Pleistocene Chinese cave hyenas and the recent Eurasian history of the spotted hyena, Crocuta crocuta

Molecular Ecology

Volumn 23, Issue 3, 2014, Pages 522-533

  Sheng, Gui Lian ^a,b   Soubrier, Julien ^b   Liu, Jin Yi ^c   Werdelin, Lars ^d   Llamas, Bastien ^b   Thomson, Vicki A ^b   Tuke, Jonathan ^b   Wu, Lian Juan ^a   Hou, Xin Dong ^a   Chen, Quan Jia ^e   Lai, Xu Long ^a   Cooper, Alan ^b  

^a CHINA UNIVERSITY OF GEOSCIENCES   (China)

^b UNIVERSITY OF ADELAIDE   (Australia)

^c INSTITUTE OF VERTEBRATE PALEONTOLOGY AND PALEOANTHROPOLOGY   (China)

^d SWEDISH MUSEUM OF NATURAL HISTORY   (Sweden)

^e JILIN UNIVERSITY   (China)

Author keywords

ancient DNA; Crocuta crocuta; divergence time; evolutionary history; Northern China

Indexed keywords

CROCUTA CROCUTA; PROTELES CRISTATUS;

CYTOCHROME B; MITOCHONDRIAL DNA;

ANCIENT DNA; ANIMAL; ASIA; BAYES THEOREM; BIOLOGICAL MODEL; CROCUTA CROCUTA; DIVERGENCE TIME; DNA SEQUENCE; EUROPE; EVOLUTION; EVOLUTIONARY HISTORY; FOSSIL; GENETICS; HYENA; MOLECULAR GENETICS; NORTHERN CHINA; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION GENETICS; REVIEW;

ANCIENT DNA; CROCUTA CROCUTA; DIVERGENCE TIME; EVOLUTIONARY HISTORY; NORTHERN CHINA;

ANIMALS; ASIA; BAYES THEOREM; BIOLOGICAL EVOLUTION; CYTOCHROMES B; DNA, MITOCHONDRIAL; EUROPE; FOSSILS; GENETICS, POPULATION; HYAENIDAE; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 84892965018     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12576     Document Type: Review

References (53)

