A genetic comparison of two alleged subspecies of P hilippine cynomolgus macaques
dc.contributor.author | Smith, David Glenn | en_US |
dc.contributor.author | Ng, Jillian | en_US |
dc.contributor.author | George, Debra | en_US |
dc.contributor.author | Trask, Jessica Satkoski | en_US |
dc.contributor.author | Houghton, Paul | en_US |
dc.contributor.author | Singh, Balbir | en_US |
dc.contributor.author | Villano, Jason | en_US |
dc.contributor.author | Kanthaswamy, Sreetharan | en_US |
dc.date.accessioned | 2014-09-03T16:51:56Z | |
dc.date.available | WITHHELD_13_MONTHS | en_US |
dc.date.available | 2014-09-03T16:51:56Z | |
dc.date.issued | 2014-09 | en_US |
dc.identifier.citation | Smith, David Glenn; Ng, Jillian; George, Debra; Trask, Jessica Satkoski; Houghton, Paul; Singh, Balbir; Villano, Jason; Kanthaswamy, Sreetharan (2014). "A genetic comparison of two alleged subspecies of P hilippine cynomolgus macaques." American Journal of Physical Anthropology 155(1): 136-148. | en_US |
dc.identifier.issn | 0002-9483 | en_US |
dc.identifier.issn | 1096-8644 | en_US |
dc.identifier.uri | https://hdl.handle.net/2027.42/108326 | |
dc.description.abstract | Two subspecies of cynomolgus macaques ( Macaca fascicularis ) are alleged to co‐exist in the Philippines, M. f. philippensis in the north and M. f. fascicularis in the south. However, genetic differences between the cynomolgus macaques in the two regions have never been studied to document the propriety of their subspecies status. We genotyped samples of cynomolgus macaques from Batangas in southwestern Luzon and Zamboanga in southwestern Mindanao for 15 short tandem repeat (STR) loci and sequenced an 835 bp fragment of the mtDNA of these animals. The STR genotypes were compared with those of cynomolgus macaques from southern Sumatra, Singapore, Mauritius and Cambodia, and the mtDNA sequences of both Philippine populations were compared with those of cynomolgus macaques from southern Sumatra, Indonesia and Sarawak, Malaysia. We conducted STRUCTURE and PCA analyses based on the STRs and constructed a median joining network based on the mtDNA sequences. The Philippine population from Batangas exhibited much less genetic diversity and greater genetic divergence from all other populations, including the Philippine population from Zamboanga. Sequences from both Batangas and Zamboanga were most closely related to two different mtDNA haplotypes from Sarawak from which they are apparently derived. Those from Zamboanga were more recently derived than those from Batangas, consistent with their later arrival in the Philippines. However, clustering analyses do not support a sufficient genetic distinction of cynomolgus macaques from Batangas from other regional populations assigned to subspecies M. f. fascicularis to warrant the subspecies distinction M. f. philippensis . Am J Phys Anthropol 155:136–148, 2014. © 2014 Wiley Periodicals, Inc. | en_US |
dc.publisher | van Nostrand Rheinhold | en_US |
dc.publisher | Wiley Periodicals, Inc. | en_US |
dc.subject.other | Subspecies | en_US |
dc.subject.other | Macaca Fascicularis | en_US |
dc.subject.other | Mitochondrial DNA | en_US |
dc.subject.other | Short Tandem Repeat (STR) | en_US |
dc.title | A genetic comparison of two alleged subspecies of P hilippine cynomolgus macaques | en_US |
dc.type | Article | en_US |
dc.rights.robots | IndexNoFollow | en_US |
dc.subject.hlbsecondlevel | Anthropology | en_US |
dc.subject.hlbtoplevel | Social Sciences | en_US |
dc.description.peerreviewed | Peer Reviewed | en_US |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/108326/1/ajpa22564.pdf | |
dc.identifier.doi | 10.1002/ajpa.22564 | en_US |
dc.identifier.source | American Journal of Physical Anthropology | en_US |
dc.identifier.citedreference | Satkoski Trask JA, Houghton P, George DA, Kanthaswamy S, Smith DG. 2013a. Population and landscape genetics of an introduced species ( M. fascicularis ) on the Island of Mauritius. PLoS One 8: e53001. | en_US |
dc.identifier.citedreference | Osada N, Hashimoto K, Kameoka Y, Hirata M, Tanuma R, Uno Y, Inoue I, Hida M, Suzuki Y, Sugano S, Terao K, Kusuda J, Takahashi I. 2008. Large‐scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta. BMC Genom 9: 90. | en_US |
dc.identifier.citedreference | Perelman P, Johnson WE, Roos C, Seuanez HN, Horvath JE, Moreira MAM, 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: e1001342. | en_US |
dc.identifier.citedreference | Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945 – 959. | en_US |
dc.identifier.citedreference | Pritchard JK, Wen W. 2003. Documentation for STRUCTURE Software: Version 2. Chicago: Department of Human Genetics, University of Chicago. | en_US |
