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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] [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] [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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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: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [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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Gani M, Rovie-Ryan JJ, Sitam FT, Kulaimi NAM, Zheng CC, Atiqah AN, Rahim NMA, Mohammed AA. Taxonomic and genetic assessment of captive White-Handed Gibbons ( Hylobateslar) in Peninsular Malaysia with implications towards conservation translocation and reintroduction programmes. Zookeys 2022; 1076:25-41. [PMID: 34975272 PMCID: PMC8674214 DOI: 10.3897/zookeys.1076.73262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/25/2021] [Indexed: 11/29/2022] Open
Abstract
Conservation translocation and reintroduction for the purpose of repopulating and reinforcing extirpated or depleted populations has been recognised as an important conservation tool, particularly for gibbon conservation in the immediate future. Feasibility assessments involving multiple factors, including taxonomic and genetic assessment of rescued and captive gibbons, are imperative prior to translocation and reintroduction programmes. In this study, we attempt to determine the subspecies and origin of captive Hylobateslar, White-handed gibbons, from Peninsular Malaysia to assist in future translocation and reintroduction programmes. A total of 12 captive and rescued H.lar samples were analysed using the control region segment of mitochondrial DNA. Sequence analyses and phylogenetic trees constructed using neighbour-joining, maximum likelihood, Bayesian inference, and network methods congruently differentiate all 12 captive individuals used in this study from other H.lar subspecies suggesting that these individuals belong to the H.larlar subspecies. In addition, two populations of H.l.lar were observed: (1) a southern population consisting of all 12 individuals from Peninsular Malaysia, and (2) a possible northern population represented by three individuals (from previous studies), which might have originated from the region between the Isthmus of Kra, Surat Thani-Krabi depression, and Kangar-Pattani. Our findings suggest that the complete control region segment can be used to determine the subspecies and origin of captive H.lar.
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Affiliation(s)
- Millawati Gani
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia
| | - Jeffrine J Rovie-Ryan
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia
| | - Frankie Thomas Sitam
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia
| | - Noor Azleen Mohd Kulaimi
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia
| | - Chew Cheah Zheng
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia.,Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi Selangor, Malaysia Universiti Kebangsaan Malaysia Bangi Malaysia
| | - Aida Nur Atiqah
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia.,Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi Selangor, Malaysia Universiti Kebangsaan Malaysia Bangi Malaysia
| | - Nur Maisarah Abd Rahim
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia.,Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia Universiti Putra Malaysia Serdang Malaysia
| | - Ahmad Azhar Mohammed
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia
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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] [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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Rovie-Ryan JJ, Khan FAA, Abdullah MT. Evolutionary pattern of Macaca fascicularis in Southeast Asia inferred using Y-chromosomal gene. BMC Ecol Evol 2021; 21:26. [PMID: 33588750 PMCID: PMC7885488 DOI: 10.1186/s12862-021-01757-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/28/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND We analyzed a combined segment (2032-bp) of the sex-determining region and the testis-specific protein of the Y-chromosome (Y-DNA) gene to clarify the gene flow and phylogenetic relationships of the long-tailed macaques (Macaca fascicularis) in Southeast Asia. Phylogenetic relationships were constructed using the maximum likelihood, Bayesian inference, and the median-joining network from a total of 164 adult male M. fascicularis from 62 localities in Malaysia, including sequences from the other regions from previous studies. RESULTS Based on Y-DNA, we confirm the presence of two lineages of M. fascicularis: the Indochinese and Sundaic lineages. The Indochinese lineage is represented by M. fascicularis located northwards of the Surat Thani-Krabi depression region and is introgressed by the Macaca mulatta Y-DNA. The Sundaic lineage is free from such hybridization event, thus defined as the original carrier of the M. fascicularis Y-DNA. We further revealed that the Sundaic lineage differentiated into two forms: the insular and the continental forms. The insular form, which represents the ancestral form of M. fascicularis, consists of two haplotypes: a single homogenous haplotype occupying the island of Borneo, Philippines, and southern Sumatra; and the Javan haplotype. The more diverse continental form consists of 17 haplotypes in which a dominant haplotype was shared by individuals from southern Thai Peninsular (south of Surat Thani-Krabi depression), Peninsular Malaysia, and Sumatra. Uniquely, Sumatra contains both the continental and insular Y-DNA which can be explained by a secondary contact hypothesis. CONCLUSIONS Overall, the findings in this study are important: (1) to help authority particularly in Malaysia on the population management activities including translocation and culling of conflict M. fascicularis, (2) to identify the unknown origin of captive M. fascicularis used in biomedical research, and; (3) the separation between the continental and insular forms warrants for the treatment as separate management units.
