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Weinbauer G, Mecklenburg L. Does Geographical Origin of Long-Tailed Macaques ( Macaca fascicularis) Matter in Drug Safety Assessment?: A Literature Review and Proposed Conclusion. Toxicol Pathol 2022; 50:552-559. [PMID: 35608013 DOI: 10.1177/01926233221095443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Long-tailed macaques are the predominant nonhuman primate species for the nonclinical safety testing of biopharmaceuticals. This species comprises 9 subspecies with Macaca fascicularis fascicularis naturally occurring in Southeast Asia. Since the 17th century, M. f. fascicularis also occurs on Mauritius. Cynomolgus macaques do not naturally occur in China, but are bred in many farms across the country. The current shortage in animal supply raises the question whether geographical animal origin matters and if animals from different geographical regions can be combined on a drug development program or even a single experiment. This article reviews geographical animal origin in relation to selected endpoints that are relevant in nonclinical drug safety testing. Animals from different countries within Asia mainland do not appear to show any meaningful difference. Very little data are available for animals from Asia island. Mauritian animals show consistent differences from Asian animals in several clinical and anatomical pathology parameters. For developmental parameters, animals from Mauritius and Asia are comparable with the exception that Mauritian animals mature faster. In the authors' view, differences between the geographical clusters can be accounted for as long as baseline and reference data are available.
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Mitogenomics of macaques (Macaca) across Wallace's Line in the context of modern human dispersals. J Hum Evol 2020; 146:102852. [DOI: 10.1016/j.jhevol.2020.102852] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/28/2020] [Accepted: 06/28/2020] [Indexed: 11/17/2022]
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Yao L, Witt K, Li H, Rice J, Salinas NR, Martin RD, Huerta-Sánchez E, Malhi RS. Population genetics of wild Macaca fascicularis with low-coverage shotgun sequencing of museum specimens. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 173:21-33. [PMID: 32643146 PMCID: PMC8329942 DOI: 10.1002/ajpa.24099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 05/10/2020] [Accepted: 05/15/2020] [Indexed: 11/12/2022]
Abstract
OBJECTIVES Long-tailed macaques (Macaca fascicularis) are widely distributed throughout the mainland and islands of Southeast Asia, making them a useful model for understanding the complex biogeographical history resulting from drastic changes in sea levels throughout the Pleistocene. Past studies based on mitochondrial genomes (mitogenomes) of long-tailed macaque museum specimens have traced their colonization patterns throughout the archipelago, but mitogenomes trace only the maternal history. Here, our objectives were to trace phylogeographic patterns of long-tailed macaques using low-coverage nuclear DNA (nDNA) data from museum specimens. METHODS We performed population genetic analyses and phylogenetic reconstruction on nuclear single nucleotide polymorphisms (SNPs) from shotgun sequencing of 75 long-tailed macaque museum specimens from localities throughout Southeast Asia. RESULTS We show that shotgun sequencing of museum specimens yields sufficient genome coverage (average ~1.7%) for reconstructing population relationships using SNP data. Contrary to expectations of divergent results between nuclear and mitochondrial genomes for a female philopatric species, phylogeographical patterns based on nuclear SNPs proved to be closely similar to those found using mitogenomes. In particular, population genetic analyses and phylogenetic reconstruction from the nDNA identify two major clades within M. fascicularis: Clade A includes all individuals from the mainland along with individuals from northern Sumatra, while Clade B consists of the remaining island-living individuals, including those from southern Sumatra. CONCLUSIONS Overall, we demonstrate that low-coverage sequencing of nDNA from museum specimens provides enough data for examining broad phylogeographic patterns, although greater genome coverage and sequencing depth would be needed to distinguish between very closely related populations, such as those throughout the Philippines.
