Species Identification of Rehabilitated Critically Endangered Orangutans Through DNA Forensic: Implication for Conservation

Main Article Content

Christy Lavenia
Dwi Sendi Priyono
Donan Satria Yudha
Tuty Arisuryanti


Rehabilitating and releasing orangutans back into the wild is one of the conservation strategies being pursued to conserve orangutans. However, the species determination between Sumatran, Tapanuli, and Bornean orangutans is essential for reintroduction to avoid outbreeding depression, which could lead to DNA hybridisation and increase the probability of recessive characters. Here, we reported on an investigation of three orangutans in which DNA forensic techniques were used to identify the species before release and reintroduction to their habitat. By applying DNA forensic, the orangutan was successfully confirmed with high probabilities (100%) by identifying two orangutan species, Pongo abelii and Pongo pygmaeus wurmbii. Based on ambiguous morphology, we found the possibility of orangutan species being misidentified in rehabilitation. This case report demonstrates the importance of molecular diagnostics to identify the orangutan species. We also provide workflow recommendations from genetic aspect for rehabilitated orangutans. These recommendations will enable decision-makers to consider genetics when assessing future management decisions, which will help ensure that the orangutan species is effectively conserved.

Article Details

How to Cite
Species Identification of Rehabilitated Critically Endangered Orangutans Through DNA Forensic: Implication for Conservation. (2024). Tropical Life Sciences Research, 35(1), 120–134. https://doi.org/10.21315/tlsr2024.35.1.7
Original Article


Abdul-Manan M N, Abd Rahman M-R, Rahman N A, Osman N A, Abdul-Latiff M A, Dharmalingam S and Zain B M M. (2020). Effectiveness of nuclear gene in species and subspecies determination of captive orangutans. Biodiversitas Journal of Biological Diversity 21(8): 3665–3669. https://doi.org/10.13057/biodiv/d210832

Banes G L, Fountain E D, Karklus A, Fulton R S, Antonacci-Fulton L, Nelson J O. (2022). Nine out of ten samples were mistakenly switched by the Orang-utan Genome Consortium. Scientific Data 9(1): 485. https://doi.org/10.1038/s41597-022- 01602-0

Banes G L, Fountain E D, Karklus A, Huang H M, Jang-Liaw N H, Burgess D L, Wendt J, Moehlenkamp C and Mayhew G F. (2020). Genomic targets for high-resolution inference of kinship, ancestry and disease susceptibility in orang-utans (genus: Pongo). BMC Genomics 21(1): 1–9. https://doi.org/10.1186/s12864-020-07278-3

Beck B B, Rodrigues M, Stoinski T, Travis D A, Unwin S and Walkup K. (2007). Best practice guidelines for the re-introduction of great apes. Gland, Switzerland: SSC Primate Specialist Group of the World Conservation Union.

Bertola L D, Miller S M, Williams V L, Naude V N, Coals P, Dures S G, Henschel P, Chege M, Sogbohossou E A and Ndiaye A. (2022). Genetic guidelines for translocations: Maintaining intraspecific diversity in the lion (Panthera leo). Evolutionary Applications 15(1): 22–39. https://doi.org/10.1111/eva.13318

Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu C-H, Xie D, Suchard M A, Rambaut A and Drummond A J. (2014). BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10(4): e1003537. https://doi.org/10.1371/journal.pcbi.1003537

Bourret V, Albert V, April J, Côté G and Morissette O. (2020). Past, present and future contributions of evolutionary biology to wildlife forensics, management and conservation. Evolutionary Applications 13(6): 1420–1434. https://doi.org/10.1111/eva.12977

Cocks L. (2007). Factors affecting mortality, fertility, and well-being in relation to species differences in captive orangutans. International Journal of Primatology 28(2): 421– 428. https://doi.org/10.1007/s10764-007-9116-x

Cooper J E and Cooper M E. (2013). Wildlife forensic investigation: Principles and practice. Boca Raton, FL: CRC Press. https://doi.org/10.1201/b14553

Cortés-Ortiz L, Duda Jr TF, Canales-Espinosa D, García-Orduña F, Rodríguez-Luna E and Bermingham E. (2007). Hybridization in large-bodied New World primates. Genetics 176(4): 2421–2425. https://doi.org/10.1534/genetics.107.074278

Cortés-Ortiz L, Mondragón E and Cabotage J. (2010). Isolation and characterization of microsatellite loci for the study of Mexican howler monkeys, their natural hybrids, and other Neotropical primates. Conservation Genetics Resources 2: 21–26. https://doi.org/10.1007/s12686-009-9124-6

Courtenay J, Groves C and Andrews P. (1988). Inter- and intra-island variation? An assessment of the differences between Bornean and Sumatran orang-utans. In J H Schwartz (eds.), Orang-utan biology. Oxford: Oxford University Press, 19-30.

