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Fan Z, Zhang R, Zhou A, Hey J, Song Y, Osada N, Hamada Y, Yue B, Xing J, Li J. Genomic Evidence for the Complex Evolutionary History of Macaques (Genus Macaca). J Mol Evol 2024; 92:286-299. [PMID: 38634872 DOI: 10.1007/s00239-024-10166-z] [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: 11/16/2023] [Accepted: 03/20/2024] [Indexed: 04/19/2024]
Abstract
The genus Macaca is widely distributed, occupies a variety of habitats, shows diverse phenotypic characteristics, and is one of the best-studied genera of nonhuman primates. Here, we reported five re-sequencing Macaca genomes, including one M. cyclopis, one M. fuscata, one M. thibetana, one M. silenus, and one M. sylvanus. Together with published genomes of other macaque species, we combined 20 genome sequences of 10 macaque species to investigate the gene introgression and genetic differences among the species. The network analysis of the SNV-fragment trees indicates a reticular phylogeny of macaque species. Combining the results from various analytical methods, we identified extensive ancient introgression events among macaque species. The multiple introgression signals between different species groups were also observed, such as between fascicularis group species and silenus group species. However, gene flow signals between fascicularis and sinica group were not as strong as those between fascicularis group and silenus group. On the other hand, the unidirect gene flow in M. arctoides probably occurred between the progenitor of M. arctoides and the common ancestor of fascicularis group. Our study also shows that the genetic backgrounds and genetic diversity of different macaques vary dramatically among species, even among populations of the same species. In conclusion, using whole genome sequences and multiple methods, we have studied the evolutionary history of the genus Macaca and provided evidence for extensive introgression among the species.
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Affiliation(s)
- Zhenxin Fan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Rusong Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Anbo Zhou
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Jody Hey
- Department of Biology, Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, USA
| | - Yang Song
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Naoki Osada
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido, 060-0814, Japan
| | - Yuzuru Hamada
- National Primate Research Center of Thailand, Chulalongkorn University, Bangkok, Thailand
| | - Bisong Yue
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Jinchuan Xing
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Jing Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.
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Rivas-González I, Rousselle M, Li F, Zhou L, Dutheil JY, Munch K, Shao Y, Wu D, Schierup MH, Zhang G. Pervasive incomplete lineage sorting illuminates speciation and selection in primates. Science 2023; 380:eabn4409. [PMID: 37262154 DOI: 10.1126/science.abn4409] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/19/2023] [Indexed: 06/03/2023]
Abstract
Incomplete lineage sorting (ILS) causes the phylogeny of some parts of the genome to differ from the species tree. In this work, we investigate the frequencies and determinants of ILS in 29 major ancestral nodes across the entire primate phylogeny. We find up to 64% of the genome affected by ILS at individual nodes. We exploit ILS to reconstruct speciation times and ancestral population sizes. Estimated speciation times are much more recent than genomic divergence times and are in good agreement with the fossil record. We show extensive variation of ILS along the genome, mainly driven by recombination but also by the distance to genes, highlighting a major impact of selection on variation along the genome. In many nodes, ILS is reduced more on the X chromosome compared with autosomes than expected under neutrality, which suggests higher impacts of natural selection on the X chromosome. Finally, we show an excess of ILS in genes with immune functions and a deficit of ILS in housekeeping genes. The extensive ILS in primates discovered in this study provides insights into the speciation times, ancestral population sizes, and patterns of natural selection that shape primate evolution.
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Affiliation(s)
- Iker Rivas-González
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | | | - Fang Li
- BGI-Research, BGI-Wuhan, Wuhan 430074, China
- Institute of Animal Sex and Development, ZhejiangWanli University, Ningbo 315104, China
- BGI-Research, BGI-Shenzhen, Shenzhen 518083, China
| | - Long Zhou
- Evolutionary & Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou 310058, China
- Women's Hospital, School of Medicine, Zhejiang University, Shangcheng District, Hangzhou 310006, China
| | - Julien Y Dutheil
- Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute of Evolution Sciences of Montpellier (ISEM), CNRS, University of Montpellier, IRD, EPHE, 34095 Montpellier, France
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic and Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Guojie Zhang
- Evolutionary & Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou 310058, China
- Women's Hospital, School of Medicine, Zhejiang University, Shangcheng District, Hangzhou 310006, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
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Kumpai P, Hamada Y, Kanthaswamy S, Malaivijitnond S. Gene flow from rhesus (Macaca mulatta) to cynomolgus macaques (M. fascicularis) and effects of introgressive hybridization on reproduction in two biomedically relevant non-human primate species. J Med Primatol 2022; 51:108-118. [PMID: 35132636 DOI: 10.1111/jmp.12570] [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: 12/14/2021] [Revised: 01/24/2022] [Accepted: 01/28/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND We compared the reproductive patterns of wild Indochinese and Sundaic cynomolgus macaques (Mf) exhibiting different levels of genetic admixture with rhesus macaques (Mm). METHODS Ten adult females from each Indochinese (WHM) and Sundaic (KN/KTK) Mf populations, which exhibited 50% and 15% of Mm autosomal SNPs, were selected as focal animals. Animals were observed for 12 months, and the frequencies of sexual proceptivity, attractivity and receptivity, number of newborns, and changes in sex skin were recorded. RESULTS Both populations showed all three sexual behaviors throughout the year, but they were classified as moderately seasonal breeders because their 3-month birth counts were as high as ~50%. The fecundity of WHM was lower than the KN/KTK. Changes in sex skin of WHM were more prone to Mm's pattern than the KN/KTK. CONCLUSION The introgressive gene flow from Mm to Mf does not affect Mf's sexual behaviors; however, it can impact fecundity and physiological (sex skin) changes.
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Affiliation(s)
- Prangmas Kumpai
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Yuzuru Hamada
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi, Thailand
| | - Sree Kanthaswamy
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University West Campus, Glendale, Arizona, USA.,California National Primate Research Center, University of California, Davis, California, USA
| | - 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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4
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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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5
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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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6
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Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression. PLoS Biol 2020; 18:e3000954. [PMID: 33270638 PMCID: PMC7738166 DOI: 10.1371/journal.pbio.3000954] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 12/15/2020] [Accepted: 11/02/2020] [Indexed: 12/17/2022] Open
Abstract
Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here, we present new reference genome assemblies for 3 Old World monkey (OWM) species: Colobus angolensis ssp. palliatus (the black and white colobus), Macaca nemestrina (southern pig-tailed macaque), and Mandrillus leucophaeus (the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place. Combining three newly sequenced primate genomes with other published genomes, this study adapts a little-known method for detecting ancient introgression to genome-scale data, revealing multiple previously unknown examples of hybridization between primate species.
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7
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Chaney ME, Romine MG, Piontkivska H, Tosi AJ. Diversifying selection detected in only a minority of xenobiotic-metabolizing CYP1-3 genes among primate species. Xenobiotica 2020; 50:1406-1412. [PMID: 32558606 DOI: 10.1080/00498254.2020.1785580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 10/24/2022]
Abstract
1. Primates exhibit a high degree of among-species dietary diversity, which likely exposes them to varying levels of xenobiotic compounds. Here, we examined the evolution of primate CYP1-3 gene families, and we classified the 15 CYP1-3 gene subfamilies as either xenobiotic-metabolizing (XM) or endogenous-metabolizing (EM) based on sources in the P450 literature. 2. We predicted that XM P450s would show (1) greater variability in gene-copy number and (2) more evidence of diversifying selection and, especially on codons that encode the substrate-recognition sites (SRSs) for the final enzymes. 3. Counter to our first prediction, EM and XM P450s showed similar levels of variation in gene-copy number. We did find, however, that four XM P450 subfamilies (CYP2C, CYP2D, CYP2E, and CYP3A) showed evidence of diversifying selection while no EM subfamilies demonstrated any consistent signal of diversifying selection. Of these four, CYP2C, CYP2D, and CYP3A showed significant links between SRSs and diversifying selection. 4. These results reveal an amount of evolutionary dynamism that would not be expected when viewing P450 subfamilies along a simple binary EM/XM spectrum. We recommend that comparative studies of cytochrome P450 evolution should focus on the CYP2C, CYP2D, CYP2E, and CYP3A subfamilies.
