Genetic Variation Within Four Captive Chital (Axis axis) Populations in Indonesia

Muhammad Zulfiqar Meizar Pratama(1), Zuliyati Rohmah(2), Tuty Arisuryanti(3*)

(1) Laboratory of Genetics and Breeding, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta 55281
(2) Laboratory of Animal Structure and Development, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta 55281
(3) Laboratory of Genetics and Breeding, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta 55281
(*) Corresponding Author


Chital is a native animal from South Asia. Chital had been introduced to many countries, including Indonesia. Chital was first introduced to Indonesia in 1811 at Bogor Palace and since had been kept captive around Indonesia. Currently, no research had been done concerning the genetic variation of Indonesian chital. Therefore, the purpose of this research was to analyze genetic variation and phylogenetic relationship of chital from Pusat Inovasi Agroteknologi Universitas Gadjah Mada (PIAT UGM), Prambanan Temple, Gembira Loka Zoo, and Bogor Palace, based on mitochondrial D-loop fragment. This study used a Polymerase Chain Reaction (PCR) method. DNA was extracted from faecal samples and amplified with L15995 and H16498 primers. The analysis used for this research were genetic variations, haplotype networking, and phylogenetic relationships between populations. This study detected 5 haplotypes out of 20 sequences with 10 polymorphic sites and 2 indels. The haplotype diversity and the nucleotide diversity were 0.443 and 0.002 respectively, and the genetic distance was between 0 and 2.03% (average 0.55%). This research also showed one main haplotype, labelled as haplotype 1, which consisted of all individuals from PIAT and Prambanan Temple, four individuals from Bogor Palace, and one individual from Gembira Loka. This grouping proves that the majority of chital population in Indonesia came from Bogor Palace. One individual from Gembira Loka has a considerable genetic divergence from the rest of the samples, which might indicate it originated from a different source population.



Captive, chital, D-loop, genetic variation, introduced species

Full Text:



Abbas, et al., 2016. Sequence diversity and phylogenetic analysis in Pakistani spotted deer (Axis axis). Pakistan Journal of Agricultural Sciences, 53(4), 16.5365. doi: 10.21162/PAKJAS/16.5365.

Adji, D. & Astuti, D., 2020. Profil Darah Rusa Totol (Axis axis) Betina Sehat di Pusat Inovasi Agroteknologi (PIAT), Universitas Gadjah Mada. Jurnal Sain Veteriner, 38(1), pp.7-11. doi: 10.22146/jvs.28204

Arisuryanti, T., Firdaus, N.U.N. & Hakim, L., 2020. Genetic characterization of striped snakehead (Channa striata Bloch, 1793) from Arut River, Central Kalimantan inferred from COI mitochondrial gene. AIP Conference Proceedings, 2260, 020001. doi: 10.1063/5.0015905

Darriba, D., Taboada, G.L. & Doallo, R.D.P., 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9(8), p.772. doi: 10.1038/nmeth.2109

Farquharson, K.A., Hogg, C.J. & Grueber, C.E., 2021. Offspring survival changes over generations of captive breeding. Nature Communications, 12, 3045. doi: 10.1038/s41467-021-22631-0.

Fumagalli, L. et al., 1996. Origin and evolution of homologous repeated sequences in the mitochondrial DNA control region of shrews. Mol Biol Evol, 13(1), pp.31-46. doi: 10.1093/oxfordjournals.molbev.a025568.

Garsetiasih, R. & Herlina, N., 2005. Evaluasi plasma nutfah Rusa totol (Axis axis) di halaman Istana Bogor. Buletin Plasma Nutfah, 11(1), pp.34-40. doi: 10.21082/blpn.v11n1.2005.p34-.

Gembira Loka Zoo, 2022. Koleksi Rusa Tutul. Last accessed on October 2, 2022.

Harsini, J.I. et al., 2017. Phylogenetic status and genetic diversity of corsac fox (Vulpes corsac) in Golestan Province, Iran. Turkish Journal of Zoology, 41(2), pp.250-258. doi: 10.3906/zoo-1509-52.

Hill, E. et al., 2019. Widespread hybridization in the introduced hog deer population of Victoria, Australia, and its implications for conservation. Ecology and Evolution, 9(18), pp.10828-10842. doi: 10.1002/ece3.5603.

Keulartz, J., 2015. Captivity for Conservation? Zoos at a Crossroads. Journal of Agricultural and Environmental Ethics, 28, pp.335-351. doi: 10.1007/s10806-015-9537-z.

Kumar, S., Stecher, G. & Tamura K. 2018. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology and Evolution, 35(6), pp.1547–1549. doi: 10.1093/molbev/msy096.

Leus, K., Traylor-Holzer, K. & Lacy, R.C., 2011. Genetic and demographic population management in zoos and aquariums: recent developments, future challenges and opportunities for scientific research. International Zoo Yearbook, 45. pp.213-225. doi: 10.1111/j.1748-1090.2011.00138.x.

Maddison, W.P. & Maddison, D.R., 2019. Mesquite: a modular system for evolutionary analysis. Version 3.61.

Peakall, R. & Smouse, P.E., 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics, 28, pp.2537-2539. doi: 10.1093/bioinformatics/bts460.

Purohit, D. et al., 2021. Genetic effects of long-term captive breeding on the endangered pygmy hog. PeerJ, 9. doi: 10.7717/peerj.12212.

Rambaut, A., 2019. ‘FigTree v 1.4.4.’. viewed 16 March 2022, from

Rozas, J. et al., 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution, 13(12), pp.3299-3302. doi: 10.1093/molbev/msx248.

Saccheri, I. et al., 1998. Inbreeding and extinction in a butterfly metapopulation. Nature, 392, pp.491-494.

Sankar, K. & Acharya, B., 2004. Spotted Deer. In Sankar, K. & Goyal, S.P. (ed.). Ungulates of India. ENVIS Bulletin: Wildlife Protected Areas, vol. 07, no. 1. Wildlife Institute of India. Deheradun, pp.171-180.

Šprem, N. et al., 2021. First genetic analysis of introduced axis deer from Croatia. Mammalian Biology, 101, pp.1121–1125. doi: 10.1007/s42991-021-00164-9.

Suharto, A., Asriany, A. & Ismartoyo, 2019. Pengaruh Pengunjung Terhadap Tingkah Laku dan Konsumsi Makan Rusa Totol (Axis-axis) Pada Penangkaran Rusa Totol di Fakultas Peternakan Unhas. Buletin Nutrisi dan Makanan Ternak, 13(1), pp.34-47. doi:

Taberlet, P. & Bouvet, J., 1994. Mitochondrial DNA polymorphism, phylogeography, and conservation genetics of the brown bear Ursus arctos in Europe. Proceedings of the Royal Society B: Biological Sciences, 255, pp.195-200. doi: 10.1098/rspb.1994.0028.

Wheeler, T.J. & Kececioglu, J.D., 2007. Multiple alignments by aligning alignments. Bioinformatics, 23, pp.i559-i568. doi: 10.1093/bioinformatics/btm226.


Article Metrics

Abstract views : 585 | views : 580


  • There are currently no refbacks.

Copyright (c) 2023 Journal of Tropical Biodiversity and Biotechnology

Creative Commons License
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.

Editoral address:

Faculty of Biology, UGM

Jl. Teknika Selatan, Sekip Utara, Yogyakarta, 55281, Indonesia

ISSN: 2540-9581 (online)