Da Silva M J F, Minhos T, Sa R and Bruford M. (2012). Using genetics as a tool in primate conservation. Nature Education Knowledge 3(10): 89.

Darriba D, Taboada G L, Doallo R and Posada D. (2012). jModelTest 2: More models, new heuristics and parallel computing. Nature Methods 9(8): 772. https://doi.org/10.1038/nmeth.2109

Frankham R, Briscoe D A and Ballou J D. (2002). Introduction to conservation genetics. Cambridge: Cambridge University Press. https://doi.org/10.1017/CBO9780511808999

Gippoliti S and D’Alessandro A. (2013). Great apes in the Giardino Zoologico of Rome (1910–1998): An overview. Der Zoologische Garten 82(3–4): 113–128. https://doi.org/10.1016/j.zoolgart.2013.10.002

Goldberg T L. (1997). Inferring the geographic origins of “refugee” chimpanzees in Uganda from mitochondrial DNA sequences. Conservation Biology 11(6): 1441–1446.

Goossens B, Chikhi L, Jalil MF, James S, Ancrenaz M, Lackman-Ancrenaz I and Bruford M W. (2009). Taxonomy, geographic variation and population genetics of Bornean and Sumatran orangutans. In S A Wich, S S U Atmoko, T M Setia and C P van Schaik (eds.). Orangutans: Geographic variation in behavioral ecology and conservation. Oxford: Oxford Academic, 1–13. https://doi.org/10.1093/acprof:oso/9780199213276.003.0001

Goossens B, Funk S M, Vidal C, Latour S, Jamart A, Ancrenaz M, Wickings E J, Tutin C E G and Bruford M W. (2002). Measuring genetic diversity in translocation programmes: Principles and application to a chimpanzee release project. Animal Conservation 5(3): 225–236. https://doi.org/10.1017/S1367943002002275

Gouda S, Kerry R G, Das A and Chauhan N S. (2020). Wildlife forensics: A boon for species identification and conservation implications. Forensic Science International 317: 110530. https://doi.org/10.1016/j.forsciint.2020.110530

Hirai H, Hirai Y, Morimoto M, Kaneko A, Kamanaka Y and Koga A. (2017). Night monkey hybrids exhibit de novo genomic and karyotypic alterations: The first such case in primates. Genome Biology and Evolution 9(4): 945–955. https://doi.org/10.1093/gbe/evx058

Hurst G D D and Jiggins F M. (2005). Problems with mitochondrial DNA as a marker in population, phylogeographic and phylogenetic studies: The effects of inherited symbionts. Proceedings of the Royal Society B: Biological Sciences 272(1572): 1525–1534. https://doi.org/10.1098/rspb.2005.3056

Jalil M, Cable J, Sinyor J, Lackman-Ancrenaz I, Ancrenaz M, Bruford M W and Goossens B. (2008). Riverine effects on mitochondrial structure of Bornean orang-utans (Pongo pygmaeus) at two spatial scales. Molecular Ecology 17(12): 2898–2909. https://doi.org/10.1111/j.1365-294X.2008.03793.x

Kamaluddin S N, Yaakop S, Idris W M R, Dharmalingam S, Rovie-Ryan J J and Md-Zain B M. (2018). Genetic identification of critically endangered orangutans in captivity. Journal of Sustainability Science and Management 13(2): 57–68.

Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S and Duran C. (2012). Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28(12): 1647–1649. https://doi.org/10.1093/bioinformatics/bts199

Kopp G H, Fischer J, Patzelt A, Roos C and Zinner D. (2015). Population genetic insights into the social organization of Guinea baboons (Papio papio): Evidence for female-biased dispersal. American Journal of Primatology 77(8): 878–889. https://doi.org/10.1002/ajp.22415

Letunic I and Bork P. (2016). Interactive tree of life (iTOL) v3: An online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Research 44(W1): W242–W245. https://doi.org/10.1093/nar/gkw290

MacKinnon J. (1974). The behaviour and ecology of wild orang-utans (Pongo pygmaeus). Animal Behaviour 22(1): 3–74. https://doi.org/10.1016/S0003-3472(74)80054-0

Maldonado J E, Young S, Simons L H, Stone S, Parker L D and Ortega Reyes J. (2015). Conservation genetics and phylogeny of the Arizona shrew in the “Sky Islands” of the Southwestern United States. Therya. Centro de Investigaciones Biológicas del Noroeste 6(2): 401–420. https://doi.org/10.12933/therya-15-250

Manel S, Berthier P and Luikart G. (2002). Detecting wildlife poaching: Identifying the origin of individuals with Bayesian assignment tests and multilocus genotypes. Conservation Biology 16(3): 650–659. https://doi.org/10.1046/j.1523-1739.2002.00576.x

McTavish E J and Hillis D M. (2015). How do SNP ascertainment schemes and population demographics affect inferences about population history? BMC Genomics 16(1): 1–13. https://doi.org/10.1186/s12864-015-1469-5

Meiklejohn K A, Burnham-Curtis M K, Straughan D J, Giles J and Moore M K. (2021). Current methods, future directions and considerations of DNA-based taxonomic identification in wildlife forensics. Forensic Science International: Animals and Environments 1: 100030. https://doi.org/10.1016/j.fsiae.2021.100030

Melton T, Holland C and Holland M. (2012). Forensic mitochondria DNA analysis: Current practice and future potential. Forensic Science Review 24(2): 101.

Nater A, Mattle-Greminger M P, Nurcahyo A, Nowak M G, de Manuel M, Desai T, Groves C, Pybus M, Sonay T B, Roos C, et al. (2017). Morphometric, behavioral, and genomic evidence for a new orangutan species. Current Biology 27(22): 3487–3498.e10. https://doi.org/10.1016/j.cub.2017.09.047

Nieves M, Mendez G, Ortiz A, Mühlmann M and Mudry M D. (2008). Karyological diagnosis of Cebus (Primates, Platyrrhini) in captivity: Detection of hybrids and management program applications. Animal Reproduction Science 108(1–2): 66–78. https://doi.org/10.1016/j.anireprosci.2007.07.006

Oklander L I, Caputo M, Kowalewski M, Anfuso J and Corach D. (2021). Use of genetic tools to assess predation on reintroduced howler monkeys (Alouatta caraya) in Northeastern Argentina. Primates 62(3): 521–528. https://doi.org/10.1007/s10329-021-00896-9

Oklander L I, Caputo M, Solari A and Corach D. (2020). Genetic assignment of illegally trafficked neotropical primates and implications for reintroduction programs. Scientific Reports 10(1): 1–9. https://doi.org/10.1038/s41598-020-60569-3

Palmer A, Sommer V and Msindai J N. (2021). Hybrid apes in the Anthropocene: Burden or asset for conservation? People and Nature 3(3): 573–586. https://doi.org/10.1002/pan3.10214

Perwitasari-Farajallah D. (2009). Discrimination of two species of orangutans (Pongo sp.): A rapid protocol for rehabilitation centres and zoos. Biotropia 16(2): 65–70. https://doi.org/10.11598/btb.2009.16.2.52

Peters H. (1995). Orangutan reintroduction? Development, use, and evaluation of a new method: Reintroduction. Masters’ diss., Groningen University, The Netherlands.

Priyono D S, Sofyantoro F, Putri W A, Septriani N I, Rabbani A and Arisuryanti T. (2023). A bibliometric analysis of indonesia biodiversity identification through DNA barcoding research from 2004–2021. Natural and Life Sciences Communications 22(1): e2023006.

Priyono D S, Solihin D D, Farajallah A, Irawati D and Arini D W I. (2018). Anoa, dwarf buffalo from Sulawesi, Indonesia: Identification based on DNA barcode. Biodiversitas Journal of Biological Diversity 19(6): 1985–1992.