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Affiliation(s)
- Morgan E Chaney
- Department of Anthropology, Kent State University, Kent, OH, USA
- School of Biomedical Sciences, Kent State University, Kent, OH, USA
| | - Melia G Romine
- Department of Anthropology, Kent State University, Kent, OH, USA
| | - Helen Piontkivska
- School of Biomedical Sciences, Kent State University, Kent, OH, USA
- Department of Biological Sciences, Kent State University, Kent, OH, USA
| | - Anthony J Tosi
- Department of Anthropology, Kent State University, Kent, OH, USA
- School of Biomedical Sciences, Kent State University, Kent, OH, 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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9
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Shiina T, Blancher A. The Cynomolgus Macaque MHC Polymorphism in Experimental Medicine. Cells 2019; 8:E978. [PMID: 31455025 PMCID: PMC6770713 DOI: 10.3390/cells8090978] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 02/07/2023] Open
Abstract
Among the non-human primates used in experimental medicine, cynomolgus macaques (Macaca fascicularis hereafter referred to as Mafa) are increasingly selected for the ease with which they are maintained and bred in captivity. Macaques belong to Old World monkeys and are phylogenetically much closer to humans than rodents, which are still the most frequently used animal model. Our understanding of the Mafa genome has progressed rapidly in recent years and has greatly benefited from the latest technical advances in molecular genetics. Cynomolgus macaques are widespread in Southeast Asia and numerous studies have shown a distinct genetic differentiation of continental and island populations. The major histocompatibility complex of cynomolgus macaque (Mafa MHC) is organized in the same way as that of human, but it differs from the latter by its high degree of classical class I gene duplication. Human polymorphic MHC regions play a pivotal role in allograft transplantation and have been associated with more than 100 diseases and/or phenotypes. The Mafa MHC polymorphism similarly plays a crucial role in experimental allografts of organs and stem cells. Experimental results show that the Mafa MHC class I and II regions influence the ability to mount an immune response against infectious pathogens and vaccines. MHC also affects cynomolgus macaque reproduction and impacts on numerous biological parameters. This review describes the Mafa MHC polymorphism and the methods currently used to characterize it. We discuss some of the major areas of experimental medicine where an effect induced by MHC polymorphism has been demonstrated.
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Affiliation(s)
- Takashi Shiina
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Antoine Blancher
- Centre de Physiopathologie Toulouse-Purpan (CPTP), Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (Inserm), Université Paul Sabatier (UPS), Toulouse 31000, France.
- Laboratoire d'immunologie, CHU de Toulouse, Institut Fédératif de Biologie, hôpital Purpan, 330 Avenue de Grande Bretagne, TSA40031, 31059 Toulouse CEDEX 9, France.
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10
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Boel C, Curnoe D, Hamada Y. Craniofacial Shape and Nonmetric Trait Variation in Hybrids of the Japanese Macaque (Macaca fuscata) and the Taiwanese Macaque (Macaca cyclopis). INT J PRIMATOL 2019. [DOI: 10.1007/s10764-019-00081-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization. BIOINFORMATICS AND PHYLOGENETICS 2019. [DOI: 10.1007/978-3-030-10837-3_13] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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12
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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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13
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Ikeda M, Satomura K, Sekizuka T, Hanada K, Endo T, Osada N. Comprehensive phylogenomic analysis reveals a novel cluster of simian endogenous retroviral sequences in Colobinae monkeys. Am J Primatol 2018; 80:e22882. [PMID: 29896810 DOI: 10.1002/ajp.22882] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 05/17/2018] [Accepted: 05/25/2018] [Indexed: 01/10/2023]
Abstract
Simian retrovirus (SRV) is a type-D betaretrovirus infectious to the Old World monkeys causing a variety of symptoms. SRVs are also present in the Old World monkey genomes as endogenous forms, which are referred to as Simian endogenous retroviruses (SERVs). Although many SERV sequences have been identified in Cercopithecinae genomes, with potential of encoding all functional genes, the distribution of SERVs in genomes and evolutionary relationship between exogeneous SRVs and SERVs remains unclear. In this study, we comprehensively investigated seven draft genome sequences of the Old World monkeys, and identified a novel cluster of SERVs in the two Rhinopithecus (R. roxellana and R. bieti) genomes, which belong to the Colobinae subfamily. The Rhinopithecus genomes harbored higher copy numbers of SERVs than the Cercopithecinae genomes. A reconstructed phylogenetic tree showed that the Colobinae SERVs formed a distinct cluster from SRVs and Cercopithecinae SERVs, and more closely related to exogenous SRVs than Cercopithecinae SERVs. Three radical amino acid substitutions specific to Cercopithecinae SERVs, which potentially affect the infectious ability of SERVs, were also identified in the proviral envelope protein. In addition, we found many integration events of SERVs were genus- or species-specific, suggesting the recent activity of SERVs in the Old World monkey genomes. The results suggest that SERVs in Cercopithecinae and Colobinae monkeys were endogenized after the divergence of subfamilies and do not transmit across subfamilies. Our findings also support the hypothesis that Colobinae SERVs are direct ancestors of SRV-6, which has a different origin from the other exogenous SRVs. These findings shed novel insight into the evolutionary history of SERVs, and may help to understand the process of endogenization of SRVs.
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Affiliation(s)
- Masaki Ikeda
- Department of Information Science and Technology, Hokkaido University, Hokkaido, Japan
| | - Kazuhiro Satomura
- Department of Information Science and Technology, Hokkaido University, Hokkaido, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kentaro Hanada
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Toshinori Endo
- Department of Information Science and Technology, Hokkaido University, Hokkaido, Japan
| | - Naoki Osada
- Department of Information Science and Technology, Hokkaido University, Hokkaido, Japan.,Global Station for Bid Data and Cybersecurity, GI-CoRE, Hokkaido University, Hokkaido, Japan
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14
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Ito T, Koyabu D. Biogeographic variation in skull morphology across the Kra Isthmus in dusky leaf monkeys. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Tsuyoshi Ito
- Department of Evolution and Phylogeny; Primate Research Institute; Kyoto University; Inuyama Aichi Japan
| | - Daisuke Koyabu
- The University Museum; The University of Tokyo; Bunkyo-ku Tokyo Japan
- Department of Humanities and Sciences; Musashino Art University
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15
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Uno Y, Uehara S, Yamazaki H. Polymorphisms of cytochrome P450 2B6 (CYP2B6) in cynomolgus and rhesus macaques. J Med Primatol 2018; 47:232-237. [PMID: 29468688 DOI: 10.1111/jmp.12336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2018] [Indexed: 11/26/2022]
Abstract
BACKGROUND Cytochrome P450 2B6 (CYP2B6) is an important drug-metabolizing enzyme and is expressed in liver. Although human CYP2B6 variants account for variable enzyme properties among individuals and populations, CYP2B6 genetic variants have not been investigated in cynomolgus macaques, widely used in drug metabolism studies. METHODS CYP2B6 was resequenced in 120 cynomolgus macaques and 23 rhesus macaques by direct sequencing. RESULTS Twenty-three non-synonymous variants were found, of which 12 and 3 were unique to cynomolgus macaques and rhesus macaques, respectively. By functional characterization using the 14 variant proteins, 8 variants (V114I, R253C, M435I, V459M, L465P, C475S, R487C, and R487H) showed different rate (>1.5-fold) of testosterone 16β-hydroxylation to wild type. However, the four variants (M435I, L465P, C475S, and R487H) were analyzed in liver microsomes, and the catalytic rates were not substantially different from wild type. CONCLUSIONS Macaque CYP2B6 was polymorphic, and the genotype could partly account for variable enzyme activities of macaque CYP2B6.