1. Anderson CNK, Ramakrishnan U, Chan YL, Hadly EA, (2004) Serial SimCoal: a population genetics model for data from multiple populations and points in time. Bioinformatics, 21, 1733-1734.
2. Austin JJ, Soubrier J, Prevosti FJ, et al,. (2013) The origins of the enigmatic Falkland Islands wolf. Nature Communications, 4, 1552.
3. Bandelt HJ, Forster P, Rohl A, (1999) Median joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37-48.
4. Barnett R, Yamaguchi N, Barnes I, Cooper A, (2006) The origin, current diversity and future conservation of the modern lion (Panthera leo). Proceedings of the Royal Society B, 273, 2119-2125.
5. Barnett R, Shapiro B, Barnes I, et al,. (2009) Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity. Molecular Ecology, 18, 1668-1677.
6. Baryshnikov GF, Tsoukala E, (2010) New analysis of the Pleistocene carnivores from Petralona cave (Macedonia, Greece) based on the collection of the Thessaloniki Aristotle university. Geobios, 43, 389-402.
7. de Bonis L, (1973) Contribution à l'étude des mammifères de l'Aquitanien de l'Agenais: rongeurs, carnivores, périssodactyles. In: Mémoires du Muséum national d'Histoire naturelle, Nouvelle Série (C) 28, pp 1-192, Paris (in French).
8. Cooper A, Poinar HN, (2001) Ancient DNA: do it right or not at all. Science, 289, 1139.
9. Diedrich C, (2008) The holotypes of the upper Pleistocene Crocuta crocuta spelaea and Panthera leo spelaea of the zoolithen cave hyena den and their palaeo- ecological interpretation. Zoological Journal of the Linnean Society, 154, 822-831.
10. Drummond AJ, Rambaut A, (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
11. Drummond AJ, Ashton B, Buxton S, et al,. (2011) Geneious v5.4, Available from http://www.geneious.com.
12. García N, Arsuaga JL, (2001) Les carnivores (Mammalia) des sites du Pléistocène ancien et moyen d'Atapuerca (Espagne). L'anthropologie, 105, 83-93. (in French with English abstract).
13. Guindon S, Dufayard J-F, Lefort V, et al,. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology, 59, 307-321.
14. Ho SYW, Phillips MJ, Cooper A, Drummond AJ, (2005) Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Molecular Biology and Evolution, 22, 1561-1568.
15. Ho SYW, Saarma U, Barnett R, Haile J, Shapiro B, (2008) The effect of inappropriate calibration: three case studies in molecular ecology. PLoS ONE, 3, 1615.
16. Ho SYW, Lanfear R, Bromham L, et al,. (2011a) Time-dependent rates of molecular evolution. Molecular Ecology, 20, 3087-3101.
17. Ho SYW, Lanfear R, Phillips MJ, et al,. (2011b) Bayesian estimation of substitution rates from ancient DNA sequences with low information content. Systematic biology, 60, 366-375.
18. Hofreiter M, Jannicke V, Serre D, Haeseler A, Paabo S, (2001) DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Research, 29, 4793-4799.
19. Hu CK, (1985) The history of Mammalian Fauna of Locality 1 of Zhoukoudian and its recent advances. In: Multi-disciplinary Study of the Peking Man Site at Zhoukoudian (eds, Wu RK, Ren M, Zhu X,), pp. 107-113. Science Press, Beijing. (In Chinese)
20. Huang WP, (1989) Taxonomy of the hyaenidae (hyaena and crocuta) of the pleistocene in China. Vertebrata Palasiatica, 27, 197-204. (in Chinese with English abstract).
21. Jenks SM, Werdelin L, (1998) Taxonomy and systematics of living hyaenas (Family Hyaenidae). In: Hyaenas: Status Survey and Conservation Action Plan (eds, Mills MGL, Hofer H,), pp. 8-17. IUCN, Gland, Switzerland.
22. Keane TM, Creevey CJ, Pentony MM, Naughton TJ, McInerney JO, (2006) Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evolutionary Biology, 6, 29.
23. Knapp M, Clarke AC, Horsburgh KA, Matisoo-Smith EA, (2011) Setting the stage-building and working in an ancient DNA laboratory. Annals of Anatomy, 194, 3-6.
24. Koepfli KP, Jenks SM, Eizirik E, et al,. (2006) Molecular systematics of the hyaenidae: relationships of a relictual lineage resolved by a molecular supermatrix. Molecular Phylogenetics and Evolution, 38, 603-620.
25. Kurtén B, (1956) The status and affinities of Hyaena sinensis Owen and Hyaena ultima Matsumoto. American Musuem Novitates, 1764, 1-48.
26. Kurtén B, (1968) Pleistocene Mammals of Europe. Weidenfeld and Nicholson, London.
