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Haris H, Othman N, Kaviarasu M, Najmuddin MF, Abdullah-Fauzi NAF, Ramli FF, Sariyati NH, Ilham-Norhakim ML, Md-Zain BM, Abdul-Latiff MAB. Ethnoprimatology reveals new extended distribution of critically endangered banded langur Presbytis femoralis (Martin, 1838) in Pahang, Malaysia: Insights from indigenous traditional knowledge and molecular analysis. Am J Primatol 2024:e23631. [PMID: 38698704 DOI: 10.1002/ajp.23631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 03/28/2024] [Accepted: 04/14/2024] [Indexed: 05/05/2024]
Abstract
The banded langur (Presbytis femoralis) is a critically endangered primate, restricted to Johor, Malaysia, with an estimated population size of less than 500 individuals. Traditionally, distribution studies on this highly threatened primate have relied on conventional methods such as DNA identification, live counting, and camera trapping. However, ethnoprimatology offers an alternative approach to data collection, involving the active participation of indigenous and local communities possessing valuable knowledge and experience with local primate species. This study employed an integrated approach incorporating ethnoprimatology by utilizing pooled local expert opinion, local surveys, interviews, and fecal DNA analysis, resulting in a novel distribution range for the banded langur. The combination of expert opinions revealed this species' most optimistic distribution scenario across Johor and Pahang, inhabiting various ecosystems, including lowland forests, peat swamps, and human-modified landscapes. Further interviews and surveys conducted within the Orang Asli community in Tasik Chini and Tasek Bera have provided additional support for the revised distribution, documenting occurrences of banded langur utilization in indigenous practices, such as food consumption, cultural beliefs, medicinal applications, and craftsmanship. Phylogenetic analysis demonstrated genetic differentiation between populations in Johor and Pahang, with the populations in the southern part of Peninsular Malaysia likely serving as ancestral sources for other populations. Consequently, this study not only elucidated the updated distribution of banded langur through DNA records and direct observations but also established the efficacy of ethnoprimatology as a precursory tool for uncovering the present distribution patterns of other primate species in Malaysia.
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Affiliation(s)
- Hidayah Haris
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Nursyuhada Othman
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Munian Kaviarasu
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
- Zoology Branch, Forest Biodiversity Division, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Muhammad Faudzir Najmuddin
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Nurfatiha Akmal Fawwazah Abdullah-Fauzi
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Farah Farhana Ramli
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Nur Hartini Sariyati
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Mohd Lokman Ilham-Norhakim
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
- Kim Ichthyologist Centre, Kg Parit Samsu, Jalan Temenggong Ahmad, Parit Jawa, Muar, Johor, Malaysia
- Akim Fishes Enterprise, 81P Pesta 2, Kg Kenangan Tun Dr Ismail, Muar, Johor, Malaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Muhammad Abu Bakar Abdul-Latiff
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
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Sariyati NH, Abdul-Latiff MAB, Aifat NR, Mohd-Ridwan AR, Osman NA, Karuppannan KV, Chan E, Md-Zain BM. Molecular phylogeny confirms the subspecies delineation of the Malayan Siamang ( Symphalangussyndactyluscontinentis) and the Sumatran Siamang ( Symphalangussyndactylussyndactylus) based on the hypervariable region of mitochondrial DNA. Biodivers Data J 2024; 12:e120314. [PMID: 38707255 PMCID: PMC11069032 DOI: 10.3897/bdj.12.e120314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/19/2024] [Indexed: 05/07/2024] Open
Abstract
Siamangs (Symphalangussyndactylus) are native to Peninsular Malaysia, Sumatra and southern Thailand and their taxonomical classification at subspecies level remains unclear. Morphologically, two subspecies were proposed as early as 1908 by Thomas namely Symphalangus s.syndactylus and Symphalanguss.continentis. Thus, this study aims to clarify the Siamang subspecies status, based on mtDNA D-loop sequences. Faecal samples were collected from wild Siamang populations at different localities in Peninsular Malaysia. A 600-bp sequence of the mitochondrial D-loop region was amplified from faecal DNA extracts and analysed along with GenBank sequences representing Symphalangus sp., Nomascus sp., Hylobates sp., Hoolock sp. and outgroups (Pongopygmaeus, Macacafascicularis and Papiopapio). The molecular phylogenetic analysis in this study revealed two distinct clades formed by S.s.syndactylus and S.s.continentis which supports the previous morphological delineation of the existence of two subspecies. Biogeographical analysis indicated that the Sumatran population lineage was split from the Peninsular Malaysian population lineage and a diversification occurrred in the Pliocene era (~ 3.12 MYA) through southward expansion. This postulation was supported by the molecular clock, which illustrated that the Peninsular Malaysian population (~ 1.92 MYA) diverged earlier than the Sumatran population (~ 1.85 MYA). This is the first study to use a molecular approach to validate the subspecies statuses of S.s.syndactylus and S.s.continentis. This finding will be useful for conservation management, for example, during Siamang translocation and investigations into illegal pet trade and forensics involving Malayan and Sumatran Siamangs.
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Affiliation(s)
- Nur Hartini Sariyati
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), 84600, Muar, Johor, MalaysiaFaculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus)84600, Muar, JohorMalaysia
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600Bangi, SelangorMalaysia
| | - Muhammad Abu Bakar Abdul-Latiff
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), 84600, Muar, Johor, MalaysiaFaculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus)84600, Muar, JohorMalaysia
| | - Nor Rahman Aifat
- Faculty of Tropical Forestry, Universiti Malaysia Sabah, 88400, Kota Kinabalu, Sabah, MalaysiaFaculty of Tropical Forestry, Universiti Malaysia Sabah, 88400Kota Kinabalu, SabahMalaysia
| | - Abd Rahman Mohd-Ridwan
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, MalaysiaCentre for Pre-University Studies, Universiti Malaysia Sarawak, 94300Kota Samarahan, SarawakMalaysia
| | - Nur Azimah Osman
- Faculty of Applied Sciences, Universiti Teknologi Mara Negeri Sembilan, 72000, Kuala Pilah, Negeri Sembilan, MalaysiaFaculty of Applied Sciences, Universiti Teknologi Mara Negeri Sembilan, 72000Kuala Pilah, Negeri SembilanMalaysia
| | - Kayal Vizi Karuppannan
- National Wildlife Forensic Laboratory (NWFL), Department of Wildlife and National Parks (PERHILITAN), 56100, Kuala Lumpur, MalaysiaNational Wildlife Forensic Laboratory (NWFL), Department of Wildlife and National Parks (PERHILITAN), 56100Kuala LumpurMalaysia
| | - Eddie Chan
- Genting Nature Adventure, Resorts World Awana Hotel, 69000, Genting Highlands, Pahang, MalaysiaGenting Nature Adventure, Resorts World Awana Hotel69000, Genting Highlands, PahangMalaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600Bangi, SelangorMalaysia
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Gani M, Mohd-Ridwan AR, Sitam FT, Kamarudin Z, Selamat SS, Awang NMZ, Karuppannan KV, Md-Zain BM. Habitat shapes the gut microbiome diversity of Malayan tigers (Panthera tigris jacksoni) as revealed through metabarcoding 16S rRNA profiling. World J Microbiol Biotechnol 2024; 40:111. [PMID: 38416247 DOI: 10.1007/s11274-023-03868-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/06/2023] [Indexed: 02/29/2024]
Abstract
The gut microbiome refers to the microorganism community living within the digestive tract. The environment plays a crucial role in shaping the gut microbiome composition of animals. The gut microbiome influences the health and behavior of animals, including the critically endangered Malayan tiger (Panthera tigris jacksoni). However, the gut microbiome composition of Malayan tigers, especially those living in their natural habitats, remains poorly understood. To address this knowledge gap, we used next-generation sequencing DNA metabarcoding techniques to analyze the gut microbiome of wild Malayan tigers using fecal samples collected from their natural habitats and in captivity. Our aim was to determine the gut microbiota composition of the Malayan tiger, considering the different types of habitat environments. The results revealed a diverse microbial community within the gut microbiome of Malayan tigers. The prominent phyla that were observed included Firmicutes, Proteobacteria, Actinobacteriota, Fusobacteriota and Bacteroidota. Beta diversity analysis revealed significant differences in gut microbiome composition of Malayan tigers that inhabited oil palm plantations, in villages and protected areas. Diversity analysis also revealed significant difference in the gut microbiome between wild and captive Malayan tigers. However, the distinctions of gut microbiome between wild and captive alpha diversity did not yield significant differences. The differences in microbiome diversity resulted from the interplay of dietary intake and environmental factors. This information will facilitate the establishment of focused conservation approaches and enhance our understanding of the effect of microbiome composition on Malayan tiger health.
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Affiliation(s)
- Millawati Gani
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- National Wildlife Forensic Laboratory (NWFL), Ex-Situ Conservation Division, Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, 56100, Kuala Lumpur, Malaysia
| | - Abd Rahman Mohd-Ridwan
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Frankie Thomas Sitam
- National Wildlife Forensic Laboratory (NWFL), Ex-Situ Conservation Division, Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, 56100, Kuala Lumpur, Malaysia
| | - Zubaidah Kamarudin
- National Wildlife Rescue Centre (NWRC), Department of Wildlife and National Parks (PERHILITAN), 35600, Sungkai, Perak, Malaysia
| | - Siti Suzana Selamat
- National Wildlife Rescue Centre (NWRC), Department of Wildlife and National Parks (PERHILITAN), 35600, Sungkai, Perak, Malaysia
| | - Nik Mohd Zamani Awang
- National Wildlife Rescue Centre (NWRC), Department of Wildlife and National Parks (PERHILITAN), 35600, Sungkai, Perak, Malaysia
| | - Kayal Vizi Karuppannan
- National Wildlife Forensic Laboratory (NWFL), Ex-Situ Conservation Division, Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, 56100, Kuala Lumpur, Malaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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Khairulmunir M, Gani M, Karuppannan KV, Mohd-Ridwan AR, Md-Zain BM. High-throughput DNA metabarcoding for determining the gut microbiome of captive critically endangered Malayan tiger ( Pantheratigrisjacksoni) during fasting. Biodivers Data J 2023; 11:e104757. [PMID: 37711366 PMCID: PMC10498273 DOI: 10.3897/bdj.11.e104757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023] Open
Abstract
The Malayan tiger (Pantheratigrisjacksoni) is a critically endangered species native to the Malaysian Peninsula. To imitate wild conditions where tigers do not hunt every day, numerous wildlife sanctuaries do not feed their tigers daily. However, the effects of fasting on the gut microbiota of captive Malayan tigers remains unknown. This study aimed to characterise the gut microbiota of captive Malayan tigers by comparing their microbial communities during fasting versus normal feeding conditions. This study was conducted at the Melaka Zoo, Malaysian Peninsula and involved Malayan tigers fasted every Monday. In total, ten faecal samples of Malayan tiger, two of Bengal tiger (outgroup) and four of lion (outgroup) were collected and analysed for metabarcoding targeting the 16S rRNA V3-V4 region. In total, we determined 14 phyla, 87 families, 167 genera and 53 species of gut microbiome across Malayan tiger samples. The potentially harmful bacterial genera found in this study included Fusobacterium, Bacteroides, Clostridium sensu stricto 1, Solobacterium, Echerichiashigella, Ignatzschineria and Negativibacillus. The microbiome in the fasting phase had a higher composition and was more diverse than in the feeding phase. The present findings indicate a balanced ratio in the dominant phyla, reflecting a resetting of the imbalanced gut microbiota due to fasting. These findings can help authorities in how to best maintain and improve the husbandry and health of Malayan tigers in captivity and be used for monitoring in ex-situ veterinary care unit.
