Mitochondrial phylogeny of leaf monkeys (genus Presbytis, Eschscholtz, 1821) with implications for taxonomy and conservation

Molecular Phylogenetics and Evolution

Volumn 59, Issue 2, 2011, Pages 311-319

  Meyer, Dirk ^a,b   Rinaldi, Ir Dones ^c   Ramlee, Hatta ^d   Perwitasari Farajallah Dyah, D ^c   Hodges, J Keith ^a   Roos, Christian ^a  

^a GERMAN PRIMATE CENTER   (Germany)

^b Göttingen Center for Biodiversity and Ecology   (Germany)

^c BOGOR AGRICULTURAL UNIVERSITY   (Indonesia)

^d AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

Asia; Colobinae; Conservation; Cytochrome b; D loop; Indonesia; Presbytis; Sundaland; Taxonomy

Indexed keywords

MITOCHONDRIAL DNA; PRIMER DNA;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CERCOPITHECIDAE; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; ENVIRONMENTAL PROTECTION; FECES; GENETICS; INDONESIA; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SPECIES DIFFERENCE; STATISTICAL MODEL;

ANIMALS; BASE SEQUENCE; BAYES THEOREM; CERCOPITHECIDAE; CONSERVATION OF NATURAL RESOURCES; DNA PRIMERS; DNA, MITOCHONDRIAL; FECES; INDONESIA; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

CERCOPITHECIDAE; COLOBINAE; HAPLORHINI; PRESBYTIS; TRACHYPITHECUS;

EID: 79955081131     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2011.02.015     Document Type: Article

References (79)