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Affiliation(s)
- Yasuhiro Uno
- Pharmacokinetics and Bioanalysis Center, Shin Nippon Biomedical Laboratories, Ltd., Kainan, Japan
| | - Shotaro Uehara
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Japan
| | - Hiroshi Yamazaki
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Japan
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16
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Bunlungsup S, Kanthaswamy S, Oldt RF, Smith DG, Houghton P, Hamada Y, Malaivijitnond S. Genetic analysis of samples from wild populations opens new perspectives on hybridization between long-tailed (Macaca fascicularis) and rhesus macaques (Macaca mulatta). Am J Primatol 2017; 79. [PMID: 29095514 DOI: 10.1002/ajp.22726] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 10/25/2017] [Accepted: 10/26/2017] [Indexed: 11/12/2022]
Abstract
In the past decade, many researchers have published papers about hybridization between long-tailed and rhesus macaques. These previous works have proposed unidirectional gene flow with the Isthmus of Kra as the zoogeographical barrier of hybridization. However, these reports analyzed specimens of unknown origin and/or did not include specimens from Thailand, the center of the proposed area of hybridization. Collected specimens of long-tailed and rhesus macaques representing all suspected hybridization areas were examined. Blood samples from four populations each of long-tailed and rhesus macaques inhabiting Thailand, Myanmar, and Laos were collected and analyzed with conspecific references from China (for rhesus macaques) and multiple countries from Sundaic regions (for long-tailed macaques). Ninety-six single nucleotide polymorphism (SNP) markers specifically designed to interrogate admixture and ancestry were used in genotyping. We found genetic admixture maximized at the hybrid zone (15-20°N), as well as admixture signals of varying strength in both directions outside of the hybrid zone. These findings show that the Isthmus of Kra is not a barrier to gene flow from rhesus to long-tailed populations. However, to precisely identify a southernmost barrier, if in fact a boundary rather than simple isolation by distance exists, the samples from peninsular Malaysia must be included in the analysis. Additionally, a long-tailed to rhesus gene flow boundary was found between northern Thailand and Myanmar. Our results suggest that selection of long-tailed and rhesus macaques, the two most commonly used non-human primates for biomedical research, should take into account not only the species identification but also the origin of and genetic admixture within and between the species.
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Affiliation(s)
- Srichan Bunlungsup
- Faculty of Science, Department of Biology, Chulalongkorn University, Bangkok, Thailand
| | - Sree Kanthaswamy
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University West Campus, Glendale, Arizona.,University of California, California National Primate Research Center, Davis, California
| | - Robert F Oldt
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University West Campus, Glendale, Arizona.,Evolutionary Biology Graduate Program, School of Life Sciences, Arizona State University, Tempe, Arizona
| | - David Glenn Smith
- Molecular Anthropology Laboratory, Department of Anthropology, University of California, Davis, California
| | | | - Yuzuru Hamada
- Evolutionary Morphology Section, Primate Research Institute, Kyoto University, Aichi, Japan
| | - 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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17
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Tung J, Barreiro LB. The contribution of admixture to primate evolution. Curr Opin Genet Dev 2017; 47:61-68. [PMID: 28923540 DOI: 10.1016/j.gde.2017.08.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/08/2017] [Accepted: 08/31/2017] [Indexed: 12/16/2022]
Abstract
Genome-wide data on genetic variation are now available for multiple primate species and populations, facilitating analyses of evolutionary history within and across taxa. One emerging theme from these studies involves the central role of admixture. Genomic data sets indicate that both ancient gene flow following initial taxonomic divergence and ongoing gene flow at current species boundaries are common. These findings are of particular interest given evidence for a complex history of admixture in our own lineage, including examples of ecologically driven adaptive introgression. Like other aspects of human biology, studies of nonhuman primates thus provide both comparative context and a living model for understanding admixture dynamics in hominins. We highlight several open questions that could be addressed in future work.
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Affiliation(s)
- Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA; Duke University Population Research Institute, Duke University, Durham, NC 27708, USA; Institute of Primate Research, National Museums of Kenya, Karen, Nairobi, Kenya.
| | - Luis B Barreiro
- Department of Pediatrics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
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18
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Wango TL, Musiega D, Mundia CN, Altmann J, Alberts SC, Tung J. Climate and Land Cover Analysis Suggest No Strong Ecological Barriers to Gene Flow in a Natural Baboon Hybrid Zone. INT J PRIMATOL 2017. [DOI: 10.1007/s10764-017-9989-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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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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20
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Nomiyama H, Osada N, Takahashi I, Terao K, Yamagata K, Yoshie O. Translational Repression of a Splice Variant of Cynomolgus Macaque CXCL1L by Its C-Terminal Sequence. J Interferon Cytokine Res 2017; 37:129-138. [PMID: 28186423 DOI: 10.1089/jir.2016.0085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We previously isolated a cDNA clone from cynomolgus macaque encoding a novel CXC chemokine that we termed CXCL1L from its close similarity to CXCL1. However, the cDNA consisted of 3 exons instead of 4 exons that were typically seen in other CXC chemokines. Here, we isolated a cDNA encoding the full-length variant of CXCL1L that we termed CXCL1Lβ. CXCL1Lβ is 50 amino acids longer than the original CXCL1L, which we now term CXCL1Lα. The CXCL1Lβ mRNA is much more abundantly expressed in the cynomolgus macaque tissues than CXCL1Lα mRNA. However, CXCL1Lβ protein was poorly produced by transfected cells compared with that of CXCL1Lα. When the coding region of the fourth exon was fused to the C-terminus of CXCL1 or even to a nonsecretory protein firefly luciferase, the fused proteins were also barely produced, although the mRNAs were abundantly expressed. The polysome profiling analysis suggested that the inhibition was mainly at the translational level. Furthermore, we demonstrated that the C-terminal 5 amino acids of CXCL1Lβ were critical for the translational repression. The present study, thus, reveals a unique translational regulation controlling the production of a splicing variant of CXCL1L. Since the CXCL1L gene is functional only in the Old World monkeys, we also discuss possible reasons for the conservation of the active CXCL1L gene in these monkeys during the primate evolution.
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Affiliation(s)
- Hisayuki Nomiyama
- 1 Department of Molecular Enzymology, Kumamoto University Graduate School of Medical Sciences , Kumamoto, Japan
| | - Naoki Osada
- 2 Division of Bioengineering and Bioinformatics, Graduate School of Information Science and Technology, Hokkaido University , Sapporo, Japan
| | - Ichiro Takahashi
- 3 Tsukuba Primate Research Center, National Institute of Biomedical Innovation , Health and Nutrition (NIBIOHN), Tsukuba, Japan
| | - Keiji Terao
- 3 Tsukuba Primate Research Center, National Institute of Biomedical Innovation , Health and Nutrition (NIBIOHN), Tsukuba, Japan
| | - Kazuya Yamagata
- 4 Department of Medical Biochemistry, Faculty of Life Sciences, Kumamoto University , Kumamoto, Japan
| | - Osamu Yoshie
- 5 The Health and Kampo Institute , Sendai, Japan
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21
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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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22
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Osada N. Genetic diversity in humans and non-human primates and its evolutionary consequences. Genes Genet Syst 2016; 90:133-45. [PMID: 26510568 DOI: 10.1266/ggs.90.133] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Genetic diversity is a key parameter in population genetics and is important for understanding the process of evolution and for the development of appropriate conservation strategies. Recent advances in sequencing technology have enabled the measurement of genetic diversity of various organisms at the nucleotide level and on a genome-wide scale, yielding more precise estimates than were previously achievable. In this review, I have compiled and summarized the estimates of genetic diversity in humans and non-human primates based on recent genome-wide studies. Although studies on population genetics demonstrated fluctuations in population sizes over time, general patterns have emerged. As shown previously, genetic diversity in humans is one of the lowest among primates; however, certain other primate species exhibit genetic diversity that is comparable to or even lower than that in humans. There exists greater than 10-fold variation in genetic diversity among primate species, and I found weak correlation with species fecundity but not with body or propagule size. I further discuss the potential evolutionary consequences of population size decline on the evolution of primate species. The level of genetic diversity negatively correlates with the ratio of non-synonymous to synonymous polymorphisms in a population, suggesting that proportionally greater numbers of slightly deleterious mutations segregate in small rather than large populations. Although population size decline is likely to promote the fixation of slightly deleterious mutations, there are molecular mechanisms, such as compensatory mutations at various molecular levels, which may prevent fitness decline at the population level. The effects of slightly deleterious mutations from theoretical and empirical studies and their relevance to conservation biology are also discussed in this review.