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Affiliation(s)
- Mohamad Khairulmunir
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43600 Bangi, SelangorMalaysia
| | - Millawati Gani
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43600 Bangi, SelangorMalaysia
- Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, Kuala Lumpur, MalaysiaDepartment of Wildlife and National Parks (PERHILITAN), KM 10 Jalan CherasKuala LumpurMalaysia
| | - Kayal Vizi Karuppannan
- Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, Kuala Lumpur, MalaysiaDepartment of Wildlife and National Parks (PERHILITAN), KM 10 Jalan CherasKuala LumpurMalaysia
| | - Abd Rahman Mohd-Ridwan
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300, Kota Samarahan, MalaysiaCentre for Pre-University Studies, Universiti Malaysia Sarawak, 94300Kota SamarahanMalaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43600 Bangi, SelangorMalaysia
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Mohd-radzi NHS, Karuppannan KV, Abdullah-fauzi NAF, Mohd-ridwan AR, Othman N, Muhammad Abu Bakar A, Gani M, Abdul-razak MFA, Md-zain BM. Figure 3 from: Mohd-Radzi NHS, Karuppannan KV, Abdullah-Fauzi NAF, Mohd-Ridwan AR, Othman N, Muhammad Abu Bakar A-L, Gani M, Abdul-Razak MFA, Md-Zain BM (2022) Determining the diet of wild Asian elephants (Elephas maximus) at human–elephant conflict areas in Peninsular Malaysia using DNA metabarcoding. Biodiversity Data Journal 10: e89752. https://doi.org/10.3897/BDJ.10.e89752. 2022. [DOI: 10.3897/bdj.10.e89752.figure3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Mohd-radzi NHS, Karuppannan KV, Abdullah-fauzi NAF, Mohd-ridwan AR, Othman N, Muhammad Abu Bakar A, Gani M, Abdul-razak MFA, Md-zain BM. Figure 7 from: Mohd-Radzi NHS, Karuppannan KV, Abdullah-Fauzi NAF, Mohd-Ridwan AR, Othman N, Muhammad Abu Bakar A-L, Gani M, Abdul-Razak MFA, Md-Zain BM (2022) Determining the diet of wild Asian elephants (Elephas maximus) at human–elephant conflict areas in Peninsular Malaysia using DNA metabarcoding. Biodiversity Data Journal 10: e89752. https://doi.org/10.3897/BDJ.10.e89752. 2022. [DOI: 10.3897/bdj.10.e89752.figure7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Mohd-radzi NHS, Karuppannan KV, Abdullah-fauzi NAF, Mohd-ridwan AR, Othman N, Muhammad Abu Bakar A, Gani M, Abdul-razak MFA, Md-zain BM. Figure 9 from: Mohd-Radzi NHS, Karuppannan KV, Abdullah-Fauzi NAF, Mohd-Ridwan AR, Othman N, Muhammad Abu Bakar A-L, Gani M, Abdul-Razak MFA, Md-Zain BM (2022) Determining the diet of wild Asian elephants (Elephas maximus) at human–elephant conflict areas in Peninsular Malaysia using DNA metabarcoding. Biodiversity Data Journal 10: e89752. https://doi.org/10.3897/BDJ.10.e89752. 2022. [DOI: 10.3897/bdj.10.e89752.figure9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Mohd-Radzi NHS, Karuppannan KV, Abdullah-Fauzi NAF, Mohd-Ridwan AR, Othman N, Muhammad Abu Bakar AL, Gani M, Abdul-Razak MFA, Md-Zain BM. Determining the diet of wild Asian elephants ( Elephasmaximus) at human-elephant conflict areas in Peninsular Malaysia using DNA metabarcoding. Biodivers Data J 2022; 10:e89752. [PMID: 36761586 PMCID: PMC9836633 DOI: 10.3897/bdj.10.e89752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/19/2022] [Indexed: 11/12/2022] Open
Abstract
Human-elephant conflict (HEC) contributes to the increasing death of Asian elephants due to road accidents, retaliatory killings and fatal infections from being trapped in snares. Understanding the diet of elephants throughout Peninsular Malaysia remains crucial to improve their habitat quality and reduce scenarios of HEC. DNA metabarcoding allows investigating the diet of animals without direct observation, especially in risky conflict areas. The aim of this study was to determine: i) the diet of wild Asian elephants from HEC areas in Peninsular Malaysia using DNA metabarcoding and ii) the influence of distinct environmental parameters at HEC locations on their feeding patterns. DNA was extracted from 39 faecal samples and pooled into 12 groups representing the different sample locations: Kuala Koh, Kenyir, Ulu Muda, Sira Batu, Kupang-Grik, Bumbun Tahan, Belum-Temengor, Grik, Kampung Pagi, Kampung Kuala Balah, Aring 10 and the National Elephant Conservation Centre, which served as a positive control for this study. DNA amplification and sequencing targeted the ribulose-bisphosphate carboxylase gene using the next-generation sequencing Illumina iSeq100 platform. Overall, we identified 35 orders, 88 families, 196 genera and 237 species of plants in the diet of the Asian elephants at HEC hotspots. Ficus (Moraceae), Curcuma (Zingiberaceae), Phoenix (Arecaceae), Maackia (Fabaceae), Garcinia (Clusiaceae) and Dichapetalum (Dichapetalaceae) were the highly abundant dietary plants. The plants successfully identified in this study could be used by the Department of Wildlife and National Parks (PERHILITAN) to create buffer zones by planting the recommended dietary plants around HEC locations and trails of elephants within Central Forest Spine (CFS) landscape.
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Affiliation(s)
- Nor Hafisa Syafina Mohd-Radzi
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43000, Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43000, Bangi, SelangorMalaysia
| | - Kayal Vizi Karuppannan
- Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, 56100, Kuala Lumpur, MalaysiaDepartment of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras56100, Kuala LumpurMalaysia
| | - Nurfatiha Akmal Fawwazah Abdullah-Fauzi
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43000, Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43000, Bangi, SelangorMalaysia
| | - Abd Rahman Mohd-Ridwan
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43000, Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43000, Bangi, SelangorMalaysia,Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, MalaysiaCentre for Pre-University Studies, Universiti Malaysia Sarawak94300 Kota Samarahan, SarawakMalaysia
| | - Nursyuhada Othman
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), 84600 Johor, MalaysiaFaculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus)84600 JohorMalaysia
| | - Abdul-Latiff Muhammad Abu Bakar
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), 84600 Johor, MalaysiaFaculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus)84600 JohorMalaysia,Oasis Integrated Group (OIG), Institute for Integrated Engineering (I2E), Universiti Tun Hussein Onn Malaysia, 86400 Parit Raja, Johor, MalaysiaOasis Integrated Group (OIG), Institute for Integrated Engineering (I2E), Universiti Tun Hussein Onn Malaysia86400 Parit Raja, JohorMalaysia
| | - Millawati Gani
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43000, Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43000, Bangi, SelangorMalaysia,Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, 56100, Kuala Lumpur, MalaysiaDepartment of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras56100, Kuala LumpurMalaysia
| | - Mohd Firdaus Ariff Abdul-Razak
- Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, 56100, Kuala Lumpur, MalaysiaDepartment of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras56100, Kuala LumpurMalaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43000, Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43000, Bangi, SelangorMalaysia
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Mohd-radzi NHS, Karuppannan KV, Abdullah-fauzi NAF, Mohd-ridwan AR, Othman N, Muhammad Abu Bakar A, Gani M, Abdul-razak MFA, Md-zain BM. Figure 12 from: Mohd-Radzi NHS, Karuppannan KV, Abdullah-Fauzi NAF, Mohd-Ridwan AR, Othman N, Muhammad Abu Bakar A-L, Gani M, Abdul-Razak MFA, Md-Zain BM (2022) Determining the diet of wild Asian elephants (Elephas maximus) at human–elephant conflict areas in Peninsular Malaysia using DNA metabarcoding. Biodiversity Data Journal 10: e89752. https://doi.org/10.3897/BDJ.10.e89752. 2022. [DOI: 10.3897/bdj.10.e89752.figure12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Osman NA, Abdul-latiff MAB, Mohd-ridwan AR, Yaakop S, Karuppannan KV, Md-zain BM. Figure 4 from: Osman NA, Abdul-Latiff MAB, Mohd-Ridwan AR, Yaakop S, Karuppannan KV, Md-Zain BM (2022) Metabarcoding data analysis revealed the plant dietary variation of long-tailed macaque Macaca fascicularis (Cercopithecidae, Cercopithecinae) living in disturbed habitats in Peninsular Malaysia. Biodiversity Data Journal 10: e89617. https://doi.org/10.3897/BDJ.10.e89617. 2022. [DOI: 10.3897/bdj.10.e89617.figure4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Osman NA, Abdul-Latiff MAB, Mohd-Ridwan AR, Yaakop S, Karuppannan KV, Md-Zain BM. Metabarcoding data analysis revealed the plant dietary variation of long-tailed macaque Macacafascicularis (Cercopithecidae, Cercopithecinae) living in disturbed habitats in Peninsular Malaysia. Biodivers Data J 2022; 10:e89617. [PMID: 36761533 PMCID: PMC9848512 DOI: 10.3897/bdj.10.e89617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/09/2022] [Indexed: 11/12/2022] Open
Abstract
The long-tailed macaque (Macacafascicularis) has a wide range in both Peninsular Malaysia and Borneo. Although the primates are especially vulnerable to habitat alterations, this primate lives in disturbed habitats due to human-induced land-use. Thus, this study presents a faecal metabarcoding approach to clarify the plant diet of long-tailed macaques from five locations in Peninsular Malaysia to represent fragmented forest, forest edge, island and recreational park habitats. We extracted genomic DNA from 53 long-tailed macaque faecal samples. We found 47 orders, 126 families, 609 genera and 818 species across these five localities. A total of 113 plant families were consumed by long-tailed macaques in Universiti Kebangsaan Malaysia, 61 in the Malaysia Genome and Vaccine Institute, 33 in Langkawi Island, 53 in Redang Island and 44 in the Cenderawasih Cave. Moraceae (33.24%) and Fabaceae (13.63%) were the most common families consumed by long-tailed macaques from the study localities. We found that habitat type impacted diet composition, indicating the flexibility of foraging activities. This research findings provide an understanding of plant dietary diversity and the adaptability of this macaque with the current alteration level that applies to long-tailed macaque conservation management interest in the future.