27. Liu JY, (1999) Study of the Late Pleistocene mammalian remains from Miaofengshan, Beijing with discussion of the migration and extinction of Crocuta crocuta ultima. Longgupo Prehistoric Culture, 1, 128-139. (In Chinese).
28. Ma AC, Tang HL, (1992) On discovery and significance of a Holocene Ailuropoda-Stegodon Fauna from Jinhua, Zhejiang. Vertebrata Palasiatica, 30, 295-312. (in Chinese with English summary).
29. Markova AK, Smirnov NG, Kozharinov AV, et al,. (1995) Late Pleistocene distribution and diversity of mammals in northern Eurasia (PALEOFAUNA Database). Paleontologia i Evolucio, 28, 5-134.
30. Martinez-Navarro B, Belmaker M, Bar-Yosef O, (2009) The large carnivores from 'Ubeidiya (early Pleistocene, Israel): biochronological and biogeographical implications. Journal of Human Evolution, 56, 514-524.
31. Poinar HN, (2003) The top 10 list: criteria of authenticity for DNA from ancient and forensic samples. International Congress Series, 1239, 575-579.
32. Qiu ZX, (1987) Die Hyaeniden aus dem Ruscinium und Villafranchium Chinas. Munchner Geowissenschaftliche Abhandlungen Reihe A, 9, 1-108. (in German).
33. Qiu ZX, Deng T, Wang BY, (2004) Early Pleistocene mammalian fauna from Longdan, Dongxiang, Gansu, China. Palaeontologia Sinica (series C), 27, 1-198.
34. Rambaut A, Drummond AJ, (2007) Tracer v 1.4. Available from: http://beast.bio.ed.ac.uk/Tracer.
35. Rohland N, Hofreiter M, (2007) Ancient DNA extraction from bones and teeth. Nature Protocols, 2, 1756-1762.
36. Rohland N, Pollack JL, Nagel D, et al,. (2005) The population history of extant and extinct hyenas. Molecular Biology and Evolution, 22, 2435-2443.
37. Römpler H, Dear PH, Krause J, et al,. (2006) Multiplex amplification of ancient DNA. Nature, 1, 720-728.
38. Shen GJ, Ku TL, Cheng H, et al,. (2001) High-precision U-series dating of locality 1 at Zhoukoudian, China. Journal of Human Evolution, 41, 679-688.
39. Tong HW, (2007) Occurrences of warm-adapted mammals in north China over the quaternary period and their paleoenvironmental significance. Science in China (series D), 50, 1327-1340.
40. Tseng ZJ, Chang CH, (2007) A study of new material of Crocuta crocuta ultima (Carnivora: Hyaenidae) from the quaternary of Taiwan. Collection and Research, 20, 9-19.
41. Turner A, (1984) The interpretation of variation in fossil specimens of spotted hyena (Crocuta crocuta Erxleben, 1777) from Sterkfontein valley sites (mammalian: Carnivora). Annals of the Transvaal Museum, 33, 399-418.
42. Turner A, (1990) The evolution of the guild of larger terrestrial carnivores during the Plio-Pleistocene in Africa. Geobios, 23, 349-368.
43. Turner A, Antón M, Werdelin L, (2008) Taxonomy and evolutionary patterns in the fossil Hyaenidae of Europe. Geobiology, 41, 677-687.
44. Watts HE, Holekamp KE, (2007) Hyena societies. Current Biology, 17, 657-660.
45. Weinstock J, Willerslev E, Sher A, et al,. (2005) Evolution, systematics, and phylogeography of Pleistocene horses in the new world: a molecular perspective. PloS Biology, 3, 1373-1379.
46. Werdelin L, (1999) Studies of fossil hyaenas: affinities of Lycyaenops rhomboideae Kretzoi from Pextlörinc, Hungary. Zoological Journal of the Linnean Society, 126, 307-317.
47. Werdelin L, Lewis ME, (2005) Plio-Pleistocene Carnivora of eastern Africa: species richness and turnover patterns. Zoological Journal of the Linnean Society, 144, 121-144.
48. Werdelin L, Lewis ME, (2008) New species of Crocuta from the early Pliocene of Kenya, with an overview of early Pliocene hyenas of eastern Africa. Journal of Vertebrate Paleontology, 28, 1162-1170.
49. Werdelin L, Solounias N, (1991) The hyaenidae: taxonomy, systematics and evolution. Fossils and Strata, 30, 1-104.
50. Werdelin L, Yamaguchi N, Johnson WE, O'Brien SJ, (2010) Felid phylogeny and evolution. In: The Biology and Conservation of Wild Felids (eds, Macdonald DM, Loveridge A,), pp. 59-82. Oxford University Press, Oxford.
51. Yamaguchi N, Cooper A, Werdelin L, Macdonald DW, (2004) Evolution of the mane and group-living in the lion (Panthera leo): a review. Journal of Zoology, 263, 329-342.
52. Zdansky O, (1924) Jungtertiäre carnivoren chinas. Palaeontologia Sinica (series C), 2, 1-149. (in German).
53. Zhou C, Lui Z, Wang Y, (2000) Climatic cycles investigated by sediment analysis in Peking Man's Cave, Zhoukoudian, China. Journal of Archaeological Science, 27, 101-109.