1. Aimi M., Bakar A. Taxonomy and distribution of Presbytis melalophos group in Sumatera, Indonesia. Primates 1992, 33:191-206.
2. Aimi M., Bakar A. Distribution and deployment of Presbytis melalophos group in Sumatera, Indonesia. Primates 1996, 37:399-409.
3. Avise J. Molecular Markers, Natural History, and Evolution 2004, Sinauer Associates, Sunderland, MA.
4. Bennett E.L., Davies A.G. The ecology of Asian colobines. Colobine Monkeys: Their Ecology, Behaviour and Evolution 1994, 129-171. Cambridge University Press, Cambridge. J.F. Davies, J.F. Oates (Eds.).
5. Brandon-Jones D. The evolution of recent Asian colobines. Recent Advances in Primatology 1978, vol. III:323-325. Academic Press, London.
6. Brandon-Jones D. Colobus and leaf monkeys. Encyclopedia of Mammals 1984, 398-410. George Allen and Unwin, London. I.D. MacDonald (Ed.).
7. Brandon-Jones D. Taxonomic affinities of the Menatwai islands surili (Bonaparte, 1856), P. potenziani. Raffles Bull. Zool. 1993, 41:331-357.
8. Brandon-Jones D. Presbytis fredericae (Sody, 1930), an endangered Colobine species endemic to Central Java, Indonesia. Primate Conserv. 1995, 16:68-70.
9. Brandon-Jones D. The zoogeography of sexual dichromatism in the Bornean grizzled surili, Presbytis comata (Desmarest, 1822). Sarawak Museum J. 1996, 5:177-200.
10. Brandon-Jones D. Presbytis species in sympatry in Borneo versus allopatry in Sumatra: an interpretation. Tropical Rainforest Research - Current Issues 1996, 71-76. Kluwer Academic Publishers, Dordrecht. D.S.E.A. Edwards (Ed.).
11. Brandon-Jones D. The Asian Colobinae as indicators of quaternary climatic change. Biol. J. Linn. Soc. 1996, 59:327-350.
12. Brandon-Jones D., Eudey A.A., Geissmann T., Groves C.P., Melnick D.J., Morales J.C., Shekelle M., Steward C.-B. Asian primate classification. Int. J. Primatol. 2004, 25:122-129.
13. Brunet M., Guy F., Pilbeam D., Mackaye H.T., Likius A., Ahounta D., Beauvilain A., Blondel C., Bocherens H., Boisserie J.R., de Bonis L., Coppens Y., Dejax J., Denys C., Duringer P., Eisenmann V., Fanone G., Fronty P., Geraads D., Lehmann T., Lihoreau F., Louchart A., Mahamat A., Merceron G., Mouchelin G., Otero O., Pelaez Campomanes P., Ponce de Leon M., Rage J.C., Sapanet M., Schuster M., Sudre J., Tassy P., Valentin X., Vignaud P., Viriot L., Zazzo A., Zollikofer C. A new hominid from the upper Miocene of Chad, Central Africa. Nature 2002, 418:145-151.
14. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 2000, 17:540-552.
15. Chasen F.N. A handlist of Malaysian mammals. Bull. Raffles Museum 1940, 15:1-209.
16. Chatterjee H.J., Ho S.Y.W., Barnes I., Groves C. Estimating the phylogeny and divergence times of primates using a supermatrix approach. BMC Evol. Biol. 2009, 9:259.
17. Cracraft, J., 1983. Species concepts and speciation analysis. In: Johnson, R.F. (Ed.), Currrent Ornithology, vol 1, pp. 159-187.
18. Craul M., Zimmermann E., Rasoloharijaona S., Randrianambinina B., Radespiel U. Unexpected species diversity of Malagasy primates (Lepilemur spp.) in the same biogeographical zone: a morphological and molecular approach with the description of two new species. BMC Evol. Biol. 2007, 7:83.
19. Delson E., Tattersall I., van Couvering J.A., Brooks A.S. Cercopithecidae. Encyclopedia of Human Evolution and Prehistory 2000, 166-171. Garland, New York. second ed. E. Delson, I. Tattersall, J.A. van Couvering, A.S. Brooks (Eds.).
20. Drummond A.J. Beast: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
21. Drummond, A.J., Ashton, B., Cheung, M., Heled, J., Kearse, M., Moir, R., Stones-Havas, S., Thierer, T., Wilson, A., 2009. Geneious. http://www.geneious.com/.
22. Drummond A.J., Ho S.Y.W., Phillips M.J., Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006, 4:e88.
23. FWI/GFW 2002. The State of the Forest: Indonesia. Bogor, Indonesia: Forest Watch Indonesia, and Washington DC: Global Forest Watch. (10.31.10). http://www.globalforestwatch.org/common/indonesia/sof.indonesia.english.low.pdf.
24. Gelman A., Rubin D. Inference from iterative simulation using multiple sequences. Stat. Sci. 1992, 7:457-511.
25. Groves C.P. The forgotten leaf-eaters, and the phylogeny of the Colobinae. Old World Monkeys: Evolution, Systematics, and Behavior 1970, 557-587. Academic Press, New York. J.R. Napier, P.H. Napier (Eds.).
26. Groves C.P. A Theory of Human and Primate Evolution 1989, Clarendon Press, Oxford and New York.
27. Groves C.P. Primate Taxonomy 2001, Smithsonian Institution Press, Washington, DC.
28. Groves C.P. The what, why and how of primate taxonomy. Int. J. Primatol. 2004, 25:1105-1126.
