; 14	11.54±0.77 10.22–13.31; 32	10.43±0.95 9.51–11.68; 5	13.84	10.10±1.19 9.26–10.94; 2	9.54±1.75 8.30–10.78; 2	12.26±0.97 11.13–13.23; 4
MTW	23.54±1.31 21.55–26.74; 14	27.70±2.25 23.44–31.77; 32	26.28±1.93 24.09–28.38; 5	35.60	26.11±3.39 23.71–28.50; 2	22.42±2.75 20.47–24.36; 2	29.99±2.31 26.59–31.69; 4
M²–M²	8.82±0.45 8.21–9.74; 14	9.02±0.44 8.37–10.33; 32	8.36±0.34 7.96–8.86; 5	10.21	8.68±0.52 8.31–9.04; 2	8.16±0.73 7.64–8.67; 2	9.24±0.62 8.42–9.88; 4
LUTR	23.94±1.28 22.33–27.45; 14	27.24±1.56 24.50–30.55; 32	27.19±2.12 24.97–29.96; 5	32.47	25.38±1.57 24.27–26.49; 2	24.29±3.00 22.17–26.41; 2	29.29±1.57 27.61–30.86; 4
LUM	8.95±0.46 8.33–10.26; 14	10.28±2.88 9.14–25.93; 32	10.34±0.65 9.70–11.19; 5	11.93	9.80±0.02 9.78–9.81; 2	9.34±1.02 8.62–10.06; 2	10.20±0.66 9.51–10.99; 4
NSL	14.55±1.17 12.41–17.37; 14	17.09±1.24 14.67–19.29; 32	16.40±1.08 15.17–17.98; 5	18.13	15.68±2.14 14.16–17.19; 2	15.60±2.14 14.08–17.11; 2	18.96±1.15 17.38–20.02; 4
BCH	16.20±0.66 15.35–17.80; 14	17.53±1.10 15.86–19.63; 32	16.87±1.51 15.69–18.99; 5	20.94	17.68±2.73 15.75–19.61; 2	14.47±0.78 13.91–15.02; 2	17.63±0.67 16.80–18.18; 4
GBFM	6.51±0.20 6.25–6.99; 13	6.63±0.28 6.04–7.05; 32	6.52±0.33 6.08–6.84; 5	6.96	6.25±0.18 6.12–6.37; 2	6.21±0.18 6.08–6.33; 2	6.58±0.52 5.91–7.19; 4
LAB	8.32±0.39 7.81–9.13; 14	9.27±0.57 8.44–11.08; 32	10.06±0.49 9.26–10.52; 5	11.09	9.19±0.81 8.61–9.76; 2	9.48±0.64 9.03–9.93; 2	10.48±0.25 10.14–10.75; 4
DAB	4.24±0.28 3.75–4.76; 14	4.93±0.89 4.01–9.21; 31	3.73±0.48 3.23–4.29; 5	5.77	3.75±0.29 3.54–3.95; 2	3.15±0.62 2.71–3.58; 2	4.91±0.76 3.88–5.72; 4
MDL	25.17±1.25 23.63–28.48; 14	26.95±1.50 23.71–29.86; 32	28.12±2.49 25.61–31.44; 5	33.40	26.28±1.75 25.04–27.51; 2	25.93±2.91 23.87–27.99; 2	28.59±1.53 27.01–30.08; 4
LBTR	19.65±1.27 18.05–22.68; 14	22.12±1.43 18.55–25.18; 32	21.67±1.43 20.11–23.33; 5	26.23	20.14±2.05 18.69–21.59; 2	19.93±2.86 17.90–21.95; 2	25.15±1.05 24.17–26.25; 4
LLM	9.43±0.46 8.81–10.34; 14	10.02±0.35 9.29–10.57; 32	10.39±0.61 9.68–11.23; 5	12.39	10.05±0.06 10.00–10.09; 2	10.25±1.16 9.43–11.07; 2	10.73±0.59 9.96–11.39; 4
LLI	8.59±1.51 6.40–10.84; 14	11.61±2.00 7.97–15.95; 32	10.11±1.72 7.80–12.05; 5	13.53	8.82±2.65 6.94–10.69; 2	10.22±2.79 8.24–12.19; 2	15.63±0.86 14.83–16.53; 4
Character abbreviations (unless specifically, all in mm): BW: Body weight (grams); HB: Head and body length; TL: Tail length; HF: Hindfoot length; GLS: Greatest length of skull; CBL: Condylobasal length; BL: Basal length; PL: Palatal length; ZMW: Zygomatic width; IOB: Interorbital breadth; FIB: Foramen infraorbital breadth; RSW: Rostrum width; MTW: Mastoid width; M²–M²: Maximum width across the upper second molars; LUTR: Length of upper tooth row; LUM: Length of upper molars; NSL: Nasal length; BCH: Braincase height; GBFM: Greatest breadth of the foramen magnum; LAB: Length of auditory bulla; DAB: Distance between auditory bulla; MDL: Mandibular length; LBTR: Length of below toothrow; LLM: Length of lower molars; LLI: Length of lower incisor. ^*: The smaller value is from a subadult individual. N/A: Not available.

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