Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data

Genes

Huan Liu¹  XiaoSen Guo¹  Sunil Kumar-Sahu¹  Yu Lin¹  HaiMeng Li¹  Xie Wang²  WenHao Xu³  Jacob Njaramba-Ngatia⁴  HuaBing Guo⁵  XiuJuan Yang⁶  RenGui Li⁷  YanChun Xu⁷  TianMing Lan⁸  Karsten Kristiansen⁸ 

[1] BGI-Shenzhen, Shenzhen 518083, China;China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China;College of Informatics, Huazhong Agricultural University, Wuhan 430070, China;College of Wildlife Resources, Northeast Forestry University, Harbin 150040, China;Forest Inventory and Planning Institute of Jilin Province, Changchun 130022, China;Heilongjiang Provincial Museum, Harbin 150001, China;Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China;Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark;

关键词: species identification;    BLAST;    ancient DNA;    next-generation sequencing;   

DOI  :  10.3390/genes10070509

来源: DOAJ

【 摘 要 】

The taxonomical identification merely based on morphology is often difficult for ancient remains. Therefore, universal or specific PCR amplification followed by sequencing and BLAST (basic local alignment search tool) search has become the most frequently used genetic-based method for the species identification of biological samples, including ancient remains. However, it is challenging for these methods to process extremely ancient samples with severe DNA fragmentation and contamination. Here, we applied whole-genome sequencing data from 12 ancient samples with ages ranging from 2.7 to 700 kya to compare different mapping algorithms, and tested different reference databases, mapping similarities and query coverage to explore the best method and mapping parameters that can improve the accuracy of ancient mammal species identification. The selected method and parameters were tested using 152 ancient samples, and 150 of the samples were successfully identified. We further screened the BLAST-based mapping results according to the deamination characteristics of ancient DNA to improve the ability of ancient species identification. Our findings demonstrate a marked improvement to the normal procedures used for ancient species identification, which was achieved through defining the mapping and filtering guidelines to identify true ancient DNA sequences. The guidelines summarized in this study could be valuable in archaeology, paleontology, evolution, and forensic science. For the convenience of the scientific community, we wrote a software script with Perl, called AncSid, which is made available on GitHub.

【 授权许可】

Unknown