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Affiliation(s)
- Naoki Osada
- Department of Population Genetics, National Institute of Genetics
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23
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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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24
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Jadejaroen J, Kawamoto Y, Hamada Y, Malaivijitnond S. An SNP marker at the STAT6 locus can identify the hybrids between rhesus (Macaca mulatta) and long-tailed macaques (M. fascicularis) in Thailand: a rapid and simple screening method and its application. Primates 2015; 57:93-102. [PMID: 26660683 DOI: 10.1007/s10329-015-0502-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/13/2015] [Indexed: 11/29/2022]
Abstract
A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay was developed to genetically discriminate rhesus (Macaca mulatta) macaques from long-tailed (M. fascicularis) macaques. The 745 bp PCR amplicon of the STAT6 locus that spans a potentially species-diagnostic single nucleotide polymorphism (SNP) marker was digested with ApaI and gel electrophoresed to give (1) two (234 and 511 bp), (2) one (745 bp) and (3) three (234, 511 and 745 bp) band patterns that correspond to the genotypes G/G (long-tailed macaque specific homozygote), A/A (rhesus macaque specific homozygote) and A/G (hybrid specific heterozygote), respectively. The diagnostic robustness and efficiency of this PCR-RFLP assay was tested on wild rhesus and long-tailed macaques inhabiting Thailand and a known hybrid population. The Indochinese and Sundaic long-tailed macaque samples (n = 18) all showed a homozygous G/G pattern, while the Indochinese rhesus macaques (n = 10) all showed a homozygous A/A pattern. The rhesus/long-tailed hybrid population at Khao Khieow Open Zoo, which resulted from an introduced group of rhesus macaques that hybridized with the indigenous long-tailed macaques about 20 years ago, revealed 47% (56/118 samples analyzed) with the heterogenous A/G genotype. In addition, the frequency of the rhesus-specific allele A significantly decreased in the hybrid population during 2006-2014, where a strong association between the STAT6 genotype and the morphology of the individuals was detected. In conclusion, a robust PCR-RFLP assay allows a simple, effective and inexpensive approach, in particular for field studies, to assess hybrid individuals between rhesus and long-tailed macaques. Although this assay cannot conclusively identify all the hybrids over two or more generations, it at least can allow the evaluation of the process of hybridization, and so it is applicable to the assessment of the status of natural or anthropogenic hybridization between the two species across their geographic range.
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Affiliation(s)
- Janya Jadejaroen
- Zoological Science Program, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Yoshi Kawamoto
- Genome Diversity Section, Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Kyoto, Japan
| | - Yuzuru Hamada
- Evolutionary Morphology Section, Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Kyoto, Japan
| | - Suchinda Malaivijitnond
- Zoological Science Program, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand. .,National Primate Research Center of Thailand, Chulalongkorn University, Saraburi, Thailand.
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25
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Hamada Y, San AM, Malaivijitnond S. Assessment of the hybridization between rhesus (Macaca mulatta) and long-tailed macaques (M. fascicularis) based on morphological characters. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 159:189-98. [PMID: 26354607 DOI: 10.1002/ajpa.22862] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 08/20/2015] [Accepted: 08/25/2015] [Indexed: 11/11/2022]
Abstract
OBJECTIVES Hybridization between rhesus (Macaca mulatta) and long-tailed (M. fascicularis) macaques has become a focal point of interest. The majority of such studies have evaluated their genetics, but not their morphological characters. MATERIALS AND METHODS We analyzed morphological characters of eight free-ranging populations of Indochinese rhesus and long-tailed macaques distributed at the proposed hybrid zone (15.75-21.58° N) in comparison with one population each of Chinese and Indian-derived rhesus macaques and three populations of Sundaic long-tailed macaques. RESULTS Chinese and Indian rhesus macaques had a heavier body mass, longer crown-rump length, shorter relative facial length and relative tail length, and a greater contrast of reddish and yellowish dorsal pelage color than the Sundaic long-tailed macaques for which the latter three parameters could be used to visually discriminate between the two species. Although the morphological characters of Indochinese rhesus and long-tailed macaques were intermediate between the Chinese/Indian rhesus and Sundaic long-tailed macaques, they were more similar to their respective conspecifics. The species-specific characters of a shorter tail (<70%) and a bipartite pelage color pattern were retained in the Indochinese rhesus macaques while the longer tail (>90%) and no bipartite pattern was found in the Indochinese long-tailed macaques. No morphological cline was observed across the species and the variations were abrupt to some extent. DISCUSSION The hybridization between rhesus and long-tailed macaques may be results of multiple contacts and isolations over a long period of time, thus their evolutionary history should not be drawn solely by genetic or morphological analysis.
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Affiliation(s)
- Yuzuru Hamada
- Evolutionary Morphology Section, Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Japan
| | - 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, Chulalongkorn University, Saraburi, Thailand
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Suzuki-Hashido N, Hayakawa T, Matsui A, Go Y, Ishimaru Y, Misaka T, Abe K, Hirai H, Satta Y, Imai H. Rapid Expansion of Phenylthiocarbamide Non-Tasters among Japanese Macaques. PLoS One 2015. [PMID: 26201026 PMCID: PMC4511751 DOI: 10.1371/journal.pone.0132016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Bitter taste receptors (TAS2R proteins) allow mammals to detect and avoid ingestion of toxins in food. Thus, TAS2Rs play an important role in food choice and are subject to complex natural selection pressures. In our previous study, we examined nucleotide variation in TAS2R38, a gene expressing bitter taste receptor for phenylthiocarbamide (PTC), in 333 Japanese macaques (Macaca fuscata) from 9 local populations in Japan. We identified a PTC “non-taster” TAS2R38 allele in Japanese macaques that was caused by a loss of the start codon. This PTC non-taster allele was only found in a limited local population (the Kii area), at a frequency of 29%. In this study, we confirmed that this allele was present in only the Kii population by analyzing an additional 264 individuals from eight new populations. Using cellular and behavioral experiments, we found that this allele lost its receptor function for perceiving PTC. The nucleotide sequences of the allele including flanking regions (of about 10 kb) from 23 chromosomes were identical, suggesting that a non-taster allele arose and expanded in the Kii population during the last 13,000 years. Genetic analyses of non-coding regions in Kii individuals and neighboring populations indicated that the high allele frequency in the Kii population could not be explained by demographic history, suggesting that positive selection resulted in a rapid increase in PTC non-tasters in the Kii population. The loss-of-function that occurred at the TAS2R38 locus presumably provided a fitness advantage to Japanese macaques in the Kii population. Because TAS2R38 ligands are often found in plants, this functional change in fitness is perhaps related to feeding habit specificity. These findings should provide valuable insights for elucidating adaptive evolutionary changes with respect to various environments in wild mammals.
