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Kenyon-Flatt B, von Cramon-Taubadel N. Intrageneric taxonomic distinction based on morphological variation in the macaque (Macaca) skeleton. Anat Rec (Hoboken) 2024; 307:118-140. [PMID: 37439127 DOI: 10.1002/ar.25283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/14/2023]
Abstract
Taxonomic classification is important for understanding the natural world, yet current methods for species assessment often focus on craniodental morphology rather than the entire skeleton. Moreover, it is currently unknown how much variation could, or should, exist intragenerically. Here, we tested whether taxonomy can be accurately predicted based on patterns of morphological variation in macaques (H1 ) and whether postcranial bones reflect subgeneric macaque taxonomy similarly, or better, than the cranium (H2 ). Data included 3D scans of cranial and postcranial bones for eight macaque species (Macaca arctoides, Macaca fascicularis, Macaca fuscata, Macaca mulatta, Macaca nemestrina, Macaca nigra, Macaca radiata, and Macaca sylvanus). Fixed anatomical and semilandmarks were applied to scans of eight skeletal elements (crania = 45; mandible = 31; scapula = 66; humerus = 38; radius = 33; os coxa = 28; femur = 40; tibia = 40). For each skeletal element, regression analyses were performed to minimize the effects of sexual dimorphism. Between-groups principal components analysis was used to visualize the major patterns of among-species morphological variation, while the strength of correct taxon classification was measured with discriminant function analysis. Results suggested accepting the alternate hypothesis that different macaque species can be distinguished morphologically. Both cranial and many postcranial elements appeared to possess a taxonomic signal, and the limb bones-especially the upper limb-are reported to be more useful for taxonomic assessment than previously realized. Theoretically, certain behaviors and/or ecogeographical factors, as well as phylogeny, influenced skeletal morphology in macaques, likely contributing to taxonomic distinctions among different species.
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Affiliation(s)
- Brittany Kenyon-Flatt
- School of Nursing, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
- Buffalo Human Evolutionary Morphology Lab, Department of Anthropology, University at Buffalo, Buffalo, New York, USA
| | - Noreen von Cramon-Taubadel
- Buffalo Human Evolutionary Morphology Lab, Department of Anthropology, University at Buffalo, Buffalo, New York, USA
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2
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Chiu KP, Stuart L, Ooi HS, Yu J, Smith DG, Pei KJC. Genome sequencing and application of Taiwanese macaque Macaca cyclopis. Sci Rep 2023; 13:11545. [PMID: 37460589 DOI: 10.1038/s41598-023-38402-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 07/07/2023] [Indexed: 07/20/2023] Open
Abstract
Formosan macaque (Macaca cyclopis) is the only non-human primate in Taiwan Island. We performed de novo hybrid assembly for M. cyclopis using Illumina paired-end short reads, mate-pair reads and Nanopore long reads and obtained 5065 contigs with a N50 of 2.66 megabases. M. cyclopis contigs > = 10 kb were assigned to chromosomes using Indian rhesus macaque (Macaca mulatta mulatta) genome assembly Mmul_10 as reference, resulting in a draft of M. cyclopis genome of 2,846,042,475 bases, distributed in 21 chromosomes. The draft genome contains 23,462 transcriptional origins (genes), capable of expressing 716,231 exons in 59,484 transcripts. Genome-based phylogenetic study using the assembled M. cyclopis genome together with genomes of four other macaque species, human, orangutan and chimpanzee showed similar result as previously reported. However, the M. cyclopis species was found to diverge from Chinese M. mulatta lasiota about 1.8 million years ago. Fossil gene analysis detected the presence of gap and pol endogenous viral elements of simian retrovirus in all macaques tested, including M. fascicularis, M. m. mulatta and M. cyclopis. However, M. cyclopis showed ~ 2 times less in number and more uniform in chromosomal locations. The constrain in foreign genome disturbance, presumably due to geographical isolation, should be able to simplify genomics-related investigations, making M. cyclopis an ideal primate species for medical research.
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Affiliation(s)
- Kuo-Ping Chiu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.
- Top Science Biotechnologies, Inc., 4F, 50-2 Dingping Rd., Sec. 1, Shiding District, New Taipei City, 223002, Taiwan.
| | - Lutimba Stuart
- Top Science Biotechnologies, Inc., 4F, 50-2 Dingping Rd., Sec. 1, Shiding District, New Taipei City, 223002, Taiwan
| | - Hong Sain Ooi
- Top Science Biotechnologies, Inc., 4F, 50-2 Dingping Rd., Sec. 1, Shiding District, New Taipei City, 223002, Taiwan
| | - John Yu
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, No.5, Fu-Shin St., Kuei Shang, Taoyuan, 333, Taiwan
| | - David Glenn Smith
- Department of Anthropology, University of California Davis, Davis, CA, USA
| | - Kurtis Jai-Chyi Pei
- Institute of Wildlife Conservation, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
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3
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Song Y, Jiang C, Li KH, Li J, Qiu H, Price M, Fan ZX, Li J. Genome-wide analysis reveals signatures of complex introgressive gene flow in macaques (genus Macaca). Zool Res 2021; 42:433-449. [PMID: 34114757 PMCID: PMC8317189 DOI: 10.24272/j.issn.2095-8137.2021.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The genus Macaca serves as an ideal research model for speciation and introgressive gene flow due to its short period of diversification (about five million years ago) and rapid radiation of constituent species. To understand evolutionary gene flow in macaques, we sequenced four whole genomes (two M. arctoides and two M. thibetana) and combined them with publicly available macaque genome data for genome-wide analyses. We analyzed 14 individuals from nine Macaca species covering all Asian macaque species groups and detected extensive gene flow signals, with the strongest signals between the fascicularis and silenus species groups. Notably, we detected bidirectional gene flow between M. fascicularis and M. nemestrina. The estimated proportion of the genome inherited via gene flow between the two species was 6.19%. However, the introgression signals found among studied island species, such as Sulawesi macaques and M. fuscata, and other species were largely attributed to the genomic similarity of closely related species or ancestral introgression. Furthermore, gene flow signals varied in individuals of the same species (M. arctoides, M. fascicularis, M. mulatta, M. nemestrina and M. thibetana), suggesting very recent gene flow after the populations split. Pairwise sequentially Markovian coalescence (PSMC) analysis showed all macaques experienced a bottleneck five million years ago, after which different species exhibited different fluctuations in demographic history trajectories, implying they have experienced complicated environmental variation and climate change. These results should help improve our understanding of the complicated evolutionary history of macaques, particularly introgressive gene flow.
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Affiliation(s)
- Yang Song
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Cong Jiang
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Kun-Hua Li
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Jing Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Hong Qiu
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Megan Price
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Zhen-Xin Fan
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Jing Li
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China. E-mail:
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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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Khanal L, Chalise MK, Fan PF, Kyes RC, Jiang XL. Multilocus phylogeny suggests a distinct species status for the Nepal population of Assam macaques ( Macaca assamensis): implications for evolution and conservation. Zool Res 2021; 42:3-13. [PMID: 33410309 PMCID: PMC7840459 DOI: 10.24272/j.issn.2095-8137.2020.279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 01/05/2021] [Indexed: 11/23/2022] Open
Abstract
Phylogenetic relationships within the sinica-group of macaques based on morphological, behavioral, and molecular characteristics have remained controversial. The Nepal population of Assam macaques ( Macaca assamensis) (NPAM), the westernmost population of the species, is morphologically distinct but has never been used in phylogenetic analyses. Here, the phylogenetic relationship of NPAM with other congeners was tested using multiple mitochondrial and Y-chromosomal loci. The divergence times and evolutionary genetic distances among macaques were also estimated. Results revealed two major mitochondrial DNA clades of macaques under the sinica-group: the first clade included M. thibetana, M. sinica, and eastern subspecies of Assam macaque ( M. assamensis assamensis); the second clade included M. radiata together with species from the eastern and central Himalaya, namely, M. leucogenys, M. munzala, and NPAM. Among the second-clade species, NPAM was the first to diverge from the other members of the clade around 1.9 million years ago. Our results revealed that NPAM is phylogenetically distinct from the eastern Assam macaques and closer to other species and hence may represent a separate species. Because of its phylogenetic distinctiveness, isolated distribution, and small population size, the Nepal population of sinica-group macaques warrants detailed taxonomic revision and high conservation priority.
