Sains
Malaysiana 53(7)(2024): 1509-1523
http://doi.org/10.17576/jsm-2024-5307-03
Molecular
Phylogenetics and Phylogeography of Malaysian Mousedeer (Tragulus kanchil) Based on Mitochondrial DNA Sequences of the
D-Loop Region
(Filogenetik Molekul dan Filogeografi Pelanduk Malaysia (Tragulus kanchil) Berdasarkan Jujukan DNA Mitokondria Kawasan
D-Loop)
MOHAMAD AZAM
AKMAL ABU-BAKAR1,2, NOR RAHMAN AIFAT3, JEFFRINE JAPNING
ROVIE-RYAN4,5, MUHAMMAD ABU BAKAR ABDUL-LATIFF6,
AHMAD AMPENG7, SHUKOR MD-NOR1 & BADRUL MUNIR MD-ZAIN1,*
1Department of Biological Sciences and Biotechnology, Faculty
of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi,
Selangor, Malaysia
2Faculty of Applied Science, Universiti Teknologi MARA
Pahang, Jengka Campus, 26400 Bandar Tun Abdul Razak, Jengka, Pahang, Malaysia
3Faculty of Tropical Forestry, Universiti Malaysia Sabah
(UMS), Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
4National Wildlife Forensic Laboratory, Ex-Situ Conservation
Division, Department of Wildlife and National Park (DWNP) Peninsular Malaysia,
KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia
5Institute of Biodiversity and Environmental Conservation
(IBEC), Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
6Faculty of Applied Sciences and Technology, Universiti Tun
Hussein Onn Malaysia (Pagoh Campus), 84600 Muar, Johor, Malaysia
7Forest Department Sarawak, Bangunan
Baitul Makmur II, Medan Raya, 93050 Petra Jaya, Kuching, Sarawak, Malaysia
Diserahkan: 22 Jun 2022/Diterima: 4 Jun 2024
Abstract
Two sympatric mousedeer species, Tragulus kanchil and Tragulus napu, inhabit the Malaysian
tropical rainforests. Previous studies have established their phylogenetic
relationships based on morphological variations; however, comprehensive genetic
data have yet to be extensively used to relate the relationships especially from
different populations. The main objectives of this study were to determine the
phylogenetic relationships, population genetics, and phylogeography of
mousedeer species based on DNA sequences of the mitochondrial D-loop region.
DNA from 32 mousedeer samples, representing various populations in Malaysia,
was sequenced and analyzed using Neighbor-Joining, Maximum Parsimony, and
Bayesian Inference approaches. The phylogenetic analyses showed two main clades
representing the populations of T.
kanchil and T. napu. The results
also showed that the T. kanchil populations in Borneo was separated from Peninsular Malaysia taxa in MP and BI
phylogenetic tree. However, Borneo population was nested in east population of
Peninsular Malaysia in NJ tree. In addition, the T. kanchil population in
Peninsular Malaysia further separated into east and west coast populations of
Titiwangsa Range. It was supported with finding in population genetic relation
that showed relatively low levels among population. This is expected because
some of the populations are isolated geographically. The divergence of these
populations is likely due to the Titiwangsa Range which acts as a barrier
separating the east and west Peninsular Malaysia populations, and the South
China Sea separates the populations of Peninsular Malaysia and Borneo.
Molecular clock tree reconstruction showed that the separation of T. kanchil and T. napu occurred around 17.11 million years ago (MYAs).
Furthermore, the T. kanchil populations from the east and west Peninsular Malaysia showed a branching
pattern from those of Borneo of about 11.04 and 9.14 MYAs, respectively. The
results of this study increase our understanding of Malaysian mousedeer
phylogeny and phylogeography.
Keywords: Mousedeer; phylogeography; Tragulus kanchil; Tragulus napu; ungulate
Abstrak
Dua spesies pelanduk Tragulus kanchil dan Tragulus napu, bersimpatrik menghuni
hutan hujan tropika Malaysia. Kajian terdahulu telah mengesahkan pertalian
filogenetik pelanduk berdasarkan variasi morfologi. Walau bagaimanapun, data
genetik yang komprehensif masih belum digunakan sepenuhnya untuk mengaitkan
hubungan terutamanya populasi yang berlainan. Objektif utama kajian ini adalah
untuk menentukan pertalian filogenetik, genetik populasi dan filogeografi
kedua-dua spesies pelanduk menggunakan jujukan DNA mitokondria kawasan D-loop.
