DNA barcoding of bats from two selected forest reserves in Peninsular Malaysia

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SAIDATUL NUR HANIM ABDUL MALEK
IZZATI ADILAH AZMIR
NUR JULIANI SHAFIE
YUZINE ESA
WAN NURHAYATI WAN HANAFI

Abstract

Abstract. Abdul Malek SNH, Azmir IA, Shafie NJ, Esa Y, Hanafi WNW. 2025. DNA barcoding of bats from two selected forest reserves in Peninsular Malaysia. Biodiversitas 26: 2843-2856. Bats (order Chiroptera) are notable for their species diversity and a variety of distinct characteristics. However, as several molecular studies have shown, morphological similarities in some taxa of this group can result in neglected diversity. DNA barcodes can help by providing an accurate, rapid, and effective method of species recognition. In this study, we used DNA barcoding to identify bats captured from two selected regions in Peninsular Malaysia: Kenyir, Terengganu and Taman Alam Liar Negeri Kenaboi (TALNK), Jelebu, Negeri Sembilan. DNA barcoding analysis was performed on 38 bat specimens to further verify the species identification of the captured bats from morphological characteristics. The COI gene (603-604 bp) was successfully sequenced from the 38 bat species, representing 3 families, 5 genera, and 15 species. The phylogenies of NJ, ML, and Bayesian methods resulted in most of the specimens of the same species being clustered together. According to the IUCN Red List, Rhinolophus trifoliatus is listed as Near Threatened (NT), whereas 14 species were listed as Least Concern (LC). The findings reported in this study confirm the usefulness of DNA barcoding to identify bat species and to measure bat diversity in Kenyir and TALNK forest reserves. Improving habitat conservation in forest reserves is necessary to guard against the disruption and extinction of bat species.

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Author Biographies

IZZATI ADILAH AZMIR, Faculty of Applied Science, Universiti Teknologi MARA. 40450 Shah Alam, Selangor Darul Ehsan, Malaysia

Senior Lecturer,

School of Biology,

Faculty of Applied Science, Universiti Teknologi MARA (UiTM), Shah Alam Branch, 40450 Shah Alam, Selangor, Malaysia.

NUR JULIANI SHAFIE, Faculty of Science and Marine Environment, Universiti Malaysia Terengganu. 21030 Kuala Nerus, Terengganu, Malaysia

Senior Lecturer,

Faculty of Science and Marine Environment, Universiti Malaysia Terengganu (UMT), 21030 Kuala Nerus, Terengganu, Malaysia.

WAN NURHAYATI WAN HANAFI, Faculty of Applied Science, Universiti Teknologi MARA. 40450 Shah Alam, Selangor Darul Ehsan, Malaysia

Senior Lecturer, 

School of Biology,

Faculty of Applied Science, Universiti Teknologi MARA (UiTM), Shah Alam Branch, 40450 Shah Alam, Selangor, Malaysia.

References

Atagana PJ, Fils EMB, Kekeunou S. 2021. Responses of bat communities (Mammalia: Chiroptera) to forest loss and habitat conversion in Southern Cameroon. Trop Conserv Sci 14: 1-8. DOI: 10.1177/19400829211010360.

Azmir IA, Esa YB, Amin SMN, Salwany MYI, Zuraina MYF. 2020. DNA barcoding analysis of larval fishes in Peninsular Malaysia. J Environ Biol 41: 1295-1308. DOI: 10.22438/jeb/41.

BakwoFils E-M, Mongombe MA, Manfothang DE, Gomeh-Djame A, Takuo JM, Bilong BCF. 2021. Patterns of bat diversity in an undisturbed forest and forest mosaic habitats of the Afromontane forest Biome of Western Cameroon. Front Ecol Evol 9: 761969. DOI: 10.3389/fevo.2021.761969.

Basith A, Abinawanto A, Kusrini E, Yasman Y. 2021. Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene. Biodiversitas 22: 4282-4290. DOI: 10.13057/biodiv/d221020.