29. Hofreiter M., Siedel H., van Neer W., Vigilant L. Mitochondrial DNA sequence from an enigmatic gorilla population (Gorilla gorilla uellensis). Am. J. Phys. Anthropol. 2003, 121:361-368.
30. Hooijer D.A. Quaternary langurs and macaques from the Malay Archipelago. Zool. Verhandelingen 1962, 55:1-64.
31. Huelsenbeck J.P., Ronquist F., Nielsen R., Bollback J.P. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 2001, 294:2310-2314.
32. IUCN, 2010. IUCN Red List of Threatened Species. Version 2010.1. (20.6.10). http://www.iucnredlist.org.
33. Kelley J. The hominoid radiation in Asia. The Primate Fossil Record 2002, 369-384. Cambridge University Press, Cambridge. W.C. Hartwig (Ed.).
34. Leakey M.G. Evolution of Theropithecus in the Turkana Basin. Theropithecus, the Rise and Fall of a Primate Genus 1993, 85-124. Cambridge University Press, Cambridge. N.G. Jablonski (Ed.).
35. Louis E.E., Engberg S.E., McGuire S.M., McCormick M.J., Randriamampionona R., Ranaivoarisoa J.F., Bailey C.A., Mittermeier R.A., Lei R. Revision of the mouse lemurs, Microcebus (Primates, Lemuriformes), of Northern and Northwestern Madagascar with descriptions of two new species at Montagne d'Ambre National Park and Antafondro Classified Forest. Primate Conserv. 2008, 23:19-38.
36. Matauschek, C., Roos, C., Heymann, E.W., in press. Mitochondrial phylogeny of tamarins (Saguinus, Hoffmannsegg 1807) with taxonomic and biogeographic implications for the S. nigricollis species group. Am. J. Phys. Anthropol., doi:10.1002/ajpa.21445.
37. Md Zain, B.M., 2001. Molecular Sytematics of the Genus Presbytis. Thesis, Columbia University, New York.
38. Md Zain, B.M., Hasan, M.H., Melnick, D.J., 2002. Defining evolutionary significant units for Presbytis melalophos conservation using mitochondrial DNA sequences. In: Omar, R., Ali Rahman, Z., Latif, M.T., Lihan, T., Adam, J.H. (Eds.), Proceedings of the Regional Symposium on Environment and Natural Resources 10-11th April 2002, Hotel Renaissance Kuala Lumpur, Malaysia, vol. 1, pp. 279-286.
39. Medway Lord. The monkeys of Sundaland: ecology and systematics of the cercopithecids of a humid equatorial environment. Old World Monkeys: Evolution 1970, 513-553. Academic Press, New York. J.R. Napier, P.H. Napier (Eds.).
40. Meijaard, E., 2004. Solving Mammalian Riddles: A Reconstruction of Tertiary and Quaternary Distribution of Mammals and their Palaeoenvironments in Island South-East Asia. Thesis, School of Archaeology and Anthropology, The Australian National University, Canberra.
41. Meijaard E., Groves C.P. The biogeographical evolution and phylogeny of the genus Presbytis. Primate Rep. 2004, 68:71-90.
42. Moritz C. Defining 'evolutionarily significant units' for conservation. Trends Ecol. Evol. 1994, 9:374-375.
43. Napier J.R., Napier P.H. Handbook of Living Primates 1967, Academic Press, London.
44. Newton P.N., Dunbar R.I.M. Colobine monkey society. Colobine Monkeys: Their Ecology, Behaviour and Evolution 1994, 311-346. Cambridge University Press, Cambridge. J.F. Davies, J.F. Oates (Eds.).
45. Nijman V. Geographic variation in pelage characteristics in Presbytis comata (Desmarest, 1822) (Mammalia: Primates, Cercopithecidae). Z. Säugetierk. 1997, 62:257-264.
46. Nijman, V., 2001. Forest (and) Primates: Conservation and Ecology of the Endemic Primates of Java and Borneo. Thesis, Amsterdam University, Wageningen, Tropenbos International.
47. Nijman V. Effects of habitat disturbance and hunting on the density and the biomass of the endemic Hose's leaf monkey Presbytis hosei (Thomas, 1889) (Mammalia: Primates: Cercopithecidae) in east Borneo. Contrib. Zool. 2004, 73:283-291.
48. Nsubuga A.M., Robbins M.M., Roeder A.D., Morin P.A., Boesch C., Vigilant L. Factors affecting the amount of genomic DNA extracted from ape faeces and the identification of an improved sample storage. Mol. Ecol. 2004, 13:2089-2094.
49. Oates G.D., Davies J.F., Delson E. The diversity of living Colobines. Colobine Monkeys: Their Ecology, Behaviour and Evolution 1994, 45-73. Cambridge University Press, Cambridge. J.F. Davies, J.F. Oates (Eds.).
50. Osterholz M., Walter L., Roos C. Phylogenetic position of the langur genera Semnopithecus and Trachypithecus among Asian colobines, and affiliations of their species groups. BMC Evol. Biol. 2008, 8:58.
51. Posada D. JModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
52. Raaum R.L., Sterner K.N., Noviello C.M., Stewart C.B., Disotell T.R. Catarrhine primate divergence dates estimated from complete mitochondrial genomes: concordance with fossil and nuclear DNA evidence. J. Hum. Evol. 2005, 48:237-257.
53. Rambaut, A., 2006. FigTree: Tree Figure Drawing Tool, Version 1.3.1. Institute of Evolutionary Biology, University of Edinburgh. http://tree.bio.ed.ac.uk/software/figtree/.