DNA daripada 32 sampel pelanduk yang mewakili populasi di Malaysia telah
dijujuk dan dianalisis menggunakan kaedah Neighbor-Joining
(NJ), Maximum Parsimony (MP) dan Bayesian
Inference (BI). Analisis filogenetik menunjukkan terhasil dua klad utama
mewakili populasi T. kanchil dan T. napu. Keputusan juga menunjukkan
populasi T. kanchil di Borneo
terpisah daripada populasi Semenanjung Malaysia berdasarkan pokok filogenetik
MP dan BI. Walau bagaimanapun, populasi Borneo masih tergolong dalam satu
kumpulan bersama populasi Timur Semenanjung Malaysia dalam pokok NJ. Selain
itu, populasi T. kanchil di
Semenanjung Malaysia terpisah kepada populasi barat dan timur Banjaran
Titiwangsa. Ini juga disokong dengan hasil analisis populasi genetik
menunjukkan tahap hubungan yang rendah antara populasi. Hal ini dijangka
disebabkan populasi ini terpisah oleh halangan geografi. Pencapahan populasi
ini berkemungkinan disebabkan Banjaran Titiwangsa bertindak sebagai penghalang
yang memisahkan populasi Timur dan Barat Semenanjung Malaysia dan Laut China
Selatan yang memisahkannya dengan populasi Borneo. Pohon jam molekul juga
menunjukkan pemisahan spesies T. kancil dan T. napu berlaku sekitar 17.11
juta tahun dahulu (JTD). Tambahan lagi, populasi T. kancil Timur dan Barat Semenanjung Malaysia menunjukkan
percambahan daripada populasi Borneo masing-masing sekitar 11.04 JTD dan 9.14
JTD. Hasil kajian ini dapat meningkatkan pemahaman tentang filogeni dan
filogeografi spesies kancil di Malaysia.
Kata kunci: Filogeografi; pelanduk; Tragulus kanchil; Tragulus napu; ungulat
RUJUKAN
Abdul-Latiff, M.A.B. & Md-Zain,
B.M. 2021. Taxonomy, evolutionary and dispersal events of pig-tailed macaque, Macaca nemestrina (Linnaeus, 1766) in
Southeast Asia with description of a new subspecies, Macaca nemestrina perakensis in Malaysia. Zool. Stud. 60: 50.
Abdul-Latiff, M.A.B., Baharuddin,
H., Abdul-Patah, P. & Md-Zain, B.M. 2019. Is Malaysia’s banded langur, Presbytis femoralis femoralis, actually Presbytis neglectus neglectus? Taxonomic
revision with new insights on the radiation history of the Presbytis species group in Southeast Asia. Primates 60: 63-79.
Abdul-Latiff, M.A.B., Ruslin, F.,
Fui, V.V., Abu, M.H., Rovie-Ryan, J.J., Abdul-Patah, P., Lakim, M., Roos, C.,
Yaakop, S. & Md-Zain, B.M. 2014a. Phylogenetic relationships of Malaysia's
long-tailed macaques, Macaca fascicularis,
based on cytochrome b sequences. Zookeys 407: 121-140.
Abdul-Latiff, M.A.B., Ruslin, F.,
Faiq, H., Hairul, M.S., Rovie-Ryan, J.J., Abdul-Patah, P., Yaakop, S. &
Md-Zain, B.M. 2014b. Continental monophyly and molecular divergence of
Peninsular Malaysia’s Macaca fascicularis
fascicularis. Biomed. Res. Int. 2014:
897682.
Abdul-Patah, P., Sasaki, H.,
Sekiguchi, T., Shukor, M.N., Mohd-Yusof, N.S., Abdul-Latiff, M.A.B. &
Md-Zain, B.M. 2020. Molecular DNA-based spatial mapping technique predicting
diversity and distribution of otters (Lutrinae) in Peninsular Malaysia using
non-invasive fecal samples. Mammal
Research 65: 691-700.
Aifat, N.R. & Md-Zain, B.M.
2021. Genetic identification of White-Handed Gibbons (Hylobates lar) in captivity. Journal of Sustainability Science
and Management 16: 316-326.