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Affiliation(s)
- Jeffrine J Rovie-Ryan
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks (DWNP) Peninsular Malaysia, KM 10 Cheras Road, 56100, Kuala Lumpur, Malaysia
- Faculty of Resource Science and Technology (FRST), Universiti Malaysia Sarawak (UNIMAS), 94300, Kota Samarahan, Sarawak, Malaysia
| | - Faisal Ali Anwarali Khan
- Faculty of Resource Science and Technology (FRST), Universiti Malaysia Sarawak (UNIMAS), 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Mohd Tajuddin Abdullah
- Institute of Tropical Biodiversity and Sustainable Development (ITBSD), Universiti Malaysia Terengganu (UMT), 21030, Kuala Nerus, Terengganu, Malaysia
- Fellow Academy of Sciences Malaysia, Level 20, West Wing, Tingkat 20, Menara MATRADE, Jalan Sultan Haji Ahmad Shah, 50480, Kuala Lumpur, 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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Haplotype and network analysis of island flying fox (Pteropus hypomelanus) using D-loop region of mitochondrial DNA to confirm subspecies designation. MAMMAL RES 2019. [DOI: 10.1007/s13364-019-00468-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Matsudaira K, Hamada Y, Bunlungsup S, Ishida T, San AM, Malaivijitnond S. Whole Mitochondrial Genomic and Y-Chromosomal Phylogenies of Burmese Long-Tailed Macaque (Macaca fascicularis aurea) Suggest Ancient Hybridization between fascicularis and sinica Species Groups. J Hered 2019; 109:360-371. [PMID: 29186474 DOI: 10.1093/jhered/esx108] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 11/17/2017] [Indexed: 01/09/2023] Open
Abstract
Macaca fascicularis aurea (Burmese long-tailed macaque) is 1 of the 10 subspecies of Macaca fascicularis. Despite having few morphological differences from other subspecies, a recent phylogeographic study showed that M. f. aurea is clearly distinct genetically from Macaca fascicularis fascicularis (common long-tailed macaque) and suggests that M. f. aurea experienced a disparate evolutionary pathway versus other subspecies. To construct a detailed evolutionary history of M. f. aurea and its relationships with other macaque species, we performed phylogenetic analyses and divergence time estimation of whole mitochondrial genomes (2 M. f. aurea, 8 M. f. fascicularis, and 16 animals of 12 macaque species) and 2871 bp of the Y chromosome (1 M. f. aurea, 2 M. f. fascicularis, and 5 animals of 5 macaque species) and haplotype network analysis of 758 bp of the Y chromosome (1 M. f. aurea, 2 M. f. fascicularis, and 21 animals of 19 macaque species). Whereas the Y chromosome of M. f. aurea clustered with those of the fascicularis species group in the phylogenetic and haplotype network analyses, its mtDNA clustered within the clade of the sinica species group. Based on this phylogenetic incongruence and the estimated divergence times, we propose that proto-M. f. aurea underwent hybridization with a population of the sinica species group between 2.5 and 0.95 MYA after divergence from the common ancestor of M. fascicularis. Hybridization and introgression might have been central in the evolution of M. f. aurea, similar to what occurred in the evolution of other macaque species and subspecies.