54. Rambaut, A., Drummond, A., 2005. Tracer v1.3: MCMC Trace Analysis Tool. Institute of Evolutionary Biology, University of Edinburgh. http://tree.bio.ed.ac.uk/software/tracer/.
55. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
56. Roos C., Nadler T., Walter L. Mitochondrial phylogeny, taxonomy and biogeography of the silvered langur species group (Trachypithecus cristatus). Mol. Phylogenet. Evol. 2008, 47:629-636.
57. SAMD, 2006. Southeast Asian Mammal Databank. http://www.ieaitaly.org/samd/.
58. Steiper M.E., Young N.M. Primate molecular divergence dates. Mol. Phylogenet. Evol. 2006, 41:384-394.
59. Sterck E.H.M., Watts D.P., van Schaik C.P. The evolution of female social relationships in nonhuman primates. Behav. Ecol. Sociobiol. 1997, 41:291-309.
60. Sterck E.H.M., Willems E.P., van Hoof J.A.R.A.M., Wich S.A. Female dispersal, inbreeding avoidance, and mate choice in Thomas langurs (Presbytis thomasi). Behaviour 2005, 142:845-868.
61. Sterner K.N., Raaum R.L., Zhang Y.-P., Stewart C.-B., Disotell T.R. Mitochondrial data support an odd-nosed colobine clade. Mol. Phylogenet. Evol. 2006, 40:1-7.
62. Swofford D. PAUP* Phylogenetic Analysis using Parsimony (* and Other Methods) 2002, Sinauer Associates, Sunderland, MA.
63. Talavera G., Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 2007, 56:564-577.
64. Thalmann O., Hebler J., Poinar H.N., Pääbo S., Vigilant L. Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes. Mol. Ecol. 2004, 13:321-335.
65. Thinh V.N., Mootnick A.R., Geissmann T., Li M., Ziegler T., Agil M., Moisson P., Nadler T., Walter L., Roos C. Mitochondrial evidence for multiple radiations in the evolutionary history of small apes. BMC Evol. Biol. 2010, 10:74.
66. Thinh V.N., Rawson B., Hallam C., Kenyon M., Nadler T., Walter L., Roos C. Phylogeny and distribution of crested gibbons (genus Nomascus) based on mitochondrial cytochrome b gene sequence data. Am. J. Primatol. 2010, 72:1047-1054.
67. Tilson R.L. Infant coloration and taxonomic affinity of the Mentawai Islands leaf monkey, Presbytis potenziani. J. Mammal. 1976, 57:766-769.
68. Ting N. Mitochondrial relationships and divergence dates of the African colobines: evidence of Miocene origins for the living colobus monkeys. J. Hum. Evol. 2008, 55:312-325.
69. Tosi A.J., Morales J.C., Melnick D.J. Paternal, maternal, and biparental molecular markers provide unique windows onto the evolutionary history of macaque monkeys. Evolution 2003, 57:1419-1435.
70. van Roosmalen M.G.M., van Roosmalen T., Mittermeier R.A. A taxonomic review of the titi monkeys, genus Callicebus Thomas, 1903, with the description of two new species, Callicebus bernhardi and Callicebus stephennashi, from Brazilian Amazonia. Neotrop. Primates 2002, 10:1-52.
71. Vignaud P., Duringer P., Mackaye H.T., Likius A., Blondel C., Boisserie J.R., de Bonis L., Eisenmann V., Etienne M.E., Geraads D., Guy F., Lehmann T., Lihoreau F., Lopez-Martinez N., Mourer-Chauvire C., Otero O., Rage J.C., Schuster M., Viriot L., Zazzo A., Brunet M. Geology and palaeontology of the Upper Miocene Toros-Menalla hominid locality, Chad. Nature 2002, 418:152-155.
72. Washburn S.L. The genera of Malayan langurs. J. Mammal. 1944, 25:289-294.
73. Whittaker D. A conservation action plan for the Mentawai primates. Primate Conserv. 2006, 20:95-105.
74. Wilson, W.L., Wilson, C.C., 1975. Species-specific vocalisations and the determination of phylogenetic affinities of the Presbytis aygula-melalophos group in Sumatra. In: Kondo, S., Kawai, M., Ehara, A. (Eds.), Contemporary Primatology, 5th International Congress of Primatology, Nagoya, August 1974, Karger, Basel, pp. 459-463.
75. Wilson C.C., Wilson W.L. Behavioral and morphological variations among primate population in Sumatra. Yearb. Phys. Anthropol. 1977, 20:207-233.
76. World Bank, 2004. Indonesia at Glance 2004. (10.31.10). http://siteresources.worldbank.org/INTEEI/Data/20856180/Indonesia.pdf.
77. Zalmout I.S., Sanders W.J., MacLatchy L.M., Gunnell G.F., Al-Mufarreh Y.A., Ali M.A., Nasser A.H., Al-Masari A.M., Al-Sobhi S.A., Nadhra A.O., Matari A.H., Wilson J.A., Gingerich P.D. New Oligocene primate from Saudi Arabia and the divergence of apes and Old World monkeys. Nature 2010, 466:360-365.
78. Ziegler T., Abegg C., Meijaard E., Perwitasari-Farajallah D., Walter L., Hodges J.K., Roos C. Molecular phylogeny and evolutionary history of Southeast Asian macaques forming the M. silenus group. Mol. Phylogenet. Evol. 2007, 42:807-816.
79. Zwickl, D.J., 2006. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets under the Maximum Likelihood Criterion. Thesis, The University of Texas at Austin.