Aifat, N.R., Yaakop, S. & Md-Zain,
B.M. 2016. Optimization of partial Cyt b gene sequence from selected ancient Presbytis museum skin specimens. Malays. Appl.
Biol. 45: 93-96.
Aifat, N.R., Abdul-Latiff, M.A.B.,
Roos, C. & Md-Zain, B.M. 2020. Taxonomic revision and evolutionary phylogeography
of dusky langur (Trachypithecus obscurus)
in Peninsular Malaysia. Zool. Stud. 59: 64.
Brunke, J., Russo, IR.M.,
Orozco-terWengel, P., Zimmermann, E., Bruford, M.W., Goossens, B. &
Radespel, U. 2020. Dispersal and genetic structure in tropical small mammal,
the Bornean tree shrew (Tupaia longipes),
in a fragmented landscape along the Kinabatangan River, Sabah, Malaysia. BMC Genet. 21: 43.
Chowdhury, S.M., Omar, A.R., Aini,
I., Hair-Bejo, M., Jamaluddin, A.A., Md-Zain, B.M. & Kono, Y. 2003.
Pathogenicity, sequence and phylogenetic analysis of Malaysian Chicken anaemia
virus obtained after low and high passages in MSB-1 cells. Arch. Virol. 148: 2437-2448.
Corbet, G.B. & Hill, J.E. 1992. The Mammals of the Indomalayan Region: A
Systematic Review. Oxford: Oxford University Press.
Drummond, A.J. & Rambaut, A.
2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7: 214.
Endo, H., Fukuta, K., Kimura, J.,
Sasaki, M., Hayashi, Y. & Oshida, T. 2004. Phylogenetic relationships among
populations of the mouse deer in the Southeast Asian Region from the nucleotide
sequence of cytochrome b gene. Mammal Study 29: 119-123.
Farida, W.R., Semiada, G.,
Handayani, T.H. & Harun. 2006. Habitat distribution and diversity of plants
of feed resources on mouse deer (Tragulus
javanicus) and barking deer (Muntiacus
muntjak) in Gunung Halimunan National Park. Tropics 15: 371-376.
Frankham, R., Ballou, J.D. &
Briscoe, D.A. 2002. Introduction to
Conservation Genetics. Cambridge: Cambridge University Press.
Halim, M., Aman-Zuki,
A., Syed-Ahmad, S.Z., Muhaimin, A.M.D., Atikah, A.R., Masri, M.M., Md-Zain,
B.M. & Yaakop, S. 2018. Exploring the abundance and DNA barcode information
of eight parasitoid wasps species (Hymenoptera), the natural enemies of the
important pest of oil palm, bagworm, Metisa
plana (Lepidoptera: Psychidae) toward the biocontrol approach and it’s
application in Malaysia. Journal of
Asia-Pacific Entomology 21(4): 1359-1365.
Hall, R. 2013. The palaeogeography
of Sundaland and Wallacea since the Late Jurassic. J. Limnol. 72: 1-17.
Hall, R. 2002. Cenozoic geological
and plate tectonic evolution of SE Asia and the SW Pacific: Computer-based
reconstruction, model and animations. J.
Asian Earth Sci. 20: 353-431.
Hall, R. 2001. Cenozoic
reconstruction of SE Asia and the SW pacific: Changing pattern of land and sea. In Faunal
and Floral Migration and Evolution in SE Asia Australasia, edited by
Metcalfe, I., Smith, J.M.B., Morwood, M. & Davidson, I. Lisse: Swets and
Zeitlinger. pp. 35-56.
Harrison,
M.E. & Chivers, D.J. 2007. The orang-utan mating system and the unflanged
male: A product of increased food stress during the late Miocene and
Pliocene? J. Hum. Evol. 52:
275-293.
Hassanin, A., Delsuc, F., Ropiquet,
A., Hammer, C., Jansen van Vuuren, B., Matthee, C., Ruiz-Garcia, M., Catzeflis,
F., Areskoug, V., Nguyen, T.T. & Couloux, A. 2012. Pattern and timing of
diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a
comprehensive analysis of mitochondrial genomes. C. R. Biol. 335: 32-50.
Houben,
A.J.P., van Mourik, C.A., Montanari, A., Coccioni, R. & Brinkhuis, H. 2012.
The Eocene-Oligocene transition: Changes in sea level, temperature, or both? Palaeogeogr. Palaeoclimatol. Palaeoecol. 335-336: 75-83.
