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中国东北鹿亚科动物亚化石的古DNA分子鉴定及系统发育分析

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  • 1 中国地质大学(武汉)环境学院 武汉 430078
    2 中国地质大学生物地质与环境地质国家重点实验室 武汉 430078
    3 中国地质大学(武汉)材料与化学学院 武汉 430078
    4 大庆博物馆 黑龙江大庆 163319
    5 青冈县古生物化石保护中心 黑龙江青冈 151600
    6 中国地质大学(武汉)地球科学学院 武汉 430074

收稿日期: 2020-05-06

  网络出版日期: 2020-10-19

基金资助

国家自然科学基金(41672017);国家自然科学基金(41972001)

Ancient DNA molecular identification and phylogenetic analysis of Cervinae subfossils from Northeast China

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  • 1 School of Environmental Studies, China University of Geosciences (Wuhan) Wuhan 430078
    2 State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan) Wuhan 430078
    3 Faculty of Materials Science and Chemistry, China University of Geosciences (Wuhan) Wuhan 430078
    4 Daqing Museum Daqing, Heilongjiang 163319
    5 Paleontological Fossil Conservation Center, Qinggang County Qinggang, Heilongjiang 151600
    6 School of Earth Sciences, China University of Geosciences (Wuhan) Wuhan 430074

Received date: 2020-05-06

  Online published: 2020-10-19

摘要

我国鹿类资源丰富,鹿亚科(Cervinae)动物有7个种在中国有分布。鹿亚科的种内系统发育研究很多,但是各物种之间进化关系仍有待进一步研究,其中从分子水平对古代材料的报道更为鲜见。对采集自黑龙江的两个距今分别为3800和5100 a的古代鹿亚科动物亚化石材料开展了古DNA研究。通过古DNA提取、古DNA双链文库构建、高通量测序及数据分析,得到了两条长度分别为16475 bp (GenBank收录号:MT784751, 序列完整度:99.83%)和16167 bp (GenBank收录号:MT784752, 序列完整度:97.96%)的线粒体基因组序列,对两个样品进行了分子鉴定。结合GenBank中现生鹿亚科动物的线粒体同源序列,构建了系统发育树。结果表明:1) 二代测序DNA片段末端碱基特性分析说明序列来自古代样品;2) 两个样品代表的个体在系统发育树中均与马鹿聚类,在物种归属中被分子鉴定为马鹿(Cervus elaphus); 3) 黑龙江的两个古代样品与现生马鹿阿拉善亚种(C. elaphus alxaicus)亲缘关系最近,而与现生马鹿东北亚种(C. elaphus xanthopygus)亲缘关系较远。结合样品年代信息,说明两例样品代表的黑龙江古代马鹿种群,不是现生马鹿东北亚种的直系母系祖先。

本文引用格式

肖博, 盛桂莲, 袁俊霞, 王斯人, 胡家铭, 陈顺港, 姬海龙, 侯新东, 赖旭龙 . 中国东北鹿亚科动物亚化石的古DNA分子鉴定及系统发育分析[J]. 古脊椎动物学报, 2020 , 58(4) : 328 -337 . DOI: 10.19615/j.cnki.1000-3118.200722

Abstract

The deer resources in China are abundant, with seven species in the sub-family Cervinae distributing in various areas. The intraspecific phylogeny of Cervinae has been widely explored, while the evolutionary relationship among different species requires further efforts, in which only few molecular studies on ancient materials have been performed. In this study, we carried out ancient DNA research on two Cervinae subfossils from northeastern China, dating of 3800 and 5100 aBP. Through ancient DNA extraction, double-stranded sequencing libraries construction, next-generation sequencing and bioinformatics data analysis, we reconstructed two mitochondria sequences with lengths of 16475 bp (GenBank accession number: MT784751, sequence integrity: 99.83%) and 16167 bp (GenBank accession numberh: MT784752, sequence integrity: 97.96%), respectively. Based on the mitochondrial homologous sequences of the extant Cervinae species in GenBank, we constructed a phylogenetic tree. The results show that: 1) both the average length and the C-to-T substitution frequencies at 5’- end of the NGS short reads indicate the data are from ancient specimens; 2) the two ancient individuals clustered with Cervus elaphus in the phylogenetic tree, and were molecularly identified as C. elaphus; 3) the two ancient samples from Heilongjiang are phylogenetically close to the extant C. elaphus alxaicus, but far from the extant C. elaphus xanthopygus. Combining the dates of the samples, we suggest that these two samples represent a population of ancient C. elaphus in Heilongjiang, which was not the direct maternal ancestor of the extant C. elaphus xanthopygus.