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Affiliation(s)
- Lu Yao
- American Museum of Natural History, New York, New York, USA
| | - Kelsey Witt
- Brown University, Providence, Rhode Island, USA
- University of California Merced, Merced, California, USA
| | - Hongjie Li
- University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan Rice
- University of California Merced, Merced, California, USA
| | - Nelson R Salinas
- American Museum of Natural History, New York, New York, USA
- Instituto de Hidrología, Metereología y Estudios Ambientales IDEAM, Bogotá, Colombia
| | - Robert D Martin
- The Field Museum of Natural History, Chicago, Illinois, USA
- University of Zürich, Zürich, Switzerland
| | | | - Ripan S Malhi
- University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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Ito T, Kanthaswamy S, Bunlungsup S, Oldt RF, Houghton P, Hamada Y, Malaivijitnond S. Secondary contact and genomic admixture between rhesus and long-tailed macaques in the Indochina Peninsula. J Evol Biol 2020; 33:1164-1179. [PMID: 33448526 DOI: 10.1111/jeb.13681] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/11/2020] [Accepted: 07/08/2020] [Indexed: 01/07/2023]
Abstract
Understanding the process and consequences of hybridization is one of the major challenges in evolutionary biology. A growing body of literature has reported evidence of ancient hybridization events or natural hybrid zones in primates, including humans; however, we still have relatively limited knowledge about the pattern and history of admixture because there have been little studies that simultaneously achieved genome-scale analysis and a geographically wide sampling of wild populations. Our study applied double-digest restriction site-associated DNA sequencing to samples from the six localities in and around the provisional hybrid zone of rhesus and long-tailed macaques and evaluated population structure, phylogenetic relationships, demographic history, and geographic clines of morphology and allele frequencies. A latitudinal gradient of genetic components was observed, highlighting the transition from rhesus (north) to long-tailed macaque distribution (south) as well as the presence of one northern population of long-tailed macaques exhibiting unique genetic structure. Interspecific gene flow was estimated to have recently occurred after an isolation period, and the migration rate from rhesus to long-tailed macaques was slightly greater than in the opposite direction. Although some rhesus macaque-biased alleles have widely introgressed into long-tailed macaque populations, the inflection points of allele frequencies have been observed as concentrated around the traditionally recognized interspecific boundary where morphology discontinuously changed; this pattern was more pronounced in the X chromosome than in autosomes. Thus, due to geographic separation before secondary contact, reproductive isolation could have evolved, contributing to the maintenance of an interspecific boundary and species-specific morphological characteristics.
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Affiliation(s)
- Tsuyoshi Ito
- Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Aichi, Japan
| | - Sreetharan Kanthaswamy
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University West Campus, Glendale, AZ, USA
| | - Srichan Bunlungsup
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,National Primate Research Center of Thailand-Chulalongkorn University, Saraburi, Thailand
| | - Robert F Oldt
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University West Campus, Glendale, AZ, USA
| | | | - Yuzuru Hamada
- Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Aichi, Japan
| | - Suchinda Malaivijitnond
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,National Primate Research Center of Thailand-Chulalongkorn University, Saraburi, Thailand
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5
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Three decades of Philippine nonhuman primate studies: research gaps and opportunities for Philippine primatology. Primates 2020; 62:233-239. [PMID: 32681352 DOI: 10.1007/s10329-020-00847-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/09/2020] [Indexed: 10/23/2022]
Abstract
The Philippines is considered a megadiverse country. However, there are few published studies on its nonhuman primate (NHP) species (Carlito syrichta, Macaca fascicularis, and Nycticebus menagensis). Understanding the nature and extent of existing NHP research in the Philippines would help us to determine research gaps and opportunities. Thus, studies on NHPs of Philippine origin were retrieved from online databases including Google Scholar, ResearchGate, Primate Lit, the Integrated Taxonomic Information System (ITIS), and relevant authors. Of a total of 107 studies on Philippine NHP from 1989 to 2019, most focused on Philippine long-tailed macaque (52.78%), and Philippine tarsier (42.59%), with far fewer on Philippine slow loris (4.63%). Fewer studies were based on fieldwork (26.17%); more were based on research on captive animals or that undertaken in the laboratory (34.58%), or used only existing specimens or data (33.64%). Studies on wild NHPs were mostly conducted in Bohol Island. In terms of the type of research, studies on diseases (38.60%) were the most prevalent for macaques; ecological studies (23.91%) for tarsiers; evolutionary, taxonomic, and systematic studies (40%), and ecological and natural history studies (40%) for lorises. Philippine researchers and collaborations with foreign researchers contributed fewer studies (43.93%) than foreign-only researchers (56.07%). In conclusion, although research on Philippine NHPs is increasing, there is a bias with regards to the species studied, the type of research, and study location. Conservation-driven studies are also lacking. These gaps offer opportunities for further research to identify threats to the survival of NHPs in the Philippines, and for the development of plans and effective strategies for their conservation.