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Affiliation(s)
- Laxman Khanal
- Central Department of Zoology, Institute of Science and Technology, Tribhuvan University, Kathmandu 44613, Nepal
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China. E-mail:
| | - Mukesh Kumar Chalise
- Central Department of Zoology, Institute of Science and Technology, Tribhuvan University, Kathmandu 44613, Nepal
- Nepal Biodiversity Research Society (NEBORS), Lalitpur 23513, Nepal
| | - Peng-Fei Fan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Randall C Kyes
- Department of Psychology, Global Health, and Anthropology, Center for Global Field Study, and Washington National Primate Research Center, University of Washington, Seattle 98195, USA
| | - Xue-Long Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China. E-mail:
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Marchewka J, Mrożek K, Leszczyński B, Wróbel A, Głąb H. Variability in the number of infraorbital foramina in rhesus macaques (Macaca mulatta) and cynomolgus macaques (Macaca fascicularis). Anat Rec (Hoboken) 2020; 304:818-831. [PMID: 32558307 DOI: 10.1002/ar.24478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/14/2020] [Accepted: 04/28/2020] [Indexed: 11/11/2022]
Abstract
This study aimed to determine the number of infraorbital foramina in monkeys of the Papionini tribe. The authors performed a μCT analysis of the morphology of the infraorbital foramina. A total number of 52 simian skulls belonged to two macaque species: Macaca mulatta and Macaca fascicularis were used in the study. The number of infraorbital foramina was counted macroscopically and with the use of a magnifying glass. Next, the skull representing the most common morphological type was selected and scanned by micro-computed tomography (μCT). The Shapiro-Wilk normality test was used in the study. To compare the differences in the number of infraorbital foramen between species, sex and sides, the Mann-Whitney U test was applied. Three infraorbital foramina were present in most individuals from the test group. The Mann-Whitney test revealed no statistically significant difference between the number of foramina on the right- and left-hand side. Likewise, no statistically significant differences between the numbers of infraorbital foramina across sexes were observed. Volumetric reconstructions revealed the presence of separate infraorbital canals for each infraorbital foramen. Craniofacial innervation in macaques is formed by complex branching patterns of cranial nerves. Variability in the number of infraorbital foramina suggests a variable maxillary innervation pattern in these animals. Based on the analysis of volumetric projections, the presence of two labial branches and a single nasal branch of the infraorbital nerve is suggested. Detailed descriptions are supported by quantitative data and μCT evidence.
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Affiliation(s)
- Justyna Marchewka
- Department of Human Biology, Institute of Biological Sciences, Cardinal Stefan Wyszynski University, Warszawa, Poland
| | - Kamil Mrożek
- Nature Education Centre, Jagiellonian University, Krakow, Poland.,Department of Anthropology, Institute of Zoology and Biomedical Research, Jagiellonian University, Krakow, Poland
| | - Bartosz Leszczyński
- Department of Medical Physics, Marian Smoluchowski Institute of Physics, Jagiellonian University, Krakow, Poland
| | - Andrzej Wróbel
- Department of Medical Physics, Marian Smoluchowski Institute of Physics, Jagiellonian University, Krakow, Poland
| | - Henryk Głąb
- Department of Anthropology, Institute of Zoology and Biomedical Research, Jagiellonian University, Krakow, Poland
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Li B, He G, Guo S, Hou R, Huang K, Zhang P, Zhang H, Pan R, Chapman CA. Macaques in China: Evolutionary dispersion and subsequent development. Am J Primatol 2020; 82:e23142. [PMID: 32452078 PMCID: PMC7378941 DOI: 10.1002/ajp.23142] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/30/2020] [Accepted: 04/08/2020] [Indexed: 11/29/2022]
Abstract
Depicting a taxonomic group's evolutionary trajectory as a function of changes in the geographical landscape and its historical distribution is critical for constructing informed conservation strategies. Based on fossil sites from the Pliocene to the Holocene, and historical records since 1175 AD, we established macaques’ dispersal pathways into and through China. These routes include internal pathways starting from the southeast corner of the Qinghai‐Tibet Plateau and Mts. Hengduan in western China, and the routes through the estuaries of the three major rivers (Yangtze, Yellow, and Pearl). Our results indicate that macaques used the three rivers and avoided the higher elevation of the plateaus to promote their radiation. They occupied the whole mainland and islands in the Pleistocene and experienced shrunken distribution in the Holocene due to climate changes and human‐induced activities. A prominent China‐wide reduction occurred between 1817 and 1917; and a remarkable retraction from central China happened between 1918 and 2018 following further eco‐social development and human expansion in central China, particularly since the second half of the last century. Starting in 1175 there was a restriction of range to higher altitudes, so that macaques have contracted their range to the west, and the Qinghai‐Tibet Plateau and Mts. Hengduan have become an important sanctuary. We predict that if the current climate and human‐induced changes are not reversed by decisive conservation actions, macaques in east and central China will likely be extinct in the near future. Major waterways used by the primates to disperse and radiate in China Primate evolution and dispersion in East Asia from the Pliocene to the Early Holocene Historically shrunk macaque distribution in China
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Affiliation(s)
- Baoguo Li
- Shaanxi Key Laboratory for Animal ConservationCollege of Life Sciences, Northwest UniversityXi'anChina
- International Centre of Biodiversity and Primate Conservation CentreDali UniversityDaliChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
| | - Gang He
- Shaanxi Key Laboratory for Animal ConservationCollege of Life Sciences, Northwest UniversityXi'anChina
| | - Songtao Guo
- Shaanxi Key Laboratory for Animal ConservationCollege of Life Sciences, Northwest UniversityXi'anChina
| | - Rong Hou
- Shaanxi Key Laboratory for Animal ConservationCollege of Life Sciences, Northwest UniversityXi'anChina
- International Centre of Biodiversity and Primate Conservation CentreDali UniversityDaliChina
- Department of AnthropologyMcGill UniversityMontrealQuebecCanada
| | - Kang Huang
- Shaanxi Key Laboratory for Animal ConservationCollege of Life Sciences, Northwest UniversityXi'anChina
| | - Pei Zhang
- Shaanxi Key Laboratory for Animal ConservationCollege of Life Sciences, Northwest UniversityXi'anChina
| | - He Zhang
- Shaanxi Key Laboratory for Animal ConservationCollege of Life Sciences, Northwest UniversityXi'anChina
| | - Ruliang Pan
- Shaanxi Key Laboratory for Animal ConservationCollege of Life Sciences, Northwest UniversityXi'anChina
- International Centre of Biodiversity and Primate Conservation CentreDali UniversityDaliChina
- School of Human Sciences, The University of Western AustraliaPerthWestern AustraliaAustralia
| | - Colin A. Chapman
- Shaanxi Key Laboratory for Animal ConservationCollege of Life Sciences, Northwest UniversityXi'anChina
- International Centre of Biodiversity and Primate Conservation CentreDali UniversityDaliChina
- Department of AnthropologyMcGill UniversityMontrealQuebecCanada
- Department of AnthropologyCenter for the Advanced Study of Human Paleobiology, The George Washington UniversityWashingtonWashington DC
- School of Life Sciences, University of KwaZulu‐NatalScottsvillePietermaritzburgSouth Africa
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Mincer ST, Russo GA. Substrate use drives the macroevolution of mammalian tail length diversity. Proc Biol Sci 2020; 287:20192885. [PMID: 32019445 DOI: 10.1098/rspb.2019.2885] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
External length is one of the most conspicuous aspects of mammalian tail morphological diversity. Factors that influence the evolution of tail length diversity have been proposed for particular taxa, including habitat, diet, locomotion and climate. However, no study to date has investigated such factors at a large phylogenetic scale to elucidate what drives tail length evolution in and across mammalian lineages. We use phylogenetic comparative methods to test a priori hypotheses regarding proposed factors influencing tail length, explore possible interactions between factors using evolutionary best-fit models, and map evolutionary patterns of tail length for specific mammalian lineages. Across mammals, substrate use is a significant factor influencing tail length, with arboreal species maintaining selection for longer tails. Non-arboreal species instead exhibit a wider range of tail lengths, secondarily influenced by differences in locomotion, diet and climate. Tail loss events are revealed to occur in the context of both long and short tails and influential factors are clade dependent. Some mammalian groups (e.g. Macaca; primates) exhibit elevated rates of tail length evolution, indicating that morphological evolution may be accelerated in groups characterized by diverse substrate use, locomotor modes and climate.
