Patterns of genetic variation within and between gibbon species

Molecular Biology and Evolution

Volumn 28, Issue 8, 2011, Pages 2211-2218

  Kim, Sung K ^a   Carbone, Lucia ^b,c   Becquet, Celine ^a   Mootnick, Alan R ^d   Li, David Jiang ^b   De Jong, Pieter J ^b   Wall, Jeffrey D ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b CHILDREN S HOSPITAL OAKLAND RESEARCH INSTITUTE   (United States)

^c OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^d Gibbon Conservation Center   (United States)

Author keywords

chromosomal rearrangements; genetic diversity; gibbon; population genetics; population history

Indexed keywords

ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; CONTROLLED STUDY; DNA EXTRACTION; DNA SEQUENCE; EFFECTIVE POPULATION SIZE; GENE FREQUENCY; GENETIC VARIABILITY; HUMAN; HYLOBATIDAE; NOMASCUS GABRIELLAE; NOMASCUS LEUCOGENY; NONHUMAN; POLYMERASE CHAIN REACTION; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; CELL LINE; GENE FLOW; GENETIC LINKAGE; GENETIC VARIATION; HYLOBATES; MUTATION; PHENOTYPE; PHYLOGENY;

HOMO; HYLOBATIDAE; NOMASCUS LEUCOGENYS;

EID: 79961055447     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msr033     Document Type: Article

References (54)

