新疆卡拉麦里山有蹄类自然保护区蒙古野驴mtDNA D-loop区的遗传多样性及系统发育研究
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摘要
蒙古野驴是生活在亚洲中部荒漠、半荒漠和荒漠草原重要的珍稀有蹄类动物。采用PCR和测序技术,我们成功测定新疆卡拉麦里山有蹄类自然保护区日常监测时获得的26匹蒙古野驴(Equus hemionus)样本的mt DNA D-loop区核酸序列,对蒙古野驴的遗传多样性及其系统发育地位进行了初步研究。研究结果发现该区域蒙古野驴核苷酸多样性较高(π=0. 20392±0. 05230),单倍型多样性与其他马科动物大致相同(Hd=0. 982±0. 020)。表明新疆卡拉麦里有蹄类自然保护区蒙古野驴的遗传多样性十分丰富。Tajima's D值为负,中性检验不显著(P> 0. 10),表明新疆卡拉麦里山有蹄类自然保护区的蒙古野驴在整体水平上并未出现过瓶颈效应或者快速扩张等历史事件。采用邻接法(NJ)和最大似然法(ML)构建单倍型之间的进化树,结合Network构建的单倍型间网络图显示2个重要分支。我们通过历史分布及地理位置推测卡拉麦里山有蹄类自然保护区的蒙古野驴可能存在外来种群的迁入。将本研究得到的蒙古野驴序列与Gen Bank检索获得的另外7种马科动物的mt DNA D-loop区基因进行比较,发现马科动物分化过程中平原斑马出现最早,山斑马首先分离出来,然后是蒙古野驴、藏野驴、努比亚野驴、细纹斑马,最后是普氏野马与非洲野马,其中与蒙古野驴最接近的物种是藏野驴。
Khulan( Equus hemionus) is a rare and endangered desert ungulates species and mainly lives in the desert and semi-desert of Eurasian areas. Using PCR and sequencing technology,we successfully determined the nucleic acid sequence in the mt DNA D-loop region of 26 khulan samples obtained during routine monitoring in the Hoofed Nature Reserve of Kalamarishan in Xinjiang.We studied the genetic diversity and phylogenetic status of Equus hemionus. The results showed that the nucleotide diversity of khulan was relatively high( π = 0. 20392 ± 0. 05230),and the haplotype diversity was roughly the same as that of other equine species( Hd = 0. 982 ± 0. 020). This showed that the genetic diversity of khulan was very rich in Mountain Kalamaili Ungulate Nature Reserve in Xinjiang. The value of Tajima's D was negative,the neutral test was not significant( P >0. 10),indicating that the khulan in Mountain Kalamaili Ungulate Nature Reserve in Xinjiang did not have the bottle-neck effect or rapid expansion and other historical events in the overall level. The evolution tree between haplotypes was constructed by using the adjacency( NJ) and maximum likelihood( ML) methods. The graph of the haplotype internetwork constructed by combining networks showed two important branches. Based on the historical distribution and geographical location,we speculate that the khulan in the Hoofed Nature Reserve of Karamari mountain may include an imported population. The sequences obtained in this study of khulan were compared with the mt DNA D-loop region genes of 7 other equine species obtained by Genbank retrieval. We found that Equus quagga first appeared in the differentiation of the equine animals,Equus zebra first separated,followed by Equus hemionus, Equus kiang, Equus asinus africanus, then Equus grevyi,and finally Equus przewalskii and Equus ferus. Khulan( Equus hemionus) had the closest relationship with the Equus kiang.