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Affiliation(s)
- Nami Suzuki-Hashido
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Takashi Hayakawa
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Atsushi Matsui
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Yasuhiro Go
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Yoshiro Ishimaru
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takumi Misaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Keiko Abe
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Hirohisa Hirai
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa, Japan
- * E-mail: (YS); (HI)
| | - Hiroo Imai
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa, Japan
- * E-mail: (YS); (HI)
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Contrasted patterns of variation and evolutionary convergence at the antiviral OAS1 gene in old world primates. Immunogenetics 2015; 67:487-99. [PMID: 26156123 PMCID: PMC4809017 DOI: 10.1007/s00251-015-0855-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 06/24/2015] [Indexed: 11/13/2022]
Abstract
The oligoadenylate synthetase 1 (OAS1) enzyme acts as an innate sensor of viral infection and plays a major role in the defense against a wide diversity of viruses. Polymorphisms at OAS1 have been shown to correlate with differential susceptibility to several infections of great public health significance, including hepatitis C virus, SARS coronavirus, and West Nile virus. Population genetics analyses in hominoids have revealed interesting evolutionary patterns. In Central African chimpanzee, OAS1 has evolved under long-term balancing selection, resulting in the persistence of polymorphisms since the origin of hominoids, whereas human populations have acquired and retained OAS1 alleles from Neanderthal and Denisovan origin. We decided to further investigate the evolution of OAS1 in primates by characterizing intra-specific variation in four species commonly used as models in infectious disease research: the rhesus macaque, the cynomolgus macaque, the olive baboon, and the Guinea baboon. In baboons, OAS1 harbors a very low level of variation. In contrast, OAS1 in macaques exhibits a level of polymorphism far greater than the genomic average, which is consistent with the action of balancing selection. The region of the enzyme that directly interacts with viral RNA, the RNA-binding domain, contains a number of polymorphisms likely to affect the RNA-binding affinity of OAS1. This strongly suggests that pathogen-driven balancing selection acting on the RNA-binding domain of OAS1 is maintaining variation at this locus. Interestingly, we found that a number of polymorphisms involved in RNA-binding were shared between macaques and chimpanzees. This represents an unusual case of convergent polymorphism.
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Osada N, Hettiarachchi N, Adeyemi Babarinde I, Saitou N, Blancher A. Whole-genome sequencing of six Mauritian Cynomolgus macaques (Macaca fascicularis) reveals a genome-wide pattern of polymorphisms under extreme population bottleneck. Genome Biol Evol 2015; 7:821-30. [PMID: 25805843 PMCID: PMC5322541 DOI: 10.1093/gbe/evv033] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Cynomolgus macaques (Macaca fascicularis) were introduced to the island of Mauritius by humans around the 16th century. The unique demographic history of the Mauritian cynomolgus macaques provides the opportunity to not only examine the genetic background of well-established nonhuman primates for biomedical research but also understand the effect of an extreme population bottleneck on the pattern of polymorphisms in genomes. We sequenced the whole genomes of six Mauritian cynomolgus macaques and obtained an average of 20-fold coverage of the genome sequences for each individual. The overall level of nucleotide diversity was 23% smaller than that of the Malaysian cynomolgus macaques, and a reduction of low-frequency polymorphisms was observed. In addition, we also confirmed that the Mauritian cynomolgus macaques were genetically closer to a representative of the Malaysian population than to a representative of the Indochinese population. Excess of nonsynonymous polymorphisms in low frequency, which has been observed in many other species, was not very strong in the Mauritian samples, and the proportion of heterozygous nonsynonymous polymorphisms relative to synonymous polymorphisms is higher within individuals in Mauritian than Malaysian cynomolgus macaques. Those patterns indicate that the extreme population bottleneck made purifying selection overwhelmed by the power of genetic drift in the population. Finally, we estimated the number of founding individuals by using the genome-wide site frequency spectrum of the six samples. Assuming a simple demographic scenario with a single bottleneck followed by exponential growth, the estimated number of founders (∼20 individuals) is largely consistent with previous estimates.
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Affiliation(s)
- Naoki Osada
- Division of Evolutionary Genetics, National Institute of Genetics, Mishima, Japan Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Japan
| | - Nilmini Hettiarachchi
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Japan Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Isaac Adeyemi Babarinde
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Japan Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Naruya Saitou
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Japan Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Antoine Blancher
- Laboratoire d'Immunogénétique Moléculaire (LIMT, EA3034), Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse III, France
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Shively CA, Day SM. Social inequalities in health in nonhuman primates. Neurobiol Stress 2015; 1:156-63. [PMID: 27589665 PMCID: PMC4721459 DOI: 10.1016/j.ynstr.2014.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 11/07/2014] [Accepted: 11/12/2014] [Indexed: 01/31/2023] Open
Abstract
Overall health has been linked to socioeconomic status, with the gap between social strata increasing each year. Studying the impact of social position on health and biological functioning in nonhuman primates has allowed researchers to model the human condition while avoiding ethical complexities or other difficulties characteristic of human studies. Using female cynomolgus macaques (Macaca fascicularis), our lab has examined the link between social status and stress for 30 years. Female nonhuman primates are especially sensitive to social stressors which can deleteriously affect reproductive health, leading to harmful consequences to their overall health. Subordinates have lower progesterone concentrations during the luteal phase of menstrual cycle, which is indicative of absence or impairment of ovulation. Subordinate animals receive more aggression, less affiliative attention, and are more likely to exhibit depressive behaviors. They also express higher stress-related biomarkers such as increased heart rates and lower mean cortisol. While no differences in body weight between dominant and subordinate animals are observed, subordinates have lower bone density and more visceral fat than their dominant counterparts. The latter increases risk for developing inflammatory diseases. Differences are also observed in neurological and autonomic function. A growing body of data suggests that diet composition may amplify or diminish physiological stress responses which have deleterious effects on health. More experimental investigation of the health effects of diet pattern is needed to further elucidate these differences in an ongoing search to find realistic and long-term solutions to the declining health of individuals living across the ever widening socioeconomic spectrum.
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Key Words
- 5-HT, Serotonin
- ACTH, Adrenocorticotropic hormone
- ANS, Autonomic nervous system
- CAA, Coronary artery atherosclerosis
- CRH, Corticotropin-releasing hormone
- CSF, Cerebrospinal fluid
- HDL-C, High-density lipoprotein cholesterol
- HPA, Hypothalamic-pituitary-adrenal
- HR, Heart rate
- HVA, Homovanillic acid
- IGF-1, Insulin-like growth factor-1
- Mediterranean diet
- Nonhuman primates
- PET, Positron emission tomography
- Social status
- Social stress
- TPC, Total plasma cholesterol
- TPH, Tryptophan hydroxylase
- Western diet
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Affiliation(s)
- Carol A. Shively
- Department of Pathology/Comparative Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston–Salem, NC 27157-1040, USA
| | - Stephen M. Day
- Integrative Physiology & Pharmacology Graduate Program, Department of Pathology/Comparative Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston–Salem, NC 27157-1040, USA
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Interspecific introgressive origin of genomic diversity in the house mouse. Proc Natl Acad Sci U S A 2014; 112:196-201. [PMID: 25512534 DOI: 10.1073/pnas.1406298111] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
We report on a genome-wide scan for introgression between the house mouse (Mus musculus domesticus) and the Algerian mouse (Mus spretus), using samples from the ranges of sympatry and allopatry in Africa and Europe. Our analysis reveals wide variability in introgression signatures along the genomes, as well as across the samples. We find that fewer than half of the autosomes in each genome harbor all detectable introgression, whereas the X chromosome has none. Further, European mice carry more M. spretus alleles than the sympatric African ones. Using the length distribution and sharing patterns of introgressed genomic tracts across the samples, we infer, first, that at least three distinct hybridization events involving M. spretus have occurred, one of which is ancient, and the other two are recent (one presumably due to warfarin rodenticide selection). Second, several of the inferred introgressed tracts contain genes that are likely to confer adaptive advantage. Third, introgressed tracts might contain driver genes that determine the evolutionary fate of those tracts. Further, functional analysis revealed introgressed genes that are essential to fitness, including the Vkorc1 gene, which is implicated in rodenticide resistance, and olfactory receptor genes. Our findings highlight the extent and role of introgression in nature and call for careful analysis and interpretation of house mouse data in evolutionary and genetic studies.