Basri HH, Mohamed NZ, Shafie NJ, Abdullah MT. 2022. Comparative diversity of bats in two contrasting habitats in Terengganu. Borneo J Resour Sci Technol 12 (2): 24-38. DOI: 10.33736/bjrst.4559.2022.

Benítez ÁJ, Ricardo-Caldera D, Atencia-Pineda M, Ballesteros-Correa J, Chacón-Pacheco J, Hoyos-López R. 2021. DNA barcoding of bats (Chiroptera) from the Colombian northern region. Mammalia 85 (5): 462-470. DOI: 10.1515/mammalia-2020-0138.

Bingpeng X, Heshan L, Zhilan Z, Chunguang W, Yanguo W, Jianjun W. 2018. DNA barcoding for identification of fish species in the Taiwan Strait. PLoS One 13: e0198109. DOI: 10.1371/journal.pone.0198109.

Buckles EL. 2014. Chiroptera (bats). In: Miller RE, Fowler ME (eds). Fowler's Zoo and Wild Animal Medicine. Saunders, United States. DOI: 10.1016/B978-1-4557-7397-8.00035-9.

Clare EL, Lim BK, Engstrom MD, Eger JL, Hebert PDN. 2007. DNA barcoding of Neotropical bats: Species identification and discovery within Guyana. Mol Ecol Notes 7 (2): 184-190. DOI: 10.1111/j.1471-8286.2006.01657.x.

Cruz-Salazar B, Ruiz-Montoya L, Mendoza-Sáenz VH, Riechers-Pérez A, García-Bautista M. 2018. Genetic diversity of tropical bats and its relationship with ecological role in a tropical semievergreen rain forest in El Ocote Biosphere Reserve, Chiapas, Mexico. Trop Conserv Sci 11: 1-21. DOI: 10.1177/1940082917752473.

Elangovan V, Mathur V, Kumar M, Priya YS. 2018. Diversity and conservation of Chiropteran fauna. In: Sivaperuman C, Venkataraman K (eds). Indian Hotspots. Springer, Singapore. DOI: 10.1007/978-981-10-6605-4_3.

Fahim MMH, Hassan W, Afsin A, Rahman MM, Rahman MT, Lim SJ, Oh Y, Park YC, Faruquee HM, Rahman MM. 2024. Molecular identification of fruit bats, natural host of Nipah virus in Bangladesh, based on DNA barcode. J Ecol Environ 48: 17. DOI: 10.5141/jee.24.003.

Fatma NAH, Wan Juliana WA, Shaharuddin MI, Wickneswari R. 2016. Community stand structure of rehabilitated forest at Kenaboi Forest Reserve, Negeri Sembilan, Malaysia. AIP Conf Proc 1784: 060013. DOI: 10.1063/1.4966851.

Fatma NAH, Wan Juliana WA, Shaharuddin MI, Wickneswari R. 2020. Stand structure of Shorea and spatial distribution of Shorea acuminata in a rehabilitated area of Kenaboi Forest Reserve. J Trop For Sci 32 (3): 257-267. DOI: 10.26525/jtfs2020.32.3.257.

Foley NM, Thong VD, Soisook P, Goodman SM, Armstrong KN, Jacobs DS, Puechmaille SJ, Teeling EC. 2015. How and why overcome the impediments to resolution: Lessons from rhinolophid and hipposiderid bats. Mol Biol Evol 32 (2): 313-333. DOI: 10.1093/molbev/msu329.

Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome C Oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3 (5): 294-299.

Francis C. 2019. Field Guide to the Mammals of South-East Asia. 2nd eds. Bloomsbury Publishing, London.

Frick WF, Kingston T, Flanders J. 2020. A review of the major threats and challenges to global bat conservation. Ann NY Acad Sci 1469 (1): 5-25. DOI: 10.1111/nyas.14045.

Gaudioso PJ, Martínez JJ, Barquez RM, Díaz MM. 2020. Evolution of scapula shape in several families of bats (Chiroptera, Mammalia). J Zool Syst Evol Res 58 (4): 1374-1394. DOI: 10.1111/jzs.12383.