dc.identifier.citedreference | Raymond M, Rousset F. 1995. GENEPOP: population genetics software for exact tests and ecumenicism. J Hered 86: 248 – 249. | en_US |
dc.identifier.citedreference | Saitou N, Nei M. 1987. The neighbor‐joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406 – 425. | en_US |
dc.identifier.citedreference | Sathiamurthy E, Voris HK. 2006. Pleistocene sea level maps for the sunda shelf. Chicago, IL: The Field Museum. | en_US |
dc.identifier.citedreference | Satkoski J, George D, Smith DG, Kanthaswamy S. 2008a. Genetic characterization of wild and captive rhesus macaques in China. J Med Primatol 37: 67 – 80. | en_US |
dc.identifier.citedreference | Satkoski J, Malhi RS, Kanthaswamy S, Tito RY, Malladi V, Smith DG. 2008b. Pyrosequencing as a method for SNP identification in the rhesus macaque ( Macaca mulatta ). BMC Genom 9: 256. | en_US |
dc.identifier.citedreference | Satkoski Trask JA, Garnica WT, Kanthaswamy S, Malhi RS, Smith DG. 2011. 4040 SNPs for genomic analysis in the rhesus macaque ( Macaca mulatta ). Genomics 98: 352 – 358. | en_US |
dc.identifier.citedreference | Satkoski Trask JA, Smith DG, Houghton P, Lerche N, Kanthaswamy S. 2013b. Single nucleotide polymorphisms reveal patterns of allele sharing across a species boundary in Macaca mulatta and M. fascicularis. Am J Primatol 75: 135 – 144. | en_US |
dc.identifier.citedreference | Schneider S, Roessli D, Excofflier L. 2000. ARLEQUIN 2.001: a software for population genetic data analysis. Switzerland: Laboratory of Genetics and Biometry, University of Geneva. | en_US |
dc.identifier.citedreference | Smith DG, George DA, Kanthaswamy S, McDonough J. 2006. Identification of country of origin and admixture between Indian and Chinese rhesus macaques. Intern J Primatol 27: 881 – 898. | en_US |
dc.identifier.citedreference | Smith DG, McDonough JW, George DA. 2007. Mitochondrial DNA variation within and among regional populations of longtail macaques ( Macaca fascicularis ) in relation to other species of the fascicularis group of macaques. Am J Primatol 69: 182 – 198. | en_US |
dc.identifier.citedreference | Sussman RW, Tattersall I. 1986. Distribution, abundance, and putative ecological strategy of Macaca fascicularis on the island of Mauritius, southwestern Indian Ocean. Folia Primatolog 46: 28 – 43. | en_US |
dc.identifier.citedreference | Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585 – 596. | en_US |
dc.identifier.citedreference | Tamura K, Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10: 512 – 526. | en_US |
dc.identifier.citedreference | Tamura K, Nei M, Kumar S. 2004. Prospects for inferring very large phylogenies by using the neighbor‐joining method. Proc Natl Acad Sci USA 101: 11030 – 11035. | en_US |
dc.identifier.citedreference | Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731 – 2739. | en_US |
dc.identifier.citedreference | Tosi AJ, Coke CS. 2007. Comparative phylogenetics offer new insights into the biogeographic history of Macaca fascicularis and the origin of the Mauritian macaques. Mol Phylogenet Evol 42: 498 – 504. | en_US |
dc.identifier.citedreference | Tosi AJ, Morales JC, Melnick DJ. 2003. Paternal, maternal, and biparental molecular markers provide unique windows onto the evolutionary history of macaque monkeys. Evolution 57: 1419 – 1435. | en_US |
dc.identifier.citedreference | Voris HK. Maps of pleistocene sea levels in Southeast Asia: Shorelines, river systems and time durations. 2000. J Biogeogr 27: 1153 – 1167. | en_US |
dc.identifier.citedreference | Wallace AR. 1876. The geographical distribution of animals. London: Macmillan. | en_US |
dc.identifier.citedreference | Watterson GA. 1975. On the number of segregating sites in genetical models without recombination. Theoret Pop Biol 7: 256 – 276. | en_US |
dc.identifier.citedreference | Weir BS, Cockerham CC. 1984. Estimating F‐statistics for the analysis of population structure. Evolution 38: 1358 – 1370. | en_US |
dc.identifier.citedreference | Yeh FC, Boyle TJB. 1997. Population genetic analysis of co‐dominant and dominant markers and quantitative traits. Belgian J Botany 129: 157. | en_US |
dc.identifier.citedreference | Abegg C, Thierry B. 2002. Macaca evolution and dispersal in insular south‐east Asia. Biol J Linn Soc 75: 555 – 576. | en_US |
dc.identifier.citedreference | Arnason U, Gullberg A, Burquete AS, Janke A. 2000. Molecular estimates of primate divergences and new hypotheses for primate dispersal and the origin of modern humans. Hereditas 133: 217 – 228. | en_US |