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Affiliation(s)
- Nur Azimah Osman
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43000 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43000 Bangi, SelangorMalaysia,School of Biology, Faculty of Applied Sciences, Universiti Teknologi Mara Negeri Sembilan, 72000 Kuala Pilah, Negeri Sembilan, MalaysiaSchool of Biology, Faculty of Applied Sciences, Universiti Teknologi Mara Negeri Sembilan72000 Kuala Pilah, Negeri SembilanMalaysia,Special Interest Group (ECONATREA), School of Biology, Faculty of Applied Sciences, Universiti Teknologi Mara Negeri Sembilan, 72000 Kuala Pilah, Negeri Sembilan, MalaysiaSpecial Interest Group (ECONATREA), School of Biology, Faculty of Applied Sciences, Universiti Teknologi Mara Negeri Sembilan72000 Kuala Pilah, Negeri SembilanMalaysia
| | - Muhammad Abu Bakar Abdul-Latiff
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), 84000, Muar, Johor, MalaysiaFaculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus)84000, Muar, JohorMalaysia,Oasis Integrated Group (OIG), Institute for Integrated Engineering (I²E), Universiti Tun Hussein Onn Malaysia, 86400 Parit Raja, Johor, MalaysiaOasis Integrated Group (OIG), Institute for Integrated Engineering (I²E), Universiti Tun Hussein Onn Malaysia86400 Parit Raja, JohorMalaysia
| | - Abd Rahman Mohd-Ridwan
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, MalaysiaCentre for Pre-University Studies, Universiti Malaysia Sarawak94300 Kota Samarahan, SarawakMalaysia
| | - Salmah Yaakop
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43000 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43000 Bangi, SelangorMalaysia
| | - Kayal Vizi Karuppannan
- Department of Wildlife and National Parks (DWNP) KM10, Jalan Cheras, 56100 Kuala Lumpur, MalaysiaDepartment of Wildlife and National Parks (DWNP) KM10, Jalan Cheras56100 Kuala LumpurMalaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43000 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43000 Bangi, SelangorMalaysia
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Mohd-yusof NS, Abdul-latiff MAB, Mohd-ridwan AR, Badrulisham AS, Othman N, Yaakop S, Md-nor S, Md-zain BM. Figure 6 from: Mohd-Yusof NS, Abdul-Latiff MAB, Mohd-Ridwan AR, Badrulisham AS, Othman N, Yaakop S, Md-Nor S, Md-Zain BM (2022) First report on metabarcoding analysis of gut microbiome in Island Flying Fox (Pteropus hypomelanus) in island populations of Malaysia. Biodiversity Data Journal 10: e69631. https://doi.org/10.3897/BDJ.10.e69631. 2022. [DOI: 10.3897/bdj.10.e69631.figure6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Mohd-Yusof NS, Abdul-Latiff MAB, Mohd-Ridwan AR, Badrulisham AS, Othman N, Yaakop S, Md-Nor S, Md-Zain BM. First report on metabarcoding analysis of gut microbiome in Island Flying Fox ( Pteropushypomelanus) in island populations of Malaysia. Biodivers Data J 2022; 10:e69631. [PMID: 36761502 PMCID: PMC9848629 DOI: 10.3897/bdj.10.e69631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 02/09/2022] [Indexed: 01/12/2023] Open
Abstract
Flying fox (Pteropushypomelanus) belongs to the frugivorous bats, which play a crucial role in maintaining proper functioning of an ecosystem and conservation of the environment. Bats are well-known carriers of pathogenic viruses, such as BatCov RaTG13 from the coronavirus family that share 90.55% with SARS-CoV-2, the pathogen causing recent global pandemic coronavirus disease 19 (COVID-19). However, bats' possible role as a carrier of pathogenic bacteria is less explored. Here, using metabarcoding analysis through high-throughput sequencing, we explored the gut microbiome composition of different island populations on the east and west coasts of Peninsula Malaysia. The 16S rRNA gene in samples from Redang Island, Langkawi Island, Pangkor Island and Tinggi Island was amplified. Bacterial community composition and structure were analysed with α and β diversity metrics. A total of 25,658 operational taxonomic units at 97% similarity were assigned to eight phyla, 44 families, 61 genera and 94 species of microbes. The Proteobacteria was the dominant phylum in all populations. Meanwhile, the genera Enterobacter, Pseudomonas and Klebsiella, isolated in this study, were previously found in the rectum of other fruit bats. Our analyses suggest that Redang Island and Langkawi Island have high bacteria diversity. Thus, we found geographic locality is a strong predictor of microbial community composition and observed a positive correlation between ecological features and bacterial richness.
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Affiliation(s)
- Nur Syafika Mohd-Yusof
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600Bangi, SelangorMalaysia
| | - Muhammad Abu Bakar Abdul-Latiff
- Faculty of Applied Sciences and Technology Universiti Tun Hussein Onn Malaysia (Pagoh Campus), KM1 Jalan Panchor 84600, Muar, Johor, MalaysiaFaculty of Applied Sciences and Technology Universiti Tun Hussein Onn Malaysia (Pagoh Campus), KM1 Jalan Panchor 84600Muar, JohorMalaysia
| | - Abd Rahman Mohd-Ridwan
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600Bangi, SelangorMalaysia,Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, MalaysiaCentre for Pre-University Studies, Universiti Malaysia Sarawak, 94300Kota Samarahan, SarawakMalaysia
| | - Aqilah Sakinah Badrulisham
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600Bangi, SelangorMalaysia
| | - Nursyuhada Othman
- Faculty of Applied Sciences and Technology Universiti Tun Hussein Onn Malaysia (Pagoh Campus), KM1 Jalan Panchor 84600, Muar, Johor, MalaysiaFaculty of Applied Sciences and Technology Universiti Tun Hussein Onn Malaysia (Pagoh Campus), KM1 Jalan Panchor 84600Muar, JohorMalaysia
| | - Salmah Yaakop
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600Bangi, SelangorMalaysia
| | - Shukor Md-Nor
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600Bangi, SelangorMalaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600Bangi, SelangorMalaysia
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Mohd-yusof NS, Abdul-latiff MAB, Mohd-ridwan AR, Badrulisham AS, Othman N, Yaakop S, Md-nor S, Md-zain BM. Figure 8 from: Mohd-Yusof NS, Abdul-Latiff MAB, Mohd-Ridwan AR, Badrulisham AS, Othman N, Yaakop S, Md-Nor S, Md-Zain BM (2022) First report on metabarcoding analysis of gut microbiome in Island Flying Fox (Pteropus hypomelanus) in island populations of Malaysia. Biodiversity Data Journal 10: e69631. https://doi.org/10.3897/BDJ.10.e69631. 2022. [DOI: 10.3897/bdj.10.e69631.figure8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Abdul-Patah P, Sasaki H, Sekiguchi T, Shukor MN, Mohd-Yusof NS, Abdul-Latiff MAB, Md-Zain BM. Correction to: Molecular DNA-based spatial mapping technique predicting diversity and distribution of otters (Lutrinae) in Peninsular Malaysia using non-invasive fecal samples. MAMMAL RES 2022. [DOI: 10.1007/s13364-022-00630-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abdullah-Fauzi NAF, Karuppannan KV, Mohd-Radzi NHS, Gani M, Mohd-Ridwan AR, Othman N, Haris H, Sariyati NH, Aifat NR, Abdul-Latiff MAB, Abdul-Razak MFA, Md-Zain BM. Determining the Dietary Preferences of Wild Asian Elephants ( Elephas maximus) in Taman Negara National Park, Malaysia Based on Sex and Age using trnL DNA Metabarcoding Analysis. Zool Stud 2022; 61:e60. [PMID: 37007822 PMCID: PMC10061209 DOI: 10.6620/zs.2022.61-60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 08/11/2022] [Indexed: 04/04/2023]
Abstract
The world's largest terrestrial mammal, Asian elephants, are known to have enormous feeding needs. Several factors such as season, sex, age, and daily activities influence the amount of food required by an individual. Generally, captive elephants have a limited choice of food on a daily basis compared with that of elephants in the wild. Elephants in captivity are fed according to a prepared feeding schedule, whereas wild elephants are free to choose the type of plants that they consume in their natural habitat. In the past, ecological observations have been widely used to determine the diet of wild elephants. However, the molecular approach has never been carried out. In the present study, we aimed to; 1) identify the plant diet of wild Asian elephants in Taman Negara National Park (TNNP) according to their sex and age using high-throughput DNA metabarcoding; and 2) determine the dietary formulation of captive elephants based on the generated plant metabarcoding database. DNA was extracted from 24 individual fecal samples collected using noninvasive sampling techniques from TNNP and the National Elephant Conservation Centre (NECC) Kuala Gandah. Seven pooled samples from male adult, female adult, male subadult, female subadult, male juvenile, female juvenile, and captive elephants were amplified and sequenced targeting the trnL region (50-150 base pairs). The CLC Genomic Workbench and PAST 4.02 software were used for data analysis. In total, 24 orders, 41 families, 233 genera, and 306 species of plants were successfully detected in the diet of the Asian elephants. The most abundant plant genera consumed were Sporobolus (21.88%), Musa (21.48%), and Ficus (10.80%). Plant variation was lower in samples from male elephants than in those from female elephants. The plant species identified were correlated with the nutrient benefits required by elephants. Adults and subadults consumed more plant species than were consumed by juvenile elephants. However, there was no significant difference between ages and sexes. The findings of this study can be used as guidance by the Department of Wildlife and National Parks for the management of captive elephants, especially in NECC Kuala Gandah.
