基于线粒体基因的新疆托氏兔遗传多样性和种群遗传结构评价

doi:10.11843/j.issn.0366-6964.2022.01.011

Abstract

Abstract: The purpose of this study is to evaluate the level of genetic diversity and explore the genetic structure between subspecies of Lepus tolai in Xinjiang by molecular genetics methods. In this study, the CO1 and D-LOOP gene sequences of mitochondrial DNA were obtained from 78 Tolai hares from the northern, northwestern, central and eastern regions of Xinjiang by PCR amplification and sequencing, and then the data were analyzed by bioinformatics methods. The results showed that 68 haplotypes were defined from the combined sequence of 78 samples of Xinjiang Tolai hare, and relatively high haplotype diversity (h=0.996±0.002) and nucleotide diversity (π=0.049±0.023) were detected. The phylogenetic relationship and median-joining network showed that the Tolai hare samples used in this study were divided into three branches (Clade A-C), in which Clade A and C contained the majority of hares from the northern and northwest groups of Xinjiang, belong to the Lepus tolai lehmanni, while the majority of hares in Clade B were from the central and eastern regions of Xinjiang, belong to the Lepus tolai centrasiaticus. Except for few mixed samples of Tolai hare, the clustering of the rest majority was consistent with their distribution range and geographical distance. The results of AMOVA analysis, Fst and gene flow showed that the genetic differentiation between subspecies of Tolai hare was larger and the gene flow was smaller, while the genetic differentiation within subspecies was relatively small and the gene flow was relatively large. The results of neutral test showed that the Tajima’D value of Xinjiang Tolai hare population was 1.075 (P>0.05), and Fu`s Fs was -15.100 (P<0.01). The mismatch distribution of nucleotide indicated a multi-peak phenomenon, and EBSPs analysis showed that the population expansion occurred at about 0.01 Ma. The results of comprehensive analysis based on CO1 and D-LOOP gene showed that Xinjiang Tolai hare was rich in genetic diversity and had an obvious systematic geographical distribution pattern. There was a strong gene flow and a small genetic differentiation between northern and northwest groups of L. t. lehmanni. However, there was a distinct differentiation between the central and eastern groups of L. t. centrasiaticus, which was probably due to the greater geographical distance. In addition, Tolai hare has recently experienced a population expansion.

Key words: Xinjiang Lepus tolai, CO1, D-LOOP, genetic diversity, genetic structure

CLC Number:

S829.1

MAMAT Miregul, ZHOU Shiyu, LIU Peng, MENG Yang, NIE Wenyue, TENG Peichen, SHAN Wenjuan. Evaluation of Genetic Diversity and Population Genetic Structure of Tolai Hare in Xinjiang Based on Mitochondrial DNA[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(1): 112-121.