Gu X-M, He S-Y, Ao L. 2008. Molecular phylogenetics among three families of bats (Chiroptera: Rhinolophidae, Hipposideridae, and Vespertilionidae) based on partial sequences of the mitochondrial 12S and 16S rRNA genes. Zool Stud 47 (3): 368-378.

Guo Y, Gong Y, He Y-M, Yang B-G, Zhang W-Y, Chen B-E, Huang Y-F, Zhao Y-J, Zhang D-P, Ma Y-H, Chu M-X, E G-X. 2022. Investigation of mitochondrial DNA genetic diversity and phylogeny of goats worldwide. J Integr Agric 21 (6): 1830-1837. DOI: 10.1016/S2095-3119(21)63882-0.

Hasan NH, Abdullah MT. 2011. A morphological analysis of Malaysian Kerivoula (Chiroptera, Vespertilionidae). Mamm Stud 36 (2): 87-97. DOI: 10.3106/041.036.0207.

Hazwani ARN, Shahfiz MA, Faradiana NMF, Kaviarasu M, Alwani NZ, Farhan MS. 2021. Notes on roundleaf bats (Hipposideridae) at selected forest reserves of Central Forest Spine (CFS) landscapes in Peninsular Malaysia. IOP Conf Ser: Earth Environ Sci 736: 012048. DOI: 10.1088/1755-1315/736/1/012048.

Hebert PDN, Cywinska A, Ball SL, deWaard JR. 2003. Biological identifications through DNA barcodes. Proc R Soc London Ser B: Biol Sci 270 (1512): 313-321. DOI: 10.1098/rspb.2002.2218.

Hughes AC, Satasook C, Bates PJJ, Soisook P, Sritongchuay T, Jones G, Bumrungsri S. 2010. Echolocation call analysis and presence-only modelling as conservation monitoring tools for rhinolophoid bats in Thailand. Acta Chiropterol 12 (2): 311-327. DOI: 10.3161/150811010X537891.

Idnan M, Javid A, Tayyab M, Hussain A, Mansoor S, Bukhari SM, Irfan, Shahbaz M, Rehman KU, Andleeb S, Azam SM, Ali W. 2021. Molecular identification of genus Pipistrellus (Mammalia: Chiroptera) from Fata region, Pakistan. Braz J Biol 83: e246322. DOI: 10.1590/1519-6984.246322.

Ingala MR, Simmons NB, Wultsch C, Krampis K, Provost KL, Perkins SL. 2021. Molecular diet analysis of neotropical bats based on fecal DNA metabarcoding. Ecol Evol 11 (12): 7474-7491. DOI: 10.1002/ece3.7579.

Kammerer R, Mansfeld M, Hänske J, Mißbach S, He X, Köllner B, Mouchantat S, Zimmermann W. 2017. Recent expansion and adaptive evolution of the carcinoembryonic antigen family in bats of the Yangochiroptera subgroup. BMC Genomics 18 (1): 717. DOI: 10.1186/s12864-017-4106-7.

Kingston T, Lim BL, Akbar Z. 2006. Bats of Krau Wildlife Reserve. Penerbit Universiti Kebangsaan Malaysia, Bangi, Malaysia.

Korine C, Adams R, Russo D, Fisher-Phelps M, Jacobs D. 2016. Bats and water: Anthropogenic alterations threaten global bat populations. In: Voigt C, Kingston T (eds). Bats in the Anthropocene: Conservation of Bats in a Changing World. Springer, Cham. DOI: 10.1007/978-3-319-25220-9_8.

Kruskop SV, Artyushin IV. 2021. Chiropteran (Chiroptera; Mammalia) taxonomy in light of modern methods and approaches. Russ J Theriol 20 (2): 111-128. DOI: 10.15298/rusjtheriol.20.2.01.

