Ancient DNA molecular identification and phylogenetic analysis of Cervinae subfossils from Northeast China
Received date: 2020-05-06
Online published: 2020-10-19
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.
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 . Ancient DNA molecular identification and phylogenetic analysis of Cervinae subfossils from Northeast China[J]. Vertebrata Palasiatica, 2020 , 58(4) : 328 -337 . DOI: 10.19615/j.cnki.1000-3118.200722
| [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 |
/
| 〈 |
|
〉 |