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Bailey N, Ruiz C, Tosi A, Stevison L. Genomic analysis of the rhesus macaque ( Macaca mulatta) and the cynomolgus macaque ( Macaca fascicularis) uncover polygenic signatures of reinforcement speciation. Ecol Evol 2023; 13:e10571. [PMID: 37849934 PMCID: PMC10577069 DOI: 10.1002/ece3.10571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 10/19/2023] Open
Abstract
Speciation can involve phases of divergent adaptation in allopatry and ecological/reproductive character displacement in sympatry or parapatry. Reproductive character displacement can result as a means of preventing hybridization, a process known as reinforcement speciation. In this study, we use whole-genome sequencing (WGS) of two closely related primate species that have experienced introgression in their history, the rhesus (Macaca mulatta) and cynomolgus (M. fascicularis) macaques, to identify genes exhibiting reproductive character displacement and other patterns consistent with reinforcement speciation. Using windowed scans of various population genetic statistics to identify signatures of reinforcement, we find 184 candidate genes associated with a variety of functions, including an overrepresentation of multiple neurological functions and several genes involved in sexual development and gametogenesis. These results are consistent with a variety of genes acting in a reinforcement process between these species. We also find signatures of introgression of the Y-chromosome that confirm previous studies suggesting male-driven introgression of M. mulatta into M. fascicularis populations. This study uses WGS to find evidence of the process of reinforcement in primates that have medical and conservation relevance.
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Affiliation(s)
- Nick Bailey
- Department of Biological SciencesAuburn UniversityAuburnAlabamaUSA
| | - Cody Ruiz
- Department of AnthropologyKent State UniversityKentOhioUSA
| | - Anthony Tosi
- Department of AnthropologyKent State UniversityKentOhioUSA
| | - Laurie Stevison
- Department of Biological SciencesAuburn UniversityAuburnAlabamaUSA
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2
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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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Phadphon P, Kanthaswamy S, Oldt RF, Hamada Y, Malaivijitnond S. Population Structure of Macaca fascicularis aurea, and their Genetic Relationships with M. f. fascicularis and M. mulatta Determined by 868 RADseq-Derived Autosomal SNPs-A consideration for biomedical research. J Med Primatol 2022; 51:33-44. [PMID: 34825374 PMCID: PMC8849537 DOI: 10.1111/jmp.12554] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND This study examined the population structure of Macaca fascicularis aurea and their genetic relationships with M. f. fascicularis and M. mulatta. METHODS The study analyzed 868 RADseq-derived SNPs from samples representing the entire distribution range of M. f. aurea, including their inter- and intraspecific hybrid zones. RESULTS The study supports a M. mulatta/Indochinese M. f. fascicularis, Sundaic M. f. fascicularis, and M. f. aurea trichotomy; M. f. aurea was genetically distinct from both forms of M. f. fascicularis and M. mulatta. Hybridization between M. f. aurea and M. f. fascicularis occurred in two directions: south-north (8°25' to 15°56') and west-east (98°28' to 99°02'). Low levels of M. mulatta introgression were also detected in M. f. aurea. CONCLUSION This study showcases a complicated scenario of genetic relationships between the M. fascicularis subspecies and between M. fascicularis and M. mulatta and underscores the importance of these taxa's population structure and genetic relationships for biomedical research.