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Uno Y, Uehara S, Kohara S, Murayama N, Yamazaki H. Polymorphisms of CYP2D17 in Cynomolgus and Rhesus Macaques: an Evidence of the Genetic Basis for the Variability of CYP2D-Dependent Drug Metabolism. Drug Metab Dispos 2014; 42:1407-10. [DOI: 10.1124/dmd.114.059220] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Barbisin M, Vanni S, Schmädicke AC, Montag J, Motzkus D, Opitz L, Salinas-Riester G, Legname G. Gene expression profiling of brains from bovine spongiform encephalopathy (BSE)-infected cynomolgus macaques. BMC Genomics 2014; 15:434. [PMID: 24898206 PMCID: PMC4061447 DOI: 10.1186/1471-2164-15-434] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 05/07/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Prion diseases are fatal neurodegenerative disorders whose pathogenesis mechanisms are not fully understood. In this context, the analysis of gene expression alterations occurring in prion-infected animals represents a powerful tool that may contribute to unravel the molecular basis of prion diseases and therefore discover novel potential targets for diagnosis and therapeutics. Here we present the first large-scale transcriptional profiling of brains from BSE-infected cynomolgus macaques, which are an excellent model for human prion disorders. RESULTS The study was conducted using the GeneChip® Rhesus Macaque Genome Array and revealed 300 transcripts with expression changes greater than twofold. Among these, the bioinformatics analysis identified 86 genes with known functions, most of which are involved in cellular development, cell death and survival, lipid homeostasis, and acute phase response signaling. RT-qPCR was performed on selected gene transcripts in order to validate the differential expression in infected animals versus controls. The results obtained with the microarray technology were confirmed and a gene signature was identified. In brief, HBB and HBA2 were down-regulated in infected macaques, whereas TTR, APOC1 and SERPINA3 were up-regulated. CONCLUSIONS Some genes involved in oxygen or lipid transport and in innate immunity were found to be dysregulated in prion infected macaques. These genes are known to be involved in other neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. Our results may facilitate the identification of potential disease biomarkers for many neurodegenerative diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Giuseppe Legname
- Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy.
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Matosiuk M, Borkowska A, Świsłocka M, Mirski P, Borowski Z, Krysiuk K, Danilkin AA, Zvychaynaya EY, Saveljev AP, Ratkiewicz M. Unexpected population genetic structure of European roe deer in Poland: an invasion of the mtDNA genome from Siberian roe deer. Mol Ecol 2014; 23:2559-72. [PMID: 24697866 DOI: 10.1111/mec.12745] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 03/31/2014] [Accepted: 03/31/2014] [Indexed: 11/30/2022]
Abstract
Introgressive hybridization is a widespread evolutionary phenomenon which may lead to increased allelic variation at selective neutral loci and to transfer of fitness-related traits to introgressed lineages. We inferred the population genetic structure of the European roe deer (Capreolus capreolus) in Poland from mitochondrial (CR and cyt b) and sex-linked markers (ZFX, SRY, DBY4 and DBY8). Analyses of CR mtDNA sequences from 452 individuals indicated widespread introgression of Siberian roe deer (C. pygargus) mtDNA in the European roe deer genome, 2000 km from the current distribution range of C. pygargus. Introgressed individuals constituted 16.6% of the deer studied. Nearly 75% of them possessed haplotypes belonging to the group which arose 23 kyr ago and have not been detected within the natural range of Siberian roe deer, indicating that majority of present introgression has ancient origin. Unlike the mtDNA results, sex-specific markers did not show signs of introgression. Species distribution modelling analyses suggested that C. pygargus could have extended its range as far west as Central Europe after last glacial maximum. The main hybridization event was probably associated with range expansion of the most abundant European roe deer lineage from western refugia and took place in Central Europe after the Younger Dryas (10.8-10.0 ka BP). Initially, introgressed mtDNA variants could have spread out on the wave of expansion through the mechanism of gene surfing, reaching high frequencies in European roe deer populations and leading to observed asymmetrical gene flow. Human-mediated introductions of C. pygargus had minimal effect on the extent of mtDNA introgression.
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Affiliation(s)
- Maciej Matosiuk
- Institute of Biology, University of Bialystok, Świerkowa 20B, 15-950, Białystok, Poland
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Fan Z, Zhao G, Li P, Osada N, Xing J, Yi Y, Du L, Silva P, Wang H, Sakate R, Zhang X, Xu H, Yue B, Li J. Whole-genome sequencing of tibetan macaque (Macaca Thibetana) provides new insight into the macaque evolutionary history. Mol Biol Evol 2014; 31:1475-89. [PMID: 24648498 PMCID: PMC4032132 DOI: 10.1093/molbev/msu104] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Macaques are the most widely distributed nonhuman primates and used as animal models in biomedical research. The availability of full-genome sequences from them would be essential to both biomedical and primate evolutionary studies. Previous studies have reported whole-genome sequences from rhesus macaque (Macaca mulatta) and cynomolgus macaque (M. fascicularis, CE), both of which belong to the fascicularis group. Here, we present a 37-fold coverage genome sequence of the Tibetan macaque (M. thibetana; TM). TM is an endemic species to China belonging to the sinica group. On the basis of mapping to the rhesus macaque genome, we identified approximately 11.9 million single-nucleotide variants), of which 3.9 million were TM specific, as assessed by comparison two Chinese rhesus macaques (CR) and two CE genomes. Some genes carried TM-specific homozygous nonsynonymous variants (TSHNVs), which were scored as deleterious in human by both PolyPhen-2 and SIFT (Sorting Tolerant From Intolerant) and were enriched in the eye disease genes. In total, 273 immune response and disease-related genes carried at least one TSHNV. The heterozygosity rates of two CRs (0.002617 and 0.002612) and two CEs (0.003004 and 0.003179) were approximately three times higher than that of TM (0.000898). Polymerase chain reaction resequencing of 18 TM individuals showed that 29 TSHNVs exhibited high allele frequencies, thus confirming their low heterozygosity. Genome-wide genetic divergence analysis demonstrated that TM was more closely related to CR than to CE. We further detected unusual low divergence regions between TM and CR. In addition, after applying statistical criteria to detect putative introgression regions (PIRs) in the TM genome, up to 239,620 kb PIRs (8.84% of the genome) were identified. Given that TM and CR have overlapping geographical distributions, had the same refuge during the Middle Pleistocene, and show similar mating behaviors, it is highly likely that there was an ancient introgression event between them. Moreover, demographic inferences revealed that TM exhibited a similar demographic history as other macaques until 0.5 Ma, but then it maintained a lower effective population size until present time. Our study has provided new insight into the macaque evolutionary history, confirming hybridization events between macaque species groups based on genome-wide data.
