Genetic Variation and Phylogenetic Analysis of Philippine Scrubfowl (Megapodius cumingii) Based on Mitochondrial NADH Dehydrogenase Subunit 2 (ND2) Gene

Jihan Winarti, I Made Budiarsa, Manap Trianto, I Nengah Kundera, Mursito S. Bialangi, Abdul Ashari

Abstract


Central Sulawesi is one of the provinces in Indonesia with high avian diversity, including the Philippine scrubfowl (Megapodius cumingii). This species belongs to the family Megapodiidae and is distributed in the Philippines, parts of eastern Borneo, and several small islands in Indonesia. This study aimed to analyze the genetic variation and phylogenetic relationships of Megapodius cumingii from Poat Island based on sequences of the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene. Genomic DNA extracted from blood samples of the Philippine scrubfowl was isolated using the gSYNC™ DNA Extraction Kit (Geneaid), amplified using the Polymerase Chain Reaction (PCR) method with primers L5145 (forward) and H6394 (reverse), and visualized by 1% agarose gel electrophoresis. The PCR products were purified using the QIAquick PCR Purification Kit. Sequence data were analyzed using BLAST for species confirmation, DnaSP v6.12.03 for genetic variation analysis, and MEGA 11 for phylogenetic tree reconstruction using the Maximum Likelihood and Neighbor-Joining methods. The results showed that the 1.072 base pair ND2 gene sequences generated three haplotypes, with a haplotype diversity value of 0.667 and a nucleotide diversity of 0.00249. The nucleotide base composition of the ND2 gene was dominated by A+T (52.03%) compared to G+C (47.95%). Phylogenetic tree reconstruction using both methods produced consistent topologies, in which all Megapodius cumingii samples from Poat Island formed a monophyletic clade with high bootstrap support, indicating strong and stable genetic relationships.

Keywords


Genetic variation; phylogenetics; Megapodius cumingii; NADH Dehydrogenase Subunit 2 (ND2); mitochondria

Full Text:

PDF

References


Astuti, D. (2017). Struktur genetik populasi burung betet jawa (Psittacula alexandri alexandri) berdasarkan sekuen DNA mitokondria gen ND2. Jurnal Biologi Indonesia, 14(1), 1-8. https://doi.org/10.47349/jbi/13012017/117

Bashari, H., Mangangue, B., & Mangangue, A. (2017). Incubation strategy of Philippine Scrubfowl Megapodius cumingii on Manumpitaeng islet, North Sulawesi, Indonesia. BirdingASIA, 82-85.

BirdLife International. (2021). Megapodius cumingii. The IUCN Red List of Threatened Species

Birks SM & Edwards SV (2002). "A phylogeny of the Megapodes (Aves: Megapodiidae) based on nuclear & mitochondrial DNA sequences." Molecular Phylogenetics and Evolution, 23(3), 408-421. https://doi.org/10.1016/S1055-7903(02)00002-7

Budiarsa, I. M., Artama, I. W. T., Sembiring, L., & Situmorang, J. (2019). Analisis Filogenetik Burung Maleo (Macrocephalon maleo) Berdasarkan Sekuen Intron Satu Gen Rhodopsin (RDP1) Nukleus. Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati, 15(2), 160–166. https://doi.org/10.24002/biota.v15i2.2693

Claramunt, S., & Cracraft, J. (2015). A new time tree reveals Earth history’s imprint on the evolution of modern birds. Science advances, 1(11), e1501005. https://www.science.org/doi/10.1126/sciadv.1501005

Elliott, A., & Kirwan, G. M. (2020). Philippine Megapode (Megapodius cumingii). Birds of the World. https://doi.org/10.2173/bow.tabscr1.01

Elvyra, R. (2023). The DNA barcode of cytb on selais bungkuk fish (Hemisilurus heterorhynchus Bleeker) originating from Riau, Indonesia. Jurnal Biologi Tropis, 23(3), 429-435. https://doi.org/10.29303/jbt.v23i3.5233

