Kai HE, Naiqing HU, Joseph D. ORKIN, Daw Thida NYEIN, Chi MA, Wen XIAO, Pengfei FAN, Xuelong JIANG. Molecular phylogeny and divergence time of Trachypithecus: with implications for the taxonomy of T. phayrei. Zoological Research, 2012, 33(E5-6): 104-110. doi: 10.3724/SP.J.1141.2012.E05-06E104
Citation: Kai HE, Naiqing HU, Joseph D. ORKIN, Daw Thida NYEIN, Chi MA, Wen XIAO, Pengfei FAN, Xuelong JIANG. Molecular phylogeny and divergence time of Trachypithecus: with implications for the taxonomy of T. phayrei. Zoological Research, 2012, 33(E5-6): 104-110. doi: 10.3724/SP.J.1141.2012.E05-06E104

Molecular phylogeny and divergence time of Trachypithecus: with implications for the taxonomy of T. phayrei

doi: 10.3724/SP.J.1141.2012.E05-06E104
Funds:  This work was supported by the Fund of State Key Laboratory of Genetics Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (GREKF12-06)
  • Received Date: 2012-09-06
  • Rev Recd Date: 2012-11-15
  • Publish Date: 2012-12-08
  • The genus Trachypithecus is the most diverse langur taxon, distributed in southwestern China, south and southeastern Asia. In this study, we include 16 recognized Trachypithecus species to reconstruct the phylogeny with particular concern to the taxonomy of the three subspecies of T. phayrei using multiple genes. Our results support a sister-relationship between T. p. phayrei and T. p. shanicus. However, the mitochondrial CYT B gene supported T. p. crepuscula as a distinct species, but the nuclear PRM1 gene suggested a closer relationship between T. p. crepuscula and T. p. phayrei. The incongruence between nuclear and mitochondrial genes suggests that hybridization may have occurred, a fact that would benefit from re-examination using multiple unlinked nuclear genes.
  • loading
  • [1]
    Aiello LC, Collard M. 2001. Palaeoanthropology: Our newest oldest ancestor? Nature, 410(6828): 526-527.
    [2]
    Bandelt HJ, Forster P, Röhl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol, 16(1): 37-48.
    [3]
    Benefit BR, Pickford M. 1986. Miocene fossil cercopithecoids from Kenya. Am J Phys Anthropol, 69(4): 441-464.
    [4]
    Bleisch B, Brockelman W, Timmins RJ, Nadler T, Thun S, Das J, Yongcheng L. 2008. Trachypithecus phayrei. IUCN 2012. IUCN Red List of Threatened Species. Version 2012.1. [www.iucnredlist.org].
    [5]
    Bradley RD, Baker RJ. 2001. A test of the genetic species concept: Cytochrome-b sequences and mammals. J Mammal, 82(4): 960-973.
    [6]
    Brandley MC, Schmitz A, Reeder TW. 2005. Partitioned bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Syst Biol, 54(3): 373-390.
    [7]
    Brandon-Jones D. 1996. The Asian Colobinae (Mammalia: Cercopithecidae) as indicators of quaternary climatic change. Biol J Linn Soc, 59(3): 327-350.
    [8]
    Brown JM, Lemmon AR. 2007. The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics. Syst Biol, 56(4): 643-655.
    [9]
    Chatterjee HJ, Ho SYW, Barnes I, Groves C. 2009. Estimating the phylogeny and divergence times of primates using a supermatrix approach. BMC Evol Biol, 9(1): 259.
    [10]
    Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol, 4(5): 699-710.
    [11]
    Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol, 29(8): 1969-1973.
    [12]
    Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res, 32(5): 1792-1797.
    [13]
    Gebo DL, MacLatchy L, Kityo R, Deino A, Kingston J, Pilbeam D. 1997. A hominoid genus from the early Miocene of Uganda. Science, 276(5311): 401-404.