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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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Day GQ, Ng J, Oldt RF, Houghton PW, Smith DG, Kanthaswamy S. DNA-based Determination of Ancestry in Cynomolgus Macaques ( Macaca fascicularis). JOURNAL OF THE AMERICAN ASSOCIATION FOR LABORATORY ANIMAL SCIENCE : JAALAS 2018; 57:432-442. [PMID: 30165920 PMCID: PMC6159685 DOI: 10.30802/aalas-jaalas-17-000147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/29/2017] [Accepted: 02/26/2018] [Indexed: 11/05/2022]
Abstract
Interest in the genetic composition of cynomolgus macaques (Macaca fascicularis) has increased due to the rising demand for NHP models in human biomedical research. Significant genetic differences among regional populations of cynomolgus macaques can confound interpretations of research results because they do not solely reflect differences in experimental treatment effects. Therefore, the common origin of cynomolgus macaques used as research subjects should be verified by using region-specific genetic markers to minimize the influence of underlying genetic variation among animals selected as research subjects on phenotypes under study. We compared the effectiveness of 18 short tandem repeat (STR) markers with that of 83 single-nucleotide polymorphism (SNP) markers to differentiate the ancestry of cynomolgus macaques from 6 different populations (Cambodia, Sumatra, Mauritius, Singapore, and the islands of Luzon and Zamboanga in the Philippines). Genetic diversity indices such as allele numbers and expected heterozygosity based on SNP were lower and exhibited lower standard errors than those provided by STR, probably because, unlike STR, most SNP are biallelic and consequently exhibit maximal expected heterozygosity values of 0.50. However, the standard error of estimates of observed heterozygosity based on SNP was higher than that for STR, perhaps reflecting sampling errors. Only 27 SNP were required to match the resolving power of 17 STR to detect population structure, that is, 1.6 SNP:1 STR. Whereas STR only differentiated the Mauritian population from all other populations, SNP detected 4 genetically distinct groups (Cambodia, Singapore-Sumatra, Mauritius, and Zamboanga). SNP are poised to become as valuable as STR for understanding and detecting genetic structure among cynomolgus macaques. Although STR will remain an important tool for cynomolgus macaque population studies, SNP have the potential to become the mainstream marker type.
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Affiliation(s)
- George Q Day
- Molecular Anthropology Laboratory, University of California, Davis, California
| | - Jillian Ng
- Molecular Anthropology Laboratory, University of California, Davis, California
| | - Robert F Oldt
- Molecular Anthropology Laboratory, University of California, Davis, California, School of Mathematics and Natural Sciences, Arizona State University at the West Campus, Glendale, Arizona
| | | | - David Glenn Smith
- Molecular Anthropology Laboratory, California National Primate Research Center, University of California, Davis, California
| | - Sree Kanthaswamy
- California National Primate Research Center, University of California, Davis, California, School of Mathematics and Natural Sciences, Arizona State University at the West Campus, Glendale, Arizona;,
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8
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Yao L, Li H, Martin RD, Moreau CS, Malhi RS. Tracing the phylogeographic history of Southeast Asian long-tailed macaques through mitogenomes of museum specimens. Mol Phylogenet Evol 2017; 116:227-238. [PMID: 28863929 DOI: 10.1016/j.ympev.2017.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 05/23/2017] [Accepted: 08/13/2017] [Indexed: 12/01/2022]
Abstract
The biogeographical history of Southeast Asia is complicated due to the continuous emergences and disappearances of land bridges throughout the Pleistocene. Here, we use long-tailed macaques (Macaca fascicularis), which are widely distributed throughout the mainland and islands of Southeast Asia, asa model for better understanding the biogeographical patterns of diversification in this geographically complex region. A reliable intraspecific phylogeny including individuals from localities on oceanic islands, continental islands, and the mainland is needed to trace relatedness along with the pattern and timing of colonization in this region. We used high-throughput sequencing techniques to sequence mitochondrial genomes (mitogenomes) from 95 Southeast Asian M. fascicularis specimens housed at natural history museums around the world. To achieve a comprehensive picture, we more than tripled the mitogenome sample size for M. fascicularis from previous studies, and for the first time included documented samples from the Philippines and several small Indonesian islands. Confirming the result from a previous, recent intraspecific phylogeny for M. fascicularis, the newly reconstructed phylogeny of 135 specimens divides the samples into two major clades: Clade A includes haplotypes from the mainland and some from northern Sumatra, while Clade B includes all insular haplotypes along with lineages from southern Sumatra. This study resolves a previous disparity by revealing a disjunction in the origin of Sumatran macaques, with separate lineages originating within the two major clades, suggesting that at least two major migrations to Sumatra occurred. However, our dated phylogeny reveals that the two major clades split ∼1.88Ma, which is earlier than in previously published phylogenies. Our new data reveal that most Philippine macaque lineages diverged from the Borneo stock within the last ∼0.06-0.43Ma. Finally, our study provides insight into successful sequencing of DNA across museums and shotgun sequencing of DNA specimens asa method to sequence the mitogenome.