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Affiliation(s)
- Nurfatiha Akmal Fawwazah Abdullah-Fauzi
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia. E-mail: (Md-Zain); (Abdullah-Fauzi); (Mohd-Radzi)
| | - Kayal Vizi Karuppannan
- Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia. E-mail: (Karuppannan); (Gani); (Abdul-Razak)
| | - Nor Hafisa Syafina Mohd-Radzi
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia. E-mail: (Md-Zain); (Abdullah-Fauzi); (Mohd-Radzi)
| | - Millawati Gani
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia. E-mail: (Md-Zain); (Abdullah-Fauzi); (Mohd-Radzi)
- Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia. E-mail: (Karuppannan); (Gani); (Abdul-Razak)
| | - Abd Rahman Mohd-Ridwan
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia. E-mail: (Md-Zain); (Abdullah-Fauzi); (Mohd-Radzi)
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia. E-mail: (Mohd-Ridwan)
| | - Nursyuhada Othman
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, 84600 Johor, Malaysia. E-mail: (Othman); (Haris); (Sariyati); (Abdul-Latiff)
- Oasis Integrated Group (OIG), Institute for Integrated Engineering (I2E), Universiti Tun Hussein Onn Malaysia, 86400 Parit Raja, Johor, Malaysia
| | - Hidayah Haris
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, 84600 Johor, Malaysia. E-mail: (Othman); (Haris); (Sariyati); (Abdul-Latiff)
- Oasis Integrated Group (OIG), Institute for Integrated Engineering (I2E), Universiti Tun Hussein Onn Malaysia, 86400 Parit Raja, Johor, Malaysia
| | - Nur Hartini Sariyati
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, 84600 Johor, Malaysia. E-mail: (Othman); (Haris); (Sariyati); (Abdul-Latiff)
- Oasis Integrated Group (OIG), Institute for Integrated Engineering (I2E), Universiti Tun Hussein Onn Malaysia, 86400 Parit Raja, Johor, Malaysia
| | - Nor Rahman Aifat
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia. E-mail: (Md-Zain); (Abdullah-Fauzi); (Mohd-Radzi)
- Faculty of Tropical Forestry, Universiti Malaysia Sabah (UMS), Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia. E-mail: (Aifat)
| | - Muhammad Abu Bakar Abdul-Latiff
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, 84600 Johor, Malaysia. E-mail: (Othman); (Haris); (Sariyati); (Abdul-Latiff)
- Oasis Integrated Group (OIG), Institute for Integrated Engineering (I2E), Universiti Tun Hussein Onn Malaysia, 86400 Parit Raja, Johor, Malaysia
| | - Mohd Firdaus Ariff Abdul-Razak
- Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia. E-mail: (Karuppannan); (Gani); (Abdul-Razak)
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia. E-mail: (Md-Zain); (Abdullah-Fauzi); (Mohd-Radzi)
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Najmuddin MF, Haris H, Norazlimi N, Ruslin F, Matsuda I, Md-Zain BM, Abdul-Latiff MAB. Dietary Habits of Free-ranging Banded Langur ( Presbytis femoralis) in a Secondary-human Modified Forest in Johor, Malaysia. Zool Stud 2021; 60:e67. [PMID: 35774255 PMCID: PMC9168899 DOI: 10.6620/zs.2021.60-67] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/09/2021] [Indexed: 06/15/2023]
Abstract
Banded langurs, Presbytis femoralis, are distributed in southern Peninsular Malaysia, i.e., Johor and its borders including Singapore. It has been estimated that there are only < 250 mature individuals of P. femoralis in Malaysia and Singapore, and the species is currently considered Critically Endangered. The dietary information of P. femoralis and even other closely related species has rarely been reported. This study, therefore, aimed to describe the species dietary habits and discuss interaction between their feeding behaviour and its surrounding. This study was conducted from February to November 2018, with 15 sampling days each month. We collected a total of 186 sighting hours, using a scan sampling method with 10-min intervals, on a five-langur focal group. We identified 29 species based on 47 items consumed by the banded langur, mostly young leaves (51%) followed by fruits (45%), and flowers (3.8%). The study group spent slightly more time consuming non-cultivated plants but relied on cultivated plants for the fruits. Over 75% of fruit feeding involved consuming cultivar plants; in most cases (73%), they ate only the pulp, not the seeds. Since the cultivated plants were planted in human settlement, there is an urgent need to implement conservation measures to untangle the human-langur conflicts-for instance, reforestation of a buffer region using non-cultivated plants. There is a potential to build upon our new findings with more detailed investigations, such as more extensive ecological factors influencing the dietary adaptation which would be necessary to support conservation efforts and management decisions of this species.
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Affiliation(s)
- Mohd Faudzir Najmuddin
- Oasis Integrated Group (OIG), Institute for Integrated Engineering (I2E), Universiti Tun Hussein Onn Malaysia, Parit Raja 86400, Johor. E-mail: (Abdul-Latiff); (Najmuddin); (Haris)
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar 84600, Johor, Malaysia, Johor. E-mail: (Norazlimi)
| | - Hidayah Haris
- Oasis Integrated Group (OIG), Institute for Integrated Engineering (I2E), Universiti Tun Hussein Onn Malaysia, Parit Raja 86400, Johor. E-mail: (Abdul-Latiff); (Najmuddin); (Haris)
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar 84600, Johor, Malaysia, Johor. E-mail: (Norazlimi)
| | - Noratiqah Norazlimi
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar 84600, Johor, Malaysia, Johor. E-mail: (Norazlimi)
| | - Farhani Ruslin
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia. E-mail: (Ruslin); (Md-Zain)
| | - Ikki Matsuda
- Chubu University Academy of Emerging Sciences, 1200, Matsumoto-cho, Kasugai-shi, Aichi 487-8501, Japan. E-mail: . ac.jp (Matsuda)
- Wildlife Research Center of Kyoto University, Japan
- Japan Monkey Centre, Japan
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Sabah, Malaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia. E-mail: (Ruslin); (Md-Zain)
| | - Muhammad Abu Bakar Abdul-Latiff
- Oasis Integrated Group (OIG), Institute for Integrated Engineering (I2E), Universiti Tun Hussein Onn Malaysia, Parit Raja 86400, Johor. E-mail: (Abdul-Latiff); (Najmuddin); (Haris)
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar 84600, Johor, Malaysia, Johor. E-mail: (Norazlimi)
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Abdul-Latiff MAB, Md-Zain BM. 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 2021; 60:e50. [PMID: 35003344 PMCID: PMC8685347 DOI: 10.6620/zs.2021.60-50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 06/06/2021] [Indexed: 01/24/2023]
Abstract
The pig-tailed macaque, Macaca nemestrina, which is distributed in Peninsular Malaysia, Thailand, Borneo, and Sumatra, has been the subject of unstable and changing taxonomic entity in the M. nemestrina group. This species is involved with a human-macaque conflict in Malaysia and at the same time played an important role in the ethnozoological culture of Malaysian. Even so, comprehensive phylogenetic, population genetics and biogeographical analysis of M. nemestrina in Malaysia are non-existent after decades of intensive research on the genus itself. Thus, we conducted the first comprehensive genetic study of M. nemestrina in Malaysia, based on three mitochondrial loci-Cytochrome b (567 bp), D-loop (398 bp), and COI (577 bp)-from 27 individuals representing Malaysia, plus an additional 26 sequences of Southeast Asian macaques from Genbank. Comparative biogeographical analysis in this study supports the positions of M. nemestrina in M. nemestrina groups as opposed to the silenus or Sulawesi groups. Results from this study also indicate that Bornean populations are the first extant lineages to separate from the other examined lineages of M. nemestrina, M. leonina, M. pagensis, and M. siberu in Southeast Asia. Molecular clock analysis suggested that M. nemestrina arrived in the Malay Peninsula about 0.32 million years ago (MYA). Our results indicate that the population of pig-tailed macaque from Perak (west Peninsular Malaysia) differs genetically based on all phylogenetic and population genetic analyses. Morphologically, Perak's pig-tailed macaque shows brighter coloration than M. n. nemestrina. Thus, we proposed a new subspecies for Perak's pig-tailed macaque as Macaca nemestrina perakensis distributed in the state of Perak, Peninsular Malaysia. This research helps resolve the taxonomic position and population genetics of pig-tailed macaque in Malaysia, which contribute directly to conservation and management of the species in Malaysia.
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Affiliation(s)
- Muhammad Abu Bakar Abdul-Latiff
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia. E-mail: (Md-Zain); or (Abdul-Latiff
- Oasis Integrated Group (OIG), Institute for Integrated Engineering (I2E), Universiti Tun Hussein Onn Malaysia, 86400 Parit Raja, Johor, Malaysia
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), 84600, Muar, Johor, Malaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia. E-mail: (Md-Zain); or (Abdul-Latiff
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Kamaluddin SN, Matsuda I, Md-Zain BM. Activity Budget and Postural Behaviors in Orangutans on Bukit Merah Orang Utan Island for Assessing Captive Great Ape Welfare. J APPL ANIM WELF SCI 2021; 25:244-255. [PMID: 33843367 DOI: 10.1080/10888705.2021.1910032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Assessments of the welfare status of captive and semi-captive animals often compare how their expression of natural behaviors differs from that of free-ranging conspecifics. From December 2015-2016, we recorded and analyzed the activity budget and postural behaviors of three orangutans in Bukit Merah Orang Utan Island (BMOUI) to evaluate their welfare status. The orangutans' activity budget was dominated by resting (60%), feeding (13%), playing (14%), and moving (9%). Behavioral categories followed a similar trend: resting > feeding > moving > playing, except that the subadult male spent significantly more time playing than the two adults. The most predominant posture was sitting (47.0%), followed by pronograde standing (29.4%), lying (10.5%), and clinging (4.5%). Our results suggest that orangutans on BMOUI engage in less feeding but more resting, and show less postural diversity than free-ranging individuals. We propose that appropriate interventions to shift activity budgets, especially feeding vs. resting, and postural behaviors of captive orangutans toward those found in free-ranging orangutans might be beneficial for their welfare and survival.
