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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
Vertebrata Palasiatica    2020, 58 (4): 328-337.   DOI: 10.19615/j.cnki.1000-3118.200722
Abstract   (124 HTML4 PDF(pc) (1569KB)(116)  

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.


Fig. 1 Samples of Cervus sp. from Taiping, Zhaodong (A) and Niaohe, Binxian (B), Heilongjiang
A. CADG522, metacarpus; B. CADG527, radius
Extracts from the Article
利用Bioedit 7.0.9.0 (Hall, 1999)对测得的序列进行排列对比并辅以人工校对,以所得两个样品的古DNA序列与36个鹿亚科动物和一个外类群驼鹿( Alces alces)的同源序列(15109 bp, 不包含D-loop区)在CIPRES网站( http://www.phylo.org )使用PartitionFinder2 (Cognato and Vogler, 2001)和RAxML V8.0 (Alexandros, 2014)通过500次自举检验估计节点构建系统发育树,碱基替换模型(model for substitution)选择GTRCAT。系统发育树的展示输出通过 Figtree v1.4.2 (Rambaut, 2009)完成。分析中所用序列信息见表2, 序列选取兼顾鹿亚科在中国分布的4属9种。同时,与样品聚类较近的中国马鹿5亚种和梅花鹿选取了当前GenBank中所收录的所有高质量序列。
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