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Affiliation(s)
- Lu Yao
- Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th St., Culver Hall 402, Chicago, IL 60637, USA; Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, IL 60605, USA.
| | - Hongjie Li
- Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave., 109 Davenport Hall, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 W Gregory Dr., Urbana, IL 61820, USA
| | - Robert D Martin
- Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th St., Culver Hall 402, Chicago, IL 60637, USA; Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, IL 60605, USA; Institute of Evolutionary Medicine, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Corrie S Moreau
- Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th St., Culver Hall 402, Chicago, IL 60637, USA; Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, IL 60605, USA
| | - Ripan S Malhi
- Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave., 109 Davenport Hall, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 W Gregory Dr., Urbana, IL 61820, USA
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Divis PCS, Lin LC, Rovie-Ryan JJ, Kadir KA, Anderios F, Hisam S, Sharma RSK, Singh B, Conway DJ. Three Divergent Subpopulations of the Malaria Parasite Plasmodium knowlesi. Emerg Infect Dis 2017; 23:616-624. [PMID: 28322705 PMCID: PMC5367419 DOI: 10.3201/eid2304.161738] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Multilocus microsatellite genotyping of Plasmodium knowlesi isolates previously indicated 2 divergent parasite subpopulations in humans on the island of Borneo, each associated with a different macaque reservoir host species. Geographic divergence was also apparent, and independent sequence data have indicated particularly deep divergence between parasites from mainland Southeast Asia and Borneo. To resolve the overall population structure, multilocus microsatellite genotyping was conducted on a new sample of 182 P. knowlesi infections (obtained from 134 humans and 48 wild macaques) from diverse areas of Malaysia, first analyzed separately and then in combination with previous data. All analyses confirmed 2 divergent clusters of human cases in Malaysian Borneo, associated with long-tailed macaques and pig-tailed macaques, and a third cluster in humans and most macaques in peninsular Malaysia. High levels of pairwise divergence between each of these sympatric and allopatric subpopulations have implications for the epidemiology and control of this zoonotic species.
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10
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Zhang X, Meng Y, Houghton P, Liu M, Kanthaswamy S, Oldt R, Ng J, Trask JS, Huang R, Singh B, Du H, Smith DG. Ancestry, Plasmodium cynomolgi prevalence and rhesus macaque admixture in cynomolgus macaques (Macaca fascicularis) bred for export in Chinese breeding farms. J Med Primatol 2017; 46:31-41. [PMID: 28266719 PMCID: PMC7571188 DOI: 10.1111/jmp.12256] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2017] [Indexed: 01/07/2023]
Abstract
BACKGROUND Most cynomolgus macaques (Macaca fascicularis) used in the United States as animal models are imported from Chinese breeding farms without documented ancestry. Cynomolgus macaques with varying rhesus macaque ancestry proportions may exhibit differences, such as susceptibility to malaria, that affect their suitability as a research model. METHODS DNA of 400 cynomolgus macaques from 10 Chinese breeding farms was genotyped to characterize their regional origin and rhesus ancestry proportion. A nested PCR assay was used to detect Plasmodium cynomolgi infection in sampled individuals. RESULTS All populations exhibited high levels of genetic heterogeneity and low levels of inbreeding and genetic subdivision. Almost all individuals exhibited an Indochinese origin and a rhesus ancestry proportion of 5%-48%. The incidence of P. cynomolgi infection in cynomolgus macaques is strongly associated with proportion of rhesus ancestry. CONCLUSIONS The varying amount of rhesus ancestry in cynomolgus macaques underscores the importance of monitoring their genetic similarity in malaria research.