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Affiliation(s)
- Poompat Phadphon
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sree Kanthaswamy
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University West Campus, Glendale, AZ, USA,California National Primate Research Center, University of California, Davis, CA, USA,Correspondence to: Suchinda Malaivijitnond, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand. Tel./Fax: +66-2-2185275; ; Sree Kanthaswamy, School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University West Campus, Glendale, AZ, USA. Tel.: (602) 543-3405;
| | - Robert F. Oldt
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University West Campus, Glendale, AZ, USA,Evolutionary Biology Graduate Program, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Yuzuru Hamada
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi 18110, Thailand
| | - Suchinda Malaivijitnond
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand,National Primate Research Center of Thailand, Chulalongkorn University, Saraburi 18110, Thailand,Correspondence to: Suchinda Malaivijitnond, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand. Tel./Fax: +66-2-2185275; ; Sree Kanthaswamy, School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University West Campus, Glendale, AZ, USA. Tel.: (602) 543-3405;
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Colman K, Andrews RN, Atkins H, Boulineau T, Bradley A, Braendli-Baiocco A, Capobianco R, Caudell D, Cline M, Doi T, Ernst R, van Esch E, Everitt J, Fant P, Gruebbel MM, Mecklenburg L, Miller AD, Nikula KJ, Satake S, Schwartz J, Sharma A, Shimoi A, Sobry C, Taylor I, Vemireddi V, Vidal J, Wood C, Vahle JL. International Harmonization of Nomenclature and Diagnostic Criteria (INHAND): Non-proliferative and Proliferative Lesions of the Non-human Primate ( M. fascicularis). J Toxicol Pathol 2021; 34:1S-182S. [PMID: 34712008 PMCID: PMC8544165 DOI: 10.1293/tox.34.1s] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The INHAND (International Harmonization of Nomenclature and Diagnostic Criteria for Lesions Project (www.toxpath.org/inhand.asp) is a joint initiative of the Societies of Toxicologic Pathology from Europe (ESTP), Great Britain (BSTP), Japan (JSTP) and North America (STP) to develop an internationally accepted nomenclature for proliferative and nonproliferative lesions in laboratory animals. The purpose of this publication is to provide a standardized nomenclature for classifying microscopic lesions observed in most tissues and organs from the nonhuman primate used in nonclinical safety studies. Some of the lesions are illustrated by color photomicrographs. The standardized nomenclature presented in this document is also available electronically on the internet (http://www.goreni.org/). Sources of material included histopathology databases from government, academia, and industrial laboratories throughout the world. Content includes spontaneous lesions as well as lesions induced by exposure to test materials. Relevant infectious and parasitic lesions are included as well. A widely accepted and utilized international harmonization of nomenclature for lesions in laboratory animals will provide a common language among regulatory and scientific research organizations in different countries and increase and enrich international exchanges of information among toxicologists and pathologists.
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Affiliation(s)
- Karyn Colman
- Novartis Institutes for BioMedical Research, Cambridge, MA,
USA
| | - Rachel N. Andrews
- Wake Forest School of Medicine, Department of Radiation
Oncology, Winston-Salem, NC, USA
| | - Hannah Atkins
- Penn State College of Medicine, Department of Comparative
Medicine, Hershey, PA, USA
| | | | - Alys Bradley
- Charles River Laboratories Edinburgh Ltd., Tranent,
Scotland, UK
| | - Annamaria Braendli-Baiocco
- Roche Pharma Research and Early Development, Pharmaceutical
Sciences, Roche Innovation Center Basel, Switzerland
| | - Raffaella Capobianco
- Janssen Research & Development, a Division of Janssen
Pharmaceutica NV, Beerse, Belgium
| | - David Caudell
- Department of Pathology, Section on Comparative Medicine,
Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Mark Cline
- Department of Pathology, Section on Comparative Medicine,
Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Takuya Doi
- LSIM Safety Institute Corporation, Ibaraki, Japan
| | | | | | - Jeffrey Everitt
- Department of Pathology, Duke University School of
Medicine, Durham, NC, USA
| | | | | | | | - Andew D. Miller
