Evaluating the Phylogenetic Position of Chinese Tree Shrew (Tupaia belangeri chinensis) Based on Complete Mitochondrial Genome: Implication for Using Tree Shrew as an Alternative Experimental Animal to Primates in Biomedical Research

Ling Xu; Shi-Yi Chen; Wen-Hui Nie; Xue-Long Jiang; Yong-Gang Yao

doi:10.1016/j.jgg.2012.02.003

Volume 39 Issue 3

Mar. 2012

Turn off MathJax

Article Contents

Article Navigation > Journal of Genetics and Genomics > 2012 > 39(3): 131-137

PDF( 282 KB)

Evaluating the Phylogenetic Position of Chinese Tree Shrew (Tupaia belangeri chinensis) Based on Complete Mitochondrial Genome: Implication for Using Tree Shrew as an Alternative Experimental Animal to Primates in Biomedical Research

doi: 10.1016/j.jgg.2012.02.003

a
Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
b
Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
c
Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Ya’an, Sichuan 625014, China
d
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China

More Information

Corresponding author: E-mail address: ygyaozh@gmail.com (Yong-Gang Yao)
Received Date: 2011-10-13
Accepted Date: 2012-01-05
Rev Recd Date: 2011-12-25

Available Online: 2012-02-18

Publish Date: 2012-03-20

Abstract

Abstract

Tree shrew (Tupaia belangeri) is currently placed in Order Scandentia and has a wide distribution in Southeast Asia and Southwest China. Due to its unique characteristics, such as small body size, high brain-to-body mass ratio, short reproductive cycle and life span, and low-cost of maintenance, tree shrew has been proposed to be an alternative experimental animal to primates in biomedical research. However, there are some debates regarding the exact phylogenetic affinity of tree shrew to primates. In this study, we determined the mtDNA entire genomes of three Chinese tree shrews (T. belangeri chinensis) and one Malayan flying lemur (Galeopterus variegatus). Combined with the published data for species in Euarchonta, we intended to discern the phylogenetic relationship among representative species of Dermoptera, Scandentia and Primates. The mtDNA genomes of Chinese tree shrews and Malayan flying lemur shared similar gene organization and structure with those of other mammals. Phylogenetic analysis based on 12 concatenated mitochondrial protein-encoding genes revealed a closer relationship between species of Scandentia and Glires, whereas species of Dermoptera were clustered with Primates. This pattern was consistent with previously reported phylogeny based on mtDNA data, but differed from the one reconstructed on the basis of nuclear genes. Our result suggested that the matrilineal affinity of tree shrew to primates may not be as close as we had thought. The ongoing project for sequencing the entire genome of Chinese tree shrew will provide more information to clarify this important issue.
- Chinese tree shrew,
- mtDNA,
- Phylogeny,
- Animal model,
- Flying lemur

FullText(HTML)

References(22)

References

[1]	Abascal, F., Zardoya, R., Posada, D. ProtTest: selection of best-fit models of protein evolution Bioinformatics, 21 (2005),pp. 2104-2105
[2]	Altekar, G., Dwarkadas, S., Huelsenbeck, J.P. et al. Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference Bioinformatics, 20 (2004),pp. 407-415
[3]	Arnason, U., Adegoke, J.A., Bodin, K. et al. Mammalian mitogenomic relationships and the root of the eutherian tree Proc. Natl. Acad. Sci. USA, 99 (2002),pp. 8151-8156
[4]	Cao, J., Yang, E.B., Su, J.J. et al. The tree shrews: adjuncts and alternatives to primates as models for biomedical research J. Med. Primatol., 32 (2003),pp. 123-130
[5]	Chen, S.Y., Xu, L., Lu, L.B. et al. Genetic diversity and matrilineal structure in Chinese tree shrews inhabiting Kunming, China Zool. Res., 32 (2011),pp. 17-23
[6]	Fuchs, E., Corbach-Söhle, S.
[7]	Galtier, N., Nabholz, B., Glémin, S. et al. Mitochondrial DNA as a marker of molecular diversity: a reappraisal Mol. Ecol., 18 (2009),pp. 4541-4550
[8]	Helgen, K.M.
[9]	Janečka, J.E., Miller, W., Pringle, T.H. et al. Molecular and genomic data identify the closest living relative of primates Science, 318 (2007),pp. 792-794
[10]	Lindblad-Toh, K., Garber, M., Zuk, O. et al. A high-resolution map of human evolutionary constraint using 29 mammals Nature, 478 (2011),pp. 476-482
[11]	Lowe, T.M., Eddy, S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence Nucleic Acids Res., 25 (1997),pp. 955-964
[12]	Murphy, W.J., Eizirik, E., O'Brien, S.J. et al. Resolution of the early placental mammal radiation using Bayesian phylogenetics Science, 294 (2001),pp. 2348-2351
[13]	Nie, W., Fu, B., O'Brien, P.C. et al. Flying lemurs—‘the flying tree shrews’? Molecular cytogenetic evidence for a Scandentia-Dermoptera sister clade BMC Biol., 6 (2008),p. 18
[14]	Peng, Y.Z., Ye, Z.Z., Zou, R.J. et al.
[15]	Roberts, T.E., Lanier, H.C., Sargis, E.J. et al. Molecular phylogeny of treeshrews (Mammalia: Scandentia) and the timescale of diversification in Southeast Asia Mol. Phylogenet. Evol., 60 (2011),pp. 358-372
[16]	Ronquist, F., Huelsenbeck, J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models Bioinformatics, 19 (2003),pp. 1572-1574
[17]	Seiffert, E.R., Simons, E.L., Attia, Y. Fossil evidence for an ancient divergence of lorises and galagos Nature, 422 (2003),pp. 421-424
[18]	Schmitz, J., Ohme, M., Zischler, H. Mol. Biol. Evol., 17 (2000),pp. 1334-1343
[19]	Tamura, K., Peterson, D., Peterson, N. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods Mol. Biol. Evol., 28 (2011),pp. 2731-2739
[20]	van der Worp, H.B., Howells, D.W., Sena, E.S. et al. Can animal models of disease reliably inform human studies? PLoS Med., 7 (2010),p. e1000245
[21]	Waddell, P.J., Cao, Y., Hauf, J. et al. Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid-invariant sites-LogDet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo, and elephant Syst. Biol., 48 (1999),pp. 31-53
[22]	Wang, Y.X. Zool. Res., 8 (1987),pp. 213-230