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Affiliation(s)
- Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Guang Zhao
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Peng Li
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Naoki Osada
- Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Jinchuan Xing
- Department of Genetics, Rutgers, the State University of New Jersey
| | - Yong Yi
- Experimental Animal Institute of Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, People's Republic of China
| | - Lianming Du
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Pedro Silva
- Research Center in Biodiversity and Genetic Resources, University of Porto (CIBIO-UP), Campus Agrário de Vairão, Vila do Conde, Portugal
| | - Hongxing Wang
- Experimental Animal Institute of Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, People's Republic of China
| | - Ryuichi Sakate
- Laboratory of Rare Disease Biospecimen, Department of Disease Bioresources Research, National Institute of Biomedical Innovation, Ibaraki, Osaka, Japan
| | - Xiuyue Zhang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Huailiang Xu
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, People's Republic of China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Jing Li
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
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Moyes CL, Henry AJ, Golding N, Huang Z, Singh B, Baird JK, Newton PN, Huffman M, Duda KA, Drakeley CJ, Elyazar IRF, Anstey NM, Chen Q, Zommers Z, Bhatt S, Gething PW, Hay SI. Defining the geographical range of the Plasmodium knowlesi reservoir. PLoS Negl Trop Dis 2014; 8:e2780. [PMID: 24676231 PMCID: PMC3967999 DOI: 10.1371/journal.pntd.0002780] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 02/23/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The simian malaria parasite, Plasmodium knowlesi, can cause severe and fatal disease in humans yet it is rarely included in routine public health reporting systems for malaria and its geographical range is largely unknown. Because malaria caused by P. knowlesi is a truly neglected tropical disease, there are substantial obstacles to defining the geographical extent and risk of this disease. Information is required on the occurrence of human cases in different locations, on which non-human primates host this parasite and on which vectors are able to transmit it to humans. We undertook a systematic review and ranked the existing evidence, at a subnational spatial scale, to investigate the potential geographical range of the parasite reservoir capable of infecting humans. METHODOLOGY/PRINCIPAL FINDINGS After reviewing the published literature we identified potential host and vector species and ranked these based on how informative they are for the presence of an infectious parasite reservoir, based on current evidence. We collated spatial data on parasite occurrence and the ranges of the identified host and vector species. The ranked spatial data allowed us to assign an evidence score to 475 subnational areas in 19 countries and we present the results on a map of the Southeast and South Asia region. CONCLUSIONS/SIGNIFICANCE We have ranked subnational areas within the potential disease range according to evidence for presence of a disease risk to humans, providing geographical evidence to support decisions on prevention, management and prophylaxis. This work also highlights the unknown risk status of large parts of the region. Within this unknown category, our map identifies which areas have most evidence for the potential to support an infectious reservoir and are therefore a priority for further investigation. Furthermore we identify geographical areas where further investigation of putative host and vector species would be highly informative for the region-wide assessment.
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Affiliation(s)
- Catherine L. Moyes
- Spatial Ecology and Epidemiology Group, Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Andrew J. Henry
- Spatial Ecology and Epidemiology Group, Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Nick Golding
- Spatial Ecology and Epidemiology Group, Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Zhi Huang
- Spatial Ecology and Epidemiology Group, Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Balbir Singh
- Malaria Research Centre, Universiti Malaysia Sarawak, Kuching, Sarawak, Malaysia
| | - J. Kevin Baird
- Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia
- Centre for Tropical Medicine, University of Oxford, Oxford, United Kingdom
| | - Paul N. Newton
- Centre for Tropical Medicine, University of Oxford, Oxford, United Kingdom
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Michael Huffman
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Kirsten A. Duda
- Spatial Ecology and Epidemiology Group, Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Chris J. Drakeley
- Department of Immunology and Infection, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Nicholas M. Anstey
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Qijun Chen
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Zoonosis, Jilin University, Changchun, China
| | - Zinta Zommers
- Division of Early Warning and Assessment, United Nations Environment Programme, Nairobi, Kenya
| | - Samir Bhatt
- Spatial Ecology and Epidemiology Group, Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Peter W. Gething
- Spatial Ecology and Epidemiology Group, Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Simon I. Hay
- Spatial Ecology and Epidemiology Group, Department of Zoology, University of Oxford, Oxford, United Kingdom
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
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Osada N, Nakagome S, Mano S, Kameoka Y, Takahashi I, Terao K. Finding the factors of reduced genetic diversity on X chromosomes of Macaca fascicularis: male-driven evolution, demography, and natural selection. Genetics 2013; 195:1027-35. [PMID: 24026095 PMCID: PMC3813834 DOI: 10.1534/genetics.113.156703] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 08/28/2013] [Indexed: 11/18/2022] Open
Abstract
The ratio of genetic diversity on X chromosomes relative to autosomes in organisms with XX/XY sex chromosomes could provide fundamental insight into the process of genome evolution. Here we report this ratio for 24 cynomolgus monkeys (Macaca fascicularis) originating in Indonesia, Malaysia, and the Philippines. The average X/A diversity ratios in these samples was 0.34 and 0.20 in the Indonesian-Malaysian and Philippine populations, respectively, considerably lower than the null expectation of 0.75. A Philippine population supposed to derive from an ancestral population by founding events showed a significantly lower ratio than the parental population, suggesting a demographic effect for the reduction. Taking sex-specific mutation rate bias and demographic effect into account, expected X/A diversity ratios generated by computer simulations roughly agreed with the observed data in the intergenic regions. In contrast, silent sites in genic regions on X chromosomes showed strong reduction in genetic diversity and the observed X/A diversity ratio in the genic regions cannot be explained by mutation rate bias and demography, indicating that natural selection also reduces the level of polymorphism near genes. Whole-genome analysis of a female cynomolgus monkey also supported the notion of stronger reduction of genetic diversity near genes on the X chromosome.
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Affiliation(s)
- Naoki Osada
- Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka 4118540, Japan
- Department of Genetics, The Graduate University of Advanced Studies (SOKENDAI), Mishima, Shizuoka 4118540, Japan
| | - Shigeki Nakagome
- The Institute of Statistical Mathematics, Tachikawa, Tokyo 1908562, Japan
| | - Shuhei Mano
- The Institute of Statistical Mathematics, Tachikawa, Tokyo 1908562, Japan
| | - Yosuke Kameoka
- Department of Disease Bioresources Research, National Institute of Biomedical Innovation, Osaka 5670085 Japan
| | - Ichiro Takahashi
- Department of Disease Bioresources Research, National Institute of Biomedical Innovation, Osaka 5670085 Japan
| | - Keiji Terao
- Tsukuba Primate Research Center, National Institute of Biomedical Innovation, Tsukuba 3050843, Japan
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Goswami DB, Ogawa LM, Ward JM, Miller GM, Vallender EJ. Large-scale polymorphism discovery in macaque G-protein coupled receptors. BMC Genomics 2013; 14:703. [PMID: 24119066 PMCID: PMC3907043 DOI: 10.1186/1471-2164-14-703] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 10/04/2013] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND G-protein coupled receptors (GPCRs) play an inordinately large role in human health. Variation in the genes that encode these receptors is associated with numerous disorders across the entire spectrum of disease. GPCRs also represent the single largest class of drug targets and associated pharmacogenetic effects are modulated, in part, by polymorphisms. Recently, non-human primate models have been developed focusing on naturally-occurring, functionally-parallel polymorphisms in candidate genes. This work aims to extend those studies broadly across the roughly 377 non-olfactory GPCRs. Initial efforts include resequencing 44 Indian-origin rhesus macaques (Macaca mulatta), 20 Chinese-origin rhesus macaques, and 32 cynomolgus macaques (M. fascicularis). RESULTS Using the Agilent target enrichment system, capture baits were designed for GPCRs off the human and rhesus exonic sequence. Using next generation sequencing technologies, nearly 25,000 SNPs were identified in coding sequences including over 14,000 non-synonymous and more than 9,500 synonymous protein-coding SNPs. As expected, regions showing the least evolutionary constraint show greater rates of polymorphism and greater numbers of higher frequency polymorphisms. While the vast majority of these SNPs are singletons, roughly 1,750 non-synonymous and 2,900 synonymous SNPs were found in multiple individuals. CONCLUSIONS In all three populations, polymorphism and divergence is highly concentrated in N-terminal and C-terminal domains and the third intracellular loop region of GPCRs, regions critical to ligand-binding and signaling. SNP frequencies in macaques follow a similar pattern of divergence from humans and new polymorphisms in primates have been identified that may parallel those seen in humans, helping to establish better non-human primate models of disease.
