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

Tao Zhang, Meng-Long Lei, Hao Zhou, Zhong-Zheng Chen, Peng Shi. 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. Zoological Research, 2022, 43(3): 331-342. doi: 10.24272/j.issn.2095-8137.2022.045
Citation: Tao Zhang, Meng-Long Lei, Hao Zhou, Zhong-Zheng Chen, Peng Shi. 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. Zoological Research, 2022, 43(3): 331-342. 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

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

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
  • 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。
  • 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.

    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.

    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.

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

    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)

    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
    fontanieriifontanieriifontanieriifontanieriifontanieriifontanieriifontanierii
    (fontanierii)cansuscansus(fontanierii)rothschildicansuscansus
    (cansus)(cansus)rothschildi(baileyi)rufescensbaileyibaileyi
    (baileyi)(rufescens)rufescens(cansus)smithiirothschildismithii
    rothschildirothschildi(rufescens)(rufescens)cansusrufescensrothschildi
    smithiismithii(baileyi)rothschildismithii(rothschildi*)
    baileyi(rothschildi)(hubeiensis*)
    (hubeiensis)rufescens
    smithiimuliensis
    Recognized species (subspecies) are presented, but not synonyms. *: These two subspecies were not verified in present study but followed Li & Chen (1989).
    下载: 导出CSV

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

    VariableEospalax muliensisE. baileyiE. cansusE. fontanieriiE. rothschildiE. rufescensE. smithii
    n=14n=34n=5n=1n=2n=2*n=4
    BW155.64±43.78
    118.24–280.22; 12
    248.44±73.20
    133.63–384.33; 34
    N/AN/AN/AN/AN/A
    HB168.92±14.64
    145.00–204.00; 12
    191.47±16.03
    160.00–220.00; 34
    N/AN/AN/AN/AN/A
    TL52.86±8.82
    45.00–70.00; 7
    N/AN/AN/AN/AN/AN/A
    HF28.00±2.08
    25.00–32.00; 7
    N/AN/AN/AN/AN/AN/A
    GLS40.52±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
    50.9441.83±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
    CBL38.15±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
    49.3639.62±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
    BL35.87±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
    46.2937.58±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
    PL27.02±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
    35.9331.33±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
    ZMW26.25±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
    37.0129.06±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
    IOB7.11±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
    8.537.81±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
    FIB6.24±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
    8.627.60±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
    RSW8.99±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
    13.8410.10±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
    MTW23.54±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
    35.6026.11±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–M28.82±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
    10.218.68±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
    LUTR23.94±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
    32.4725.38±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
    LUM8.95±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
    11.939.80±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
    NSL14.55±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
    18.1315.68±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
    BCH16.20±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
    20.9417.68±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
    GBFM6.51±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
    6.966.25±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
    LAB8.32±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
    11.099.19±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
    DAB4.24±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
    5.773.75±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
    MDL25.17±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
    33.4026.28±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
    LBTR19.65±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
    26.2320.14±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
    LLM9.43±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
    12.3910.05±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
    LLI8.59±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
    13.538.82±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.
    下载: 导出CSV
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  • 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

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