Lim BK, Hernandez LMA. 2016. DNA barcoding of Jamaican bats: Implications to Neotropical biodiversity. Mitochondrial DNA A DNA Mapp Seq Anal 27: 3013-3019. DOI: 10.3109/19401736.2015.1063047.

Lim L-S, Struebig MJ, Zalipah MN, Mohd-Adnan A, Senawi J, Zubaid A, Mohd Sah SA, Rossiter SJ. 2019. Bats from the understorey of lowland tropical rainforests across Peninsular Malaysia. J Bat Res Conserv 12 (1): 68-82. DOI: 10.14709/BarbJ.12.1.2019.10.

Lim V-C, Ramli R, Bhassu S, Wilson J-J. 2017. A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library. PLoS One 12: e0179555. DOI: 10.1371/journal.pone.0179555.

Marina MT, Chubo JK, Senawi J, Nur Farrazuin J, Ahmad Badrul Amin AR. 2021. Current status of bat diversity and conservation in Universiti Putra Malaysia and its forest reserves. J Sustain Sci Manag 16 (7): 237-259. DOI: 10.46754/jssm.2021.10.018.

Miller GS. 1907. The Families and Genera of Bats (No. 57). US Government Printing Office, USA.

Mohammad Noor NA, Rahim NAA, Ahmad NII, Abdullah MT. 2019. Taxonomic composition of non-volant small mammal assemblages in Tasik Kenyir, Hulu Terengganu, Terengganu. In: Abdullah M, Mohammad A, Nor Zalipah M, Safiih Lola M (eds). Greater Kenyir Landscapes. Springer, Cham. DOI: 10.1007/978-3-319-92264-5_17.

Mohd-Hanif RMD, Nur-Aida MT, Zahirunisa AR, Mohd-Ridwan AR, Abdullah MT. 2015. Contribution of regenerated forest in conservation of bats in Peninsular Malaysia. J Trop For Sci 27 (4): 506-516.

Monadjem A, Demos TC, Dalton DL, Webala PW, Musila S, Peterhans JCK, Patterson BD. 2021. A revision of pipistrelle-like bats (Mammalia: Chiroptera: Vespertilionidae) in East Africa with the description of new genera and species. Zool J Linn Soc 191 (4): 1114-1146. DOI: 10.1093/zoolinnean/zlaa087/5903787.

Mota TFM, Fabrin TMC, Diamante NA, de Oliveira AV, Filho HO, Prioli AJ, Prioli SMAP. 2022. DNA Barcode is efficient for identifying bat species. J Mamm Evol 29 (1): 1-13. DOI: 10.1007/s10914-021-09563-8.

Mubarok H, Handayani NSN, Maryanto I, Arisuryanti T. 2023. Phylogenetic and genetic variation analysis of lesser short-nosed fruit bat Cynopterus brachyotis (Müller 1838) on Java Island, Indonesia, inferred from mitochondrial D-loop. J Genet Eng Biotechnol 21 (1): 1. DOI: 10.1186/s43141-022-00460-y.

Nasir NM, Nasir DM, Ramli R. 2021. Diversity of bats in three selected forest types in Peninsular Malaysia. Turk J Zool 45 (2): 142-155. DOI: 10.3906/zoo-1912-50.

Novella-Fernandez R, Juste J, Ibañez C, Nogueras J, Osborne PE, Razgour O. 2022. The role of forest structure and composition in driving the distribution of bats in Mediterranean regions. Sci Rep 12: 3224. DOI: 10.1038/s41598-022-07229-w.

Park S, Noh P, Choi Y-S, Joo S, Jeong G, Kim S-S. 2019. Population genetic structure based on mitochondrial DNA analysis of Ikonnikov’s whiskered bat (Myotis ikonnikovi-Chiroptera: Vespertilionidae) from Korea. J Ecol Environ 43: 45. DOI: 10.1186/s41610-019-0140-5.

Phillipps Q, Phillipps K. 2016. Phillipps' Field Guide to the Mammals of Borneo and Their Ecology: Sabah, Sarawak, Brunei, and Kalimantan John Beaufoy Publishing Ltd., Oxford, United Kingdom.