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Affiliation(s)
- Kazunari Matsudaira
- Department of Biology, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand.,National Primate Research Center of Thailand, Chulalongkorn University, Saraburi, Thailand
| | - Yuzuru Hamada
- Evolutionary Morphology Section, Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Srichan Bunlungsup
- Department of Biology, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| | - Takafumi Ishida
- Unit of Human Biology and Genetics, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Aye Mi San
- Department of Zoology, University of Yangon, Kamayut, Yangon, Myanmar
| | - Suchinda Malaivijitnond
- Department of Biology, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand.,National Primate Research Center of Thailand, Chulalongkorn University, Saraburi, Thailand
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Veron G, Debruille A, Kayser P, Fernandez DAP, Bourgeois A. Genetic diversity and structure of the binturong Arctictis binturong (Carnivora: Viverridae) – status of the elusive Palawan binturong and implications for conservation. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractThe binturong or bearcat is a forest mesocarnivore ranging from Nepal to Indonesia and the Philippines. Several subspecies of binturongs are recognized but a revision is needed. The binturong from Palawan was described as a species and is now considered a subspecies, but its status has never been checked using molecular approaches. Owing to its restricted range and the pressure on its habitat, the Palawan binturong may be endangered. It is, therefore, of crucial importance to clarify its taxonomic status, particularly for the management of captive populations. We sequenced one nuclear and two mitochondrial markers for binturongs from locations across the species range and from zoos. Our results provide an assessment of the genetic polymorphism and structure within the binturong, resulting in two groups, corresponding to the Indochinese and the Sundaic regions. Within the latter were found the Palawan binturongs on one side, and an individual from Sulu archipelago (a locality not reported before) on the other side. The Palawan binturongs form a monophyletic group, genetically close to Bornean binturongs, which suggests that they may have dispersed from Borneo, and represents a lineage worth preserving, but which is not a separate species nor a separate subspecies.
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Affiliation(s)
- Géraldine Veron
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP 51, Paris Cedex, France
| | - Agathe Debruille
- Arctictis Binturong Conservation (ABConservation), 4 rue de la chamoiserie, Gentilly, France
| | - Pauline Kayser
- Arctictis Binturong Conservation (ABConservation), 4 rue de la chamoiserie, Gentilly, France
- Ménagerie le Zoo du Jardin des Plantes de Paris, Muséum National d’Histoire Naturelle, Paris, France
| | | | - Aude Bourgeois
- Ménagerie le Zoo du Jardin des Plantes de Paris, Muséum National d’Histoire Naturelle, Paris, France
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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] [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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12
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Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis. Sci Rep 2019; 9:8504. [PMID: 31186469 PMCID: PMC6560038 DOI: 10.1038/s41598-019-44870-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/20/2019] [Indexed: 11/08/2022] Open
Abstract
Macaca fascicularis, also known as the cynomolgus macaque, is an important non-human primate animal model used in biomedical research. It is an Old-World primate widely distributed in Southeast Asia and is one of the most abundant macaque species in Malaysia. However, the genetic structure of wild cynomolgus macaque populations in Malaysia has not been thoroughly elucidated. In this study, we developed genic-simple sequence repeat (genic-SSR) markers from an in-house transcriptome dataset generated from the Malaysian cynomolgus macaque via RNA sequencing, and applied these markers on 26 cynomolgus macaque individuals. A collection of 14,751 genic-SSRs were identified, where 13,709 were perfect SSRs. Dinucleotide repeats were the most common repeat motifs with a frequency of 65.05%, followed by trinucleotide repeats (20.55%). Subsequently, we designed 300 pairs of primers based on perfect di- and trinucleotide SSRs, in which 105 SSRs were associated with functional genes. A subset of 30 SSR markers were randomly selected and validated, yielding 19 polymorphic markers with an average polymorphism information content value of 0.431. The development of genic-SSR markers in this study is indeed timely to provide useful markers for functional and population genetic studies of the cynomolgus macaque and other related non-human primate species.