dc.identifier.citedreference | Bandelt H‐J, Forster P, Roehl A. 1999. Median‐joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16: 37 – 48. | en_US |
dc.identifier.citedreference | Barker G, Barton H, Beavitt P, Bird M, Daly P, Doherty C, Gilbertson D, Hunt C, Krigbaum J, Lewis H, Manser J, McLaren S, Paz V, Piper P, Pyatt B, Rabett R, Reynolds T, Rose J, Rushworth G, Stephens M. 2002. Prehistoric foragers and farmers in Southeast Asia: renewed investigations at Niah Cave, Sarawak. Proc Prehist Soc 68: 147 – 164. | en_US |
dc.identifier.citedreference | Delson E. 1980. Fossil macaques, phyletic relationships and a scenario of deployment. In: Lindburg DG, editor. The macaques. Studies in ecology, behavior and evolution. New York: van Nostrand Rheinhold. p 10 – 30. | en_US |
dc.identifier.citedreference | Esselstyn JA, Widmann P, Heaney LR. 2004. The mammals of Palawan Island, Philippines. Proc Biol Soc Wash 117: 271 – 302. | en_US |
dc.identifier.citedreference | Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol 14: 2611 – 2620. | en_US |
dc.identifier.citedreference | Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783 – 791. | en_US |
dc.identifier.citedreference | Felsenstein J. 2004. PHYLIP (Phylogeny Inference Package) version 3.6b. Distributed by the author. Seattle: Department of Genome Sciences, University of Washington. | en_US |
dc.identifier.citedreference | Fooden J. 1991. Systematic review of Philippine macaques (Primates, Cercopithecidae: Macaco, fascicularis subspp.). Fieldiana: Zoology, N.S., No. 64:1–44. Field Museum of Natural History. | en_US |
dc.identifier.citedreference | Fooden J. 2000. Systematic review of the rhesus macaque, Macaca mulatta (Zimmermann, 1780). Fieldiana Zool 96: 1 – 180. | en_US |
dc.identifier.citedreference | Fooden J. 2006. Comparative review of fascicularis ‐group species of macaques (primates: Macaca ). Fieldiana Zool: 1 – 43. | en_US |
dc.identifier.citedreference | Forster P, Harding R, Torroni A, Bandelt H‐J. 1996. Origin and evolution of Native American mtDNA variation: a reappraisal. Am J Hum Genet 59: 935 – 945. | en_US |
dc.identifier.citedreference | Groves C. 2001. Primate taxonomy. Washington: Smithsonian Institution Press. p 229 – 232. | en_US |
dc.identifier.citedreference | Heaney LR. 1986. Biogeography of mammals in SE Asia: estimates of rates of colonization, extinction and speciation. Biol J Linn Soc 28: 127 – 165. | en_US |
dc.identifier.citedreference | Hubisz MJ, Falush D, Stephens M, Pritchard JK. 2009. Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour 2009; 9: 1322 – 1332. | en_US |
dc.identifier.citedreference | Jombart T. 2008. Adegenet: a R package for the multivariate analysis of genetic markers, Bioinformatics 24: 1403 – 1405. | en_US |
dc.identifier.citedreference | Kanthaswamy S, Trask JS, George D, Kou A, Erickson B, Smith DG. 2008. Hybridization and stratification of nuclear genetic variation in Macaca mulatta and M. fascicularis. Int J Primatol 29: 1295 – 1311. | en_US |
dc.identifier.citedreference | Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P. 2004. Micro‐Checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4: 535 – 538. | en_US |
dc.identifier.citedreference | Kanthaswamy S, Trask JS, George DA, Kou AK, Hoffman LN, Doherty TB, Erickson BJ‐A, Houghton P, Smith DG. 2013. The genetic composition of cynomolgus macaque populations ( Macaca cynomolgus ) used in biomedical research. J Med Primatol 42: 120 – 131. | en_US |
dc.identifier.citedreference | Lambert AB, Meñez C, Villanoy L, David LT. 2006. Movement of water across passages connecting Philippine Inland Sea Basins (Marine Science Institute, University of the Philippines). | en_US |
dc.identifier.citedreference | Lawler SH, Sussman RW, Taylor LL. 1995. Mitochondrial DNA of the Mauritian macaques ( Macaca fascicularis ): an example of the founder effect. Am J Phys Anthropol 96: 133 – 141. | en_US |
dc.identifier.citedreference | Li J, Han K, Xing J, Kim H‐S, Rogers JA, Ryder OA, Disotell T, Bisong Yue B, Batzer MA. 2009. Phylogeny of the macaques (Cercopithecidae: Macaca ) based on Alu elements. Gene 448: 242 – 249. | en_US |
dc.identifier.citedreference | Ling B, Veazey RS, Luckay A, Penedo C, Xu K, Lifson JD, Marx P. 2002. SIVmac pathogenesis in rhesus macaques of Chinese and Indian origin compared with primary HIV infections in humans. AIDS 16: 1489 – 1496. | en_US |
dc.identifier.citedreference | Malhi RS, Sickler B, Lin D, Satkoski J, George D, Kanthaswamy S, Smith DG. 2007. MamuSNP: a resource for rhesus macaque ( Macaca mulatta ) genomics. PLoS One 2: e438. | en_US |
dc.owningcollname | Interdisciplinary and Peer-Reviewed |
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