References 36

[1]	SMITH A T,XIE Y.A guide to the mammals of China[M].Princeton:Princeton University Press,2008.
[2]	相雨,杨奇森,夏霖.中国兔属动物的分类现状和分布[J].四川动物,2004,23(4):391-397.XIANG Y,YANG Q S,XIA L.Distribution and taxonomy of genus Lepus (Hares) in China[J].Sichuan Journal of Zoology,2004,23(4):391-397.(in Chinese)
[3]	罗泽珣.中国野兔[M].北京:中国林业出版社,1988.LUO Z X.The Chinese hare[M].Beijing:China Forestry Publishing House,1988.(in Chinese)
[4]	WU C H,WU J P,BUNCH T D,et al.Molecular phylogenetics and biogeography of Lepus in eastern Asia based on mitochondrial DNA sequences[J].Mol Phylogenet Evol,2005,37(1):45-61.
[5]	WANG J L,YANG G.Complete mitogenome of cape hare Lepus capensis (Lagomorpha:Leporidae) and its phylogenetic considerations[J].Acta Theriol Sin,2012,32(1):1-11.
[6]	程承,葛德燕,夏霖,等.中国“草兔”头骨的形态计量学研究[J].兽类学报,2012,32(4):275-286.CHENG C,GE D Y,XIA L,et al.Morphometrics study on the so called ‘Cape hare’ (Lagomorpha:Leporidae:Lepus) in China[J].Acta Theriologica Sinica,2012,32(4):275-286.(in Chinese)
[7]	SMITH A T,JOHNSTON C H,ALVES P C,et al.Lagomorphs:pikas,rabbits,and hares of the world[M].Baltimore:Johns Hopkins University Press,2018.
[8]	单文娟,代慧英,张玉琮.基于线粒体基因的新疆三种野兔分类及遗传多样性[J].畜牧兽医学报,2020,51(10):2403-2412.SHAN W J,DAI H Y,ZHANG Y C.Classification and genetic diversity of three hare species in Xinjiang based on mitochondrial DNA[J].Acta Veterinaria et Zootechnica Sinica,2020,51(10):2403-2412.(in Chinese)
[9]	LIU J,YU L,ARNOLD M L,et al.Reticulate evolution:frequent introgressive hybridization among Chinese hares (genus lepus) revealed by analyses of multiple mitochondrial and nuclear DNA loci[J].BMC Evol Biol,2011,11(1):223.
[10]	WU Y H,XIA L,ZHANG Q,et al.Bidirectional introgressive hybridization between Lepus capensis and Lepus yarkandensis[J].Mol Phylogenet Evol,2011,59(3):545-555.
[11]	单文娟,刘江,马合木提·哈力克.新疆草兔的种群遗传结构和亚种分化[J].动物学研究,2011,32(2):179-187.SHAN W J,LIU J,HALIK M.Genetic structure and subspecies divergence of Lepus capensis in Xinjiang[J].Zoological Research,2011,32(2):179-187.(in Chinese)
[12]	SHAN W J,TURSUN M,ZHOU S Y,et al.The complete mitochondrial genome sequence of Lepus tolai in Xinjiang[J]. Mitochondrial DNA B,2020,5(2):1336-1337.
[13]	张玉琮,曾婉琴,许盼,等.新疆野兔DNA条形码筛选[J].畜牧兽医学报,2020,51(2):270-278.ZHANG Y C,ZENG W Q,XU P,et al.The screening of DNA barcode for hares in Xinjiang[J].Acta Veterinaria et Zootechnica Sinica,2020,51(2):270-278.(in Chinese)
[14]	张玉琮,代慧英,单文娟.基于SRY基因鉴定新疆野兔性别[J].野生动物学报,2019,40(1):83-86.ZHANG Y C,DAI H Y,SHAN W J.Sex identification of Hares in Xinjiang based on SRY gene[J].Chinese Journal of Wildlife, 2019,40(1):83-86.(in Chinese)
[15]	代慧英,单文娟.基于头骨形态指标的新疆野兔年龄鉴定[J].黑龙江畜牧兽医,2021(1):138-141.DAI H Y,SHAN W J.Age identification of Xinjiang hare based on skull morphology indexes[J].Heilongjiang Animal Science and Veterinary Medicine,2021(1):138-141.(in Chinese)
[16]	潘清华,王应祥,岩崑.中国哺乳动物彩色图鉴[M].北京:中国林业出版社,2007.PAN Q H,WANG Y X,YAN K.A field guide to the mammals of China[M].Beijing:China Forestry Press House,2007.(in Chinese)
[17]	常卫利,兰文旭.阿勒泰严厉打击非法捕猎蒙古兔行动初见成效[J].新疆林业,2009(1):16.CHANG W L,LAN W X.Altay to crack down on illegal hunting of Tolai hare action has achieved initial results[J].Forestry of Xinjiang,2009(1):16.(in Chinese)
[18]	SHAN W J,LIU J,YU L,et al.Genetic consequences of postglacial colonization by the endemic Yarkand hare (Lepus yarkandensis) of the arid Tarim Basin[J].Chin Sci Bull,2011,56(13):1370-1382.
[19]	LARKIN M A,BLACKSHIELDS G,BROWN N P,et al.Clustal W and clustal X version 2.0[J].Bioinformatics, 2007,23(21): 2947-2948.
[20]	KUMAR S,STECHER G,LI M,et al.MEGA X:molecular evolutionary genetics Analysis across computing platforms[J].Mol Biol Evol,2018,35(6):1547-1549.
