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Ancient DNA sequences from Coelodonta antiquitatis in China reveal its divergence and phylogeny

Science China Earth Sciences volume 57, pages 388–396 (2014)Cite this article

Abstract

Ancient DNA data have supported a sister relationship between woolly rhinoceros and extant Sumatran rhinoceros. This relationship has been used to explore the divergent times for the woolly rhinoceros from their relatives. Complete and partial ancient DNA sequences of the mitochondrial cytochrome b (cyt b) gene were retrieved from bones of the late Pleistocene Coelodonta antiquitatis excavated from northern and northeastern China. The newly obtained sequences together with the European and northern Asian Coelodonta antiquitatis sequences from GenBank were used to estimate the evolutionary divergence time. Phylogenetic analyses showed the exchange of genetic information between the Chinese individuals and Coelodonta antiquitatis of north Asia, which also indicated a more recent evolutionary timescale (3.8–4.7 Ma) than previous molecular estimations (17.5–22.8 or 21–26 Ma) for woolly rhinoceros based on the fossil calibration of outgroups. This new timescale was more consistent with the fossil record of the earliest known genus Coelodonta.

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References

  • Álvarez-Lao D, García-García N. 2006. A new site from the Spanish middle Pleistocene with cold-resistant faunal elements: La Parte (Asturias, Spain). Quatern Int, 142–143: 107–118

    Article  Google Scholar 

  • Arnason U, Gullberg A. 1996. Cytochrome b nucleotide sequences and the identification of five primary lineages of extant cetaceans. Mol Biol Evol, 13: 407–417

    Article  Google Scholar 

  • Bandelt H J, Forster P, Rohl A. 1999. Median joining networks for inferring intraspecific phylogenies. Mol Biol Evol, 16: 37–48

    Article  Google Scholar 

  • Binladen J, Wiuf C, Gilbert M T P, et al. 2006. Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. Genetics, 172: 733–741

    Article  Google Scholar 

  • Birungi J, Arctander P. 2001. Molecular systematics and phylogeny of the reduncini (Artiodactyla: Bovidae) inferred from the analysis of mitochondrial cytochrome b gene sequences. J Mamm Evol, 8: 125–147

    Article  Google Scholar 

  • Brown W M, George J R, Wilson A C. 1979. Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci USA, 76: 1967–1971

    Article  Google Scholar 

  • Burridge C P, Craw D, Fletcher D, et al. 2008. Geological dates and molecular rates: fish DNA sheds light on time dependency. Mol Biol Evol, 25: 624–633

    Article  Google Scholar 

  • Cai B Q, Yin J C. 1992. Late Pleistocene fossil mammals from Qinggang, Heilongjiang Province (in Chinese with English abstract). Bull Chin Acad Geol Sci, 25: 131–138

    Google Scholar 

  • Debruyne R, Barriel V, Tassy P. 2003. Mitochondrial cytochrome b of the Lyakhov mammoth (Proboscidea, Mammalia): New data and phylogenetic analyses of Elephantidae. Mol Phylogenet Evol, 26, 421–434

    Article  Google Scholar 

  • Deng T. 2002. The earliest known woolly rhino discovered in the Linxia Basin, Gansu Province, China (in Chinese with English abstract). Geol Bull Chin, 21: 604–608

    Google Scholar 

  • Deng T. 2006. Neogene rhinoceroses of the Linxia Basin (Gansu, China). Courier Forschungsinstitut Senckenberg, 256: 43–56

    Google Scholar 

  • Deng T. 2008. Comparison between woolly rhino forelimbs from Longdan, northwestern China and Tologi, Transbaikalian region. Quatern Int, 179: 196–207

    Article  Google Scholar 

  • Deng T, Wang X M, Fortelius M, et al. 2011. Out of Tibet: Pliocene woolly rhino suggests high-plateau origin of Ice Age megaherbivores. Science, 333: 1285–1288

    Article  Google Scholar 

  • Drummond A J, Rammbaut A. 2007. BAEST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol, 7: 214

    Article  Google Scholar 

  • Elias S A, Crocker B. 2008. The Bering Land Bridge: a moisture barrier to the dispersal of steppe-tundra biota. Quatern Sci Rev, 27: 2473–2483

    Article  Google Scholar 

  • Enk J M, Yesner D R, Crossen K J, et al. 2009. Phylogeographic analysis of the mid-Holocene mammoth from Qagnax Cave, St. Paul Island, Alaska. Palaeogeogr Palaeoclimat Palaeoecol, 273: 184–190

    Article  Google Scholar 

  • Geng R Q, Wang L P, Ji D J, et al. 2011. Phylogenetic relationships among domestic Chinese Bovinae species based on mitochondrial cytochrome b gene sequences (in Chinese with English abstract). Sci Agr Sin, 44: 4081–4087

    Google Scholar 

  • Gilbert M T P, Drautz D I, Lesk A M, et al. 2008. Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proc Natl Acad Sci USA, 105: 8327–8332

    Article  Google Scholar 

  • Hofreiter M, Jannicke V, Serre D, et al. 2001. DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res, 29: 4793–4799