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Affiliation(s)
- Sarah T Mincer
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Gabrielle A Russo
- Department of Anthropology, Stony Brook University, Stony Brook, NY 11794, USA
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9
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Roos C, Kothe M, Alba DM, Delson E, Zinner D. The radiation of macaques out of Africa: Evidence from mitogenome divergence times and the fossil record. J Hum Evol 2019; 133:114-132. [DOI: 10.1016/j.jhevol.2019.05.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 04/14/2019] [Accepted: 05/31/2019] [Indexed: 01/30/2023]
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10
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Fan Z, Zhou A, Osada N, Yu J, Jiang J, Li P, Du L, Niu L, Deng J, Xu H, Xing J, Yue B, Li J. Ancient hybridization and admixture in macaques (genus Macaca) inferred from whole genome sequences. Mol Phylogenet Evol 2018; 127:376-386. [PMID: 29614345 DOI: 10.1016/j.ympev.2018.03.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 03/23/2018] [Accepted: 03/30/2018] [Indexed: 12/25/2022]
Abstract
The evolutionary history of the stump-tailed macaque (Macaca arctoides) and its genetic relationship to other macaques is a subject of continuing controversy. Here, we have reported the first genome sequences of two stump-tailed macaques and one Assamese macaque (M. assamensis). Additionally, we have investigated the genetic diversity between macaque species and analyzed ancient hybridization events. Genome-wide analyses demonstrated that the stump-tailed macaque is more closely related to sinica species than to fascicularis/mulatta species. This topology contradicts the mitochondrial sequence-based phylogeny that places the stump-tailed macaque into the fascicularis/mulatta group. However, our results further show that stump-tailed macaques have genetic backgrounds distinct from sinica species, and present evidence of gene flows with rhesus macaques. We suggest that an ancient introgression occurred after stump-tailed macaques diverged from sinica species. The distinct gene flow between proto-arctoides and proto-mulatta resulted in the transfer of rhesus macaque-type mitochondria into proto-arctoides. The rhesus macaque-type mitochondria remained in populations because of genetic drift during the bottleneck. The PSMC results and morphological and geographic evidence are consistent with the mitochondria capture pattern in the stump-tailed macaque. The molecular clock estimates suggest that the mitochondrial transference into stump-tailed macaques occurred 0.4-1.4 million years ago. Furthermore, we detected extensive admixtures between different macaque species, indicating that gene flow has played an important role in the evolutionary history of the genus Macaca.
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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
| | - Anbo Zhou
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Naoki Osada
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido 060-0814, Japan
| | - Jianqiu Yu
- Chengdu Zoo, Institute of Chengdu Wildlife, Chengdu 610081, People's Republic of China
| | - Juan Jiang
- 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
| | - Peng 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
| | - Lianming Du
- 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
| | - Lili Niu
- Chengdu Zoo, Institute of Chengdu Wildlife, Chengdu 610081, People's Republic of China
| | - Jiabo Deng
- Chengdu Zoo, Institute of Chengdu Wildlife, Chengdu 610081, People's Republic of China
| | - Huailiang Xu
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, People's Republic of China
| | - Jinchuan Xing
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - 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.
| | - 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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11
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Jiang J, Yu J, Li J, Li P, Fan Z, Niu L, Deng J, Yue B, Li J. Mitochondrial Genome and Nuclear Markers Provide New Insight into the Evolutionary History of Macaques. PLoS One 2016; 11:e0154665. [PMID: 27135608 PMCID: PMC4852913 DOI: 10.1371/journal.pone.0154665] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/18/2016] [Indexed: 01/20/2023] Open
Abstract
The evolutionary history of macaques, genus Macaca, has been under debate due to the short times of divergence. In this study, maternal, paternal, and biparental genetic systems were applied to infer phylogenetic relationships among macaques and to trace ancient hybridization events in their evolutionary history. Using a PCR display method, 17 newly phylogenetically informative Alu insertions were identified from M. assamensis. We combined presence/absence analysis of 84 Alu elements with mitochondrial genomes as well as nuclear sequences (five autosomal genes, two Y chromosomal genes, and one X chromosomal fragment) to reconstruct a robust macaque phylogeny. Topologies generated from different inherited markers were similar supporting six well defined species groups and a close relationship of M. assamensis and M. thibetana, but differed in the placing of M. arctoides. Both Alu elements and nuclear genes supported that M. arctoides was close to the sinica group, whereas the mitochondrial data clustered it into the fascicularis/mulatta lineage. Our results reveal that a sex-biased hybridization most likely occurred in the evolutionary history of M. arctoides, and suggest an introgressive pattern of male-mediated gene flow from the ancestors of M. arctoides to the M. mulatta population followed by nuclear swamping. According to the estimation of divergence dates, the hybridization occurred around 0.88~1.77 mya (nuclear data) or 1.38~2.56 mya (mitochondrial data). In general, our study indicates that a combination of various molecular markers could help explain complicated evolutionary relationships. Our results have provided new insights into the evolutionary history of macaques and emphasize that hybridization might play an important role in macaque evolution.
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Affiliation(s)
- Juan Jiang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064 Sichuan, China
| | - Jianqiu Yu
- Chengdu Zoo, Institute of Chengdu Wildlife, Chengdu 610081, China
| | - Jing Li
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Peng Li
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064 Sichuan, China
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064 Sichuan, China
| | - Lili Niu
- Chengdu Zoo, Institute of Chengdu Wildlife, Chengdu 610081, China
| | - Jiabo Deng
- Chengdu Zoo, Institute of Chengdu Wildlife, Chengdu 610081, China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Jing Li
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064 Sichuan, China
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12
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Liedigk R, Kolleck J, Böker KO, Meijaard E, Md-Zain BM, Abdul-Latiff MAB, Ampeng A, Lakim M, Abdul-Patah P, Tosi AJ, Brameier M, Zinner D, Roos C. Mitogenomic phylogeny of the common long-tailed macaque (Macaca fascicularis fascicularis). BMC Genomics 2015; 16:222. [PMID: 25887664 PMCID: PMC4371801 DOI: 10.1186/s12864-015-1437-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/06/2015] [Indexed: 12/31/2022] Open
Abstract
Background Long-tailed macaques (Macaca fascicularis) are an important model species in biomedical research and reliable knowledge about their evolutionary history is essential for biomedical inferences. Ten subspecies have been recognized, of which most are restricted to small islands of Southeast Asia. In contrast, the common long-tailed macaque (M. f. fascicularis) is distributed over large parts of the Southeast Asian mainland and the Sundaland region. To shed more light on the phylogeny of M. f. fascicularis, we sequenced complete mitochondrial (mtDNA) genomes of 40 individuals from all over the taxon’s range, either by classical PCR-amplification and Sanger sequencing or by DNA-capture and high-throughput sequencing. Results Both laboratory approaches yielded complete mtDNA genomes from M. f. fascicularis with high accuracy and/or coverage. According to our phylogenetic reconstructions, M. f. fascicularis initially diverged into two clades 1.70 million years ago (Ma), with one including haplotypes from mainland Southeast Asia, the Malay Peninsula and North Sumatra (Clade A) and the other, haplotypes from the islands of Bangka, Java, Borneo, Timor, and the Philippines (Clade B). The three geographical populations of Clade A appear as paraphyletic groups, while local populations of Clade B form monophyletic clades with the exception of a Philippine individual which is nested within the Borneo clade. Further, in Clade B the branching pattern among main clades/lineages remains largely unresolved, most likely due to their relatively rapid diversification 0.93-0.84 Ma. Conclusions Both laboratory methods have proven to be powerful to generate complete mtDNA genome data with similarly high accuracy, with the DNA-capture and high-throughput sequencing approach as the most promising and only practical option to obtain such data from highly degraded DNA, in time and with relatively low costs. The application of complete mtDNA genomes yields new insights into the evolutionary history of M. f. fascicularis by providing a more robust phylogeny and more reliable divergence age estimations than earlier studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1437-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rasmus Liedigk
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany.
| | - Jakob Kolleck
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany.
| | - Kai O Böker
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany. .,Junior Research Group Medical RNA Biology, Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany.
| | - Erik Meijaard
- Borneo Futures Project, People & Nature Consulting International, Country Woods house 306, JL. WR Supratman, Pondok Ranji, Ciputat, 15412, Jakarta, Indonesia. .,School of Archaeology & Anthropology, Building 14, Australian National University, Canberra, ACT 0200, Australia. .,School of Biological Sciences, University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Badrul Munir Md-Zain
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
| | - Muhammad Abu Bakar Abdul-Latiff
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
| | - Ahmad Ampeng
- Sarawak Forest Department Hq, Wisma Sumber Alam Jalan Stadium, 93660, Petra Jaya Kuching, Sarawak, Malaysia.
| | - Maklarin Lakim
- Sabah Parks, Research and Education Division, PO Box 10626, 88806, Kota Kinabalu, Sabah, Malaysia.
| | - Pazil Abdul-Patah
- Department of Wildlife and National Parks, Km 10, Jalan Cheras, 50664, Kuala Lumpur, Malaysia.
| | - Anthony J Tosi
- Department of Anthropology, Kent State University, 238 Lowry Hall, Kent, OH, 44242, USA.
| | - Markus Brameier
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany.