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Affiliation(s)
- Dharmendra B Goswami
- New England Primate Research Center, Harvard Medical School, One Pine Hill Drive, Southborough, MA 01772, USA.
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Higashino A, Sakate R, Kameoka Y, Takahashi I, Hirata M, Tanuma R, Masui T, Yasutomi Y, Osada N. Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome. Genome Biol 2012; 13:R58. [PMID: 22747675 PMCID: PMC3491380 DOI: 10.1186/gb-2012-13-7-r58] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 07/02/2012] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The genetic background of the cynomolgus macaque (Macaca fascicularis) is made complex by the high genetic diversity, population structure, and gene introgression from the closely related rhesus macaque (Macaca mulatta). Herein we report the whole-genome sequence of a Malaysian cynomolgus macaque male with more than 40-fold coverage, which was determined using a resequencing method based on the Indian rhesus macaque genome. RESULTS We identified approximately 9.7 million single nucleotide variants (SNVs) between the Malaysian cynomolgus and the Indian rhesus macaque genomes. Compared with humans, a smaller nonsynonymous/synonymous SNV ratio in the cynomolgus macaque suggests more effective removal of slightly deleterious mutations. Comparison of two cynomolgus (Malaysian and Vietnamese) and two rhesus (Indian and Chinese) macaque genomes, including previously published macaque genomes, suggests that Indochinese cynomolgus macaques have been more affected by gene introgression from rhesus macaques. We further identified 60 nonsynonymous SNVs that completely differentiated the cynomolgus and rhesus macaque genomes, and that could be important candidate variants for determining species-specific responses to drugs and pathogens. The demographic inference using the genome sequence data revealed that Malaysian cynomolgus macaques have experienced at least three population bottlenecks. CONCLUSIONS This list of whole-genome SNVs will be useful for many future applications, such as an array-based genotyping system for macaque individuals. High-quality whole-genome sequencing of the cynomolgus macaque genome may aid studies on finding genetic differences that are responsible for phenotypic diversity in macaques and may help control genetic backgrounds among individuals.
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Uno Y, Osada N. CpG site degeneration triggered by the loss of functional constraint created a highly polymorphic macaque drug-metabolizing gene, CYP1A2. BMC Evol Biol 2011; 11:283. [PMID: 21961956 PMCID: PMC3199271 DOI: 10.1186/1471-2148-11-283] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 10/01/2011] [Indexed: 11/29/2022] Open
Abstract
Background Elucidating the pattern of evolutionary changes in drug-metabolizing genes is an important subject not only for evolutionary but for biomedical research. We investigated the pattern of divergence and polymorphisms of macaque CYP1A1 and CYP1A2 genes, which are major drug-metabolizing genes in humans. In humans, CYP1A2 is specifically expressed in livers while CYP1A1 has a wider gene expression pattern in extrahepatic tissues. In contrast, macaque CYP1A2 is expressed at a much lower level than CYP1A1 in livers. Interestingly, a previous study has shown that Macaca fascicularis CYP1A2 harbored unusually high genetic diversity within species. Genomic regions showing high genetic diversity within species is occasionally interpreted as a result of balancing selection, where natural selection maintains highly diverged alleles with different functions. Nevertheless many other forces could create such signatures. Results We found that the CYP1A1/2 gene copy number and orientation has been highly conserved among mammalian genomes. The signature of gene conversion between CYP1A1 and CYP1A2 was detected, but the last gene conversion event in the simian primate lineage occurred before the Catarrhini-Platyrrhini divergence. The high genetic diversity of macaque CYP1A2 therefore cannot be explained by gene conversion between CYP1A1 and CYP1A2. By surveying CYP1A2 polymorphisms in total 91 M. fascicularis and M. mulatta, we found several null alleles segregating in these species, indicating functional constraint on CYP1A2 in macaques may have weakened after the divergence between humans and macaques. We propose that the high genetic diversity in macaque CYP1A2 is partly due to the degeneration of CpG sites, which had been maintained at a high level by purifying selection, and the rapid degeneration process was initiated by the loss of functional constraint on macaque CYP1A2. Conclusions Our findings show that the highly polymorphic CYP1A2 gene in macaques has not been created by balancing selection but by the burst of CpG site degeneration after loss of functional constraint. Because the functional importance of CYP1A1/2 genes is different between humans and macaques, we have to be cautious in extrapolating a drug-testing data using substrates metabolized by CYP1A genes from macaques to humans, despite of their somewhat overlapping substrate specificity.
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Affiliation(s)
- Yasuhiro Uno
- Pharmacokinetics and Bioanalysis Center, Shin Nippon BiomedicalLaboratories, Ltd., Kainan, Wakayama 642-0017, Japan
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Osada N. Phylogenetic inconsistency caused by ancient sex-biased gene migration. PLoS One 2011; 6:e25549. [PMID: 21980490 PMCID: PMC3183042 DOI: 10.1371/journal.pone.0025549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 09/07/2011] [Indexed: 12/25/2022] Open
Abstract
Inferences of ancient sex-biased migration patterns using sex-linked genetic markers are usually difficult because of a stochastic process of allele fixation. Nevertheless, incongruent phylogenetic trees between different sex-linked markers and between sex-linked and autosomal markers are frequently interpreted as a signature of sex-biased migration without further statistical evaluation. I investigated the types of incongruent phylogenetic trees from which past sex-biased migration events can be statistically supported under the coalescent model. In the case of mammals, detecting a sex-biased migration pattern is not guaranteed by comparing the phylogenetic pattern of mitochondrial and Y-chromosomal loci. Likewise, evidence of introgression at a mitochondrial locus, but not at autosomal loci, does not support the hypothesis of an ancient female-biased migration pattern with statistical significance. In contrast, evidence of introgression at ≥ 5 unlinked autosomal loci, but not at a Y-chromosomal locus, would reject the null hypothesis of a sexually equal migration rate with statistical significance. A similar argument can be made to infer a male-biased migration pattern. Furthermore, the investigation of many recombining sex-biased markers such as X-chromosomal loci in mammals has the potential to efficiently detect ancient sex-biased demographic patterns.
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Affiliation(s)
- Naoki Osada
- Department of Population Genetics, National Institute of Genetics, Mishima, Japan.
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Osada N, Akashi H. Mitochondrial-nuclear interactions and accelerated compensatory evolution: evidence from the primate cytochrome C oxidase complex. Mol Biol Evol 2011; 29:337-46. [PMID: 21890478 DOI: 10.1093/molbev/msr211] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Accelerated rates of mitochondrial protein evolution have been proposed to reflect Darwinian coadaptation for efficient energy production for mammalian flight and brain activity. However, several features of mammalian mtDNA (absence of recombination, small effective population size, and high mutation rate) promote genome degradation through the accumulation of weakly deleterious mutations. Here, we present evidence for "compensatory" adaptive substitutions in nuclear DNA- (nDNA) encoded mitochondrial proteins to prevent fitness decline in primate mitochondrial protein complexes. We show that high mutation rate and small effective population size, key features of primate mitochondrial genomes, can accelerate compensatory adaptive evolution in nDNA-encoded genes. We combine phylogenetic information and the 3D structure of the cytochrome c oxidase (COX) complex to test for accelerated compensatory changes among interacting sites. Physical interactions among mtDNA- and nDNA-encoded components are critical in COX evolution; amino acids in close physical proximity in the 3D structure show a strong tendency for correlated evolution among lineages. Only nuclear-encoded components of COX show evidence for positive selection and adaptive nDNA-encoded changes tend to follow mtDNA-encoded amino acid changes at nearby sites in the 3D structure. This bias in the temporal order of substitutions supports compensatory weak selection as a major factor in accelerated primate COX evolution.
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Affiliation(s)
- Naoki Osada
- Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Mishima, Japan.
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