- Cornell University College of Veterinary Medicine, Ithaca,
NY, USA
| | | | - Shigeru Satake
- Shin Nippon Biomedical Laboratories, Ltd., Kagoshima and
Tokyo, Japan
| | | | - Alok Sharma
- Covance Laboratories, Inc., Madison, WI, USA
| | | | | | | | | | | | - Charles Wood
- Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT,
USA
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Oldt RF, Bussey KJ, Settles ML, Fass JN, Roberts JA, Reader JR, Komandoor S, Abrich VA, Kanthaswamy S. MYBPC3 Haplotype Linked to Hypertrophic Cardiomyopathy in Rhesus Macaques ( Macaca mulatta). Comp Med 2020; 70:358-367. [PMID: 32753092 PMCID: PMC7574221 DOI: 10.30802/aalas-cm-19-000108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/13/2020] [Accepted: 02/07/2020] [Indexed: 11/05/2022]
Abstract
In humans, abnormal thickening of the left ventricle of the heart clinically defines hypertrophic cardiomyopathy (HCM), a common inherited cardiovascular disorder that can precede a sudden cardiac death event. The wide range of clinical presentations in HCM obscures genetic variants that may influence an individual's susceptibility to sudden cardiac death. Although exon sequencing of major sarcomere genes can be used to detect high-impact causal mutations, this strategy is successful in only half of patient cases. The incidence of left ventricular hypertrophy (LVH) in a managed research colony of rhesus macaques provides an excellent comparative model in which to explore the genomic etiology of severe HCM and sudden cardiac death. Because no rhesus HCM-associated mutations have been reported, we used a next-generation genotyping assay that targets 7 sarcomeric rhesus genes within 63 genomic sites that are orthologous to human genomic regions known to harbor HCM disease variants. Amplicon sequencing was performed on 52 macaques with confirmed LVH and 42 unrelated, unaffected animals representing both the Indian and Chinese rhesus macaque subspecies. Bias-reduced logistic regression uncovered a risk haplotype in the rhesus MYBPC3 gene, which is frequently disrupted in both human and feline HCM; this haplotype implicates an intronic variant strongly associated with disease in either homozygous or carrier form. Our results highlight that leveraging evolutionary genomic data provides a unique, practical strategy for minimizing population bias in complex disease studies.
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Affiliation(s)
- Robert F Oldt
- School of Mathematical and Natural Sciences, Arizona State University at the West Campus, Glendale, Arizona; Evolutionary Biology Graduate Program, School of Life Sciences, Arizona State University at the West Campus, Glendale, Arizona;,
| | - Kimberly J Bussey
- School of Mathematical and Natural Sciences, Arizona State University at the West Campus, Glendale, Arizona; BEYOND Center for Fundamental Concepts in Science, Arizona State University at the West Campus, Glendale, Arizona
| | - Matthew L Settles
- Bioinformatics Core, UC Davis Genome Center, University of California, Davis, California
| | - Joseph N Fass
- Bioinformatics Core, UC Davis Genome Center, University of California, Davis, California
| | - Jeffrey A Roberts
- California National Primate Research Center, University of California, Davis, California
| | - J Rachel Reader
- California National Primate Research Center, University of California, Davis, California
| | | | - Victor A Abrich
- Division of Cardiovascular Diseases, Mayo Clinic, Scottsdale, Arizona
| | - Sreetharan Kanthaswamy
- School of Mathematical and Natural Sciences, Arizona State University at the West Campus, Glendale, Arizona; Evolutionary Biology Graduate Program, School of Life Sciences, Arizona State University at the West Campus, Glendale, Arizona; California National Primate Research Center, University of California, Davis, California
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6
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Wang S, Duan Y, Yan Y, Adar C, Braslavsky I, Chen B, Huang T, Qiu S, Li X, Inglis BM, Ji W, Si W. Improvement of sperm cryo-survival of cynomolgus macaque (Macaca fascicularis) by commercial egg-yolk-free freezing medium with type III antifreeze protein. Anim Reprod Sci 2019; 210:106177. [PMID: 31635783 DOI: 10.1016/j.anireprosci.2019.106177] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 08/24/2019] [Accepted: 09/04/2019] [Indexed: 11/26/2022]
Abstract