Khulan( Equus hemionus) is a rare and endangered desert ungulates species and mainly lives in the desert and semi-desert of Eurasian areas. Using PCR and sequencing technology,we successfully determined the nucleic acid sequence in the mt DNA D-loop region of 26 khulan samples obtained during routine monitoring in the Hoofed Nature Reserve of Kalamarishan in Xinjiang.We studied the genetic diversity and phylogenetic status of Equus hemionus. The results showed that the nucleotide diversity of khulan was relatively high( π = 0. 20392 ± 0. 05230),and the haplotype diversity was roughly the same as that of other equine species( Hd = 0. 982 ± 0. 020). This showed that the genetic diversity of khulan was very rich in Mountain Kalamaili Ungulate Nature Reserve in Xinjiang. The value of Tajima's D was negative,the neutral test was not significant( P >0. 10),indicating that the khulan in Mountain Kalamaili Ungulate Nature Reserve in Xinjiang did not have the bottle-neck effect or rapid expansion and other historical events in the overall level. The evolution tree between haplotypes was constructed by using the adjacency( NJ) and maximum likelihood( ML) methods. The graph of the haplotype internetwork constructed by combining networks showed two important branches. Based on the historical distribution and geographical location,we speculate that the khulan in the Hoofed Nature Reserve of Karamari mountain may include an imported population. The sequences obtained in this study of khulan were compared with the mt DNA D-loop region genes of 7 other equine species obtained by Genbank retrieval. We found that Equus quagga first appeared in the differentiation of the equine animals,Equus zebra first separated,followed by Equus hemionus, Equus kiang, Equus asinus africanus, then Equus grevyi,and finally Equus przewalskii and Equus ferus. Khulan( Equus hemionus) had the closest relationship with the Equus kiang.
引文
[1]高行宜.新疆的珍稀动物——野驴[J].干旱区研究,1987,48(3):46.
[2]彭向前.卡拉麦里山蒙古野驴的现状与保护[J].野生动物学报,2015,36(2):162-165.
[3]汪松.中国濒危动物红皮书[M].北京:科学出版社,1998.
[4]楚国忠,梁崇歧,阮云秋,等.卡拉麦里山有蹄类野生动物保护区野驴的夏季栖息地及种群数量[J].动物学报,1985,31(2):178-186.
[5]葛炎,刘楚光,初红军,等.新疆卡拉麦里山自然保护区蒙古野驴的资源现状[J].干旱区研究,2003,20(1):32-34,66.
[6]岳建兵,胡德夫,彭向前,等.卡拉麦里山有蹄类自然保护区蒙古野驴的数量与分布[J].林业资源管理,2008(5):111-115.
[7]初红军,蒋志刚,葛炎,等.卡拉麦里山有蹄类自然保护区蒙古野驴和鹅喉羚种群密度和数量[J].生物多样性,2009,17(4):414-422.
[8]刘伟,杨维康,黄怡,等.蒙古野驴(Equus hemionus)昼间行为时间分配初探[J].干旱区地理,2012,35(4):607-614.
[9]吴洪潘,初红军,王渊,等.卡拉麦里山有蹄类自然保护区水源地蒙古野驴的活动节律:基于红外相机监测数据[J].生物多样性,2014,22(6):752-757.
[10]岳建兵.卡拉麦里有蹄类自然保护区蒙古野驴的种群数量分布及食性选择的研究[D].北京:北京林业大学,2006.
[11]初红军,蒋志刚,兰文旭,等.蒙古野驴、鹅喉羚和家畜的食物重叠[J].动物学报,2008,54(6):941-954.
[12]刘伟,杨维康,徐文轩.蒙古野驴的秋季食性分析[J].兽类学报,2008,28(1):33-36.
[13]徐文轩,杨维康,乔建芳.卡拉麦里山自然保护区蒙古野驴的食性[J].兽类学报,2009,29(4):427-431.
[14] Feh C,Munkhtuya B,Enkhbold S,et al. Ecology and social structure of the Gobi khulan Equus hemionus subsp in the Gobi B National Park,Mongolia[J]. Biological Conservation,2001,101(1):51-61.
[15] Kaczensky P,Kuehn R,Lhagvasuren B,et al. Connectivity of the asiatic wild ass population in the Mongolian Gobi[J]. Biological Conservation,2011,144(2):920-929.
[16]海棠,黄金龙,赵一萍,等.蒙古家马和蒙古野马mt DNA Dloop区遗传多样性及母系起源分析[J].黑龙江畜牧兽医,2014(9):68-70.
[17] Ivankovic A,Kavar T,Caput P,et al. Genetic diversity of three donkey populations in the Croatian coastal region[J]. Animal Genetics,2015,33(3):169-177.
[18] Rosel P E,Haygood M G,Perrin W F. Phylogenetic relationships among the true porpoises(Cetacea:Phocoenidae)[J]. Molecular Phylogenetics and Evolution,1995,4(4):463-474.
[19]刘小艳,张家骅. mt DNA D-loop在家畜遗传多样性和系统分化中的应用[J].四川畜牧兽医,2007,34(11):25-26.
[20]周慧,李迪强,张于光,等.藏羚羊mt DNA D-loop区遗传多样性研究[J].遗传,2006,28(3):299-305.