Fan, P., Song, G., Qiao, H., Zhang, D., Ji, Y., Qu, Y., & Lei, F. (2024). Revaluation of the genetic diversity area relationship by integrating nucleotide and haplotype diversity. Current Zoology. https://doi.org/10.1093/cz/zoae078

Frankham, R., Ballou, J. D., Ralls, K., Eldridge, M., Dudash, M. R., Fenster, C. B., & Sunnucks, P. (2017). Genetic management of fragmented animal and plant populations. Oxford University Press. https://doi.org/10.1093/oso/9780198783398.001.0001

Grant, W. A. S., & Bowen, B. W. (1998). Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. Journal of heredity, 89(5), 415-426. https://doi.org/10.1093/jhered/89.5.415

Harris, R. B., Birks, S. M., & Leaché, A. D. (2014). Incubator birds: Biogeographical origins and evolution of underground nesting in megapodes (Galliformes: Megapodiidae). Journal of Biogeography, 41(11), 2045-2056. https://doi.org/10.1111/jbi.12357

Hoban, S., Campbell, C. D., da Silva, J. M., Ekblom, R., Funk, W. C., Garner, B. A., & Hunter, M. E. (2021). Genetic diversity is considered important but interpreted narrowly in country reports to the Convention on Biological Diversity: Current actions and indicators are insufficient. Biological Conservation, 261, 109233. https://doi.org/10.1016/j.biocon.2021.109233

Hosseini Farash, B. R., Shamsian, S. A., Berenji, F., Najafzadeh, M. J., Zarean, M., Mahmoudi Gorgi, B., Soleimanian, S., Nakhaei, E., & Jarahi, L. (2025). Molecular characterization and phylogenetic analysis of cryptosporidium spp. in pediatric acute gastroenteritis: Epidemiological insights from northeastern Iran. New Microbes and New Infections, 101622. https://doi.org/10.1016/j.nmni.2025.101622

Khan, H. A., Arif, I. A., Altwaijry, N. A., & Ahamed, A. (2023). DNA barcodes of Saudi Arabian birds: Implications for species identification and diversity analysis. Journal of King Saud University-Science, 35(8), 102887. https://doi.org/10.1016/j.jksus.2023.102887

Kumar, S., Nei, M., Dudley, J., & Tamura, K. (2008). MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in bioinformatics, 9(4), 299-306. https://doi.org/10.1093/bib/bbn017

Mailloux, R. J. (2024). The emerging importance of the ?-keto acid dehydrogenase complexes in serving as intracellular and intercellular signaling platforms for the regulation of metabolism. Redox Biology, 72, 103155. https://doi.org/10.1016/j.redox.2024.103155

Novitasari, Budiarsa, I. M., Suleman, S. M., Kundera, I. N., Jayanti, Z. D., & Trianto, M. (2025). Burung Gosong Filipina (Megapodius cumingii) di Sulawesi Tengah: Variasi Haplotipe dan Hubungan Filogenetik Berdasarkan Gen EEF2. Bioscientist: Jurnal Ilmiah Biologi, 13(3), 2086-2095. https://doi.org/10.33394/bioscientist.v13i3.17540

Paguntalan, L. J., Oquendo, M. F. J. M., Bonares, B. A., & Villegas, G. M. (2021). Ecology of Philippine scrubfowl Megapodius cumingii on Palwan with notes on other islands. Journal of Asian Ornithology, 37, 99-106.

Prum, R. O., Berv, J. S., Dornburg, A., Field, D. J., Townsend, J. P., Lemmon, E. M., & Lemmon, A. R. (2015). A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature, 526(7574), 569-573.). https://doi.org/10.1038/nature15697

Quek, M. C., Chin, N. L., Tan, S. W., Yusof, Y. A., & Law, C. L. (2018). Molecular identification of species and production origins of edible bird's nest using FINS and SYBR green I based real-time PCR. Food Control, 84, 118-127. https://doi.org/10.1016/j.foodcont.2017.07.027

Radley, P. M., Davis, R. A., Dekker, R. W., Molloy, S. W., Blake, D., & Heinsohn, R. (2018). Vulnerability of megapodes (Megapodiidae, Aves) to climate change and related threats. Environmental Conservation, 45(4), 396-406. https://doi.org/10.1017/S0376892918000152

