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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

发表日期:2020-07-22来源:放大 缩小

编辑: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

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。
关键词:黑龙江,鹿亚科,古DNA, 分子鉴定,系统发育分析
卷期:第58卷,第4期

 

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

XIAO Bo, SHENG Gui-Lian, YUAN Jun-Xia, WANG Si-Ren, HU Jia-Ming,
 CHEN Shun-Gang, JI Hai-Long, HOU Xin-Dong, LAI Xu-Long
 

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 numbers: MT784751, sequence integrity: 99.83%) and 16167 bp (GenBank accession numbers: 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.
Key words   Heilongjiang, China, Cervinae, ancient DNA, molecular identification, phylogenetic analysis

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