1. Genomes Project Consortium Durbin RM, Abecasis GR, et al. (542 co-authors). 2010. A map of human genome variation from population-scale sequencing. Nature 467:1061-1073.
2. Becquet C, Przeworski M. 2007. A new approach to estimate parameters of speciation models with application to apes. Genome Res. 17:1505-1519. (Pubitemid 47529435)
3. Becquet C, Przeworski M. 2009. Learning about modes of speciation by computational approaches. Evolution 63:2547-2562.
4. Brown JD, O'Neill RJ. 2010. Chromosomes, conflict and epigenetics: chromosomal speciation revisited. Annu Rev Genomics Hum Genet. 11:291-316.
5. Bush GL, Case SM, Wilson AC, Patton JL. 1977. Rapid speciation and chromosomal evolution in mammals. Proc Natl Acad Sci USA. 74:3942-3945.
6. Carbone L, Harris RA, Vessere GM, et al. (12 co-authors). 2009. Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution. PLoS Genet. 5:e1000538.
7. Carbone L, Mootnick AR, Nadler T, Moisson P, Ryder O, Roos C, de Jong PJ. 2009. A chromosomal inversion unique to the northern white-cheeked gibbon. PLoS One. 4:e4999.
8. Carbone L, Vessere GM, ten Hallers BF, et al. (14 co-authors). 2006. A high-resolution map of synteny disruptions in gibbon and human genomes. PLoS Genet. 2:e223.
9. Crow JF, Kimura M. 1970. An introduction to population genetics theory. Minneapolis, MN: Burgess Publishing.
10. Dutrillaux B, Rethore MO, Prieur M, Lejeune J. 1973. Analysis of the structure of chromatids of Gorilla gorilla. Comparison with Homo sapiens and Pan troglodytes. Humangenetik 20:343-354.
11. Ewing B, Hillier L, Wendl MC, Green P. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175-185. (Pubitemid 28177229)
12. Felsenstein J. 1989. PHYLIP-phylogeny inference package (version 3.2). Cladistics 5:164-166.
13. Fischer A, Pollack J, Thalmann O, Nickel B, Paabo S. 2006. Demographic history and genetic differentiation in apes. Curr Biol. 16:1133-1138. (Pubitemid 43815750)
14. Fontdevila A. 2005. Hybrid genome evolution by transposition. Cytogenet Genome Res. 110:49-55. (Pubitemid 41159882)
15. Geissmann T. 1995. Gibbon systematics and species identification. Int Zoo News. 42:467-501.
16. Glazko GV, Nei M. 2003. Estimation of divergence times for major lineages of primate species. Mol Biol Evol. 20:424-434. (Pubitemid 36427177)
17. Groves CP. 1972. Systematics and phylogeny of gibbon. In: Rumbaugh DM, editor. Gibbon and Siamang, evolution, ecology behavior, and captive maintenance. Basel (Switzerland): S. Karger. Vol. 1 p. 1-89.
18. Groves CP. 2001. Primate taxonomy. Washington (DC): Smithsonian Institution Press.
19. Hayashi S, Hayasaka K, Takenaka O, Horai S. 1995. Molecular phylogeny of gibbons inferred from mitochondrial DNA sequences: preliminary report. J Mol Evol. 41:359-365.
20. Hey J, Nielsen R. 2004. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167:747-760. (Pubitemid 38931862)
21. ST. Nat Rev Genet. 10:639-650.
22. Hudson RR, Slatkin M, Maddison WP. 1992. Estimation of levels of gene flow from DNA sequence data. Genetics 132:583-589.
23. IUCN. 2009. IUCN red list of threatened species 2009.2. 2009. [cited 2010 Oct. 1]. Available from: http://www.iucnredlist.org
24. Kong A, Gudbjartsson D, Sainz J, et al. (16 co-authors). 2002. A highresolution recombination map of the human genome. Nat Genet. 31:241-247.
25. Kumar S, Filipski A, Swarna V, Walker A, Hedges SB. 2005. Placing confidence limits on the molecular age of the human-chimpanzee divergence. Proc Natl Acad Sci USA. 102:18832-18847.
26. Malécot G. 1948. Les mathématiques de l'héré dié. Paris (France): Masson.
27. Marshall JT, Marshall ER. 1976. Gibbons and their territorial songs. Science 193:235-237.
28. Marshall JT, Marshall ER. 1978. The Gibbons. Gainesville (FL): ARA records. (Long playing phonograph disc)
29. Marshall JT, Sugardjito J. 1986. Gibbon systematics. In: Swindler DR, Erwin J, editors. Comparative primate biology. New York: AR Liss. p. 137-185.
30. Marshall JT, Sugardjito J, Markaya M. 1984. Gibbons of the lar group: relationships based on voice. In: Preuschoft H, Chivers DJ, Brockelman WY, Creel N, editors. The Lesser apes. Edinburgh (UK): Edinburgh University Press. p. 533-541.
31. Matsudaira K, Ishida T. 2010. Phylogenetic relationships and divergence dates of the whole mitochondrial genome sequences among three gibbon genera. Mol Phylogenet Evol. 55:454-459.
32. Meijaard E, Groves CP. 2006. The geography of mammals and rivers in mainland southeast Asia. In: Primate Biogeography: progress and prospects. New York: Springer. p. 305-329.
33. Meng XL. 1994. Posterior predictive p-values. Ann Stat. 22:1142-1160.
34. Misceo D, Capozzi O, Roberto R, Dell'oglio MP, Rocchi M, Stanyon R, Archidiacono N. 2008. Tracking the complex flow of chromosome rearrangements from the Hominoidea Ancestor to extant Hylobates and Nomascus Gibbons by high-resolution synteny mapping. Genome Res. 18:1530-1537.
35. Monda K, Simmons RE, Kressirer P, Su B, Woodruff DS. 2007. Mitochondrial DNA hypervariable region-1 sequence variation and phylogeny of the concolor gibbons, Nomascus. Am J Primatol. 69:1-22.
36. Mootnick AR. 2006. Gibbon (Hylobatidae) species identification recommended for rescue or breeding centers. Primate Conserv. 21:103-138.
37. Mootnick AR, Fan P-F. 2011. A comparative study of crested gibbons (Nomascus). Am J Primatol. 73(2):135-154.
38. Mootnick AR, Xiaoming W, Moisson P, Chan BPL, Fellowes JR, Nadler T. 2007. Hainan gibbon, Nomascus hainanus (Thomas, 1892). In: Mittermeier RA, Ratsimbazafy J, Rylands JB, et al., editors. Primates in peril: the World's 25 most endangered primates, 2006-2008. Arlington (TX): IUCN/SSC Primate Specialist group. p. 16-17.
39. Morley RJ, Flenley JR. 1987. Late Cainozoic vegetational and environmental changes in the Malay Archipelago. In: Whitmore TC, editor. Biogeographical Evolution of the Malay Archipelago. Oxford: Clarendon Press. p. 50-59.
40. Muller S, Hollatz M, Wienberg J. 2003. Chromosomal phylogeny and evolution of gibbons (Hylobatidae). Hum Genet. 113:493-501. (Pubitemid 37383764)
41. Nei M, Li WH. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A. 76:5269-5273. (Pubitemid 10236121)
42. Nielsen R, Wakeley J. 2001. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158:885-896. (Pubitemid 32552323)
43. O'Neil RJ, O'Neil MJ, Graves JA. 1998. Undermethylation associated with retroelement activation and chromosome remodeling in an interspecific mammalian hybrid. Nature 393:68-72. (Pubitemid 28240255)
44. Roach JC, Glusman G, Smit AF, et al. (15 co-authors). 2010. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328:636-639.
45. Tajima F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437-460. (Pubitemid 14247444)
46. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595. (Pubitemid 19274682)
47. Takacs Z, Morales JC, Geissmann T, Melnick DJ. 2005. A complete species-level phylogeny of the Hylobatidae based on mitochondrial ND3-ND4 gene sequence. Mol Phylogenet Evol. 36:456-467. (Pubitemid 41138884)
48. Van Ngoc T, Mootnick AR, Geissmann T, Vu Ngoc T, Nadler T, Roos C. 2010. A new species of crested gibbon from the central Annamite mountain range. Vietnam J Primatol. 4:1-12.
49. Van Ngoc T, Mootnick AR, Li M, Ziegler T, Agil M, Moisson P, Nadler T, Walter L, Roos C. 2010. Mitochondrial evidence for multiple radiations in the evolutionary history of small apes. BMC Evol Biol. 10:74.
50. van Tuinen P, Mootnick AR, Kingswood SC, Hale DW, Kumamoto AT. 1999. Complex, compound inversion/translocation polymorphism in an ape: presumptive intermediate stage in the karyotypic evolution of the agile gibbon Hylobates agilis. Am J Phys Anthropol. 110:129-142. (Pubitemid 29466215)
51. Wall JD, Cox MP, Mendez FL, Woerner A, Severson T, Hammer MF. 2008. A novel DNA sequence database for analyzing human demographic history. Genome Res. 18:1354-1361.
52. Watterson G. 1975. On the number of segregating sites in genetical models without recombination. Theor Popul Biol. 7:256-276.
53. Whittaker DJ, Morales JC, Melnick DJ. 2007. Resolution of the Hylobates phylogeny: congruence of mitochondrial D-loop sequences with molecular, behavioral, and morphological datasets. Mol Phylogenet Evol. 45:620-628. (Pubitemid 47532760)
54. Wright S. 1951. The genetical structure of populations. Ann Eugen. 15:323-354.