Huelsenbeck, J.P. & Ronquist, F.
2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
Hurzaid, A., Jaafar, I., Awang, Z.
& Siti-Azizah, M.N. 2014. Genetic structure of the Asian Grass Frog, Fejevarya limnocharis (Amphibia: Anura:
Dicroglossidae) of Peninsular Malaysia: A preliminary report. Zool. Stud. 53: 77.
Kamaruddin, K.R. & Esa, Y. 2009.
Phylogeny and phylogeography of Barbonymus
schwanenfeldii (Cyprinidae) from Malaysia inferred using partial cytochrome b mtDNA gene. Journal of Tropical Biology and Conservation 5: 1-13.
Khalil, A.R.A., Setiawan, A.,
Rustiati, E.L., Harianto, S.P. & Nurarifin, I. 2019. Keragaman dan
kelimpahan Artiodactyla menggunakan kamera jebak di Kesatuan Pengelolaan Hutan
I Pesisir Barat. Jurnal Sylva Lestari 7:
350-358.
Kim, K.S., Tanaka, K., Ismail, D.B.,
Maruyama, S., Matsubayashi, H., Endo, H., Fukuta, K. & Kimura, J. 2004.
Cytogenetic comparison of the lesser mousedeer (Tragulus javanicus) and the greater mousedeer (T. napu). Caryologia 57:
229-243.
Kocher, T.D., Thomas, W.K., Meyer,
A., Edwards, S.V., Paabo, S., Villablanca, F.X. & Wilson, A.C. 1989.
Dynamics of mitochondrial DNA evolution in animals: Amplification and
sequencing with conserved primers. Proc.
Natl. Acad. Sci. 86: 6196-6200.
Kumar, S., Stecher, G., Li, M.,
Knyaz, C. & Tamura, K. 2018. MEGA X: Molecular evolutionary genetics
analysis across computing platforms. Mol.
Biol. Evol. 35: 1547-1549.
Kusuda, S., Adachi, I., Fujioka, K.,
Nakamura, M., Amano-Hanzawa, N., Goto, N., Furuhashi, S. & Doi, O. 2013.
Reproductive characteristics of female lesser mouse deers (Tragulus javanicus) based on fecal progestagens and breeding
records. Anim. Reprod. Sci. 137:
69-73.
Kuznetsov, G.V. & Borissenko,
A.V. 2004. A new record of Tragulus
versicolor (Artiodactyla, Tragulidae) from Vietnam, and its sympatric
occurrence with T. kanchil. Russian J.
Theriol. 3: 9-13.
Loo, A.H.B., Tan, H.T.W., Kumar,
P.P. & Saw, L.G. 2001. Intraspecific variation in Licuala glabra Griff. (Palmae) in Peninsular Malaysia–a morphometric
analysis. Biol. J. Linn Soc. 72:
115-128.
Matsubayashi, H. & Sukor, J.R.A.
2005. Activity and habitat use of lesser mousedeer and greater mouse-deer
species, Tragulus javanicus dan Tragulus napu, in Sabah, Malaysia,
Borneo. Malay. Nat. J. 57: 235-241.
Md-Zain, B.M., Lee, S.J., Lakim, M.,
Ampeng, A. & Mahani, M.C. 2010. Phylogenetic position of Tarsius bancanus based on partial
Cytochrome b DNA sequences. Journal of Biological Sciences 10:
348-354.
Meijaard, E. & Groves, C.P.
2004. A taxonomic revision of the Tragulus mousedeer (Artiodactyla). Zool. J.
Linn Soc. 140: 63-102.
Meijaard, E., Umilaela & de
Wijeyeratne, G.S. 2010. Aquatic escape behaviour in mousedeer provides insight
into tragulid evolution. Mamm. Biol. 75:
471-473.
Mètais, G., Chaimanee, Y., Jaeger,
J.J. & Ducrocq, S. 2007. Eocene bunoselenodont Artiodactyla from southern
Thailand and the early evolution of Ruminantia in South Asia. Naturwissens 94: 493-498.
Mètais, G., Chaimanee, Y., Jaeger,
J.J. & Ducrocq, S. 2001. New remains of primitive ruminants from Thailand:
Evidence of the early evolution of the Ruminantia in Asia. Zool. Scr. 30: 231-248.