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Affiliation(s)
- Siti Norsyuhada Kamaluddin
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Ikki Matsuda
- Chubu University Academy of Emerging Sciences, Kasugai-shi, Aichi, Japan.,Wildlife Research Center of Kyoto University, Kyoto, Japan.,Japan Monkey Centre, Inuyama, Aichi, Japan.,Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia.,Bukit Merah Orang Utan Island Foundation, Perak, Malaysia
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Ampeng A, Liam J, Simpson B, Traelholt C, Md Nor S, Abdan-Saleman MSB, Osman S, Zakaria SA, Md-Zain BM. First Bornean orangutan sighting in Usun Apau National Park, Sarawak. Biodivers Data J 2021; 9:e60753. [PMID: 33531863 PMCID: PMC7846550 DOI: 10.3897/bdj.9.e60753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/15/2021] [Indexed: 11/12/2022] Open
Abstract
Wildlife surveys were conducted in Usun Apau National Park (UANP), Sarawak from Oct 2017 to Oct 2020. This was the first attempt to document fauna diversity in Usun Apau National Park on the UANP plateau at 1200-1400 m a.s.l. On 17 September 2020, 10 AM, we observed an orangutan individual, Pongo pygmaeus, over a period of one minute at Libut Camp UANP (E: 114039'.546, N: 2052'36.44) at 1,020 m a.s.l. We also recorded four nests and orangutan vocalisation twice. This observation is important for Bornean orangutan conservation as this was the first orangutan sighting in UANP and well outside the species distribution range for in Sarawak.
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Affiliation(s)
- Ahmad Ampeng
- Sarawak Forest Department, Petra Jaya, Kuching, Malaysia Sarawak Forest Department, Petra Jaya Kuching Malaysia
| | - Jack Liam
- Sarawak Forest Department, Petra Jaya, Kuching, Malaysia Sarawak Forest Department, Petra Jaya Kuching Malaysia
| | - Boyd Simpson
- Copenhagen Zoo, Department of Research & Conservation, Frederiksberg, Denmark Copenhagen Zoo, Department of Research & Conservation Frederiksberg Denmark
| | - Carl Traelholt
- Copenhagen Zoo, Department of Research & Conservation, Frederiksberg, Denmark Copenhagen Zoo, Department of Research & Conservation Frederiksberg Denmark
| | - Shukor Md Nor
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia Bangi, Selangor Malaysia
| | | | - Syafiani Osman
- Sarawak Forest Department, Petra Jaya, Kuching, Malaysia Sarawak Forest Department, Petra Jaya Kuching Malaysia
| | - Shaffeqe Affendy Zakaria
- Sarawak Forest Department, Petra Jaya, Kuching, Malaysia Sarawak Forest Department, Petra Jaya Kuching Malaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia Bangi, Selangor Malaysia
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Abdul-Patah P, Sasaki H, Sekiguchi T, Shukor MN, Mohd-Yusof NS, Abdul-Latiff MAB, Md-Zain BM. Molecular DNA-based spatial mapping technique predicting diversity and distribution of otters (Lutrinae) in Peninsular Malaysia using non-invasive fecal samples. MAMMAL RES 2020. [DOI: 10.1007/s13364-020-00532-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Najmuddin MF, Haris H, Othman N, Zahari F, Mohd-Ridwan AR, Md-Zain BM, Shahrool-Anuar R, Ayeb O, Othman I, Abdul-Latiff MAB. Data on First Record of Brown Morph Banded Langur ( Presbytis femoralis), Leucistic Dusky Leaf Monkey ( Trachypithecus obscurus) in Malaysia and Review of Morph Diversity in Langur (Colobinae). Data Brief 2020; 31:105727. [PMID: 32548216 PMCID: PMC7284059 DOI: 10.1016/j.dib.2020.105727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 11/25/2022] Open
Abstract
Morphism refer to polymorphic species, in which multiple colour variants coexist within a population. Morphism in primates is common and langurs also exhibit certain characteristics of morphism, such as conspicuous natal coats. Banded langurs (Presbytis femoralis) and dusky leaf monkey (Trachypithecus obscurus) exhibits the same characteristics of conspicuous natal coats, but these coats are only limited to infants and changed when they reached adulthood. This article reports the first discovery of rare brown morph of two adult male banded langurs and one leucistic adult female dusky leaf monkey in Malaysia. We also conducted a systematic literature search to review the diversity of morphism in leaf monkey globally.
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Affiliation(s)
- Mohd Faudzir Najmuddin
- Centre of Research for Sustainable Uses of Natural Resources, Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh campus), KM 1, Jalan Panchor, 84600 Muar, Johor, Malaysia
| | - Hidayah Haris
- Centre of Research for Sustainable Uses of Natural Resources, Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh campus), KM 1, Jalan Panchor, 84600 Muar, Johor, Malaysia
| | - Nursyuhada Othman
- Centre of Research for Sustainable Uses of Natural Resources, Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh campus), KM 1, Jalan Panchor, 84600 Muar, Johor, Malaysia
| | - Fatin Zahari
- Centre of Research for Sustainable Uses of Natural Resources, Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh campus), KM 1, Jalan Panchor, 84600 Muar, Johor, Malaysia
| | - Abd Rahman Mohd-Ridwan
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia.,Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, 43600 Bangi, Malaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, 43600 Bangi, Malaysia
| | - Rohani Shahrool-Anuar
- Panz village, Lot 147 Lorong Bahtera, Kg Johor Lama, 81940 Kota Tinggi, Johor, Malaysia
| | - Othman Ayeb
- Rimbawi Geo Discovery, No 109A, Kg Kubang Badak, Mukim Ayer Hangat, 07000 Pulau Langkawi, Malaysia
| | - Iqramullah Othman
- Rimbawi Geo Discovery, No 109A, Kg Kubang Badak, Mukim Ayer Hangat, 07000 Pulau Langkawi, Malaysia
| | - Muhammad Abu Bakar Abdul-Latiff
- Centre of Research for Sustainable Uses of Natural Resources, Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh campus), KM 1, Jalan Panchor, 84600 Muar, Johor, Malaysia
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23
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Rosli N, Sitam FT, Rovie-Ryan JJ, Gan HM, Lee YP, Hartini Ithnin, Millawati Gani, Mohd Firdaus Ariff Abdul Razak, Md-Zain BM, Abdullah MT. The complete mitochondrial genome of Malayan Gaur ( Bos gaurus hubbacki) from Peninsular Malaysia. Mitochondrial DNA B Resour 2019; 4:2535-2536. [PMID: 33365614 PMCID: PMC7706526 DOI: 10.1080/23802359.2019.1640085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Here, we present the first complete mitochondrial genome of Malayan Gaur (Bos gaurus hubbacki) inferred using next-generation sequencing. The mitogenome is 16,367 bp in length with the structural organization of a typical bovine mitochondrial arrangement comprising 13 protein-coding genes, 21 tRNAs, and 2 rRNAs. No internal stop codon was found in the protein-coding genes. Phylogenetic tree analysis revealed that Malayan gaur is more closely related to Burmese banteng instead of gaur.
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Affiliation(s)
- Norsyamimi Rosli
- National Wildlife Forensic Laboratory (NWFL), Department of Wildlife and National Parks, Kuala Lumpur, Malaysia.,Institute of Tropical Biodiversity and Sustainable Development, Faculty of Science and Technology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Frankie Thomas Sitam
- National Wildlife Forensic Laboratory (NWFL), Department of Wildlife and National Parks, Kuala Lumpur, Malaysia.,Institute of Tropical Biodiversity and Sustainable Development, Faculty of Science and Technology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Jeffrine Japning Rovie-Ryan
- National Wildlife Forensic Laboratory (NWFL), Department of Wildlife and National Parks, Kuala Lumpur, Malaysia.,Institute of Tropical Biodiversity and Sustainable Development, Faculty of Science and Technology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Han Ming Gan
- Department of Genomics Facility, Monash University Malaysia, Selangor, Malaysia.,School of Life & Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Australia
| | - Yin Peng Lee
- Department of Genomics Facility, Monash University Malaysia, Selangor, Malaysia.,School of Life & Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Australia
| | - Hartini Ithnin
- National Wildlife Forensic Laboratory (NWFL), Department of Wildlife and National Parks, Kuala Lumpur, Malaysia
| | - Millawati Gani
- National Wildlife Forensic Laboratory (NWFL), Department of Wildlife and National Parks, Kuala Lumpur, Malaysia
| | | | - Badrul Munir Md-Zain
- School of Environment and Natural Resource Sciences, Faculty of Sciences and Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Mohd Tajuddin Abdullah
- Institute of Tropical Biodiversity and Sustainable Development, Faculty of Science and Technology, Universiti Malaysia Terengganu, Terengganu, Malaysia.,School of Marine and Environmental Sciences, Universiti Malaysia Terengganu, Terengganu, Malaysia
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24
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Md-Zain BM, Abdul-Aziz A, Aifat NR, Mohd-Yusof NS, Zulkifli NA, Japning JRR, Rosli N, Yaakop S. Sequence variation data of the mitochondrial DNA D-loop region of the captive Malayan Gaur ( Bos gaurus hubbacki). Data Brief 2019; 24:103532. [PMID: 31193484 PMCID: PMC6531834 DOI: 10.1016/j.dib.2018.11.117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 11/20/2018] [Accepted: 11/22/2018] [Indexed: 11/18/2022] Open
Abstract
This article contains data of the sequence variation in the mitochondrial DNA D-loop region of the Malayan gaur (Bos gaurus hubbacki), locally known as the seladang, from two captive centers. Thirty fecal samples of Malayan gaur were collected from Jenderak Selatan Wildlife Conservation Center (Pahang) and the Sungkai Wildlife Reserve (Perak) for DNA extraction and amplification with polymerase chain reactions. DNA sequences were then analyzed using neighbor joining (NJ) and maximum parsimony (MP) methods. Based on the 652 base pairs obtained, we found seven variable characters with a value of 1%. The genetic distance between the two captive centers was 0.001. Haplotype analyses detected only four haplotypes between these two captive centers. Both NJ and MP trees demonstrate that all individuals in the Jenderak and Sungkai captive centers are in the same clade. Genetic variation of the Malayan gaur in these centers is considered low, possibly because individuals share the same common parent. This sequence variation data are of paramount importance for designing a proper breeding and management program of the Malayan gaur in the future.