[21]郭彦斌,刘丑生,王慧,等.利用mt DNA D-loop区研究中国10个绵羊品种的遗传多样性与起源[J].农业生物技术学报,2012,20(7):799-806.
[22]初红军.卡拉麦里山有蹄类自然保护区蒙古野驴(Equus hemionus)和鹅喉羚(Gazella subgutturosa)食性、种群和栖息地研究[D].西宁:中国科学院西北高原生物研究所,2008.
[23] Luo Yongjun,Chen Yu,Liu Fuyu,et al. Mitochondrial genome sequence of the Tibetan wild ass(Equus kiang)[J]. Mitochondrial DNA,2011,22(1/2):6-8.
[24]王小斌,秦芳,张云生,等.蒙古马mt DNA D-loop区遗传多样性与多重母系起源[J].西北农林科技大学学报:自然科学版,2010,38(3):47-51.
[25]阿地力江·卡德尔.新疆地方马品种与普氏野马(E. przewalskii)mt DNA遗传多样性及亲缘关系研究[D].乌鲁木齐:新疆大学,2008.
[26] Khaire D,Atkulwar A,Farahand S,et al. Low genetic diversity of the endangered Indian wild ass Equus hemionus khur,as revealed by microsatellite analyses[J]. Journal of Genetics,2017,96(S1):31-34.
[27] Nasiri-Moghadam N, Aliabadian M, Kaboli M, et al. Genetic structure of the Persian wild ass(Equus hemionus onager)in Touran Biosphere Reserve and Bahram-e-goor Protected Area[J]. Taxonomy&Biosystematics,2014,6(18):3.
[28] Brown G G,Gadaleta G,Pepe G,et al. Structural conservation and variation in the D-loop-containing region of vertebrate mitochondrial DNA[J]. Journal of Molecular Biology,1986,192(3):503-511.
[29] Burt W H,Ellerman J R,Morrison-Scott T C S. Check list of palaearctic and Indian mammals[J]. Journal of Mammalogy,1952,33(3):401.
[30]中国科学院青海甘肃综合考察队.青海甘肃兽类调查报告[M].北京:科学出版社,1964.
[31] Corbet G B. The mammals of the Palaearctic Region:a taxonomic review[J]. Quarterly Review of Biology,1978,60(3078):1-113.
[32]冯祚建,蔡桂全,郑昌琳.西藏哺乳类名录[J].兽类学报,1984,4(4):341-358.
[33]郑生武.中国西北地区珍稀濒危动物志[M].北京:中国林业出版社,1994.
[34] GRoves C P,Mazák V. On some taxonomic problems of Asiatic wild asses; with the description of a new subspecies(Perissodactyla;Equidae)[J]. Zeitschrift für Sugetierkunde,1967,32:321-355.
[35] Ryder O A,Chemnick L G. Chromosomal and molecular evolution in Asiatic wild asses[J]. Genetica,1990,83(1):67-72.
[36] Steiner C C,Mitelberg A,Tursi R,et al. Molecular phylogeny of extant equids and effects of ancestral polymorphism in resolving species-level phylogenies[J]. Molecular Phylogenetics and Evolution,2012,65(2):573-581.
[37] Vilstrup J T,Seguin-Orlando A,Stiller M A,et al. Mitochondrial phylogenomics of modern and ancient equids[J]. PLo S One,2013,8(2):e55950.
[38] Rosenbom S,Costa V,Chen Shanyuan,et al. Reassessing the evolutionary history of ass-like equids:insights from patterns of genetic variation in contemporary extant populations[J]. Molecular Phylogenetics and Evolution,2015,85:88-96.
[39] Khaire D,Atkulwar A,Farah S,et al. Mitochondrial DNA analyses revealed low genetic diversity in the endangered Indian wild ass Equus hemionus khur[J]. Mitochondrial DNA Part A,2017,28(5):681-686.
[40] Orlando L,Mashkour M,Burke A,et al. Geographic distribution of an extinct equid(Equus hydruntinus:Mammalia, Equidae)revealed by morphological and genetical analyses of fossils[J]. Molecular Ecology,2006,15(8):2083-2093.
[41] Jansen T,Forster P,Levine M A,et al. Mitochondrial DNA and the origins of the domestic horse[J]. Proceedings of the National Academy of Sciences of the United States of America,2002,99(16):10905-10910.