    Article  Google Scholar 

  • Ho S Y W, Phillips M J, Cooper A, et al. 2005. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol, 22: 1561–1568

    Article  Google Scholar 

  • Ho S Y W, Lanfear R, Bromham L, et al. 2011. Time-dependent rates of molecular evolution. Mol Ecol, 20: 3087–3101

    Article  Google Scholar 

  • Huang W B. 1979. Discovery of woolly rhinoceros fossils in Fuchengmen, Beijing and the late Pleistocene climate (in Chinese). Vertebr Palasiat, 2: 172–175

    Google Scholar 

  • Irwin D M, Kocher T D, Wilson A C. 1991. Evolution of the cytochrome b gene of mammals. J Mol Evol, 32: 128–144

    Article  Google Scholar 

  • Jiang P. 1982. Preliminary probe on Mammuthus-Coelodonta fauna of northeastern China (in Chinese with English abstract). J Northeast Normal Univ (Nat Sci Ed), 1: 105–115

    Google Scholar 

  • Jiang P. 1991. Discovery of a comparatively complete skeleton of Coelodonta in Fuyu, Jilin (in Chinese with English abstract). Acta Anthropol Sin, 10: 78–82

    Google Scholar 

  • Jin C Z, Xu Q Q, Li C T. 1984. The Quaternary mammalian faunas from Qingshantou Site, Jilin Province (in Chinese with English abstract). Vertebr Palasiat, 4: 314–323

    Google Scholar 

  • Kahlke R D, Lacombat F. 2008. The earliest immigration of woolly rhinoceros (Coelodonta tologoijensis, Rhinocerotidae, Mammalia) into Europe and its adaptive evolution in Palaearctic cold stage mammal faunas. Quatern Sci Rev, 27: 1951–1961

    Article  Google Scholar 

  • Krause J, Dear P H, Pollack J L, et al. 2006. Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature, 439: 724–727

    Article  Google Scholar 

  • Lai X L, Qi S H. 2005. DNA preservation of late Pleistocene materials from China. Abstract of 15th Goldschimidt Conference. Geochem Cosmochem Acta, 69(Suppl): A347–A347

    Google Scholar 

  • Li Z Y, Dong W. 2007. Mammalian fauna from the Lingjing Paleolithic site in Xuchang, Henan Province (in Chinese with English abstract). Acta Anthropol Sin, 26: 345–360

    Google Scholar 

  • Lister A M, Sher A V. 2001. The origin and evolution of the woolly mammoth. Science, 294: 1094–1097

    Article  Google Scholar 

  • Lorenzen E D, Nogués-Bravo D, Orlando L, et al. 2011. Quaternary megafauna to climate and humans. Nature, 479: 359–364

    Article  Google Scholar 

  • Lu Y Q, Li Y, Jin C Z. 1986. Mammalian remains from the late Pleistocene of Wurji, Nei Mongol (in Chinese with English abstract). Vertebr Palasiat, 2: 152–162

    Google Scholar 

  • Luo B, Wang Y Z, Huang Q P, et al. 1983. The discovery of the Picea and Coelodonta antiquitalis symbionsis in Tianjin and its significances (in Chinese with English abstract). Sci Geol Sin, 2: 160–164

    Google Scholar 

  • Ma G Q, Gao T, Sun D R. 2010. Discussion of relationship between Collichthys lucidus and C. Niveatus based on 16S rRNA and cyt b gene sequences (in Chinese with English abstract). South Chin Fisheries Sci, 6: 13–20

    Google Scholar 

  • Miller W, Drautz D I, Ratan A, et al. 2008. Sequencing the nuclear genome of the extinct woolly mammoth. Nature, 456: 387–390

    Article  Google Scholar 

  • Nie Z S, Li H, Ma B Q. 2008. Fossil fauna in the late stage of late Pleistocene in the Hetao Basin, Inner Mongolia (in Chinese with English abstract). Quatern Sci, 28: 14–25

    Google Scholar 

  • Noro M, Masuda R, Dubrovo I A, et al. 1998. Molecular phylogenetic inference of the woolly mammoth Mammuthus primigenius, based on complete sequences of mitochondrial cytochrome b and 12S ribosomal RNA genes. J Mol Evol, 46: 314–326

    Article  Google Scholar 

  • Orlando L, Leonard J A, Thenot A L, et al. 2003. Ancient DNA analysis reveals woolly rhino evolutionary relationships. Mol Phylogenet Evol, 28: 485–499

    Article  Google Scholar 

  • Pääbo S, Poinar H, Serre D, et al. 2004. Genetic analyses from ancient DNA. Annual Rev Gen, 38: 645–679

    Article  Google Scholar 

  • Pei S W. 2001. Discovery of Coelondonta antiquitatis from Hutouliang in Nihewan Basin (in Chinese with English abstract). Vert PalAsiat, 1: 72–75

    Google Scholar 

  • Rogaev E I, Moliaka Y K, Malyarchuk B A, et al. 2006. Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius. PLoS Biol, 4: 403–410

    Article  Google Scholar 

  • Rohland N, Hofreiter M. 2007a. Comparison and optimization of ancient DNA extraction. BioTechniques, 42: 343–352

