Short sequence effect of ancient DNA on mammoth phylogenetic analyses

doi:10.1007/s11707-009-0010-z

Front Earth Sci Chin

0, Vol.

Issue () : 100-106 https://doi.org/10.1007/s11707-009-0010-z

RESEARCH ARTICLE

Short sequence effect of ancient DNA on mammoth phylogenetic analyses

Guilian SHENG^1,2, Lianjuan WU¹, Xindong HOU^1,2, Junxia YUAN¹, Shenghong CHENG¹, Bojian ZHONG¹, Xulong LAI¹(

)

1. Key Laboratory of Biogeology and Environmental Geology of Ministry of Education, China University of Geosciences, Wuhan 430074, China; 2. Institute of Ecology & Environment, China University of Geosciences, Wuhan 430074, China

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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

Corresponding Author(s): LAI Xulong,Email:xllai@cug.edu.cn

Issue Date: 05 March 2009

Cite this article:

Guilian SHENG,Lianjuan WU,Xindong HOU, et al. Short sequence effect of ancient DNA on mammoth phylogenetic analyses[J]. Front Earth Sci Chin, 0, (): 100-106.

URL:

https://academic.hep.com.cn/fesci/EN/10.1007/s11707-009-0010-z
https://academic.hep.com.cn/fesci/EN/Y0/V/I/100

Fig.1 Location of the sampling site (indicated by the star)

Tab.1 Primers used in this study

Tab.2 Data sets studied herein

Fig.2 Gel electrophoresis image of PCR products with primer pair Cb-EC & Cb-ED. M. 100 bp DNA ladder; 1. negative control; 5. 164 bp product; 2-4 & 6-7. PCR products with other PCR primers showing no target segments amplified

Fig.3 Gel electrophoresis image of PCR products with primer pair Cb-ELL&Cb-ELH. M. 100 bp DNA ladder; 1. negative control; 2. 138 bp product; 3-7. PCR products with other PCR primers showing no target fragments amplified

Fig.4 Aligned DNA sequences of the 119 bp fragment of cyt from , , and the outgroup taxon . Dots represent identical bases to . _EF408550, the individual collected from Northeast China

Fig.5 Phylogenetic trees based on (a) whole mitochondrial genome; (b) complete cyt gene; and (c) partial cyt gene of the Elephantidae. Numbers on internal branches are bootstrap values derived from 1000 replications. Numbers to the right side of nodes represent bootstrap values by neighbor-joining method, while numbers to the left side of nodes indicate bootstrap values by minimum evolution method. The bar represents 1% sequence divergence. “_ EF408550” in (c) is the woolly mammoth individual collected from Northeast China

Tab.3 Sister taxa and bootstrap probability when using different sequences as dataset to reconstruct the Elephantidae phylogeny

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 doi: 10.1016/S1055-7903(02)00292-0
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(5846): 1927-1930 doi: 10.1126/science.1146971
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 doi: 10.1038/370333b0
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 doi: 10.1007/BF02515385
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 doi: 10.1038/nature04432
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 doi: 10.1093/bib/5.2.150
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 doi: 10.1007/PL00006308
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 doi: 10.1007/PL00006160
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: e73, 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): e207, 1663-1671
17	Shoshani J (1998). Understanding proboscidean evolution: A formidable task. Trends in Ecology and Evolution , 13: 480-487 doi: 10.1016/S0169-5347(98)01491-8
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 doi: 10.1098/rspb.2000.0978
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 doi: 10.1007/BF02109479
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 doi: 10.1093/nar/22.22.4673
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): e241, 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 doi: 10.1006/mpev.1996.0398
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 doi: 10.1080/10020070612330008
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)

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