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany.
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany. .,Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany.
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13
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Emperador S, Pacheu-Grau D, Bayona-Bafaluy MP, Garrido-Pérez N, Martín-Navarro A, López-Pérez MJ, Montoya J, Ruiz-Pesini E. An MRPS12 mutation modifies aminoglycoside sensitivity caused by 12S rRNA mutations. Front Genet 2015; 5:469. [PMID: 25642242 PMCID: PMC4294204 DOI: 10.3389/fgene.2014.00469] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 12/19/2014] [Indexed: 01/22/2023] Open
Abstract
Several homoplasmic pathologic mutations in mitochondrial DNA, such as those causing Leber hereditary optic neuropathy or non-syndromic hearing loss, show incomplete penetrance. Therefore, other elements must modify their pathogenicity. Discovery of these modifying factors is not an easy task because in multifactorial diseases conventional genetic approaches may not always be informative. Here, we have taken an evolutionary approach to unmask putative modifying factors for a particular homoplasmic pathologic mutation causing aminoglycoside-induced and non-syndromic hearing loss, the m.1494C>T transition in the mitochondrial DNA. The mutation is located in the decoding site of the mitochondrial ribosomal RNA. We first looked at mammalian species that had fixed the human pathologic mutation. These mutations are called compensated pathogenic deviations because an organism carrying one must also have another that suppresses the deleterious effect of the first. We found that species from the primate family Cercopithecidae (old world monkeys) harbor the m.1494T allele even if their auditory function is normal. In humans the m.1494T allele increases the susceptibility to aminoglycosides. However, in primary fibroblasts from a Cercopithecidae species, aminoglycosides do not impair cell growth, respiratory complex IV activity and quantity or the mitochondrial protein synthesis. Interestingly, this species also carries a fixed mutation in the mitochondrial ribosomal protein S12. We show that the expression of this variant in a human m.1494T cell line reduces its susceptibility to aminoglycosides. Because several mutations in this human protein have been described, they may possibly explain the absence of pathologic phenotype in some pedigree members with the most frequent pathologic mutations in mitochondrial ribosomal RNA.
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Affiliation(s)
- Sonia Emperador
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain ; Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza Zaragoza, Spain ; Centros de Investigación Biomédica en Red de Enfermedades Raras, Universidad de Zaragoza Zaragoza, Spain
| | - David Pacheu-Grau
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain
| | - M Pilar Bayona-Bafaluy
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain
| | - Nuria Garrido-Pérez
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain
| | - Antonio Martín-Navarro
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain
| | - Manuel J López-Pérez
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain ; Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza Zaragoza, Spain ; Centros de Investigación Biomédica en Red de Enfermedades Raras, Universidad de Zaragoza Zaragoza, Spain
| | - Julio Montoya
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain ; Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza Zaragoza, Spain ; Centros de Investigación Biomédica en Red de Enfermedades Raras, Universidad de Zaragoza Zaragoza, Spain
| | - Eduardo Ruiz-Pesini
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain ; Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza Zaragoza, Spain ; Centros de Investigación Biomédica en Red de Enfermedades Raras, Universidad de Zaragoza Zaragoza, Spain ; Fundación ARAID, Universidad de Zaragoza Zaragoza, Spain
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14
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Russo GA. Postsacral Vertebral Morphology in Relation to Tail Length Among Primates and Other Mammals. Anat Rec (Hoboken) 2014; 298:354-75. [DOI: 10.1002/ar.23004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/29/2014] [Accepted: 07/08/2014] [Indexed: 12/11/2022]
Affiliation(s)
- Gabrielle A. Russo
- Department of Anthropology; Stony Brook University; Stony Brook New York 11794-8081 USA
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15
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Hasan MK, Feeroz MM, Jones-Engel L, Engel GA, Kanthaswamy S, Smith DG. Diversity and molecular phylogeny of mitochondrial DNA of rhesus macaques (Macaca mulatta) in Bangladesh. Am J Primatol 2014; 76:1094-104. [PMID: 24810278 DOI: 10.1002/ajp.22296] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 03/26/2014] [Accepted: 04/01/2014] [Indexed: 11/06/2022]
Abstract
While studies of rhesus macaques (Macaca mulatta) in the eastern (e.g., China) and western (e.g., India) parts of their geographic range have revealed major genetic differences that warrant the recognition of two different subspecies, little is known about genetic characteristics of rhesus macaques in the transitional zone extending from eastern India and Bangladesh through the northern part of Indo-China, the probable original homeland of the species. We analyzed genetic variation of 762 base pairs of mitochondrial DNA from 86 fecal swab samples and 19 blood samples from 25 local populations of rhesus macaque in Bangladesh collected from January 2010 to August 2012. These sequences were compared with those of rhesus macaques from India, China, and Myanmar. Forty-six haplotypes defined by 200 (26%) polymorphic nucleotide sites were detected. Estimates of gene diversity, expected heterozygosity, and nucleotide diversity for the total population were 0.9599 ± 0.0097, 0.0193 ± 0.0582, and 0.0196 ± 0.0098, respectively. A mismatch distribution of paired nucleotide differences yielded a statistically significantly negative value of Tajima's D, reflecting a population that rapidly expanded after the terminal Pleistocene. Most haplotypes throughout regions of Bangladesh, including an isolated region in the southwestern area (Sundarbans), clustered with haplotypes assigned to the minor haplogroup Ind-2 from India reflecting an east to west dispersal of rhesus macaques to India. Haplotypes from the southeast region of Bangladesh formed a cluster with those from Myanmar, and represent the oldest rhesus macaque haplotypes of Bangladesh. These results are consistent with the hypothesis that rhesus macaques first entered Bangladesh from the southeast, probably from Indo-China, then dispersed westward throughout eastern and central India.
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Affiliation(s)
- M Kamrul Hasan
- Molecular Anthropology Laboratory, Department of Anthropology, University of California, Davis (UC Davis), California
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16
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Abdul-Latiff MAB, Ruslin F, Fui VV, Abu MH, Rovie-Ryan JJ, Abdul-Patah P, Lakim M, Roos C, Yaakop S, Md-Zain BM. Phylogenetic relationships of Malaysia's long-tailed macaques, Macaca fascicularis, based on cytochrome b sequences. Zookeys 2014; 407:121-40. [PMID: 24899832 PMCID: PMC4042704 DOI: 10.3897/zookeys.407.6982] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 04/22/2014] [Indexed: 12/03/2022] Open
Abstract
Phylogenetic relationships among Malaysia's long-tailed macaques have yet to be established, despite abundant genetic studies of the species worldwide. The aims of this study are to examine the phylogenetic relationships of Macaca fascicularis in Malaysia and to test its classification as a morphological subspecies. A total of 25 genetic samples of M. fascicularis yielding 383 bp of Cytochrome b (Cyt b) sequences were used in phylogenetic analysis along with one sample each of M. nemestrina and M. arctoides used as outgroups. Sequence character analysis reveals that Cyt b locus is a highly conserved region with only 23% parsimony informative character detected among ingroups. Further analysis indicates a clear separation between populations originating from different regions; the Malay Peninsula versus Borneo Insular, the East Coast versus West Coast of the Malay Peninsula, and the island versus mainland Malay Peninsula populations. Phylogenetic trees (NJ, MP and Bayesian) portray a consistent clustering paradigm as Borneo's population was distinguished from Peninsula's population (99% and 100% bootstrap value in NJ and MP respectively and 1.00 posterior probability in Bayesian trees). The East coast population was separated from other Peninsula populations (64% in NJ, 66% in MP and 0.53 posterior probability in Bayesian). West coast populations were divided into 2 clades: the North-South (47%/54% in NJ, 26/26% in MP and 1.00/0.80 posterior probability in Bayesian) and Island-Mainland (93% in NJ, 90% in MP and 1.00 posterior probability in Bayesian). The results confirm the previous morphological assignment of 2 subspecies, M. f. fascicularis and M. f. argentimembris, in the Malay Peninsula. These populations should be treated as separate genetic entities in order to conserve the genetic diversity of Malaysia's M. fascicularis. These findings are crucial in aiding the conservation management and translocation process of M. fascicularis populations in Malaysia.