[42] Mashima S. Mitochondrial DNA sequences of various species of the genus Equus with special reference to the phylogenetic relationship between Przewalskii's wild horse and domestic horse[J]. Journal of Molecular Evolution,1995,41(2):180-188.
[43] Orlando L,Metcalf J L,Alberdi M T,et al. Revising the recent evolutionary history of equids using ancient DNA[J]. Proceedings of the National Academy of Sciences of the United States of America,2009,106(51):21754-21759.
[2]彭向前.卡拉麦里山蒙古野驴的现状与保护[J].野生动物学报,2015,36(2):162-165.
[3]汪松.中国濒危动物红皮书[M].北京:科学出版社,1998.
[4]楚国忠,梁崇歧,阮云秋,等.卡拉麦里山有蹄类野生动物保护区野驴的夏季栖息地及种群数量[J].动物学报,1985,31(2):178-186.
[5]葛炎,刘楚光,初红军,等.新疆卡拉麦里山自然保护区蒙古野驴的资源现状[J].干旱区研究,2003,20(1):32-34,66.
[6]岳建兵,胡德夫,彭向前,等.卡拉麦里山有蹄类自然保护区蒙古野驴的数量与分布[J].林业资源管理,2008(5):111-115.
[7]初红军,蒋志刚,葛炎,等.卡拉麦里山有蹄类自然保护区蒙古野驴和鹅喉羚种群密度和数量[J].生物多样性,2009,17(4):414-422.
[8]刘伟,杨维康,黄怡,等.蒙古野驴(Equus hemionus)昼间行为时间分配初探[J].干旱区地理,2012,35(4):607-614.
[9]吴洪潘,初红军,王渊,等.卡拉麦里山有蹄类自然保护区水源地蒙古野驴的活动节律:基于红外相机监测数据[J].生物多样性,2014,22(6):752-757.
[10]岳建兵.卡拉麦里有蹄类自然保护区蒙古野驴的种群数量分布及食性选择的研究[D].北京:北京林业大学,2006.
[11]初红军,蒋志刚,兰文旭,等.蒙古野驴、鹅喉羚和家畜的食物重叠[J].动物学报,2008,54(6):941-954.
[12]刘伟,杨维康,徐文轩.蒙古野驴的秋季食性分析[J].兽类学报,2008,28(1):33-36.
[13]徐文轩,杨维康,乔建芳.卡拉麦里山自然保护区蒙古野驴的食性[J].兽类学报,2009,29(4):427-431.
[14] Feh C,Munkhtuya B,Enkhbold S,et al. Ecology and social structure of the Gobi khulan Equus hemionus subsp in the Gobi B National Park,Mongolia[J]. Biological Conservation,2001,101(1):51-61.
[15] Kaczensky P,Kuehn R,Lhagvasuren B,et al. Connectivity of the asiatic wild ass population in the Mongolian Gobi[J]. Biological Conservation,2011,144(2):920-929.
[16]海棠,黄金龙,赵一萍,等.蒙古家马和蒙古野马mt DNA Dloop区遗传多样性及母系起源分析[J].黑龙江畜牧兽医,2014(9):68-70.
[17] Ivankovic A,Kavar T,Caput P,et al. Genetic diversity of three donkey populations in the Croatian coastal region[J]. Animal Genetics,2015,33(3):169-177.
[18] Rosel P E,Haygood M G,Perrin W F. Phylogenetic relationships among the true porpoises(Cetacea:Phocoenidae)[J]. Molecular Phylogenetics and Evolution,1995,4(4):463-474.
[19]刘小艳,张家骅. mt DNA D-loop在家畜遗传多样性和系统分化中的应用[J].四川畜牧兽医,2007,34(11):25-26.
[20]周慧,李迪强,张于光,等.藏羚羊mt DNA D-loop区遗传多样性研究[J].遗传,2006,28(3):299-305.
[21]郭彦斌,刘丑生,王慧,等.利用mt DNA D-loop区研究中国10个绵羊品种的遗传多样性与起源[J].农业生物技术学报,2012,20(7):799-806.
[22]初红军.卡拉麦里山有蹄类自然保护区蒙古野驴(Equus hemionus)和鹅喉羚(Gazella subgutturosa)食性、种群和栖息地研究[D].西宁:中国科学院西北高原生物研究所,2008.