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Ee Uli J, Yong CSY, Yeap SK, Alitheen NB, Rovie-Ryan JJ, Mat Isa N, Tan SG. RNA sequencing of kidney and liver transcriptome obtained from wild cynomolgus macaque (Macaca fascicularis) originating from Peninsular Malaysia. BMC Res Notes 2018; 11:923. [PMID: 30577850 PMCID: PMC6303865 DOI: 10.1186/s13104-018-4014-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/12/2018] [Indexed: 01/22/2023] Open
Abstract
Objective Using high-throughput RNA sequencing technology, this study aimed to sequence the transcriptome of kidney and liver tissues harvested from Peninsular Malaysia cynomolgus macaque (Macaca fascicularis). M. fascicularis are significant nonhuman primate models in the biomedical field, owing to the macaque’s biological similarities with humans. The additional transcriptomic dataset will supplement the previously described Peninsular Malaysia M. fascicularis transcriptomes obtained in a past endeavour. Results A total of 75,350,240 sequence reads were obtained via Hi-seq 2500 sequencing technology. A total of 5473 significant differentially expressed genes were called. Gene ontology functional categorisation showed that cellular process, catalytic activity, and cell part categories had the highest number of expressed genes, while the metabolic pathways category possessed the highest number of expressed genes in the KEGG pathway analysis. The additional sequence dataset will further enrich existing M. fascicularis transcriptome assemblies, and provide a dataset for further downstream studies. Electronic supplementary material The online version of this article (10.1186/s13104-018-4014-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joey Ee Uli
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Christina Seok-Yien Yong
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University, Sepang, Selangor, Malaysia
| | - Noorjahan Banu Alitheen
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Jeffrine J Rovie-Ryan
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, Kuala Lumpur, Malaysia
| | - Nurulfiza Mat Isa
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Soon Guan Tan
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 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] [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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15
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Ee Uli J, Yong CSY, Yeap SK, Rovie-Ryan JJ, Mat Isa N, Tan SG, Alitheen NB. RNA sequencing (RNA-Seq) of lymph node, spleen, and thymus transcriptome from wild Peninsular Malaysian cynomolgus macaque ( Macaca fascicularis). PeerJ 2017; 5:e3566. [PMID: 28828235 PMCID: PMC5563440 DOI: 10.7717/peerj.3566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/21/2017] [Indexed: 12/25/2022] Open
Abstract
The cynomolgus macaque (Macaca fascicularis) is an extensively utilised nonhuman primate model for biomedical research due to its biological, behavioural, and genetic similarities to humans. Genomic information of cynomolgus macaque is vital for research in various fields; however, there is presently a shortage of genomic information on the Malaysian cynomolgus macaque. This study aimed to sequence, assemble, annotate, and profile the Peninsular Malaysian cynomolgus macaque transcriptome derived from three tissues (lymph node, spleen, and thymus) using RNA sequencing (RNA-Seq) technology. A total of 174,208,078 paired end 70 base pair sequencing reads were obtained from the Illumina Hi-Seq 2500 sequencer. The overall mapping percentage of the sequencing reads to the M. fascicularis reference genome ranged from 53–63%. Categorisation of expressed genes to Gene Ontology (GO) and KEGG pathway categories revealed that GO terms with the highest number of associated expressed genes include Cellular process, Catalytic activity, and Cell part, while for pathway categorisation, the majority of expressed genes in lymph node, spleen, and thymus fall under the Global overview and maps pathway category, while 266, 221, and 138 genes from lymph node, spleen, and thymus were respectively enriched in the Immune system category. Enriched Immune system pathways include Platelet activation pathway, Antigen processing and presentation, B cell receptor signalling pathway, and Intestinal immune network for IgA production. Differential gene expression analysis among the three tissues revealed 574 differentially expressed genes (DEG) between lymph and spleen, 5402 DEGs between lymph and thymus, and 7008 DEGs between spleen and thymus. Venn diagram analysis of expressed genes revealed a total of 2,630, 253, and 279 tissue-specific genes respectively for lymph node, spleen, and thymus tissues. This is the first time the lymph node, spleen, and thymus transcriptome of the Peninsular Malaysian cynomolgus macaque have been sequenced via RNA-Seq. Novel transcriptomic data will further enrich the present M. fascicularis genomic database and provide future research potentials, including novel transcript discovery, comparative studies, and molecular markers development.