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Affiliation(s)
- Badrul Munir Md-Zain
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
- Corresponding author.
| | - Aqilah Abdul-Aziz
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Nor Rahman Aifat
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Nur Syafika Mohd-Yusof
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Nadiatur Akmar Zulkifli
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | | | - Norsyamimi Rosli
- Department of Wildlife and National Parks (DWNP), KM10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia
| | - Salmah Yaakop
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
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25
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Nadia AS, Md-Zain BM, Dharmalingam S, Fairuz A, Hani-Kartini A. Serological survey of Leptospirosis in high-risk rangers and wild animals from ex-situ captive centers. Trop Biomed 2019; 36:443-452. [PMID: 33597405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Leptospirosis is a bacterial disease caused by pathogenic Leptospira that infect both human and animals. This study was conducted to determine the seroprevalence of leptospirosis among rangers and wild animals in two ex-situ captive centers, Bukit Merah Orangutan Island (BMOUI) and Taiping Zoo, Perak and to identify the risk factors responsible for the leptospiral seropositivity. Blood samples from rangers and animals of BMOUI and Taiping Zoo were taken to determine the presence of antibodies against Leptospira through microscopic agglutination test (MAT) using 21 serovars of Leptospira commonly found in Malaysia as antigens. Structured surveys in identifying risk factors were given to each ranger from both study sites. It was observed that Rattus exulans (1/10) (10.0%), Rattus rattus (1/5) (20.0%), Niniventer fulvescens (1/1) (100.0%), Callosciurus notatus (0/6) (0.0%), Tupaia tana (1/1) (100.0%), Pongo pygmaeus (5/10) (50.0%) and BMOUI rangers (8/18) (44.4%) were positive for leptospiral antibodies. Samples obtained from Taiping Zoo also revealed the presence of leptospiral antibodies in R. rattus (0/19) (0.0%), R. exulans (1/2) (50.0%) and rangers (2/5) (40.0%). Among the positive cases, most human and animal samples from both study sites reacted with serovar Lepto 175. Our surveys indicated no significant associations between seroprevalence of leptospiral antibodies with rangers' age (p = 0.82), sex (p = 0.85), ethnicity (p = 0.65), educational level (p = 0.88) and working experience (p = 0.82). In terms of risk factors, no significant associations between seroprevalence of leptospiral antibodies with knowledge on leptospirosis (p = 0.82), working hours (p = 0.53), smoking (p = 0.85), crossing rivers/pools/stagnant water while working (p = 0.90) and wearing full personal protective equipment (PPE) (p = 0.73). This study provides epidemiological data on leptospirosis in rangers and animals from BMOUI and Taiping Zoo which is of paramount importance for improving strategies in prevention of the disease.
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Affiliation(s)
- A S Nadia
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600 Selangor, Malaysia
| | - B M Md-Zain
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600 Selangor, Malaysia
| | - S Dharmalingam
- Bukit Merah Orang Utan Island Foundation, Semanggol, Taiping, Perak, Malaysia
| | - A Fairuz
- Bacteriology Department, Institute for Medical Research, Kuala Lumpur, Malaysia
| | - A Hani-Kartini
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600 Selangor, Malaysia
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Abdul-Latiff MAB, Baharuddin H, Abdul-Patah P, Md-Zain BM. 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 2018; 60:63-79. [PMID: 30471014 DOI: 10.1007/s10329-018-0699-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 11/08/2018] [Indexed: 11/26/2022]
Abstract
The disjunct distribution of Presbytis femoralis subspecies across Sumatra (P. f. percura), southern (P. f. femoralis) and northern (P. f. robinsoni) Peninsular Malaysia marks the unique vicariance events in the Sunda Shelf. However, the taxonomic positions and evolutionary history of P. f. femoralis are unresolved after decades of research. To elucidate this evolutionary history, we analyzed 501 base pairs of the mitochondrial HVSI gene from 25 individuals representing Malaysia's banded langur, with the addition of 29 sequences of Asian Presbytis from Genbank. Our results revealed closer affinity of P. f. femoralis to P. m. mitrata and P. m. sumatrana while maintaining the monophyletic state of P. f. femoralis as compared to P. f. robinsoni. Two central theses were inferred from the results; (1) P. f. femoralis does not belong in the same species classification as P. f. robinsoni, and (2) P. f. femoralis is the basal lineage of the Presbytis in Peninsular Malaysia. Proving the first hypothesis through genetic analysis, we reassigned P. f. femoralis of Malaysia to Presbytis neglectus (Schlegel's banded langur) (Schlegel in Revue Methodique, Museum d'Histoire Naturelle des Pays-Bas 7:1, 1876) following the International Code of Zoological Nomenclature (article 23.3). The ancestors of P. neglectus are hypothesized to have reached southern Peninsular Malaysia during the Pleistocene and survived in refugium along the western coast. Consequently, they radiated upward, forming P. f. robinsoni and P. siamensis resulting in the highly allopatric distribution in Peninsular Malaysia. This study has successfully resolved the taxonomic position of P. neglectus in Peninsular Malaysia while providing an alternative biogeographic theory for the Asian Presbytis.
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Affiliation(s)
- Muhammad Abu Bakar Abdul-Latiff
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- Centre of Research for Sustainable Uses of Natural Resources (CoR-SUNR), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), KM1, Jalan Panchor, 84600, Muar, Johor, Malaysia
| | - Hanisah Baharuddin
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Pazil Abdul-Patah
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- Biodiversity Conservation Division, Department of Wildlife and National Parks (DWNP), KM10 Jalan Cheras, 56100, Kuala Lumpur, Malaysia
| | - Badrul Munir Md-Zain
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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Mohd Yussup SS, Marzukhi M, Md-Zain BM, Mamat K, Mohd Yusof FZ. Polymorphism of 11 Y Chromosome Short Tandem Repeat Markers among Malaysian Aborigines. Evol Bioinform Online 2017; 13:1176934317735318. [PMID: 29085238 PMCID: PMC5648092 DOI: 10.1177/1176934317735318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 08/23/2017] [Indexed: 12/02/2022] Open
Abstract
The conventional technique such as patrilocality suggests some substantial effects on population diversity. With that, this particular study investigated the paternal line, specifically Scientific Working Group on DNA Analysis Methods (SWGDAM)-recommended Y-STR markers, namely, DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS438, and DYS439. These markers were tested to compare 184 Orang Asli individuals from 3 tribes found in Peninsular Malaysia. As a result, the haplotype diversity and the discrimination capacity obtained were 0.9987 and 0.9076, respectively. Besides, the most diverse marker was DYS385b, whereas the least was DYS391. Furthermore, the Senoi and Proto-Malay tribes were found to be the most distant, whereas the Senoi and Negrito clans were almost similar to each other. In addition, the analysis of molecular variance analysis revealed 82% of variance within the population, but only 18% of difference between the tribes. Finally, the phylogenetic trees constructed using Neighbour Joining and UPGMA (Unweighted Pair Group Method with Arithmetic Mean) displayed several clusters that were tribe specific. With that, future studies are projected to analyse individuals based on more specific sub-tribes.
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Affiliation(s)
| | - Marlia Marzukhi
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam, Malaysia
| | - Badrul Munir Md-Zain
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Kamaruddin Mamat
- Faculty of Computer and Mathematical Sciences, Universiti Teknologi MARA (UiTM), Shah Alam, Malaysia
| | - Farida Zuraina Mohd Yusof
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam, Malaysia.,Integrative Pharmacogenomics Institute (iPROMISE), Bandar Puncak Alam, Malaysia
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Liedigk R, Kolleck J, Böker KO, Meijaard E, Md-Zain BM, Abdul-Latiff MAB, Ampeng A, Lakim M, Abdul-Patah P, Tosi AJ, Brameier M, Zinner D, Roos C. Mitogenomic phylogeny of the common long-tailed macaque (Macaca fascicularis fascicularis). BMC Genomics 2015; 16:222. [PMID: 25887664 PMCID: PMC4371801 DOI: 10.1186/s12864-015-1437-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/06/2015] [Indexed: 12/31/2022] Open
Abstract
Background Long-tailed macaques (Macaca fascicularis) are an important model species in biomedical research and reliable knowledge about their evolutionary history is essential for biomedical inferences. Ten subspecies have been recognized, of which most are restricted to small islands of Southeast Asia. In contrast, the common long-tailed macaque (M. f. fascicularis) is distributed over large parts of the Southeast Asian mainland and the Sundaland region. To shed more light on the phylogeny of M. f. fascicularis, we sequenced complete mitochondrial (mtDNA) genomes of 40 individuals from all over the taxon’s range, either by classical PCR-amplification and Sanger sequencing or by DNA-capture and high-throughput sequencing. Results Both laboratory approaches yielded complete mtDNA genomes from M. f. fascicularis with high accuracy and/or coverage. According to our phylogenetic reconstructions, M. f. fascicularis initially diverged into two clades 1.70 million years ago (Ma), with one including haplotypes from mainland Southeast Asia, the Malay Peninsula and North Sumatra (Clade A) and the other, haplotypes from the islands of Bangka, Java, Borneo, Timor, and the Philippines (Clade B). The three geographical populations of Clade A appear as paraphyletic groups, while local populations of Clade B form monophyletic clades with the exception of a Philippine individual which is nested within the Borneo clade. Further, in Clade B the branching pattern among main clades/lineages remains largely unresolved, most likely due to their relatively rapid diversification 0.93-0.84 Ma. Conclusions Both laboratory methods have proven to be powerful to generate complete mtDNA genome data with similarly high accuracy, with the DNA-capture and high-throughput sequencing approach as the most promising and only practical option to obtain such data from highly degraded DNA, in time and with relatively low costs. The application of complete mtDNA genomes yields new insights into the evolutionary history of M. f. fascicularis by providing a more robust phylogeny and more reliable divergence age estimations than earlier studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1437-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rasmus Liedigk
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany.
| | - Jakob Kolleck
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany.
| | - Kai O Böker
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany. .,Junior Research Group Medical RNA Biology, Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany.
| | - Erik Meijaard
- Borneo Futures Project, People & Nature Consulting International, Country Woods house 306, JL. WR Supratman, Pondok Ranji, Ciputat, 15412, Jakarta, Indonesia. .,School of Archaeology & Anthropology, Building 14, Australian National University, Canberra, ACT 0200, Australia. .,School of Biological Sciences, University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Badrul Munir Md-Zain
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
| | - Muhammad Abu Bakar Abdul-Latiff
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
| | - Ahmad Ampeng
- Sarawak Forest Department Hq, Wisma Sumber Alam Jalan Stadium, 93660, Petra Jaya Kuching, Sarawak, Malaysia.
| | - Maklarin Lakim
- Sabah Parks, Research and Education Division, PO Box 10626, 88806, Kota Kinabalu, Sabah, Malaysia.
| | - Pazil Abdul-Patah
- Department of Wildlife and National Parks, Km 10, Jalan Cheras, 50664, Kuala Lumpur, Malaysia.
| | - Anthony J Tosi
- Department of Anthropology, Kent State University, 238 Lowry Hall, Kent, OH, 44242, USA.
| | - Markus Brameier
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany.