    Article  Google Scholar 

  • Rohland N, Hofreiter M. 2007b. Ancient DNA extraction from bones and teeth. Nat Protoc, 2: 1756–1762

    Article  Google Scholar 

  • Scott K. 2007. The ecology of the late middle Pleistocene mammoths in Britain. Quatern Int, 169-170: 125–136

    Article  Google Scholar 

  • Subramanian S, Denver D R, Millar C D, et al. 2009. High mitogenomic evolutionary rates and time dependency. Trends Gen, 25: 482–486

    Article  Google Scholar 

  • Sun J Z, Wang Y Z. 1983. The strata of northeast China during Dali glaciations (in Chinese). J Strati, 7: 1–11

    Google Scholar 

  • Tamura K, Dudley J, Nei M, et al. 2007. MEGA 4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol, 24: 1596–1599

    Article  Google Scholar 

  • Tong H W, Claude G. 2009. Early Pleistocene Dicerorhinus sumatrensis remains from the Liucheng Gigantopithecus Cave, Guangxi, China. Geobios, 42: 525–539

    Article  Google Scholar 

  • Tougard C, Delefosse T, Hänni C M C. 2001. Phylogenetic relationships of the five extant Rhinoceros species (Rhinocerotidae, Perissodactyla) based on mitochondrial cytochrome b and 12S rRNA genes. Mol Phyl Evol, 19: 34–44

    Article  Google Scholar 

  • Triant D A, DeWoody J A. 2006. Accelerated molecular evolution in Microtus (Rodentia) as assessed via complete mitochondrial genome sequences. Genetica, 128: 95–108

    Article  Google Scholar 

  • Wei Z Y, Zhu G W. 1990. Coelodonta antiquitatis excavated from Zhaodong (in Chinese). Chin Nat, 2: 27–28

    Google Scholar 

  • Willerslev E, Gilbert M T P, Binladen J, et al. 2009. Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution. BMC Evol Biol, doi: 10.1186/1471-2148-9-95

    Google Scholar 

  • Xu G Y. 1986. Dali glacial period in Liaoning Province (in Chinese with English abstract). Liaoning Geol, 1: 60–68

    Google Scholar 

  • Xu X, Janke A, Arnason U. 1996. The complete mitochondrial DNA sequence of the greater Indian rhinoceros, Rhinoceros unicornis, and the phylogenetic relationship among Carnivora, Perissodactyla, and Artiodactyla (+ Cetacea). Mol Biol Evol, 13: 1167–1173

    Article  Google Scholar 

  • Xu X, Arnason U. 1997. The complete mitochondrial DNA sequence of the white rhinoceros, Ceratotherium simum, and comparison with the mt DNA sequence of the Indian rhinoceros, Rhinoceros unicornis. Mol Phyl Evol, 7: 189–194

    Article  Google Scholar 

  • Yang D, Watt K. Contamination controls when preparing archaeological remains for ancient DNA analysis. J Archaeol Sci, 2005, 32: 331–336

    Google Scholar 

  • Yang H, Golenberg E M, Shoshani J. 1996. Phylogenetic resolution within Elephantidae using fossil DNA sequence from American mastodon (Mammut americanum) as an outgroup. Proc Natl Acad Sci USA, 93: 1190–1194

    Article  Google Scholar 

  • Yang S J, Lai X L, Shi S H, et al. 2006. New ancient DNA sequences suggest high genetic diversity for the woolly mammoth (Mammuthus primigenius). Prog Nat Sci, 16: 379–386

    Article  Google Scholar 

  • Zheng J J, Xu Q Q, Jin C Z. 1992. Division of the late Pleistocene mammalian fauna in north China and its geographic distribution (in Chinese with English abstract). J Stratigr, 16: 171–190

    Google Scholar 

  • Zhou B X. 1978. The distribution of the woolly rhinoceros and woolly mammoth (in Chinese with English abstract). Vertebr Palasiat, 16: 47–59

    Google Scholar 

  • Zhou M Z. 1964. The Chinese fauna evolution in Quaternary (in Chinese). J Strati, 6: 274–278

    Google Scholar 

  • Zin M M T, Masanaru T, Takehisa T, et al. 2008. A new species of Dicerorhinus (Rhinocerotidae) from the Plio-Pleistocene of Myanmar. Palaeontol, 51: 1419–1433

    Article  Google Scholar 

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Authors and Affiliations

  1. State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China

    JunXia Yuan, GuiLian Sheng, XinDong Hou, XiaoYan Shuang, Jian Yi, Hong Yang & XuLong Lai

  2. Faculty of Material Science and Chemistry, China University of Geosciences, Wuhan, 430074, China

    JunXia Yuan

  3. Department of Science and Technology, Bryant University, 1150 Douglas Pike Smithfield, Rhode Island, 02917, USA

    Hong Yang

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  1. JunXia Yuan
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Yuan, J., Sheng, G., Hou, X. et al. Ancient DNA sequences from Coelodonta antiquitatis in China reveal its divergence and phylogeny. Sci. China Earth Sci. 57, 388–396 (2014). https://doi.org/10.1007/s11430-013-4702-6

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