Pounsin G, Wahab NS, Roslan A, Zahidin MA, Pesiu E, Tamrin NAM, Abdullah MT. 2018. Diversity of bats in contrasting habitats of Hulu Terengganu Dipterocarp Forest and Setiu Wetland BRIS forest with a note on preliminary study of vertical stratification of Pteropodid Bats. Trop Life Sci Res 29 (1): 51-69. DOI: 10.21315/tlsr2018.29.1.4.

Purty RS, Chatterjee S. 2016. DNA barcoding: An effective technique in molecular taxonomy. Austin J Biotechnol Bioeng 3 (1): 1059.

Ramlee MNA, Hussin MF, Roslan A, Rosmidi FH, Pesiu E, Rahim NAA, Ahmad NII, David G, Zakaria AA, Adanan NA, Basri HH, Ariffin MSA, Bartholomew CV, Zahidin MA, Lola MS, Abdullah MT. 2020. Conspectus of flora, fauna and micro-climate data in Tasik Kenyir from Mac 2015-February 2016. Data Brief 29: 105328. DOI: 10.1016/j.dib.2020.105328.

Richards CM, Falk DA, Montalvo AM. 2016. Population and ecological genetics in restoration ecology. In: Palmer MA, Zedler JB, Falk DA (eds). Foundations of Restoration Ecology. Island Press, Washington, DC. DOI: 10.5822/978-1-61091-698-1_5.

Russo D, Billington G, Bontadina F, Dekker J, Dietz M, Gazaryan S, Jones G, Meschede A, Rebelo H, Reiter G, Ruczy?ski I, Tillon L, Twisk P. 2016. Identifying key research objectives to make European forests greener for bats. Front Ecol Evol 4: 87. DOI: 10.3389/fevo.2016.00087.

Sarvananda L. 2018. Short introduction of DNA barcoding. Intl J Res 5 (4): 673-685.

Sazali SN, Besar K, Abdullah MT. 2011. Phylogenetic analysis of the Malaysian Rhinolopus and Hipposideros inferred from partial mitochondrial DNA cytochrome b gene sequences. Pertanika J Trop Agric Sci 34 (2): 281-294.

Senawi J, Norhayati A. 2021. Bats of Malaysia. Putrajaya: Kementerian Tenaga dan Sumber Asli, Malaysia.

Soisook P. 2013. Systematics, biogeography and echolocation of tube-nosed bats genus murina (Chiroptera: vespertilionidae) in mainland Southeast Asia. [Dissertation]. Prince of Songkla University, Thailand.

Sovic MG, Carstens BC, Gibbs HL. 2016. Genetic diversity in migratory bats: Results from RADseq data for three tree bat species at an Ohio windfarm. PeerJ 4: e1647. DOI: 10.7717/peerj.1647.

Sun K, Kimball RT, Liu T, Wei X, Jin L, Jiang T, Lin A, Feng J. 2016. The complex evolutionary history of big-eared horseshoe bats (Rhinolophus macrotis complex): Insights from genetic, morphological and acoustic data. Sci Rep 6: 35417. DOI: 10.1038/srep35417.

Wan Zainal Azhar WFA, Azmir IA. 2019. Genetic identification of selected ornamental fishes in Seremban, Negeri Sembilan. J Acad 7 (2): 56-66.

Yu W-H, Csorba G, Wu Y. 2020. Tube-nosed variations-a new species of the genus Murina (Chiroptera: Vespertilionidae) from China. Zool Res 41 (1): 70-77. DOI: 10.24272/j.issn.2095-8137.2020.009.

Yuzefovich AP, Artyushin IV, Skopin AE, Son NT, Kruskop SV. 2022. Taxonomic diversity of the Hipposideros larvatus species complex (Chiroptera: Hipposideridae) in mainland Asia. Zootaxa 5200 (1): 73-95. DOI: 10.11646/zootaxa.5200.1.6.

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