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. Molecular Biology and Evolution, 34(12), 3299-3302. https://doi.org/10.1093/molbev/msx248

Shafer, A. B., Wolf, J. B., Alves, P. C., Bergström, L., Bruford, M. W., Brännström, I., & Zieli?ski, P. (2015). Genomics and the challenging translation into conservation practice. Trends in ecology & evolution, 30(2), 78-87. https://doi.org/10.1016/j.tree.2014.11.009

Sinclair, J Ross; O'brien, T.G.; Kinnaird, M.F. 2002: The selection of incubation sites by the Philippine Megapode, Megapodius cumingii, in North Sulawesi, Indonesia Emu 102(2), 151-158. https://doi.org/10.1071/MU00078

Siswanto, J. E., Berlian, T., Putricahya, E., Panggalo, L. V, & Yuniani, L. (2016). Isolasi DNA pada Sampel Darah Tepi dan Swab Buccal pada Bayi Penderita ROP: Perbandingan Hasil Uji Konsentrasi dan Indeks Kemurnian. Sari Pediatri, 18(4), 270-277.

Supriatna, J. (2018). Konservasi Biodiversitas: Teori dan Praktik di Indonesia. Yayasan Pustaka Obor Indonesia.

Tala'a, A. S. (2021). Analisis Filogenetik Burung Gosong Filipina (Megapodius cumingii) Berdasarkan Gen IRF2 Intron 2 dan Pemanfaatannya sebagai Media Pembelajaran. Skripsi, (Universitas Tadulako).

Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA11: molecular evolutionary genetics analysis version 11. Molecular biology and evolution, 38(7), 3022-3027. https://doi.org/10.1093/molbev/msab120

Tavakoli MB, Moradi H, Khanahmad H, Hosseini M. Circular Mitochondrial DNA: A Geant4-DNA User Application for Evaluating Radiation-induced Damage in Circular Mitochondrial DNA. J Med Signals Sens. 7(4):213-219.

Vikar, A., & Paramitha, T. A. (2024). Perbandingan Keragaman Jenis Burung Tahun 2018 Dan 2023 Di Taman Hutan Kota Kaombona Palu Provinsi Sulawesi Tengah. Jurnal Forbis Sains, 3(1), 125-131.

Wang, B., Ye, W., Xu, Y., Zhong, X., Zhang, J., Yang, N., & Zhou, C. (2023). Climate change affects Galliformes taxonomic, phylogenetic and functional diversity indexes, shifting conservation priority areas in China. Diversity and Distributions, 29(3), 409-422. https://doi.org/10.1111/ddi.13667

Yang, Z. (2014). Molecular evolution: a statistical approach. Oxford University Press. https://doi.org/10.1093/acprof:oso/9780199602605.001.0001

Yin, M. ting, & Guo, L. (2025). Mitochondrial DNA methylation: State-of-the-art in molecular mechanisms and disease implications. Journal of Advanced Research. https://doi.org/10.1016/j.jare.2025.08.029

Yue, G. H., Feng, J. B., Xia, J. H., Cao, S. Y., & Wang, C. M. (2021). Inferring the invasion mechanisms of the red swamp crayfish in China using mitochondrial DNA sequences. Aquaculture and Fisheries, 6(1), 35-41. https://doi.org/10.1016/j.aaf.2020.04.003

Zink, R. M., & Barrowclough, G. F. (2008). Mitochondrial DNA under siege in avian phylogeography. Molecular ecology, 17(9), 2107-2121. https://doi.org/10.1111/j.1365-294X.2008.03737.x




DOI: https://doi.org/10.14421/biomedich.2026.151.433-442

Refbacks

  • There are currently no refbacks.


Bookmark and Share


Copyright (c) 2026 Jihan Winarti, I Made Budiarsa, Manap Trianto, I Nengah Kundera, Mursito S Bialangi, Abdul Ashari



Biology, Medicine, & Natural Product Chemistry
ISSN 2089-6514 (paper) - ISSN 2540-9328 (online)
Published by Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity.

CC BY NC
This work is licensed under a CC BY-NC