    [14]
    Geissmann T, Groves CP, Roos C. 2004. The Tenasserim lutung, Trachypithecus barbei (Blyth, 1847) (Primates: Cercopithecidae): Description of a live specimen, and a reassessment of phylogenetic affinities, taxonomic history, and distribution. Contrib Zool, 73(4): 271-282.
    [15]
    Gilbert CC, Goble ED, Hill A. 2010. Miocene cercopithecoidea from the Tugen Hills, Kenya. J Hum Evol, 59(5): 465-483.
    [16]
    Groves CP. 2005. Order primates // Wilson D E, Reeder D M. Mammal Species of the World: A Taxonomic and Geographic Reference. Baltimore: John Hopkins University Press, 111-184.
    [17]
    Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol, 52(5): 696-704.
    [18]
    He K, Chen JH, Gould GC, Yamaguchi N, Ai HS, Wang YX, Zhang YP, Jiang XL. 2012. An estimation of erinaceidae phylogeny: A combined analysis approach. PLoS ONE, 7(6): e39304.
    [19]
    Ho SYM. 2007. Calibrating molecular estimates of substitution rates and divergence times in birds. J Avian Biol, 38(4): 409-414.
    [20]
    Huelsenbeck J, Rannala B. 2004. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst Biol, 53(6): 904-913.
    [21]
    Irwin DM, Kocher TD, Wilson AC. 1991. Evolution of the cytochrome b gene of mammals. J Mol Evol, 32(2): 128-144.
    [22]
    Jablonski NG. 2002. Fossil Old World monkeys: the Late Neogene radiation // Hartwig WC. The Primate Fossil Record. Cambridge: Cambridge University Press, 255-299.
    [23]
    Jablonski NG, Tyler DE. 1999. Trachypithecus auratus sangiranensis, a new fossil monkey from Sangiran, central Java, Indonesia. Int J Primatol, 20(3): 319-326.
    [24]
    Karanth KP. 2008. Primate numts and reticulate evolution of capped and golden leaf monkeys (Primates: Colobinae). J Biosci, 33(5): 761-770.
    [25]
    Karanth KP, Singh L, Collura RV, Stewart CB. 2008. Molecular phylogeny and biogeography of langurs and leaf monkeys of South Asia (Primates: Colobinae). Mol Phylogenet Evol, 46(2): 683-694.
    [26]
    Larick R, Ciochon RL, Zaim Y, Sudijono, Suminto, Rizal Y, Aziz F. 2000. Lithostratigraphic context for Kln-1993.05-SNJ, a fossil colobine maxilla from Jokotingkir, Sangiran dome. Int J Primatol, 21(4): 731-759.
    [27]
    Lemmon AR, Brown JM, Stanger-Hall K, Lemmon EM. 2009. The effect of ambiguous data on phylogenetic estimates obtained by Maximum Likelihood and Bayesian Inference. Syst Biol, 58(1): 130-145.
    [28]
    Liedigk R, Van Ngoc Thinh TN, Walter L, Roos C. 2009. Evolutionary history and phylogenetic position of the Indochinese grey langur (Trachypithecus crepusculus). Vietn J Primatol, 3: 1-8.
    [29]
    Meijaard E, Groves CP. 2006. The geography of mammals and rivers in mainland Southeast Asia // Lehman SM, Fleagle JG. Primate Biogeography. New York: Springer, 305-329.
    [30]
    Nadler T, Momberg F, Dang NX, Lormee N. 2003. Vietnam Primate Conservation Status Review 2002. Part 2: Leaf Monkeys. Hanoi: Fauna and Flora International and Frankfurt Zoological Society, 145-164.
    [31]
    Nakatsukasa M, Mbua E, Yoshihiro S, Sakai T, Nakaya H, Kunimatsu Y. 2010. Earliest colobine skeletons from Nakali, Kenya. Am J Phys Anthropol, 143(3): 365-382.
    [32]
    Nsubuga AM, Robbins MM, Roeder AD, Morin PA, Boesch C, Vigilant L. 2004. Factors affecting the amount of genomic DNA extracted from ape faeces and the identification of an improved sample storage method. Mol Ecol, 13(7): 2089-2094.
