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Xi-Yao Ma, Tiao Ning, Adeniyi C. Adeola, Jie Li, Ali Esmailizadeh, Jacqueline K. Lichoti, Bernard R. Agwanda, Jainagul Isakova, Almaz A. Aldashev, Shi-Fang Wu, He-Qun Liu, Najmudinov Tojiddin Abdulloevich, Manilova Elena Afanasevna, Khudoidodov Behruz Ibrohimovich, Rahamon Akinyele Moshood Adedokun, Sunday Charles Olaogun, Oscar J. Sanke, Godwin F. Mangbon, Xi Chen, Wei-Kang Yang, Zhe Wang, Min-Sheng Peng, Sheila C. Ommeh, Yan Li, Ya-Ping Zhang. Potential dual expansion of domesticated donkeys revealed by worldwide analysis on mitochondrial sequences. Zoological Research, 2020, 41(1): 51-60. doi: 10.24272/j.issn.2095-8137.2020.007
Citation: Xi-Yao Ma, Tiao Ning, Adeniyi C. Adeola, Jie Li, Ali Esmailizadeh, Jacqueline K. Lichoti, Bernard R. Agwanda, Jainagul Isakova, Almaz A. Aldashev, Shi-Fang Wu, He-Qun Liu, Najmudinov Tojiddin Abdulloevich, Manilova Elena Afanasevna, Khudoidodov Behruz Ibrohimovich, Rahamon Akinyele Moshood Adedokun, Sunday Charles Olaogun, Oscar J. Sanke, Godwin F. Mangbon, Xi Chen, Wei-Kang Yang, Zhe Wang, Min-Sheng Peng, Sheila C. Ommeh, Yan Li, Ya-Ping Zhang. Potential dual expansion of domesticated donkeys revealed by worldwide analysis on mitochondrial sequences. Zoological Research, 2020, 41(1): 51-60. doi: 10.24272/j.issn.2095-8137.2020.007

Potential dual expansion of domesticated donkeys revealed by worldwide analysis on mitochondrial sequences

doi: 10.24272/j.issn.2095-8137.2020.007

Potential dual expansion of domesticated donkeys revealed by worldwide analysis on mitochondrial sequences

Funds: This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA2004010302), Second Tibetan Plateau Scientific Expedition and Research (STEP) Program (2019QZKK0501), National Natural Science Foundation of China (31860305), Sino-Africa Joint Research Center, Chinese Academy of Sciences (SAJC201611), and Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences. Y.L. was supported by the Young Academic and Technical Leader Raising Foundation of Yunnan Province. Samples used in this study were provided by the Animal Branch of the Germplasm Bank of Wild Species, Chinese Academy of Sciences (Large Research Infrastructure Funding)
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    #Authors contributed equally to this work
  • Figure  1.  mtDNA genome phylogeny of Equus

    A: Neighbor-joining tree; B: Maximum likelihood tree; C: Bayesian tree. Colored branches denote different categories. Red: Horse; Green: Asiatic wild ass; Yellow: Somali wild ass; Blue: Clade I lineage; Magenta: Clade II lineage.

    Figure  2.  Population characteristics between Clade I and Clade II lineages

    A: Sequence variation of mtDNA genome within each lineage. Nucleotide diversity (π) using 200 nt windows (step size=100 nt) centered at midpoint. Schematic (linearized) genetic map of mitochondrial genome is presented. B: Demographic histories for each lineage estimated using Bayesian skyline plot from mitochondrial genomes. Shadow means 95% highest posterior density intervals of effective number of females. C: Mismatch distribution for each mtDNA lineage. D: Median-joining network based on D-loop region. Red diamonds are haplotypes of horse outgroup. Green circles are haplotypes of Asiatic wild ass. Dark red circles are haplotypes of Somali wild ass. Indigo circles are haplotypes of Clade I lineage. Magenta circles are haplotypes of Clade II lineage. Circle size is proportional to frequencies of haplotypes.

    Figure  3.  Worldwide geographic distribution of two lineages plotted using “rworldmap” package in R (A) and genetic diversity of Clade I (B) and Clade II (C) lineages across China

    A: Blue: Clade I lineage; Magenta: Clade II lineage. B: Dark to light indigo indicates diversity decay. Gray regions indicate no samples available. C: Dark to light magenta indicates diversity decay. Gray regions indicate no samples available.

    Table  1.   Genetic distance and nucleotide diversity of two clades

    Pairwise distanceSD (distance)PiSD (Pi)
    Clade I lineage1.932 71.100 70.008 40.000 3
    Clade II lineage1.074 40.711 20.004 60.000 5
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  • 收稿日期:  2019-07-03
  • 刊出日期:  2020-01-01

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