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Affiliation(s)
- Xinjun Zhang
- Department of Anthropology, University of California, Davis, CA, USA
| | - Yuhuan Meng
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | | | - Mingyu Liu
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Sreetharan Kanthaswamy
- School of Mathematical and Natural Sciences, Arizona State University (ASU West Campus), Glendale, AZ, USA
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Robert Oldt
- School of Mathematical and Natural Sciences, Arizona State University (ASU West Campus), Glendale, AZ, USA
| | - Jillian Ng
- Department of Anthropology, University of California, Davis, CA, USA
| | - Jessica Satkoski Trask
- Department of Research Compliance & Integrity, Office of Research, University of California, Davis, CA, USA
| | - Ren Huang
- Guangdong Key Laboratory of Laboratory Animals, Guangzhou, China
| | - Balbir Singh
- Malaria Research Centre, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Hongli Du
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - David Glenn Smith
- Department of Anthropology, University of California, Davis, CA, USA
- California National Primate Research Center, University of California, Davis, CA, USA
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11
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Zhang X, Kadir KA, Quintanilla-Zariñan LF, Villano J, Houghton P, Du H, Singh B, Smith DG. Distribution and prevalence of malaria parasites among long-tailed macaques (Macaca fascicularis) in regional populations across Southeast Asia. Malar J 2016; 15:450. [PMID: 27590474 PMCID: PMC5010671 DOI: 10.1186/s12936-016-1494-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 08/16/2016] [Indexed: 12/17/2022] Open
Abstract
Background Plasmodium knowlesi and Plasmodium cynomolgi are two malaria parasites naturally transmissible between humans and wild macaque through mosquito vectors, while Plasmodium inui can be experimentally transmitted from macaques to humans. One of their major natural hosts, the long-tailed macaque (Macaca fascicularis), is host to two other species of Plasmodium (Plasmodium fieldi and Plasmodium coatneyi) and is widely distributed in Southeast Asia. This study aims to determine the distribution of wild macaques infected with malarial parasites by examining samples derived from seven populations in five countries across Southeast Asia. Methods Plasmodium knowlesi, P. cynomolgi, P. coatneyi, P. inui and P. fieldi, were detected using nested PCR assays in DNA samples from 276 wild-caught long-tailed macaques. These samples had been derived from macaques captured at seven locations, two each in the Philippines (n = 68) and Indonesia (n = 70), and one each in Cambodia (n = 54), Singapore (n = 40) and Laos (n = 44). The results were compared with previous studies of malaria parasites in long-tailed macaques from other locations in Southeast Asia. Fisher exact test and Chi square test were used to examine the geographic bias of the distribution of Plasmodium species in the macaque populations. Results Out of 276 samples tested, 177 were Plasmodium-positive, with P. cynomolgi being the most common and widely distributed among all long-tailed macaque populations (53.3 %) and occurring in all populations examined, followed by P. coatneyi (20.4 %), P. inui (12.3 %), P. fieldi (3.4 %) and P. knowlesi (0.4 %). One P. knowlesi infection was detected in a macaque from Laos, representing the first documented case of P. knowlesi in wildlife in Laos. Chi square test showed three of the five parasites (P. knowlesi, P. coatneyi, P. cynomolgi) with significant bias in prevalence towards macaques from Malaysian Borneo, Cambodia, and Southern Sumatra, respectively. Conclusions The prevalence of malaria parasites, including those that are transmissible to humans, varied among all sampled regional populations of long-tailed macaques in Southeast Asia. The new discovery of P. knowlesi infection in Laos, and the high prevalence of P. cynomolgi infections in wild macaques in general, indicate the strong need of public advocacy in related countries.