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany.
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany. .,Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany.
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29
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Abdul-Latiff MAB, Ruslin F, Fui VV, Abu MH, Rovie-Ryan JJ, Abdul-Patah P, Lakim M, Roos C, Yaakop S, Md-Zain BM. Phylogenetic relationships of Malaysia's long-tailed macaques, Macaca fascicularis, based on cytochrome b sequences. Zookeys 2014:121-40. [PMID: 24899832 PMCID: PMC4042704 DOI: 10.3897/zookeys.407.6982] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 04/22/2014] [Indexed: 12/03/2022] Open
Abstract
Phylogenetic relationships among Malaysia’s long-tailed macaques have yet to be established, despite abundant genetic studies of the species worldwide. The aims of this study are to examine the phylogenetic relationships of Macaca fascicularis in Malaysia and to test its classification as a morphological subspecies. A total of 25 genetic samples of M. fascicularis yielding 383 bp of Cytochrome b (Cyt b) sequences were used in phylogenetic analysis along with one sample each of M. nemestrina and M. arctoides used as outgroups. Sequence character analysis reveals that Cyt b locus is a highly conserved region with only 23% parsimony informative character detected among ingroups. Further analysis indicates a clear separation between populations originating from different regions; the Malay Peninsula versus Borneo Insular, the East Coast versus West Coast of the Malay Peninsula, and the island versus mainland Malay Peninsula populations. Phylogenetic trees (NJ, MP and Bayesian) portray a consistent clustering paradigm as Borneo’s population was distinguished from Peninsula’s population (99% and 100% bootstrap value in NJ and MP respectively and 1.00 posterior probability in Bayesian trees). The East coast population was separated from other Peninsula populations (64% in NJ, 66% in MP and 0.53 posterior probability in Bayesian). West coast populations were divided into 2 clades: the North-South (47%/54% in NJ, 26/26% in MP and 1.00/0.80 posterior probability in Bayesian) and Island-Mainland (93% in NJ, 90% in MP and 1.00 posterior probability in Bayesian). The results confirm the previous morphological assignment of 2 subspecies, M. f. fascicularis and M. f. argentimembris, in the Malay Peninsula. These populations should be treated as separate genetic entities in order to conserve the genetic diversity of Malaysia’s M. fascicularis. These findings are crucial in aiding the conservation management and translocation process of M. fascicularis populations in Malaysia.
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Affiliation(s)
- Muhammad Abu Bakar Abdul-Latiff
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Farhani Ruslin
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Vun Vui Fui
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia ; UCSI University, 1, Jalan Menara Gading, UCSI Heights, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Mohd-Hashim Abu
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | | | - Pazil Abdul-Patah
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia ; Department of Wildlife and National Parks, Km 10, Jalan Cheras, 50664, Kuala Lumpur, Malaysia
| | - Maklarin Lakim
- Sabah Parks, Research and Education Division, PO Box 10626, 88806, Kota Kinabalu, Sabah, Malaysia
| | - Christian Roos
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Salmah Yaakop
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Badrul Munir Md-Zain
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
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Shariff S, Ibrahim NJ, Md-Zain BM, Idris AB, Suhana Y, Roff MN, Yaakop S. Multiplex PCR in determination of Opiinae parasitoids of fruit flies, Bactrocera sp., infesting star fruit and guava. J Insect Sci 2014; 14:7. [PMID: 25373154 PMCID: PMC4199358 DOI: 10.1093/jis/14.1.7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 10/11/2012] [Indexed: 06/04/2023]
Abstract
Malaysia is a tropical country that produces commercial fruits, including star fruits, Averrhoa carambola L. (Oxalidales: Oxalidaceae), and guavas, Psidium guajava L. (Myrtales: Myrtaceae). There is a high demand for these fruits, and they are planted for both local consumption and export purposes. Unfortunately, there has been a gradual reduction of these fruits, which has been shown to be related to fruit fly infestation, especially from the Bactrocera species. Most parasitic wasps (Hymenoptera: Braconidae: Opiinae) are known as parasitoids of fruit fly larvae. In this study, star fruits and guavas infested by fruit fry larvae were collected from the Malaysian Agricultural Research and Development Institute. The parasitized larvae were reared under laboratory conditions until the emergence of adult parasitoids. Multiplex PCR was performed to determine the braconid species using two mitochondrial DNA markers, namely cytochrome oxidase subunit I and cytochrome b. Two benefits of using multiplex PCR are the targeted bands can be amplified simultaneously using the same reaction and the identification process of the braconid species can be done accurately and rapidly. The species of fruit flies were confirmed using the COI marker. The results obtained from our study show that Diachasmimorpha longicaudata (Ashmead) (Hymenoptera: Braconidae), Fopius arisanus (Sonan), and Pysttalia incisi (Silvestri) were parasitoids associated with Bactrocera carambolae (Drew and Hancock) (Diptera: Tephritidae) infested star fruits. Fopius arisanus was also the parasitoid associated with Bactrocera papayae (Drew and Hancock) infested guavas. Maximum parsimony was been constructed in Opiinae species to compare tree resolution between these two genes in differentiating among closely related species. The confirmation of the relationship between braconids and fruit fly species is very important, recognized as preliminary data, and highly necessary in biological control programs.
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Affiliation(s)
- S Shariff
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, University Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - N J Ibrahim
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, University Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - B M Md-Zain
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, University Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - A B Idris
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, University Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Y Suhana
- Horticulture Research Centre, Malaysian Agricultural Research and Development Institute (MARDI), 43400 Serdang, Selangor, Malaysia
| | - M N Roff
- Horticulture Research Centre, Malaysian Agricultural Research and Development Institute (MARDI), 43400 Serdang, Selangor, Malaysia
| | - S Yaakop
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, University Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
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31
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Romaino SMN, Fazly-Ann ZA, Loo SS, Hafiz MM, Hafiz MD, Iswadi MI, Kashiani P, Rosli MKA, Syed-Shabthar SMF, Md-Zain BM, Abas-Mazni O. Species identification of Malayan Gaur, Kedah-Kelantan and Bali cattle using polymerase chain reaction-restricted fragment length polymorphism. Genet Mol Res 2014; 13:406-14. [PMID: 24535867 DOI: 10.4238/2014.january.21.8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Mitochondrial DNA (mtDNA) is a useful genetic marker that can be used for species identification. The cytochrome b (Cyt b) gene is a suitable mtDNA candidate gene for use in phylogenetic analyses due to its sequence variability, which makes it appropriate for comparisons at the subspecies, species, and genus levels. This study was conducted to develop a rapid molecular method for species identification of Malayan gaur (Bos gaurus hubbacki), Kedah-Kelantan (KK) (Bos indicus), and Bali (Bos javanicus) cattle in Malaysia. DNA was extracted from blood samples of 8 Malayan gaurs, 30 KK, and 28 Bali cattle. A set of both specific and universal primers for the Cyt b gene were used in PCR amplification. DNA sequences obtained were then analyzed using BioEdit and Restriction Mapper softwares. The PCR products obtained from Cyt b gene amplification were then subjected to restriction enzyme digestion. The amplification, using both specific and universal primers, produced a 154- and a 603-bp fragment, respectively, in all three species. Two restriction enzymes, NlaIV and SspI, were used to obtain specific restriction profiles that allowed direct identification of Malayan gaur, KK, and Bali cattle. Our findings indicate that all three species can be identified separately using a combination of universal primers and the restriction enzyme SspI.
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Affiliation(s)
- S M N Romaino
- Agro-Biotechnology Institute, Malaysia (ABI), Serdang, Selangor, Malaysia
| | - Z A Fazly-Ann
- Agro-Biotechnology Institute, Malaysia (ABI), Serdang, Selangor, Malaysia
| | - S S Loo
- Agro-Biotechnology Institute, Malaysia (ABI), Serdang, Selangor, Malaysia
| | - M M Hafiz
- Agro-Biotechnology Institute, Malaysia (ABI), Serdang, Selangor, Malaysia
| | - M D Hafiz
- Agro-Biotechnology Institute, Malaysia (ABI), Serdang, Selangor, Malaysia
| | - M I Iswadi
- Agro-Biotechnology Institute, Malaysia (ABI), Serdang, Selangor, Malaysia
| | - P Kashiani
- Agro-Biotechnology Institute, Malaysia (ABI), Serdang, Selangor, Malaysia
| | - M K A Rosli
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - S M F Syed-Shabthar
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - B M Md-Zain
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - O Abas-Mazni
- Agro-Biotechnology Institute, Malaysia (ABI), Serdang, Selangor, Malaysia
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Syed-Shabthar SMF, Rosli MKA, Mohd-Zin NAA, Romaino SMN, Fazly-Ann ZA, Mahani MC, Abas-Mazni O, Zainuddin R, Yaakop S, Md-Zain BM. The molecular phylogenetic signature of Bali cattle revealed by maternal and paternal markers. Mol Biol Rep 2013; 40:5165-76. [PMID: 23686165 DOI: 10.1007/s11033-013-2619-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 04/30/2013] [Indexed: 11/28/2022]
Abstract
Bali cattle is a domestic cattle breed that can be found in Malaysia. It is a domestic cattle that was purely derived from a domestication event in Banteng (Bos javanicus) around 3,500 BC in Indonesia. This research was conducted to portray the phylogenetic relationships of the Bali cattle with other cattle species in Malaysia based on maternal and paternal lineage. We analyzed the cytochrome c oxidase I (COI) mitochondrial gene and SRY of Y chromosome obtained from five species of the Bos genus (B. javanicus, Bos gaurus, Bos indicus, Bos taurus, and Bos grunniens). The water buffalo (Bubalus bubalis) was used as an outgroup. The phylogenetic relationships were observed by employing several algorithms: Neighbor-Joining (PAUP version 4.0), Maximum parsimony (PAUP version 4.0) and Bayesian inference (MrBayes 3.1). Results from the maternal data showed that the Bali cattle formed a monophyletic clade, and together with the B. gaurus clade formed a wild cattle clade. Results were supported by high bootstrap and posterior probability values together with genetic distance data. For the paternal lineage, the sequence variation is low (with parsimony informative characters: 2/660) resulting an unresolved Neighbor-Joining tree. However, Bali cattle and other domestic cattle appear in two monophyletic clades distinct from yak, gaur and selembu. This study expresses the potential of the COI gene in portraying the phylogenetic relationships between several Bos species which is important for conservation efforts especially in decision making since cattle is highly bred and hybrid breeds are often formed. Genetic conservation for this high quality beef cattle breed is important by maintaining its genetic characters to prevent extinction or even decreased the genetic quality.