[21]	ZHANG D,GAO F L,JAKOVLIĆ I,et al.PhyloSuite:an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies[J].Mol Ecol Resour,2020,20(1):348-355.
[22]	LIBRADO P,ROZAS J.DnaSP v5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics, 2009,25(11):1451-1452.
[23]	EXCOFFIER L,LISCHER H E L.Arlequin suite ver 3.5:a new series of programs to perform population genetics analyses under Linux and Windows[J].Mol Ecol Resour,2010,10(3):564-567.
[24]	WLEIGH J W,BRYANT D.POPART:full-feature software for haplotype network construction[J].Methods Ecol Evol,2015, 6(9):1110-1116.
[25]	洪波,张锋,陈志杰,等.基于微卫星标记的中国枣食芽象甲地理种群遗传多样性分析[J].昆虫学报,2019,62(3):381-390.HONG B,ZHANG F,CHEN Z J,et al.Analysis of the genetic diversity of Scythropus yasumatsui (Coleoptera:Curculionidae) populations in China based on microsatellite markers[J].Acta Entomologica Sinica,2019,62(3):381-390.(in Chinese)
[26]	BOUCKAERT R,HELED J,KÜHNERT D,et al.BEAST 2:a software platform for Bayesian evolutionary analysis[J].PLoS Comput Biol,2014,10(4):e1003537.
[27]	MINOUDI S,PAPAPETRIDIS I,KARAISKOU N,et al.Genetic analyses of brown hare (Lepus europaeus) support limited migration and translocation of Greek populations[J].PLoS One,2018,13(10):e0206327.
[28]	KUMAR B,CHENG J L,GE D Y,et al.Phylogeography and ecological niche modeling unravel the evolutionary history of the Yarkand hare,Lepus yarkandensis (Mammalia:Leporidae),through the Quaternary[J].BMC Evol Biol,2019,19(1):113.
[29]	伊拉木江·托合塔洪,阿迪力·艾合麦提,单文娟,等.新疆兔属三物种潜在生境分布及未来气候变化的影响[J].野生动物学报,2020,41(1):70-79.TUOHETAHONG Y,AHMAT A,SHAN W J,et al.Potential habitat distribution of three species of Lepus in Xinjiang and effects of future climate change[J].Chinese Journal of Wildlife,2020,41(1):70-79.(in Chinese)
[30]	向颖,董婉未,蒋国芳,等.基于线粒体基因和核基因的中华虎凤蝶指名亚种地理种群遗传分化分析[J].昆虫学报,2020,63(11):1377-1384.XIANG Y,DONG W W,JIANG G F,et al.Analysis of the genetic differentiation among geographical populations of Luehdorfia chinensis chinensis (Lepidoptera:Papilionidae) based on mitochondrial gene and nuclear genes[J].Acta Entomologica Sinica,2020,63(11):1377-1384.(in Chinese)
[31]	张桂宁,方弟安,薛向平,等.基于细胞色素B(Cytb)基因对翘嘴鲌不同群体遗传多样性的分析[J].中国农学通报,2021,37(23):118-124.ZHANG G N,FANG D A,XUE X P,et al.Culter alburnus basilewsky in different populations:genetic diversity analysis based on Cytochrome B (Cytb) gene[J].Chinese Agricultural Science Bulletin,2021,37(23):118-124.(in Chinese)
[32]	SU B,FU Y X,WANG Y X,et al.Genetic diversity and population history of the red Panda (Ailurus fulgens) as inferred from mitochondrial DNA sequence variations[J].Mol Biol Evol,2001,18(6):1070-1076.
[33]	张玉宁,章群,黄柏炎,等.基于线粒体COⅠ基因序列的中国沿海缘边银鲈遗传多样性分析[J].海洋渔业,2021,43(2):129-136.ZHANG Y N,ZHANG Q,HUANG B Y,et al.MtDNA COⅠ sequence diversity of Gerres limbatus in coastal waters of China[J].Marine Fisheries,2021,43(2):129-136.(in Chinese)
[34]	安成邦,王伟,刘依,等.新疆全新世环境变迁与史前文化交流[J].中国科学:地球科学,2020,50(5):677-687.AN C B,WANG W,LIU Y,et al.The Holocene environmental change in Xinjiang and its impact on prehistoric cultural exchange[J].Scientia Sinica Terrae,2020,50(5):677-687.(in Chinese)
[35]	范义姣,马箫忆,刘慧,等.黄土记录的中亚干旱区东部全新世气候与环境演化[J].冰川冻土,2021,43(3):818-826.FAN Y J,MA X Y,LIU H,et al.Climatic and environmental evolution during the Holocene in the eastern Arid Central Asia recorded by loess-paleosol sequences[J].Journal of Glaciology and Geocryology,2021,43(3):818-826.(in Chinese)
[36]	CHEN F H,JIA J,CHEN J H,et al.A persistent Holocene wetting trend in arid central Asia,with wettest conditions in the late Holocene,revealed by multi-proxy analyses of loess-paleosol sequences in Xinjiang,China[J].Quaternary Sci Rev,2016,146: 134-146.

Evaluation of Genetic Diversity and Population Genetic Structure of Tolai Hare in Xinjiang Based on Mitochondrial DNA

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