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Affiliation(s)
- Muhammad Abu Bakar Abdul-Latiff
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Farhani Ruslin
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Vun Vui Fui
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- UCSI University, 1, Jalan Menara Gading, UCSI Heights, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Mohd-Hashim Abu
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | | | - Pazil Abdul-Patah
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- Department of Wildlife and National Parks, Km 10, Jalan Cheras, 50664, Kuala Lumpur, Malaysia
| | - Maklarin Lakim
- Sabah Parks, Research and Education Division, PO Box 10626, 88806, Kota Kinabalu, Sabah, Malaysia
| | - Christian Roos
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Salmah Yaakop
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Badrul Munir Md-Zain
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
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17
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Shattuck MR, Satkoski-Trask J, Deinard A, Tito RY, Smith DG, Malhi RS. The evolutionary history of SLC6A4 and the role of plasticity in Macaca. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 153:605-16. [PMID: 24375078 DOI: 10.1002/ajpa.22460] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 12/03/2013] [Indexed: 11/07/2022]
Abstract
Serotonin has been repeatedly indicated as a biological marker of behavior. In particular, the serotonin transporter gene, SLC6A4, has been the focus of a large body of research. Interestingly, both rhesus macaques (Macaca mulatta) and humans have independently evolved a number of shared polymorphisms for this gene, which is indicative of parallel evolution between the two species. However, little is known about the evolution of this gene, particularly within macaques. Although there are several hypotheses as to the adaptive values of various polymorphisms, few authors have gone beyond theoretical discussion. Here, we examined the genetic variation in SLC6A4 within and between several species of macaques and investigate whether selection has played a significant role in its evolutionary history. In addition, we assayed the promoter region polymorphism, 5-HTTLPR, which is known to play a significant role in regulating both serotonin turnover and behavior. In examining the distribution of the 5-HTTLPR polymorphism, we identified significant differences between Indian and Chinese populations of Macaca mulatta; furthermore, we discovered its presence in Macaca cyclopis, which has not been described before. In regard to the evolutionary history of SLC6A4, we found little evidence for selection and conclude that SLC6A4 largely evolved through neutral processes, possibly due to its potential role in regulating behavioral plasticity. However, we also found very low levels of linkage between the coding regions and 5-HTTLPR. Because we limited evolutionary analyses to the coding regions, it is possible that the promoter region shows a distinct evolutionary history from SLC6A4.
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Affiliation(s)
- Milena R Shattuck
- Department of Anthropology, University of Illinois, Urbana, IL, 61801
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18
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Wu SJ, Luo J, Li QQ, Wang YQ, Murphy RW, Blair C, Wu SF, Yue BS, Zhang YP. Ecological genetics of Chinese rhesus macaque in response to mountain building: all things are not equal. PLoS One 2013; 8:e55315. [PMID: 23405134 PMCID: PMC3566204 DOI: 10.1371/journal.pone.0055315] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 12/21/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Pliocene uplifting of the Qinghai-Tibetan Plateau (QTP) and Quaternary glaciation may have impacted the Asian biota more than any other events. Little is documented with respect to how the geological and climatological events influenced speciation as well as spatial and genetic structuring, especially in vertebrate endotherms. Macaca mulatta is the most widely distributed non-human primate. It may be the most suitable model to test hypotheses regarding the genetic consequences of orogenesis on an endotherm. METHODOLOGY AND PRINCIPAL FINDINGS Using a large dataset of maternally inherited mitochondrial DNA gene sequences and nuclear microsatellite DNA data, we discovered two maternal super-haplogroups exist, one in western China and the other in eastern China. M. mulatta formed around 2.31 Ma (1.51-3.15, 95%), and divergence of the two major matrilines was estimated at 1.15 Ma (0.78-1.55, 95%). The western super-haplogroup exhibits significant geographic structure. In contrast, the eastern super-haplogroup has far greater haplotypic variability with little structure based on analyses of six variable microsatellite loci using Structure and Geneland. Analysis using Migrate detected greater gene flow from WEST to EAST than vice versa. We did not detect signals of bottlenecking in most populations. CONCLUSIONS Analyses of the nuclear and mitochondrial datasets obtained large differences in genetic patterns for M. mulatta. The difference likely reflects inheritance mechanisms of the maternally inherited mtDNA genome versus nuclear biparentally inherited STRs and male-mediated gene flow. Dramatic environmental changes may be responsible for shaping the matrilineal history of macaques. The timing of events, the formation of M. mulatta, and the divergence of the super-haplogroups, corresponds to both the uplifting of the QTP and Quaternary climatic oscillations. Orogenesis likely drove divergence of western populations in China, and Pleistocene glaciations are likely responsible for genetic structuring in the eastern super-haplogroup via geographic isolation and secondary contact.
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Affiliation(s)
- Shan-Jin Wu
- Laboratory for Conservation and Utilization of Bio-resources, School of Life Science, Yunnan University, Kunming, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
| | - Jing Luo
- Laboratory for Conservation and Utilization of Bio-resources, School of Life Science, Yunnan University, Kunming, China
| | - Qing-Qing Li
- School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Yan-Qin Wang
- Laboratory for Conservation and Utilization of Bio-resources, School of Life Science, Yunnan University, Kunming, China
| | - Robert W. Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
- Centre for Biodiversity and Conservation Biology, Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Christopher Blair
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
| | - Bi-Song Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
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Variability of tail length in hybrids of the Japanese macaque (Macaca fuscata) and the Taiwanese macaque (Macaca cyclopis). Primates 2012; 53:397-411. [DOI: 10.1007/s10329-012-0317-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Accepted: 07/10/2012] [Indexed: 10/28/2022]
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Biswas J, Borah DK, Das A, Das J, Bhattacharjee PC, Mohnot SM, Horwich RH. The enigmatic Arunachal macaque: its biogeography, biology and taxonomy in Northeastern India. Am J Primatol 2011; 73:458-73. [PMID: 21246593 DOI: 10.1002/ajp.20924] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 12/21/2010] [Accepted: 12/21/2010] [Indexed: 11/09/2022]
Abstract
The purpose of this study was to determine the taxonomic status of an unidentified enigmatic macaque seen by scientists since the late 1990s in Arunachal Pradesh, India. We surveyed 49 troops of enigmatic macaques in four districts of Arunachal Pradesh. The population studied is from the macaque sinica-group as defined by the reproductive organs. The main species-separating trait in the sinica-group is tail length to head and body length ratio that decreases with latitude and elevation. We gathered data on morphology, pelage descriptions, tail to head and body ratios and tail to hind foot ratios from photos and live animals (43 individuals from 36 areas) within the range of and between the two subspecies of the Assamese macaque (Macaca assamensis). We compared the data to six western Assamese macaques and studies of Assamese macaques and related species. We found great variability in tail length, pelage color, facial skin color, and facial and hair patterns. The tail/head-body and tail/foot ratios, although varied, supported the hypothesis that these enigmatic forms were part of a population of Assamese macaques found in the gap between the two subspecies ranges and were not a new species as described earlier. Instead, we found evidence that darker pelage, larger body size, and shorter tails occur at higher elevations and latitudes similar to the general trend in the sinica-group's adaptations to colder climates. Thus, the population may be important for its variation, throwing light on the speciation process and how the northern species of Tibetan macaques evolved from an ancestor similar to the Assamese macaques as adaptations to a colder climate.