Miller, K.G., Kominz, M.A.,
Browning, J.V., Wright, J.D., Mountain, G.S., Katz, M.E., Sugarman, P.J.,
Cramer, B.S., Christie-Blick, N. & Pekar, S.F. 2005. The Phanerozoic record
of global sea-level change. Science 310:
1293-1298.
Mohd-Ridwan, A.R. & Abdullah,
M.T. 2012. Population genetics of the cave-dwelling dusky fruit bat, Penthetor lucasi, based on four
populations in Malaysia. Pertanika J.
Trop. Agric. Sci. 3: 459-484.
Mohd-Yusof, N.S., Senawi, J., Nor,
S.M. & Md-Zain, B.M. 2020. Haplotype and network analysis of Island Flying
Fox (Pteropus hypomelanus) using
D-Loop region of mitochondrial DNA to confirm subspecies designation. Mammal Research 65: 375-385.
Nur-Syuhada, N., Magintan, D.,
Siti-Hajar, A.R., Aisah, M.S. & Shukor, M.N. 2016. The wildlife research
& rescue programme for mammals at Hulu Terengganu Hydroelectric Project
(HTHEP), Terengganu, Peninsular Malaysia. In AIP Conference Proceedings 1784(1): 060036. AIP Publishing LLC.
Posada, D. & Crandall, K.A.
1998. Modeltest: Testing the model of DNA substitution. Bioinformatics 14: 817-818.
Rosli, M.K., Zamzuriada, A.S.,
Syed-Shabthar, S.M., Mahani, M.C., Abas-Mazni, O. & Md-Zain, B.M. 2011.
Optimization of 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.
Rozas, J., Ferrer-Mata, A.,
Sanchez-DelBarrio, J.C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S.E. &
Sanchez-Gracia, A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large
data sets. Mol. Biol. Evol. 34:
3299-3302.
Rubinoff, D. & Hollad, B.S.
2005. Between two extremes:mitochondrial DNA is neither the panacea nor the
nemesis of phylogenetic and taxonomic inference. Syst. Biol. 54: 952-961.
Sum, J.S., Lee, W.C., Amir, A.,
Braima, K.A., Jeffery, J., Abdul-Aziz, N.M., Mun-Yik, F. & Yee-Ling, L.
2014. Phylogenetic study of six species of Anopheles mosquitoes in Peninsular Malaysia based on
inter-transcribed spacer region 2 (ITS2) of ribosomal DNA. Parasit Vectors 7: 309.
Syed-Shabthar, S.M., Rosli, M.K.,
Mohd-Zin, N.A., Romaino, S.M., Fazly-Ann, Z.A, Mahani, M.C., Abas-Mazni, O.,
Zainuddin, R., Yaakop, S. & Md-Zain, B.M. 2013. The molecular phylogenetic
signature of Bali cattle revealed by maternal and paternal markers. Mol. Biol. Rep. 40: 5165-5176.
Timmins, R. & Duckworth,
J.W. 2015. Tragulus kanchil. The
IUCN Red List of Threatened Species 2015: e.T136297A61978576.
van Dort, M. 1988. Note on the skull
size in the sympatric mouse deer species, Tragulus
javanicus (Osbeck, 1765) and Tragulus
napu (F. Cuvier, 1822). Zeitschrift
für Säugetierkunde 53: 124-125.
Vislobokova, I.A. 2013. On the
origin of Cetartiodactyla: Comparison of data on evolutionary morphology and
molecular biology. Paleontol. J. 47:
321-334.
Voris, H.K. 2000. Maps of
Pleistocene sea levels in Southeast Asia: Shoreline, river systems and time
durations. Journal of Biogeogr. 27:
1153-1167.
Whitlock, M.C. & McCauley, D.E. 1999.
Indirect measures of gene flow and migration: FST≠1/(4Nm+1). Heredity 82:
117-125.
Wirdateti, W. & Nugraha, T.P.
2016. Variasi dan filogeni Kancil dan Napu (Tragulus spp.) di Indonesia menggunakan gen 12s rRNA mitokondria. Jurnal Veteriner Maret 17: 22-29.
Wright,
S. 1965. The interpretation of population structure by F-statistics with
special regard to systems of mating. Evolution 19:
395-420.
*Pengarang untuk surat-menyurat; email: abgbadd@ukm.edu.my
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