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Affiliation(s)
- Xinjun Zhang
- Department of Anthropology, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Khamisah Abdul Kadir
- Malaria Research Centre, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | | | - Jason Villano
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, 2800 Plymouth Rd., Ann Arbor, MI, 48109, USA
| | - Paul Houghton
- Primate Products, Inc., PO Box 1588, Immokalee, FL, 34143, USA
| | - Hongli Du
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China
| | - Balbir Singh
- Malaria Research Centre, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - David Glenn Smith
- Department of Anthropology, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA.
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12
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Bunlungsup S, Imai H, Hamada Y, Gumert MD, San AM, Malaivijitnond S. Morphological characteristics and genetic diversity of Burmese long-tailed Macaques (Macaca fascicularis aurea). Am J Primatol 2015; 78:441-455. [DOI: 10.1002/ajp.22512] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 10/23/2015] [Accepted: 11/21/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Srichan Bunlungsup
- Department of Biology, Faculty of Science; 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
| | - Michael D. Gumert
- Division of Psychology, School of Humanities and Social Sciences; Nanyang Technological University; Singapore
| | - Aye Mi San
- Department of Zoology; Mawlamyine University; Mawlamyine Myanmar
| | - Suchinda Malaivijitnond
- Department of Biology, Faculty of Science; Chulalongkorn University; Bangkok Thailand
- National Primate Research Center of Thailand; Saraburi Thailand
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Hawks J. Biological Anthropology in 2014: Beyond the Traditional. AMERICAN ANTHROPOLOGIST 2015. [DOI: 10.1111/aman.12241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- John Hawks
- Department of Anthropology; University of Wisconsin-Madison; Madison WI 53706
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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: 44] [Impact Index Per Article: 4.9] [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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Ng J, Trask JS, Houghton P, Smith DG, Kanthaswamy S. Use of genome-wide heterospecific single-nucleotide polymorphisms to estimate linkage disequilibrium in rhesus and cynomolgus macaques. Comp Med 2015; 65:62-9. [PMID: 25730759 PMCID: PMC4396931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/25/2014] [Accepted: 10/27/2014] [Indexed: 06/04/2023]
Abstract
Rhesus and cynomolgus macaques are frequently used in biomedical research, and the availability of their reference genomes now provides for their use in genome-wide association studies. However, little is known about linkage disequilibrium (LD) in their genomes, which can affect the design and success of such studies. Here we studied LD by using 1781 conserved single-nucleotide polymorphisms (SNPs) in 183 rhesus macaques (Macaca mulatta), including 97 purebred Chinese and 86 purebred Indian animals, and 96 cynomolgus macaques (M. fascicularis fascicularis). Correlation between loci pairs decayed to 0.02 at 1146.83, 2197.92, and 3955.83 kb for Chinese rhesus, Indian rhesus, and cynomolgus macaques, respectively. Differences between the observed heterozygosity and minor allele frequency (MAF) of pairs of these 3 taxa were highly statistically significant. These 3 nonhuman primate taxa have significantly different genetic diversities (heterozygosity and MAF) and rates of LD decay. Our study confirms a much lower rate of LD decay in Indian than in Chinese rhesus macaques relative to that previously reported. In contrast, the especially low rate of LD decay in cynomolgus macaques suggests the particular usefulness of this species in genome-wide association studies. Although conserved markers, such as those used here, are required for valid LD comparisons among taxa, LD can be assessed with less bias by using species-specific markers, because conserved SNPs may be ancestral and therefore not informative for LD.
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Affiliation(s)
- Jillian Ng
- Molecular Anthropology Laboratory, Department of Anthropology, University of California, Davis, California, USA
| | - Jessica Satkoski Trask
- Molecular Anthropology Laboratory, California National Primate Research Center, University of California, Davis, California, USA
| | | | - David G Smith
- Molecular Anthropology Laboratory, Department of Anthropology, California National Primate Research Center, University of California, Davis, California, USA
| | - Sree Kanthaswamy
- Molecular Anthropology Laboratory, Department of Anthropology, California National Primate Research Center, Department of Environmental Toxicology, University of California, Davis, USA; California, School of Mathematics and Natural Sciences, Arizona State University (ASU) at the West Campus, Glendale, Arizona, USA.
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