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Affiliation(s)
- Jihosuo Biswas
- Primate Research Centre NE India, Guwahati, Assam, India
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Sun B, Li J, Zhu Y, Xia D. Mitochondrial DNA variation in Tibetan macaque (Macaca thibetana). FOLIA ZOOLOGICA 2010. [DOI: 10.25225/fozo.v59.i4.a5.2010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Binghua Sun
- School of Life Science, Anhui University, 3 Feixi road, 230039 Hefei, China
- Anhui Key Laboratory of Eco-engineering and Bio-technique, 3 Feixi road, 230039 Hefei, China
| | - Jinhua Li
- School of Life Science, Anhui University, 3 Feixi road, 230039 Hefei, China
- Anhui Key Laboratory of Eco-engineering and Bio-technique, 3 Feixi road, 230039 Hefei, China
| | - Yong Zhu
- School of Life Science, Anhui University, 3 Feixi road, 230039 Hefei, China
- Anhui Key Laboratory of Eco-engineering and Bio-technique, 3 Feixi road, 230039 Hefei, China
| | - Dongpo Xia
- School of Life Science, Anhui University, 3 Feixi road, 230039 Hefei, China
- Anhui Key Laboratory of Eco-engineering and Bio-technique, 3 Feixi road, 230039 Hefei, China
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Evans BJ, Pin L, Melnick DJ, Wright SI. Sex-linked inheritance in macaque monkeys: implications for effective population size and dispersal to Sulawesi. Genetics 2010; 185:923-37. [PMID: 20407130 PMCID: PMC2907209 DOI: 10.1534/genetics.110.116228] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 04/19/2010] [Indexed: 11/18/2022] Open
Abstract
Sex-specific differences in dispersal, survival, reproductive success, and natural selection differentially affect the effective population size (N(e)) of genomic regions with different modes of inheritance such as sex chromosomes and mitochondrial DNA. In papionin monkeys (macaques, baboons, geladas, mandrills, drills, and mangabeys), for example, these factors are expected to reduce N(e) of paternally inherited portions of the genome compared to maternally inherited portions. To explore this further, we quantified relative N(e) of autosomal DNA, X and Y chromosomes, and mitochondrial DNA using molecular polymorphism and divergence information from pigtail macaque monkeys (Macaca nemestrina). Consistent with demographic expectations, we found that N(e) of the Y is lower than expected from a Wright-Fisher idealized population with an equal proportion of males and females, whereas N(e) of mitochondrial DNA is higher. However, N(e) of 11 loci on the X chromosome was lower than expected, a finding that could be explained by pervasive hitchhiking effects on this chromosome. We evaluated the fit of these data to various models involving natural selection or sex-biased demography. Significant support was recovered for natural selection acting on the Y chromosome. A demographic model with a skewed sex ratio was more likely than one with sex-biased migration and explained the data about as well as an ideal model without sex-biased demography. We then incorporated these results into an evaluation of macaque divergence and migration on Borneo and Sulawesi islands. One X-linked locus was not monophyletic on Sulawesi, but multilocus data analyzed in a coalescent framework failed to reject a model without migration between these islands after both were colonized.
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Affiliation(s)
- Ben J Evans
- Department of Biology, McMaster University, Life Sciences Building, Hamilton, Ontario L8S 4K1, Canada.
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Li J, Han K, Xing J, Kim HS, Rogers J, Ryder OA, Disotell T, Yue B, Batzer MA. Phylogeny of the macaques (Cercopithecidae: Macaca) based on Alu elements. Gene 2009; 448:242-9. [PMID: 19497354 PMCID: PMC2783879 DOI: 10.1016/j.gene.2009.05.013] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 05/26/2009] [Accepted: 05/27/2009] [Indexed: 10/20/2022]
Abstract
Genus Macaca (Cercopithecidae: Papionini) is one of the most successful primate radiations. Despite previous studies on morphology and mitochondrial DNA analysis, a number of issues regarding the details of macaque evolution remain unsolved. Alu elements are a class of non-autonomous retroposons belonging to short interspersed elements that are specific to the primate lineage. Because retroposon insertions show very little homoplasy, and because the ancestral state (absence of the SINE) is known, Alu elements are useful genetic markers and have been utilized for analyzing primate phylogenentic relationships and human population genetic relationships. Using PCR display methodology, 298 new Alu insertions have been identified from ten species of macaques. Together with 60 loci reported previously, a total of 358 loci are used to infer the phylogenetic relationships of genus Macaca. With regard to earlier unresolved issues on the macaque evolution, the topology of our tree suggests that: 1) genus Macaca contains four monophyletic species groups; 2) within the Asian macaques, the silenus group diverged first, and members of the sinica and fascicularis groups share a common ancestor; 3) Macaca arctoides are classified in the sinica group. Our results provide a robust molecular phylogeny for genus Macaca with stronger statistical support than previous studies. The present study also illustrates that SINE-based approaches are a powerful tool in primate phylogenetic studies and can be used to successfully resolve evolutionary relationships between taxa at scales from the ordinal level to closely related species within one genus.
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Affiliation(s)
- Jing Li
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Kyudong Han
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Jinchuan Xing
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Korea
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Oliver A. Ryder
- San Diego Zoo's Institute for Conservation Research, San Diego, California 92112, USA
| | - Todd Disotell
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York 10003, USA
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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Juliandi B, Suryobroto B, Perwitasari-Farajallah D. The ischial callosities of Sulawesi macaques. Am J Primatol 2009; 71:1021-31. [PMID: 19746442 DOI: 10.1002/ajp.20745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Berry Juliandi
- Division of Animal Biosystematic and Ecology, Department of Biology, Bogor Agricultural University, Bogor, Indonesia.
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25
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Identification of novel MHC class I sequences in pig-tailed macaques by amplicon pyrosequencing and full-length cDNA cloning and sequencing. Immunogenetics 2009; 61:689-701. [PMID: 19777225 DOI: 10.1007/s00251-009-0397-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Accepted: 09/11/2009] [Indexed: 12/21/2022]
Abstract
Pig-tailed macaques (Macaca nemestrina) provide important animal models in biomedical research, but utility of this species for HIV and other disease pathogenesis research is limited by incomplete knowledge of major histocompatibility complex (MHC) class I genetics. Here, we describe comprehensive MHC class I genotyping of 24 pig-tailed macaques, using pyrosequencing to evaluate a 367- bp complementary DNA (cDNA)-PCR amplicon spanning the highly polymorphic peptide-binding region of MHC class I transcripts. We detected 29 previously described Mane transcripts, 90 novel class I sequences, and eight shared MHC class IB haplotypes. We used this genotyping data to inform full-length MHC class I cDNA allele discovery, characterizing 66 novel full-length transcripts. These new full-length sequences nearly triple the number of Mane-B cDNA sequences previously characterized. The comprehensive genotypes and full-length Mane transcripts described herein add value to pig-tailed macaques as model organisms in biomedical research; furthermore, the coordinated method for MHC genotyping and allele discovery is extensible to other less well-characterized nonhuman primate species.