[23] Luo Yongjun,Chen Yu,Liu Fuyu,et al. Mitochondrial genome sequence of the Tibetan wild ass(Equus kiang)[J]. Mitochondrial DNA,2011,22(1/2):6-8.
[24]王小斌,秦芳,张云生,等.蒙古马mt DNA D-loop区遗传多样性与多重母系起源[J].西北农林科技大学学报:自然科学版,2010,38(3):47-51.
[25]阿地力江·卡德尔.新疆地方马品种与普氏野马(E. przewalskii)mt DNA遗传多样性及亲缘关系研究[D].乌鲁木齐:新疆大学,2008.
[26] Khaire D,Atkulwar A,Farahand S,et al. Low genetic diversity of the endangered Indian wild ass Equus hemionus khur,as revealed by microsatellite analyses[J]. Journal of Genetics,2017,96(S1):31-34.
[27] Nasiri-Moghadam N, Aliabadian M, Kaboli M, et al. Genetic structure of the Persian wild ass(Equus hemionus onager)in Touran Biosphere Reserve and Bahram-e-goor Protected Area[J]. Taxonomy&Biosystematics,2014,6(18):3.
[28] Brown G G,Gadaleta G,Pepe G,et al. Structural conservation and variation in the D-loop-containing region of vertebrate mitochondrial DNA[J]. Journal of Molecular Biology,1986,192(3):503-511.
[29] Burt W H,Ellerman J R,Morrison-Scott T C S. Check list of palaearctic and Indian mammals[J]. Journal of Mammalogy,1952,33(3):401.
[30]中国科学院青海甘肃综合考察队.青海甘肃兽类调查报告[M].北京:科学出版社,1964.
[31] Corbet G B. The mammals of the Palaearctic Region:a taxonomic review[J]. Quarterly Review of Biology,1978,60(3078):1-113.
[32]冯祚建,蔡桂全,郑昌琳.西藏哺乳类名录[J].兽类学报,1984,4(4):341-358.
[33]郑生武.中国西北地区珍稀濒危动物志[M].北京:中国林业出版社,1994.
[34] GRoves C P,Mazák V. On some taxonomic problems of Asiatic wild asses; with the description of a new subspecies(Perissodactyla;Equidae)[J]. Zeitschrift für Sugetierkunde,1967,32:321-355.
[35] Ryder O A,Chemnick L G. Chromosomal and molecular evolution in Asiatic wild asses[J]. Genetica,1990,83(1):67-72.
[36] Steiner C C,Mitelberg A,Tursi R,et al. Molecular phylogeny of extant equids and effects of ancestral polymorphism in resolving species-level phylogenies[J]. Molecular Phylogenetics and Evolution,2012,65(2):573-581.
[37] Vilstrup J T,Seguin-Orlando A,Stiller M A,et al. Mitochondrial phylogenomics of modern and ancient equids[J]. PLo S One,2013,8(2):e55950.
[38] Rosenbom S,Costa V,Chen Shanyuan,et al. Reassessing the evolutionary history of ass-like equids:insights from patterns of genetic variation in contemporary extant populations[J]. Molecular Phylogenetics and Evolution,2015,85:88-96.
[39] Khaire D,Atkulwar A,Farah S,et al. Mitochondrial DNA analyses revealed low genetic diversity in the endangered Indian wild ass Equus hemionus khur[J]. Mitochondrial DNA Part A,2017,28(5):681-686.
[40] Orlando L,Mashkour M,Burke A,et al. Geographic distribution of an extinct equid(Equus hydruntinus:Mammalia, Equidae)revealed by morphological and genetical analyses of fossils[J]. Molecular Ecology,2006,15(8):2083-2093.
[41] Jansen T,Forster P,Levine M A,et al. Mitochondrial DNA and the origins of the domestic horse[J]. Proceedings of the National Academy of Sciences of the United States of America,2002,99(16):10905-10910.
[42] Mashima S. Mitochondrial DNA sequences of various species of the genus Equus with special reference to the phylogenetic relationship between Przewalskii's wild horse and domestic horse[J]. Journal of Molecular Evolution,1995,41(2):180-188.
[43] Orlando L,Metcalf J L,Alberdi M T,et al. Revising the recent evolutionary history of equids using ancient DNA[J]. Proceedings of the National Academy of Sciences of the United States of America,2009,106(51):21754-21759.