Short Communication: Effectiveness of nuclear gene in species and subspecies determination of captive orangutans
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Abstract. Abdul-Manan MN, Mohd-Ridwan AR, Aifat NR, Osman NA, Abdul-Latiff MA, Dharmalingam S, Md-Zain BM. 2020. Short Communication: Effectiveness of nuclear gene in species and subspecies determination of captive orangutans. Biodiversitas 21: 3665-3669. Genetic identification of captive orangutans is of paramount importance in providing a correct identity that is essential for captive management. Thus, the utility of nuclear DNA sequences was tested in this study to identify the genetic identity of captive orangutans at Bukit Merah Orang Utan Island. Out of 24 DNA samples that were successfully extracted, only 10 orangutan samples were successfully sequenced for the von Willebrand factor (vWF) gene. From the results, this gene was able to separate the genus Pongo at the species level. Distance and character analyses indicated that a clear separation between P. pygmaeus and P. abelii at the species level. However, the degree of separation at species level was indicated in tree topology with moderate bootstrap values. At the subspecies level of P. pygmaeus, this gene was unable to show a clear separation between three Bornean subspecies. All the subspecies were formed clade together with each other. The vMF gene is a good nuclear gene for the study of phylogenetic relationships of orangutans in captivity at the species level, but the genetic identification at subspecies level in the genus level remains unclear. We suggest that future studies should involve multiple independent nuclear markers to increase the probability of getting reliable results.
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References
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Roos C, Boonratana R, Supriatna J, Fellowes JR, Groves CP, Nash SD, Rylands AB, Mittermeier RA. 2014. An updated taxonomy and conservation status review of Asian primates. Asian Primates J 4: 2-38.
Rosli MKA, Zamzuriada AS, Syed-Shabthar SMF, Mahani MC, Abas-Mazni O, Md-Zain BM. 2011. Optimization PCR conditions to amplify Cyt b, COI and 12S rRNA gene fragments of Malayan gaur (Bos gaurus hubbacki) mtDNA. Genet Mol Res 10: 2554-2568.
Steiper ME. (2006). Population history, biogeography, and taxonomy of orangutans (Genus: Pongo) based on a population genetic meta-analysis of multiple loci. Journal of Human Evolution 50(5): 509-522.
Swofford DL. 2002 Phylogenetic analysis using parsimony and other methods version 4.0 beta version. Sinauer Associates, Sunderland
Warren KS, Verschoor EJ, Langenhuijzen S, Swan RA, Vigilant L, Heeney JL. 2001. Speciation and intrasubspecific variation of Bornean orangutans, Pongo pygmaeus pygmaeus. Mol Biol Evol 18: 472-480.
Yaacov DB, Arbel-Thau K, Zilka Y, Ovadia O, Bouskila A, Mishmar D. (2012). Mitochondrial DNA variation, but not nuclear DNA, sharply divides morphologically identical chameleons along an ancient geographic barrier. PLoS One 7: e31372.
Zainudin R, Shukor MN, Norhayati A, Md-Zain BM, Mustafa AR. 2010. Genetic structure of Hylarana erythraea (Amphibia: Anura: Ranidae) from Malaysia. Zool Stud 49: 88-702.
Zhang DX, Hewitt GM. 2003. Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Mol Ecol 12: 563-584.
Zhang Y, Ryder OA, Zhang YP. 2001. Genetic divergence of orangutan subspecies (Pongo pygmaeus). J Mol Evol 52: 516-526.
Zhi L, Karesh WB, Janczewski DN, Frazier-Taylor H, Sajuthi D, Gombek F, Andau M, Martenson JS, O’Brien SJ. 1996. Genomic differentiation among natural populations of orang-utan (Pongo pygmaeus). Curr Biol 6: 1326-1336.
Aifat NR, Yaakop S, Md-Zain BM. 2016. Optimization of partial Cyt b gene sequence from selected ancient Presbytis museum skin specimens. Malays Appl Biol 45: 93-96.
Ancrenaz M, Gumal M, Marshall AJ, Meijaard E, Wich SA, Husson S. 2016. Pongo pygmaeus (errata version published in 2018). The IUCN Red List of Threatened Species 2016. http://www.iucnredlist.org.
Banes GL, Galdikas BM. 2016. Effective characterisation of the complete orang utan mitochondrial DNA control region, in the face of persistent focus in many taxa on shorter hypervariable regions. PloS One 11: e0168715.
Chaves R, Sampaio I, Schneider MP, Schneider H, Page SL, Goodman M. 1999. The place of Callimico goeldii in the callithrichine phylogenetic tree: evidence from von Willebrand factor gene intron 11 sequences. Mol Phylogenet Evol 13: 392-404.
Goossens B, Chikhi L, Jalil MF, James S, Ancrenaz M, Lackman, Ancrenaz I, Bruford MW. (2009). Taxonomy, geographic variation and population genetics of Bornean and Sumatran orangutans. In: Wich SA, Utami Atmoko SS, Setia TM, van Schaik CP (eds). Orangutans: geographic variation in behavioral ecology and conservation. Oxford University Press, Oxford, pp 215-224.
Guo C, Du J, Wang L, Yang S, Mauricio R, Tian D, Gu T. (2016). Insertions/deletions-associated nucleotide polymorphism in Arabidopsis thaliana. Frontiers in Plant Science 7: 1792.
Kamaluddin SN, Yaakop S, Idris WMR, Dharmalingam S, Rovie-Ryan JJ, Md-Zain BM. 2018. Genetic identification of critically endangered orangutans in captivity. J Sustain Sci Manag 13: 57-68.