When nonhuman primate sperm undergoes cryopreservation in an egg yolk medium there is an increased risk that the egg yolk might adversely affect the sperm due to containing of avian pathogens. Although commercial egg-yolk-free medium for human sperm cryopreservation has been used for macaque sperm, the cryo-survival remains less than optimal. The present study, therefore, was conducted to determine the optimal concentration of antifreeze protein (AFP) III supplemented in a commercial egg-yolk-free medium for cynomolgus macaque (Macaca fascicularis) sperm cryo-survival. The function of frozen-thawed sperm was evaluated by post-thaw sperm motility, acrosome integrity, and mitochondrial function. Results indicate that the sperm motilities were greater when 0.1, 1, and 10 μg/ml of AFP III were supplemented into the sperm freezing medium (P < 0.05). In addition, the mitochondrial membrane potential was greater in the sperm cryopreserved with the medium that was supplemented with 0.1 μg/ml of AFP III (P < 0.05). The addition of AFP III at any of the concentrations, however, did not have any cryoprotection effect on the sperm acrosome, and the greatest concentrations of AFP III at 100 and 200 μg/ml had detrimental effects on acrosomal integrity (P < 0.05). Results of the present study indicated the methods used are effective for the cryopreservation of cynomolgus monkey sperm while reducing associated health risks due to avian pathogens being present in egg yolk-based extenders.
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Affiliation(s)
- Shengnan Wang
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
| | - Yanchao Duan
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
| | - Yaping Yan
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
| | - Chen Adar
- Institute of Biochemistry, Food Science, and Nutrition, Robert H. Smith Faculty of Agriculture, Food, and Environment, & Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Ido Braslavsky
- Institute of Biochemistry, Food Science, and Nutrition, Robert H. Smith Faculty of Agriculture, Food, and Environment, & Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Bingbing Chen
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
| | - Tianzhuang Huang
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
| | - Shuai Qiu
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
| | - Xi Li
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
| | - Briauna Marie Inglis
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
| | - Weizhi Ji
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
| | - Wei Si
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, Yunnan, China.
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7
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Oldt RF, Kanthaswamy S, Montes M, Schumann L, Grijalva J, Bunlungsup S, Houghton P, Smith DG, Malaivijitnond S. Population genetics of the ABO locus within the rhesus (Macaca mulatta
) and cynomolgus (M. fascicularis
) macaque hybrid zone. Int J Immunogenet 2018; 46:38-48. [DOI: 10.1111/iji.12405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 10/05/2018] [Indexed: 01/23/2023]
Affiliation(s)
- Robert F. Oldt
- School of Mathematics and Natural Sciences; Arizona State University (ASU) at the West Campus; Glendale Arizona
- Evolutionary Biology Graduate Program, School of Life Sciences; ASU; Tempe Arizona
| | - Sreetharan Kanthaswamy
- School of Mathematics and Natural Sciences; Arizona State University (ASU) at the West Campus; Glendale Arizona
- California National Primate Research Center; University of California; Davis California
| | - Mae Montes
- School of Mathematics and Natural Sciences; Arizona State University (ASU) at the West Campus; Glendale Arizona
| | - Laura Schumann
- School of Mathematics and Natural Sciences; Arizona State University (ASU) at the West Campus; Glendale Arizona
| | - Jose Grijalva
- School of Mathematics and Natural Sciences; Arizona State University (ASU) at the West Campus; Glendale Arizona
| | - Srichan Bunlungsup
- National Primate Research Center of Thailand; Chulalongkorn University; Saraburi Thailand
| | | | - David Glenn Smith
- California National Primate Research Center; University of California; Davis California
- Molecular Anthropology Laboratory, Department of Anthropology; University of California; Davis California
| | - Suchinda Malaivijitnond
- National Primate Research Center of Thailand; Chulalongkorn University; Saraburi Thailand
- Department of Biology, Faculty of Science; Chulalongkorn University; Bangkok Thailand
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8
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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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