    [33]
    O'Brien SJ, Menninger JC, Nash WG. 2006. Atlas of Mammalian Chromosomes. New Jersey: John Wiley and Sons, 714.
    [34]
    Osterholz M, Walter L, Roos C. 2008. Phylogenetic position of the langur genera Semnopithecus and Trachypithecus among Asian colobines, and genus affiliations of their species groups. BMC Evol Biol, 8(1): 58.
    [35]
    Perelman P, Johnson WE, Roos C, Seu醤ez HN, Horvath JE, Moreira MA, Kessing B, Pontius J, Roelke M, Rumpler Y, Schneider MPC, Silva A, O'Brien SJ, Pecon-Slattery J. 2011. A molecular phylogeny of living primates. PLoS Genet, 7(3): e1001342.
    [36]
    Posada D. 2008. jModelTest: phylogenetic model averaging. Mol Biol Evol, 25(7): 1253-1256.
    [37]
    Que TC, Hu YL, Zhang CC, Huang CM, Meng XJ. 2007. Observations on the Hybrid F of Trachypthecus leucocephalus and T. francioisi and its offspring. Zool Res, 28(3): 225-230.
    [38]
    Rambaut A, Drummond A. 2009. Tracer v1.5 [http://tree.bio.ed.ac.uk/ software/tracer/].
    [39]
    Sambrook J, Russell D. 2001. Molecular Cloning: A Laboratory Manual. New York: Cold Spring Harbor Laboratory Press, 2368.
    [40]
    Schempp W, M黱ch C, Roos C, Nadler T. 2008. Chromosomal and molecular studies of a hybrid between red-shanked douc langur (Pygathrix nemaeus) and Hatinh langur (Trachypithecus laotum hatinhensis). Vietnam J Primatol, 1: 55-62.
    [41]
    Schwarz G. 1978. Estimating the dimension of a model. Ann Statist, 6(2): 461-464.
    [42]
    Senut B, Pickford M, Gommery D, Mein P, Cheboi K, Coppens Y. 2001. First hominid from the Miocene (Lukeino Formation, Kenya). Comptes Rendus De L Academie Des Sciences Serie Ii Fascicule a-Sciences De La Terre Et Des Planetes, 332(2): 137-144.
    [43]
    Vallet D, Petit E, Gatti S, Levr閞o F, M閚ard N. 2008. A new 2CTAB/PCI method improves DNA amplification success from faeces of Mediterranean (Barbary macaques) and tropical (lowland gorillas) primates. Conserv Genet, 9(3): 677-680.
    [44]
    Wang XP, Yu L, Roos C, Ting N, Chen CP, Wang J, Zhang YP. 2012. Phylogenetic relationships among the colobine monkeys revisited: New insights from analyses of complete mt genomes and 44 nuclear non-coding markers. PLoS ONE, 7(4): e36274.
    [45]
    Wang YX, Jiang XL, Feng Q. 1999. Taxonomy, status and conservation of leaf monkeys in China. Zool Res, 20(4): 206-315 (in Chinese).
    [46]
    Wangchuk T. 2005. The Evolution, Phylogeography, and Conservation of the Golden Langur (Trachypithecus geei) in Bhutan. Ph.D. thesis. Department of Biology, University of Maryland.
    [47]
    Wangchuk T, Inouye DW, Hare MP. 2008. The emergence of an endangered species: Evolution and phylogeny of the Trachypithecus geei of Bhutan. Int J Primatol, 29(3): 565-582.
    [48]
    Zalmout IS, Sanders WJ, MacLatchy LM, Gunnell GF, Al-Mufarreh YA, Ali MA, Nasser AAH, Al-Masari AM, Al-Sobhi SA, Nadhra AO, Matari AH, Wilson JA, Gingerich PD. 2010. New Oligocene primate from Saudi Arabia and the divergence of apes and Old World monkeys. Nature, 466(7304): 360-365.
    [49]
    Zhang YP, Shi LM. 1993. Mitochondrial DNA restriction fragment length polymorphism in Presbytis phayrei and P. francoisi. Zool Res, 14(3): 263-269 (in Chinese).
  • 加载中

Catalog

    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Article Metrics

    Article views (1256) PDF downloads(1758) Cited by()
    Proportional views
    Related

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return