Short sequence effect of ancient DNA on mammoth phylogenetic analyses

Abstract

The evolution of Elephantidae has been intensively studied in the past few years, especially after 2006. The molecular approaches have made great contribution to the assumption that the extinct woolly mammoth has a close relationship with the Asian elephant instead of the African elephant. In this study, partial ancient DNA sequences of cytochrome b (cyt b) gene in mitochondrial genome were successfully retrieved from Late Pleistocene Mammuthus primigenius bones collected from Heilongjiang Province in Northeast China. Both the partial and complete homologous cyt b gene sequences and the whole mitochondrial genome sequences extracted from GenBank were aligned and used as datasets for phylogenetic analyses. All of the phylogenetic trees, based on either the partial or the complete cyt b gene, reject the relationship constructed by the whole mitochondrial genome, showing the occurrence of an effect of sequence length of cyt b gene on mammoth phylogenetic analyses.

Keywords

Mammuthus primigenius / ancient mitochondrial DNA / cytochrome b (cytb) gene / phylogenetic analysis

References

[1] Debruyne R, Barriel V, Tassy P (2003). Mitochondrial cytochrome b of the Lyakhov mammoth (Proboscidea, Mammalia): New data and phylogenetic analyses of Elephantidae. Molecular Phylogenetics and Evolution, 26: 421-434

[2] Gilbert M T P, Tomsho L P, Rendulic S, Packard M, Drautz D I, Sher A, Tikhonov A, Dalén L, Kuznetsova T, Kosintsev P (2007). Whole-genome shotgun sequencing of mitochondria from ancient hair shafts. Science, 317(<patent>5846</patent>): 1927-1930

[3] Hagelberg E, Thomas M G, Cook C E, Sher A V, Baryshnikov G F, Lister A M (1994). DNA from ancient mammoth bones. Nature, 370: 333

[4] Hauf J, Waddell P, Chalwatzis N, Joger U, Zimmermann F K (1999). The complete mitochondrial genome sequence of the African elephant (Loxodonta Africana), phylogenetic relationships of Proboscidea to other mammals, and D-loop heteroplasmy. Zoology, 102: 184-195

[5] Haynes G (1991). Mammoths, Mastodonts & Elephants: Biology, Behavior, and the Fossil Record. Cambridge: Cambridge University Press, 5-6

[6] Irwin D M, Kocher T D, Wilson A C (1991). Evolution of the cytchromobe b gene of mammals. Journal of Molecular Evolution, 32: 128-144

[7] Jin C Z, Xu Q Q, Zheng J J (1998). On the dispersal events of mammuthus during the Late Pleistocene. Vertebrata Palasiatica, 36(1): 47-53 (in Chinese with English abstract)

[8] Joger U, Garrido G (2001). Phylogenetic position of Elephas, Loxodonta and Mammuthus, based on molecular evidence. The World of Elephants-International Congress, Rome

[9] Kawamura Y (1994). Late Pleistocene to Holocene mammalian faunal succession in the Japanese Island, with comments on the Late Quaternary extinction. Archaeozoologia, 6: 7-22

[10] Krause J, Dear P H, Pollack J L, Slatkin M, Spriggs H Barnes I, Lister A M, Ebersberger I, P??bo S, Hofreiter M (2006). Multiplex amplification of the mammoth mitochondrial genome and the evolution of the Elephantidae. Nature, 439:724-727

[11] Kumar S, Tamura K, Nei M (2004). MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Briefings in Bioinformatics, 5: 150-163

[12] Li W H, Luo C C, Wu C I (1985). Evolution of DNA sequences. In: MacIntyre I L, ed. Molecular Evolutionary Genetics. New York: Plenum, 1-94

[13] Noro M, Masuda R, Dubrovo I A, Yoshida M C, Kato M (1998). Molecular phylogenetic inference of the wooly mammoth Mammuthus primigenius, based on complete sequences of mitochondrial cytochrome b and 12S ribosomal RNA gene. Journal of Molecular Evolution, 46: 314-326

[14] Ozawa T, Hayashi S, Mikhelson V M (1997). Phylogentic position of mammoth and Steller’s sea cow within Tethytheria demonstrated by mitochondrial DNA sequences. Journal of Molecular Evolution, 44: 406-413

[15] Rogaev E I, Moliaka Y K, Malyarchuk B A, Kondrashov F A, Derenko M V, Chumakov I, Grigorenko A P (2006). Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius. PLoS Biology, 4: <patent>e73</patent>, 0403-0410

[16] Rohland N, Malaspinas A, Pollack J L, Slatkin M, Matheus P, Hofreiter M (2007). Proboscidean mitogenomics: Chronology and mode of elephant evolution using mastodon as outgroup. PloS Biology, 5(8): <patent>e207</patent>, 1663-1671

[17] Shoshani J (1998). Understanding proboscidean evolution: A formidable task. Trends in Ecology and Evolution, 13: 480-487

[18] Shoshani J, Tassy P (1996). The Proboscidea: Evolution and Palaeoecology of Elephants and their Relatives. New York: Oxford University Press, 472

[19] Thomas M G, Hagelberg E, Jones H B, Yang Z, Lister A M (2000). Molecular and morphological evidence on the phylogeny of the Elephantidae. Proceedings of the Royal Society of London, Series B, 267: 2493-2500

[20] Thomas W K, P??bo S, Villablanca F X (1990). Spatial and temporal continuity of kangaroo rat populations shown by sequencing mitochondrial DNA from museum specimens. Journal of Molecular Evolution, 31: 101-112

[21] Thompson J D, Higgins D G, Gibson T J (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22: 4673-4680

[22] Weinstock J, Willerslev E, Sher A, Tong W, Ho S W, Rubenstein D, Storer J, Burns J, Martin L, Bravi C, Prieto A, Froese D, Scott E, Lai X L, Cooper A (2005). Evolution, systematics, and phylogeography of Pleistocene horses in the new world: A molecular perspective. PloS Biology, 3(8): <patent>e241</patent>, 1373-1379

[23] Yang H, Golerberg E M., Shoshani J (1997). A blind testing design for authenticating ancient DNA sequence. Molecular Phylogenetics and Evolution, 7(2): 261-265

[24] Yang S J, Lai X L, Shi S H, Cheng S H, Zhou X G, Yang X J , Yang H (2006). New ancient DNA sequences suggest high genetic diversity for the woolly mammoth (Mammuthus primigenius). Progress in Nature Science, 16(4): 380-386

[25] Zhou M Z (1959). Pleistocene mammalian fossils from the eastern border of the Tibetian plateau. China Quaternary Sciences, 2(1): 6-13 (in Chinese with English abstract)

[26] Zhou M Z, Zhang Y P (1974). Chinese Elephant Fossils. Beijing: Science Press, 13 (in Chinese with English abstract)

Acknowledgements

This work was supported by the National Natural Science Foundation of China (Grant No. 40672006), the “111” Project (B08030) and the Research Foundation of Key Laboratory of Biogeology and Environmental Geology of Ministry of Education, China University of Geosciences, Wuhan (BGEG0604). We would like to thank Michael Hofreiter and his group in Max Planck Institute for Evolutionary Anthropology for their helpful technical assistance and Heilongjiang Provincial Museum for the sample supply.

RIGHTS & PERMISSIONS

2014 Higher Education Press and Springer-Verlag Berlin Heidelberg