Kamaluddin SN, Dharmalingam S, Md-Zain BM. 2019. Positional behavior of captive Bornean Orangutan (Pongo pygmaeus) at Bukit Merah Orangutan Island, Perak, Malaysia. Biodiversitas 20: 425-429.
Kumar S, Stecher G, Tamura K. 2016. MEGA 7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33: 1870-1874.
Loken B, Spehar S, Rayadin Y. 2013. Terrestriality in the Bornean orangutan (Pongo pygmaeus morio) and implications for their ecology and conservation. Am J Primatol 75: 1129-1138
Ma J, Liu J, Shen Y, Fan Z, Yue B, Zhang X. (2019). Population genetic structure and intraspecific genetic distance of Periplaneta americana (Blattodea: Blattidae) based on mitochondrial and nuclear DNA markers. Ecology and Evolution 22: 12928-12939.
Ma X, Kelley JL, Eilertson K, Musharoff S, Degenhardt JD, Martins AL, Vinar T, Kosiol C, Siepel A, Gutenkunst RN, Bustamante CD. 2013. Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii). PLoS One 8: e77175
Md-Zain BM, Lee SJ, Lakim M, Ampeng A, Mahani MC. 2010. Phylogenetic position of Tarsius bancanus based on partial Cytochrome b DNA sequences. J Biol Sci 10: 348-354.
Md-Zain BM, Mohhoyua KS, Aifat NR, Ngadi E, Ayob N, Rovie-Ryan JJ, Ampeng A, Mohd-Ridwan AR, Blair ME, Abdul-Latiff MAB. 2019. Molecular data confirm the presence of Nycticebus bengalensis on Langkawi Island, Malaysia. Biodiversitas 20: 1115-1120.
Muir CC, Galdikas BM, Beckenbach AT. 2000. MtDNA sequence diversity of orangutans from islands of Borneo and Sumatra. J Mol Evol 51: 471-480.
Nater A, Mattle-Greminger MP, Nurcahyo A, Nowak MG, de Manuel M, Desai T, Groves C, Pybus M, Sonay TB, Roos C, Lameira AR, Wich SA, Askew J, Davila-Ross M, Fredriksson G, de Valles G, Casals F, Prado-Martinez J, Goossens B, Verschoor EJ, Warren KS, Singleton I, Marques DA, Pamungkas J, Perwitasari-Farajallah D, Rianti P, Tuuga A, Gut IG, Gut M, Orozco-terWengel P, van Schaik CP, Bertranpetit J, Anisimova M, Scally A, Marques-Bonet T, Meijaard E, Krützen M. 2017. Morphometric, behavioral, and genomic evidence for a new orangutan species. Curr Biol 27: 3487-3498.e10.
Opazo JC, Wildman DE, Prychitko T, Robert M Johnson RM, Goodman M. 2006. Phylogenetic relationships and divergence times among New World monkeys (Platyrrhini, Primates). Mol Phylogenet Evol 40: 274-280.
Rogers J, Gibbs RA. 2014. Comparative primate genomics: emerging patterns of genome content and dynamics. Nat Rev Genet 15: 347-359.
Roos C, Boonratana R, Supriatna J, Fellowes JR, Groves CP, Nash SD, Rylands AB, Mittermeier RA. 2014. An updated taxonomy and conservation status review of Asian primates. Asian Primates J 4: 2-38.
Rosli MKA, Zamzuriada AS, Syed-Shabthar SMF, Mahani MC, Abas-Mazni O, Md-Zain BM. 2011. Optimization PCR conditions to amplify Cyt b, COI and 12S rRNA gene fragments of Malayan gaur (Bos gaurus hubbacki) mtDNA. Genet Mol Res 10: 2554-2568.
Steiper ME. (2006). Population history, biogeography, and taxonomy of orangutans (Genus: Pongo) based on a population genetic meta-analysis of multiple loci. Journal of Human Evolution 50(5): 509-522.
Swofford DL. 2002 Phylogenetic analysis using parsimony and other methods version 4.0 beta version. Sinauer Associates, Sunderland
Warren KS, Verschoor EJ, Langenhuijzen S, Swan RA, Vigilant L, Heeney JL. 2001. Speciation and intrasubspecific variation of Bornean orangutans, Pongo pygmaeus pygmaeus. Mol Biol Evol 18: 472-480.
Yaacov DB, Arbel-Thau K, Zilka Y, Ovadia O, Bouskila A, Mishmar D. (2012). Mitochondrial DNA variation, but not nuclear DNA, sharply divides morphologically identical chameleons along an ancient geographic barrier. PLoS One 7: e31372.
Zainudin R, Shukor MN, Norhayati A, Md-Zain BM, Mustafa AR. 2010. Genetic structure of Hylarana erythraea (Amphibia: Anura: Ranidae) from Malaysia. Zool Stud 49: 88-702.
Zhang DX, Hewitt GM. 2003. Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Mol Ecol 12: 563-584.
Zhang Y, Ryder OA, Zhang YP. 2001. Genetic divergence of orangutan subspecies (Pongo pygmaeus). J Mol Evol 52: 516-526.
Zhi L, Karesh WB, Janczewski DN, Frazier-Taylor H, Sajuthi D, Gombek F, Andau M, Martenson JS, O’Brien SJ. 1996. Genomic differentiation among natural populations of orang-utan (Pongo pygmaeus). Curr Biol 6: 1326-1336.
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