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Affiliation(s)
- S M F Syed-Shabthar
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
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33
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Ampeng A, Md-Zain BM. Ranging patterns of critically endangered colobine, Presbytis chrysomelas chrysomelas. ScientificWorldJournal 2012; 2012:594382. [PMID: 22536146 PMCID: PMC3317630 DOI: 10.1100/2012/594382] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 12/08/2011] [Indexed: 11/17/2022] Open
Abstract
Presbytis chrysomelas chrysomelas endemic only in Sarawak and Kalimantan was categorized by IUCN as a critically endangered primate that require special attention from research and conservation perspectives. A qualitative study on ranging patterns of P. c. chrysomelas was conducted in the Samunsam Wildlife Sanctuary, Sarawak. The study was conducted over a period of 13 months from December 2004 to December 2005 with 213 days of observation. Behavioural observation covered 17 groups with special emphasis on two main groups and 1 subadult group. Scanning and focal sampling were employed as the observation methods. Results indicated that P. c. chrysomelas had vertical, straight horizontal, and cross-horizontal types of movement patterns. P. c. chrysomelas was recorded to have a short movement distance (31.8–54.3 m). Distribution, abundance types, and food resources might be the factors that shaped the patterns of movement and distance in P. c. chrysomelas.
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Affiliation(s)
- Ahmad Ampeng
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, 43600 Bangi, Malaysia
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34
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Rosli MKA, Zamzuriada AS, Syed-Shabthar SMF, Mahani MC, Abas-Mazni O, Md-Zain BM. Optimization of PCR conditions to amplify Cyt b, COI and 12S rRNA gene fragments of Malayan gaur (Bos gaurus hubbacki) mtDNA. Genet Mol Res 2011; 10:2554-68. [PMID: 22033937 DOI: 10.4238/2011.october.19.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
PCR has been extensively used for amplification of DNA sequences. We conducted a study to obtain the best amplification conditions for cytochrome b (Cyt b), cytochrome c oxidase I (COI) and 12S rRNA (12S) gene fragments of Malayan gaur mtDNA. DNA from seven Malayan gaur samples were extracted for PCR amplification. Various trials and combinations were tested to determine the best conditions of PCR mixture and profile to obtain the best PCR products for sequencing purposes. Four selected target factors for enhancing PCR, annealing temperature, concentration of primer pairs, amount of Taq polymerase, and PCR cycle duration, were optimized by keeping the amount of DNA template (50 ng/μL) and concentration of PCR buffer (1X), MgCl(2) (2.5 mM) and dNTP mixture (200 μM each) constant. All genes were successfully amplified, giving the correct fragment lengths, as assigned for both forward and reverse primers. The optimal conditions were determined to be: 0.1 μM primers for Cyt b and COI, 0.3 μM primers for 12S, 1 U Taq polymerase for all genes, 30 s of both denaturation and annealing cycles for Cyt b, 1 min of both stages for 12S and COI and annealing temperature of 58.4 ° C for Cyt b, 56.1 ° C for 12S and 51.3 ° C for COI. PCR products obtained under these conditions produced excellent DNA sequences.
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Affiliation(s)
- M K A Rosli
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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35
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Ang KC, Leow JWH, Yeap WK, Hood S, Mahani MC, Md-Zain BM. Phylogenetic relationships of the Orang Asli and Iban of Malaysia based on maternal markers. Genet Mol Res 2011; 10:640-9. [PMID: 21491374 DOI: 10.4238/vol10-2gmr1011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Malaysia remains as a crossroad of different cultures and peoples, and it has long been recognized that studying its population history can provide crucial insight into the prehistory of Southeast Asia as a whole. The earliest inhabitants were the Orang Asli in Peninsular Malaysia and the indigenous groups in Sabah and Sarawak. Although they were the earliest migrants in this region, these tribes are divided geographically by the South China Sea. We analyzed DNA sequences of 18 Orang Asli using mitochondrial DNA extracted from blood samples, each representing one sub-tribe, and from five Sarawakian Iban. Mitochondrial DNA was extracted from hair samples in order to examine relationships with the main ethnic groups in Malaysia. The D-loop region and cytochrome b genes were used as the candidate loci. Phylogenetic relationships were investigated using maximum parsimony and neighbor joining algorithms, and each tree was subjected to bootstrap analysis with 1000 replicates. Analyses of the HVS I region showed that the Iban are not a distinct group from the Orang Asli; they form a sub-clade within the Orang Asli. Based on the cytochrome b gene, the Iban clustered with the Orang Asli in the same clade. We found evidence for considerable gene flow between Orang Asli and Iban. We concluded that the Orang Asli, Iban and the main ethnic groups of Malaysia are probably derived from a common ancestor. This is in agreement with a single-route migration theory, but it does not dismiss a two-route migration theory.
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Affiliation(s)
- K C Ang
- School of Environment and Natural Resource Science, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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36
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Rosli MKA, Zakaria SS, Syed-Shabthar SMF, Zainal ZZ, Shukor MN, Mahani MC, Abas-Mazni O, Md-Zain BM. Phylogenetic relationships of Malayan gaur with other species of the genus Bos based on cytochrome b gene DNA sequences. Genet Mol Res 2011; 10:482-93. [PMID: 21476194 DOI: 10.4238/vol10-1gmr1002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The Malayan gaur (Bos gaurus hubbacki) is one of the three subspecies of gaurs that can be found in Malaysia. We examined the phylogenetic relationships of this subspecies with other species of the genus Bos (B. javanicus, B. indicus, B. taurus, and B. grunniens). The sequence of a key gene, cytochrome b, was compared among 20 Bos species and the bongo antelope, used as an outgroup. Phylogenetic reconstruction was employed using neighbor joining and maximum parsimony in PAUP and Bayesian inference in MrBayes 3.1. All tree topologies indicated that the Malayan gaur is in its own monophyletic clade, distinct from other species of the genus Bos. We also found significant branching differences in the tree topologies between wild and domestic cattle.
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Affiliation(s)
- M K A Rosli
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
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37
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Vun VF, Mahani MC, Lakim M, Ampeng A, Md-Zain BM. Phylogenetic relationships of leaf monkeys (Presbytis; Colobinae) based on cytochrome b and 12S rRNA genes. Genet Mol Res 2011; 10:368-81. [PMID: 21365553 DOI: 10.4238/vol10-1gmr1048] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Little is known about the classification and phylogenetic relationships of the leaf monkeys (Presbytis). We analyzed mitochondrial DNA sequences of cytochrome b (Cyt b) and 12S rRNA to determine the phylogenetic relationships of the genus Presbytis. Gene fragments of 388 and 371 bp of Cyt b and 12S rRNA, respectively, were sequenced from samples of Presbytis melalophos (subspecies femoralis, siamensis, robinsoni, and chrysomelas), P. rubicunda and P. hosei. The genus Trachypithecus (Cercopithecidae) was used as an outgroup. The Cyt b NJ and MP phylogeny trees showed P. m. chrysomelas to be the most primitive, followed by P. hosei, whereas 12S rRNA tree topology only indicated that these two species have close relationships with the other members of the genus. In our analysis, chrysomelas, previously classified as a subspecies of P. melalophos, was not included in either the P. m. femoralis clade or the P. m. siamensis clade. Whether or not there should be a separation at the species level remains to be clarified. The tree topologies also showed that P. m. siamensis is paraphyletic with P. m. robinsoni, and P. m. femoralis with P. rubicunda, in two different clades. Cyt b and 12S rRNA are good gene candidates for the study of phylogenetic relationships at the species level. However, the systematic relationships of some subspecies in this genus remain unclear.
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Affiliation(s)
- V F Vun
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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Md-Zain BM, Mohamad M, Ernie-Muneerah MA, Ampeng A, Jasmi A, Lakim M, Mahani MC. Phylogenetic relationships of Malaysian monkeys, Cercopithecidae, based on mitochondrial cytochrome c sequences. Genet Mol Res 2010; 9:1987-96. [PMID: 20927717 DOI: 10.4238/vol9-4gmr942] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Mitochondrial DNA cytochrome c oxidase II (COII) gene sequences of Malaysian Cercopithecidae were examined to ascertain their phylogenetic relationships. Colobinae were represented by the genera Presbytis, Trachypithecus and Nasalis, while the genus Macaca represented Cercopithecinae. DNA amplification and sequencing of the COII gene was performed on 16 samples. Symphalangus syndactylus (Hylobatidae) was used as the outgroup. Data were analyzed using both character (maximum parsimony) and distance (neighbor-joining) methods. Tree topologies indicated that Colobinae and Cercopithecinae have their own distinct monophyletic clade. This result was well supported by bootstrap values and genetic distances derived from the Kimura-2-parameter algorithm. Separation of Macaca nemestrina from M. fascicularis was also well supported by bootstrap values. In addition, tree topologies indicate a good resolution of the Colobinae phylogenetic relationships at the intergeneric level, but with low bootstrap support. The position of Nasalis remained problematic in both trees. Overall, COII is a good gene candidate for portraying the phylogenetic relationships of Malaysian primates at the inter- and intra-subfamily levels.
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Affiliation(s)
- B M Md-Zain
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia.
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Chowdhury SMZH, Omar AR, Aini I, Hair-Bejo M, Jamaluddin AA, Md-Zain BM, Kono Y. Pathogenicity, sequence and phylogenetic analysis of Malaysian Chicken anaemia virus obtained after low and high passages in MSB-1 cells. Arch Virol 2003; 148:2437-48. [PMID: 14648297 DOI: 10.1007/s00705-003-0189-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2003] [Revised: 01/01/2003] [Accepted: 07/07/2003] [Indexed: 10/26/2022]
Abstract
Specific-pathogen-free (SPF) chickens inoculated with low passage Chicken anaemia virus (CAV), SMSC-1 and 3-1 isolates produced lesions suggestive of CAV infection. Repeated passages of the isolates in cell culture until passage 60 (P60) and passage 123 produced viruses that showed a significantly reduced level of pathogenicity in SPF chickens compared to the low passage isolates. Sequence comparison indicated that nucleotide changes in only the coding region of the P60 passage isolates were thought to contribute to virus attenuation. Phylogenetic analysis indicated that SMSC-1 and 3-1 were highly divergent, but their P60 passage derivatives shared significant homology to a Japanese isolate A2.
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Affiliation(s)
- S M Z H Chowdhury
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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