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26
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Ito T, Nishimura TD, Senut B, Koppe T, Treil J, Takai M. Reappraisal of Macaca speciosa subfossilis from the Late Pleistocene of Northern Vietnam Based on the Analysis of Cranial Anatomy. INT J PRIMATOL 2009. [DOI: 10.1007/s10764-009-9365-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Bonhomme M, Cuartero S, Blancher A, Crouau-Roy B. Assessing natural introgression in 2 biomedical model species, the rhesus macaque (Macaca mulatta) and the long-tailed macaque (Macaca fascicularis). J Hered 2008; 100:158-69. [PMID: 18974398 DOI: 10.1093/jhered/esn093] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Rhesus macaque (Macaca mulatta) and long-tailed macaque (Macaca fascicularis) are the 2 most commonly used primate model species in biomedical sciences. Although morphological studies have revealed a weak hybridization at the interspecific contact zone, in the north of Indochina, a molecular study has suggested an ancient introgression from rhesus to long-tailed macaque into the Indo-Chinese peninsula. However, the gene flow between these 2 taxa has never been quantified using genetic data and theoretical models. In this study, we have examined genetic variation within and between the parapatric Chinese rhesus macaque and Indo-Chinese long-tailed macaque populations, using 13 autosomal, 5 sex-linked microsatellite loci and mitochondrial DNA sequence data. From these data, we assessed genetic structure and estimated gene flow using a Bayesian clustering approach and the "Isolation with Migration" model. Our results reveal a weak interspecific genetic differentiation at both autosomal and sex-linked loci, suggesting large population sizes and/or gene flow between populations. According to the Bayesian clustering, Chinese rhesus macaque is a highly homogeneous gene pool that contributes strongly to the current Indo-Chinese long-tailed macaque genetic makeup, whether or not current admixture is assumed. Coalescent simulations, which integrated the characteristics of the loci, pointed out 1) a higher effective population size in rhesus macaque, 2) no mitochondrial gene flow, and 3) unilateral and male-mediated nuclear gene flow of approximately 10 migrants per generation from rhesus to long-tailed macaque. These patterns of genetic structure and gene flow suggest extensive ancient introgression from Chinese rhesus macaque into the Indo-Chinese long-tailed macaque population.
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Affiliation(s)
- Maxime Bonhomme
- the Université Paul Sabatier, Laboratoire Evolution et Diversité Biologique, UMR CNRS 5174, Toulouse cedex 9, France
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Street SL, Kyes RC, Grant R, Ferguson B. Single nucleotide polymorphisms (SNPs) are highly conserved in rhesus (Macaca mulatta) and cynomolgus (Macaca fascicularis) macaques. BMC Genomics 2007; 8:480. [PMID: 18166133 PMCID: PMC2248198 DOI: 10.1186/1471-2164-8-480] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Accepted: 12/31/2007] [Indexed: 11/17/2022] Open
Abstract
Background Macaca fascicularis (cynomolgus or longtail macaques) is the most commonly used non-human primate in biomedical research. Little is known about the genomic variation in cynomolgus macaques or how the sequence variants compare to those of the well-studied related species, Macaca mulatta (rhesus macaque). Previously we identified single nucleotide polymorphisms (SNPs) in portions of 94 rhesus macaque genes and reported that Indian and Chinese rhesus had largely different SNPs. Here we identify SNPs from some of the same genomic regions of cynomolgus macaques (from Indochina, Indonesia, Mauritius and the Philippines) and compare them to the SNPs found in rhesus. Results We sequenced a portion of 10 genes in 20 cynomolgus macaques. We identified 69 SNPs in these regions, compared with 71 SNPs found in the same genomic regions of 20 Indian and Chinese rhesus macaques. Thirty six (52%) of the M. fascicularis SNPs were overlapping in both species. The majority (70%) of the SNPs found in both Chinese and Indian rhesus macaque populations were also present in M. fascicularis. Of the SNPs previously found in a single rhesus population, 38% (Indian) and 44% (Chinese) were also identified in cynomolgus macaques. In an alternative approach, we genotyped 100 cynomolgus DNAs using a rhesus macaque SNP array representing 53 genes and found that 51% (29/57) of the rhesus SNPs were present in M. fascicularis. Comparisons of SNP profiles from cynomolgus macaques imported from breeding centers in China (where M. fascicularis are not native) showed they were similar to those from Indochina. Conclusion This study demonstrates a surprisingly high conservation of SNPs between M. fascicularis and M. mulatta, suggesting that the relationship of these two species is closer than that suggested by morphological and mitochondrial DNA analysis alone. These findings indicate that SNP discovery efforts in either species will generate useful resources for both macaque species. Identification of SNPs that are unique to regional populations of cynomolgus macaques indicates that location-specific SNPs could be used to distinguish monkeys of uncertain origin. As an example, cynomolgus macaques obtained from 2 different breeding centers in China were shown to have Indochinese ancestry.
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Affiliation(s)
- Summer L Street
- Genetics Research and Informatics Program, Oregon National Primate Research Center, Oregon Health & Sciences University, Beaverton, OR 97006, USA.
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Jacquelin B, Mayau V, Brysbaert G, Regnault B, Diop OM, Arenzana-Seisdedos F, Rogge L, Coppée JY, Barré-Sinoussi F, Benecke A, Müller-Trutwin MC. Long oligonucleotide microarrays for African green monkey gene expression profile analysis. FASEB J 2007; 21:3262-71. [PMID: 17507667 DOI: 10.1096/fj.07-8271com] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Nonhuman primates, including African green monkey (AGM), are important models for biomedical research. The information on monkey genomes is still limited and no versatile gene expression screening tool is available. We tested human whole genome microarrays for cross-species reactivity with AGM transcripts using both long oligonucleotide arrays (60-mer probes) and short oligonucleotide arrays (25-mer). Using the long oligonucleotide arrays, we detected 4-fold more AGM transcripts than with the short oligonucleotide technology. The number of detected transcripts was comparable to that detected using human RNA, with 87% of the detected genes being shared between both species. The specificity of the signals obtained with the long oligonucleotide arrays was determined by analyzing the transcriptome of concanavalin A-activated CD4+ T cells vs. nonactivated T cells of two monkey species AGM and macaque. For both species, the genes showing the most significant changes in expression, such as IL-2R, were those known to be regulated in human CD4+ T cell activation. Finally, tissue specificity of the signals was established by comparing the transcription profiles of AGM brain and tonsil cells. In conclusion, the ABI human microarray platform provides a highly valuable tool for the assessment of AGM gene expression profiles.
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Affiliation(s)
- Béatrice Jacquelin
- Unité de Régulations des Infections Rétrovirales, Institut Pasteur, 25, rue du Docteur Roux, 75724 Paris cedex 15, France
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30
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Smith DG, McDonough JW, George DA. Mitochondrial DNA variation within and among regional populations of longtail macaques (Macaca fascicularis) in relation to other species of the fascicularis group of macaques. Am J Primatol 2007; 69:182-98. [PMID: 17177314 DOI: 10.1002/ajp.20337] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
An 835 base pair (bp) fragment of mitochondrial DNA (mtDNA) was sequenced to characterize genetic variation within and among 1,053 samples comprising five regional populations each of longtail macaques (Macaca fascicularis) and rhesus macaques (Macaca mulatta), and one sample each of Japanese (M. fuscata) and Taiwanese (M. cyclopis) macaques. The mtDNA haplotypes of longtail macaques clustered in two large highly structured clades (Fas1 and Fas2) of a neighbor-joining tree that were reciprocally monophyletic with respect to those representing rhesus macaques, Japanese macaques, and Taiwanese macaques. Both clades exhibited haplotypes of Indonesian and Malaysian longtail macaques widely dispersed throughout them; however, longtail macaques from Indochina, Philippines, and Mauritius each clustered in a separate well-defined clade together with one or a few Malaysian and/or Indonesian longtail macaques, suggesting origins on the Sunda shelf. Longtail macaques from Malaysia and Indonesia were far more genetically diverse, and those from Mauritius were far less diverse than any other population studied. Nucleotide diversity between mtDNA sequences of longtail macaques from different geographic regions is, in some cases, greater than that between Indian and Chinese rhesus macaques. Approximately equal amounts of genetic diversity are due to differences among animals in the same regional population, different regional populations, and different species. A greater proportion of genetic variance was explained by interspecies differences when Japanese and Taiwanese macaques were regarded as regional populations of rhesus macaques than when they were treated as separate species. Rhesus macaques from China were more closely related to both Taiwanese and Japanese macaques than to their own conspecifics from India.
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Affiliation(s)
- David Glenn Smith
- Molecular Anthropology Laboratory, Department of Anthropology, University of California-Davis, Davis, CA 95616, USA.