Priyono D S, Solihin D D, Farajallah A and Purwantara B. (2020). The first complete mitochondrial genome sequence of the endangered mountain anoa (Bubalus quarlesi) (Artiodactyla: Bovidae) and phylogenetic analysis. Journal of Asia-Pacific Biodiversity 13(2): 123–133. https://doi.org/10.1016/j.japb.2020.01.006

Rianti P, Perwitasari-Farajallah D, Sajuthi D, Pamungkas J, Nater A and Krützen M. (2015). Identification of diagnostic mitochondrial DNA single nucleotide polymorphisms specific to Sumatran orangutan (Pongo abelii) populations. HAYATI Journal of Biosciences 22(4): 149–156. https://doi.org/10.1016/j.hjb.2015.09.002

Russon A E. (2009). Orangutan rehabilitation and reintroduction: Successes, failures, and role in conservation. In S A Wich, S S U Atmoko, T M Setia and C P van Schaik (eds.), Orangutans: Geographic variation in behavioral ecology and conservation. Oxford: Oxford Academic, 327–350. https://doi.org/10.1093/acprof:oso/9780199213276.003.0023

Ryder O A and Chemnick L. (1993). Chromosomal and mitochondrial DNA variation in orang utans. Journal of Heredity 84(5): 405–409. https://doi.org/10.1093/oxfordjournals.jhered.a111362

Sakamoto Y, Ishiguro M and Kitagawa G. (1986). Akaike information criterion statistics. Dordrecht, The Netherlands: D. Reidel and Taylor & Francis.

Syndercombe Court D. (2021). Mitochondrial DNA in forensic use. Emerging Topics in Life Sciences 5(3): 415–426. https://doi.org/10.1042/ETLS20210204

Tallmon D A, Luikart G and Waples R S. (2004). The alluring simplicity and complex reality of genetic rescue. Trends in Ecology and Evolution 19(9): 489–496. https://doi.org/10.1016/j.tree.2004.07.003

Walker D N and Adrian W J. (2014). Wildlife forensic investigation principles and practice. Journal of Wildlife Diseases 50(1): 154–156. https://doi.org/10.7589/50-1-BR1

Wang W, Qiao Y, Pan W and Yao M. (2015). Low genetic diversity and strong geographical structure of the critically endangered white-headed langur (Trachypithecus leucocephalus) inferred from mitochondrial DNA control region sequences. PLoS ONE 10(6): 1–17. https://doi.org/10.1371/journal.pone.0129782

Warren K S, Nijmian I J, Lenstra J A, Swan R A, Heriyanto and Den Boer M. (2000). Microsatellite DNA variation in Bornean orangutans (Pongo pygameus). Journal of Medical Primatology 29(2): 57–62. https://doi.org/10.1034/j.1600-0684.2000.290202.x

Warren K S, Verschoor E J, Langenhuijzen S, Heriyanto, Swan R A, Vigilant L and Heeney J L. (2001). Speciation and intrasubspecific variation of Bornean orangutans, Pongo pygmaeus pygmaeus. Molecular Biology and Evolution 18(4): 472–480. https://doi.org/10.1093/oxfordjournals.molbev.a003826

Weeks A R, Sgro C M, Young A G, Frankham R, Mitchell N J, Miller K A, Byrne M, Coates D J, Eldridge M D and Sunnucks P. (2011). Assessing the benefits and risks of translocations in changing environments: A genetic perspective. Evolutionary Applications 4(6): 709–725. https://doi.org/10.1111/j.1752-4571.2011.00192.x

Widdig A, Muniz L, Minkner M, Barth Y, Bley S, Ruiz-Lambides A, Junge O, Mundry R and Kulik L. (2017). Low incidence of inbreeding in a long-lived primate population isolated for 75 years. Behavioral Ecology and Sociobiology 71(1): 1–15. https://doi.org/10.1007/s00265-016-2236-6

Wong E H, Shivji M S and Hanner R H. (2009). Identifying sharks with DNA barcodes: Assessing the utility of a nucleotide diagnostic approach. Molecular Ecology Resources 9: 243–256. https://doi.org/10.1111/j.1755-0998.2009.02653.x

Yang H, Bell T A, Churchill G A and Pardo-Manuel de Villena F. (2007). On the subspecific origin of the laboratory mouse. Nature Genetics 39(9): 1100–1107. https://doi.org/10.1038/ng2087

Zemanova M A. (2019). Poor implementation of non-invasive sampling in wildlife genetics studies. Rethinking Ecology 4: 119–132. https://doi.org/10.3897/rethinkingecology.4.32751

Zhang Y W, Ryder O A and Zhang Y P. (2001). Genetic divergence of orangutan subspecies (Pongo pygmaeus). Journal of Molecular Evolution 52(6): 516–526. https://doi.org/10.1007/s002390010182