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Affiliation(s)
- Joey Ee Uli
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Christina Seok Yien Yong
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University, Sepang, Selangor, Malaysia
| | - Jeffrine J Rovie-Ryan
- Department of Wildlife and National Parks (DWNP), Ex-Situ Conservation Division, Department of Wildlife and National Parks, Kuala Lumpur, Malaysia
| | - Nurulfiza Mat Isa
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Soon Guan Tan
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Noorjahan Banu Alitheen
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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16
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Klegarth A, Sanders S, Gloss A, Lane‐deGraaf K, Jones‐Engel L, Fuentes A, Hollocher H. Investigating biogeographic boundaries of the Sunda shelf: A phylogenetic analysis of two island populations of
Macaca fascicularis. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 163:658-670. [DOI: 10.1002/ajpa.23235] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/21/2017] [Accepted: 04/10/2017] [Indexed: 11/05/2022]
Affiliation(s)
- A.R. Klegarth
- Department of Biological SciencesUniversity of Notre DameNotre Dame Indiana
- Department of AnthropologyUniversity of WashingtonSeattle Washington
| | - S.A. Sanders
- Department of Biological SciencesUniversity of Notre DameNotre Dame Indiana
- National Center for Genome Analysis SupportPervasive Technology Institute, Indiana UniversityBloomington Indiana
| | - A.D. Gloss
- Department of Biological SciencesUniversity of Notre DameNotre Dame Indiana
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucson Arizona
| | - K.E. Lane‐deGraaf
- Department of Biological SciencesUniversity of Notre DameNotre Dame Indiana
- Department of BiologyFontbonne UniversitySt. Louis Missouri
| | - L. Jones‐Engel
- Department of AnthropologyUniversity of WashingtonSeattle Washington
- National Primate Research CenterUniversity of WashingtonSeattle Washington
| | - A. Fuentes
- Department of AnthropologyUniversity of Notre DameNotre Dame Indiana
| | - H. Hollocher
- Department of Biological SciencesUniversity of Notre DameNotre Dame Indiana
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17
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Bunlungsup S, Imai H, Hamada Y, Matsudaira K, Malaivijitnond S. Mitochondrial DNA and two Y-chromosome genes of common long-tailed macaques (Macaca fascicularis fascicularis) throughout Thailand and vicinity. Am J Primatol 2016; 79:1-13. [PMID: 27643851 DOI: 10.1002/ajp.22596] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/22/2016] [Accepted: 08/29/2016] [Indexed: 11/11/2022]
Abstract
Macaca fascicularis fascicularis is distributed over a wide area of Southeast Asia. Thailand is located at the center of their distribution range and is the bridge connecting the two biogeographic regions of Indochina and Sunda. However, only a few genetic studies have explored the macaques in this region. To shed some light on the evolutionary history of M. f. fascicularis, including hybridization with M. mulatta, M. f. fascicularis and M. mulatta samples of known origins throughout Thailand and the vicinity were analyzed by molecular phylogenetics using mitochondrial DNA (mtDNA), including the hypervariable region 1, and Y-chromosomal DNA, including SRY and TSPY genes. The mtDNA phylogenetic analysis divided M. f. fascicularis into five subclades (Insular Indonesia, Sundaic Thai Gulf, Vietnam, Sundaic Andaman sea coast, and Indochina) and revealed genetic differentiation between the two sides of the Thai peninsula, which had previously been reported as a single group of Malay peninsular macaques. From the estimated divergence time of the Sundaic Andaman sea coast subclade, it is proposed that after M. f. fascicularis dispersed throughout Southeast Asia, some populations on the south-easternmost Indochina (eastern Thailand, southern Cambodia and southern Vietnam at the present time) migrated south-westwards across the land bridge, which was exposed during the glacial period of the late Pleistocene epoch, to the southernmost Thailand/northern peninsular Malaysia. Then, some of them migrated north and south to colonize the Thai Andaman sea coast and northern Sumatra, respectively. The SRY-TSPY phylogenetic analysis suggested that male-mediated gene flow from M. mulatta southward to M. f. fascicularis was restricted south of, but close to, the Isthmus of Kra. There was a strong impact of the geographical factors in Thailand, such as the Isthmus of Kra, Nakhon Si Thammarat, and Phuket ranges and Sundaland, on M. f. fascicularis biogeography and their hybridization with M. mulatta.
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Affiliation(s)
- Srichan Bunlungsup
- Faculty of Science, Department of Biology, Chulalongkorn University, Bangkok, Thailand
| | - Hiroo Imai
- Molecular Biology Section, Primate Research Institute, Kyoto University, Aichi, Japan
| | - Yuzuru Hamada
- Evolutionary Morphology Section, Primate Research Institute, Kyoto University, Aichi, Japan
| | - Kazunari Matsudaira
- Faculty of Science, Department of Biology, Chulalongkorn University, Bangkok, Thailand
| | - Suchinda Malaivijitnond
- Faculty of Science, Department of Biology, Chulalongkorn University, Bangkok, Thailand.,National Primate Research Center of Thailand-Chulalongkorn University, Saraburi, Thailand
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18
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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] [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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