参考文献

[1] Alexandros S, 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30:1312-1313
[2] Aurelien G, Morten R M, Thomas P G et al., 2011. mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics, 27:2153-2155
[3] Cai B Q, Yin J C, 1992. Late Pleistocene fossil mammals from Qinggang, Heilongjiang Province. Bull Chinese Acad Geol Sci, 25:131-138
[4] Cognato A I, Vogler A P, 2001. Exploring data interaction and nucleotide alignment in a multiple gene analysis of Ips (Coleoptera: Scolytinae). Syst Biol, 50:758-780
[5] Dong W, Li Z Y, 2009. New cervids (Artiodactyla, Mammalia) from the Late Pleistocene of Lingjing Site in Henan Province, China. Acta Anthrop Sin, 28:319-326
[6] Dong W, Liu W H, Zhang L M et al., 2018. New materials of Cervidae (Artiodactyla, Mammalia) from Tuchengzi of Huade, Nei Mongol, North China. Vert PalAsiat, 56:157-175
[7] Emerson B C, Tate M L, 1993. Genetic analysis of evolutionary relationships among deer (Subfamily Cervinae). J Hered, 84:266-273
[8] Geist V, 1998. Deer of the World: Their Evolution, Behaviour, and Ecology. Mechanicsburg: Stackpole Book. 1-421
[9] Groves C P, Grubb P, 1987. Relationships of living deer. In: Christen M W ed. Biology and Management of the Cervidae. Washington, DC: Smithsonian Institution Press. 20-59
[10] Grubb P, 1993. Artiodactyla: Cervidae. In: Wilson D E, Reeder D M eds. Mammal Species of the World: A Taxonomic and Geographic Reference. Washington, DC: Smithsonian Institution Press. 384-392
[11] Hall T A, 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser, 41:95-98
[12] Hofreiter M, Paijmans J, Goodchild H et al., 2014. The future of ancient DNA: technical advances and conceptual shifts. BioEssays, 37: 10. 1002/bies. 201400160
[13] Korneliussen T S, Albrechtsen A, Nielsen R, 2014. ANGSD: analysis of next generation sequencing. BMC Bioinformatics, 15:356
[14] Li H, Durbin R, 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26:589-595
[15] Li H, Handsaker B, Wysoker A et al., 2009. The sequence alignment/map format and SAMtools. Bioinformatics, 25:2078-2079
[16] Li M, Wang X M, Sheng H L et al., 1998. Origin and genetic diversity of four subspecies of red deer (Cervus elaphus). Zool Res, 19:177-183
[17] Liu H T, Dong Y M, Wang L et al., 2017. Research progress on taxonomy and phylogeny of deer in China. Chinese J Wildlife, 38:514-523
[18] Liu X H, Wang Y Q, Liu Z Q et al., 2003. Phylogenetic relationships of Chinese brown frogs (Rana) based on sequence of mitochondrial cytochrome b gene. Zool Res, 22:345-350
[19] Ludt C J, Schroeder W, Rottmann O et al., 2004. Mitochondrial DNA phylogeography of red deer (Cervus elaphus). Mol Phylogenet Evol, 31:1064-1083
[20] Martin M, 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J, 17:10-12
[21] Matthias M, Martin K, 2010. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harbor Protoc, 2010: pdb. prot5448
[22] Muhmut H, Masuda R, Onuma M et al., 2002. Molecular phylogeography of the red deer (Cervus elaphus) populations in Xinjiang of China: comparison with other Asian, European and North American populations. Zool Sci, 19:485-495
[23] Neitzel H, 1987. Chromosome evolution of Cervidae: karyotypic and molecular aspects. In: Obe G, Basler A eds. Cytogenetics: Basic and Applied Aspects. Berlin/Heidelberg: Springer. 90-112
[24] Polziehn R O, Strobeck C, 2002. A phylogenetic comparison of red deer and wapiti using mitochondrial DNA. Mol Phylogenet Evol, 22:342-356
[25] Qiao F J, Li J L, Gao H et al., 2019. Molecular phylogenetics of the Alashan red deer (Cervus elaphus alxaicus) based on Cyt b DNA. Chinese J Wildlife, 40:307-311
[26]
[27] Randi E, Mucci N, Claro H F et al., 2001. A mitochondrial DNA control region phylogeny of the Cervinae: speciation in Cervus and implications for conservation. Anim Conserv Forum, 4:1-11
[28] Rohland N, Hofreiter M, 2007a. Comparison and optimization of ancient DNA extraction. Bio-Techniques, 42:343-352
[29] Rohland N, Hofreiter M, 2007b. Ancient DNA extraction from bones and teeth. Nat Protoc, 2:1756-1762
[30] Sawyer S, Krause J, Guschanski K et al., 2012. Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PloS ONE, 7:e34131
[31] Sheng H L, 1992. The Deer in China. Shanghai: East China Normal University Press. 1-251
[32] Tu J F, Xing X M, Xu J P et al., 2012. Sequence difference of mitochondrial DNA control region and genetic differentiation of Cervinae in China. J Anhui Agr Sci, 40:669-672
[33] Wang X M, Li M, Tang S X et al., 1999. Study on the resources and protection status of cloven hooves in Helan Mountain. Chinese J Zool, 34:26-29
[34] Wang Z R, Du R F, 1983. Karyotypes of Cervidae and their evolution. Acta Zool Sin, 29:214-222
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