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31
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Ziegler T, Abegg C, Meijaard E, Perwitasari-Farajallah D, Walter L, Hodges JK, Roos C. Molecular phylogeny and evolutionary history of Southeast Asian macaques forming the M. silenus group. Mol Phylogenet Evol 2006; 42:807-16. [PMID: 17208017 DOI: 10.1016/j.ympev.2006.11.015] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Revised: 11/09/2006] [Accepted: 11/16/2006] [Indexed: 10/23/2022]
Abstract
The 12 presently recognized taxa forming the Macaca silenus group represent the most diverse lineage within the genus Macaca. The present study was set up to clarify the phylogenetic relationships of the extant members of the M. silenus group and to explain their geographical distribution patterns seen today. A combined approach involving the analysis of one paternal (TSPY) and two maternal (cyt b and 12S-16S rRNA) molecular markers enabled us to resolve the phylogenetic relationships within this lineage. Our Y chromosomal marker is not informative enough to allow detailed conclusion. Based on our mitochondrial data, however, M. pagensis, endemic to the three southern Mentawai islands (Sipora, North- and South Pagai), split off early (2.4-2.6 mya) and represents a sister clade to the macaques from the northern Mentawai island of Siberut and from those of the Southeast Asian mainland, which diverged in a radiation-like splitting event about 1.5-1.7 mya. By combining our new results with available data on behavioural as well as climate and sea level changes in Southeast Asia during the Plio- and Pleistocene, we have developed two scenarios for the evolutionary history of this primate group, which may help explain the current geographical distribution of its members.
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Affiliation(s)
- Thomas Ziegler
- Department of Reproductive Biology, German Primate Centre, Kellnerweg 4, 37077 Göttingen, Germany
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32
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33
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Li QQ, Zhang YP. Phylogenetic relationships of the macaques (Cercopithecidae: Macaca), inferred from mitochondrial DNA sequences. Biochem Genet 2006; 43:375-86. [PMID: 16187162 DOI: 10.1007/s10528-005-6777-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2004] [Accepted: 08/30/2004] [Indexed: 11/24/2022]
Abstract
To study the phylogenetic relationships of the macaques, five gene fragments were sequenced from 40 individuals of eight species: Macaca mulatta, M. cyclopis, M. fascicularis, M. arctoides, M. assamensis, M. thibetana, M. silenus, and M. leonina. In addition, sequences of M. sylvanus were obtained from Genbank. A baboon was used as the outgroup. The phylogenetic trees were constructed using maximum-parsimony and Bayesian methods. Because five gene fragments were from the mitochondrial genome and were inherited as a single entity without recombination, we combined the five genes into a single analysis. The parsimony bootstrap proportions we obtained were higher than those from earlier studies based on the combined mtDNA dataset. Excluding M. arctoides, our results are generally consistent with the classification of Delson (1980). Our phylogenetic analyses agree with earlier studies suggesting that the mitochondrial lineages of M. arctoides share a close evolutionary relationship with the mitochondrial lineages of the fascicularis group of macaques (and M. fascicularis, specifically). M. mulatta (with respect to M. cyclopis), M. assamensis assamensis (with respect to M. thibetana), and M. leonina (with respect to M. silenus) are paraphyletic based on our analysis of mitochondrial genes.
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Affiliation(s)
- Qing-Qing Li
- Laboratory of Molecular Evolution and Genome Diversity, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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GIPPOLITI SPARTACO, AMORI GIOVANNI. Ancient introductions of mammals in the Mediterranean Basin and their implications for conservation. Mamm Rev 2006. [DOI: 10.1111/j.1365-2907.2006.00081.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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35
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Tanee T, Chaveerach A, Sattayasai N, Tanomtong A, Suarez SA, Nuchadomrong S. Cytogenetic and AFLP Fingerprints for Five Species of Thai Macaques. CYTOLOGIA 2006. [DOI: 10.1508/cytologia.71.303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Tawatchai Tanee
- Department of Biochemistry, Faculty of Science, Khon Kaen University
| | | | - Nison Sattayasai
- Department of Biochemistry, Faculty of Science, Khon Kaen University
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36
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Kawamoto Y. NRAMP1 polymorphism in a hybrid population between Japanese and Taiwanese macaques in Wakayama, Japan. Primates 2004; 46:203-6. [PMID: 16096901 DOI: 10.1007/s10329-004-0119-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2004] [Accepted: 09/28/2004] [Indexed: 10/26/2022]
Abstract
A macaque population produced by the hybridization of native Japanese macaques (Macaca fuscata) and introduced Taiwanese macaques (M. cyclopis) in Wakayama Prefecture was shown to possess three DNA haplotypes of the natural resistance-associated macrophage protein 1 (NRAMP1). Based on genotyping and comparison with M. fuscata populations, it was revealed that the introduced M. cyclopis population was polymorphic for the NRAMP1 locus. Extensive crossbreeding of the introduced species with the native species was confirmed using this genetic marker and the proportion of M. cyclopis genes was 57.4%. Results of statistical tests suggested non-random mating in the hybrid population.
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Affiliation(s)
- Yoshi Kawamoto
- Primate Research Institute, Kyoto University, Kanrin, Inuyama 484-8506, Japan.
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Nakatsukasa M, Ward CV, Walker A, Teaford MF, Kunimatsu Y, Ogihara N. Tail loss in Proconsul heseloni. J Hum Evol 2004; 46:777-84. [PMID: 15183676 DOI: 10.1016/j.jhevol.2004.04.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2004] [Revised: 04/07/2004] [Accepted: 04/08/2004] [Indexed: 11/20/2022]
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Marmi J, Bertranpetit J, Terradas J, Takenaka O, Domingo-Roura X. Radiation and phylogeography in the Japanese macaque, Macaca fuscata. Mol Phylogenet Evol 2004; 30:676-85. [PMID: 15012947 DOI: 10.1016/s1055-7903(03)00247-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2003] [Revised: 06/06/2003] [Indexed: 11/21/2022]
Abstract
The Japanese macaque (Macaca fuscata) presumably differentiated from eastern rhesus macaque (Macaca mulatta) populations during the Pleistocene and the two species are closely related. In order to analyse speciation and subspeciation events in the Japanese macaque and to describe historical and current relationships among their populations, we sequenced and analysed a fragment of 392bp of mitochondrial DNA (mtDNA) control region in 50 individuals belonging to six populations of Japanese macaque and compared these sequences with 89 eastern rhesus macaque control region sequences from GenBank/EMBL database. There were high genetic similarities between both species and only two positions were fixed within each species, which supports the inclusion of the Japanese macaque in a single species with eastern populations of rhesus macaques. Japanese macaque ancestors colonised Japan after the separation of the two species, estimated at between 0.31 and 0.88 million years ago (Mya). The star-like phylogeny, multimodal mismatch distribution, and lack of correlation between geographic and genetic distances are in accordance with a rapid dispersion of macaques throughout the archipelago after the arrival into Japan. The species shows low genetic variation within populations and high levels of genetic differentiation among populations with no mtDNA haplotype shared across populations. Genetic distances between Yakushima macaques (Macaca fuscata yakui) and any other population of Macaca fuscata fuscata subspecies are comparable to the distances between populations of Honshu, Awajishima, and Kyushu, not supporting the classification of Yakushima macaques as a different subspecies.
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Affiliation(s)
- Josep Marmi
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Dr. Aiguader 80, Barcelona E-08003, Spain
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Evans BJ, Supriatna J, Andayani N, Melnick DJ. Diversification of Sulawesi macaque monkeys: decoupled evolution of mitochondrial and autosomal DNA. Evolution 2004; 57:1931-46. [PMID: 14503633 DOI: 10.1111/j.0014-3820.2003.tb00599.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In macaque monkeys, females are philopatric and males are obligate dispersers. This social system is expected to differently affect evolution of genetic elements depending on their mode of inheritance. Because of this, the geographic structure of molecular variation may differ considerably in mitochondrial DNA (mtDNA) and in autosomal DNA (aDNA) in the same individuals, even though these genomes are partially co-inherited. On the Indonesian island of Sulawesi, macaque monkeys underwent an explosive diversification as a result of range fragmentation. Today, barriers to dispersal have receded and fertile hybrid individuals can be found at contact zones between parapatric species. In this study, we examine the impact of range fragmentation on Sulawesi macaque mtDNA and aDNA by comparing evolution, phylogeography, and population subdivision of each genome. Our results suggest that mtDNA is paraphyletic in some species, and that mtDNA phylogeography is largely consistent with a pattern of isolation by distance. Autosomal DNA, however, is suggestive of fragmentation, in that interspecific differentiation across most contact zones is significant but intraspecific differentiation between contact zones is not. Furthermore, in mtDNA, most molecular variation is partitioned between populations within species but in aDNA most variation is partitioned within populations. That mtDNA has a different geographic structure than aDNA (and morphology) in these primates is a probable consequence of (1) a high level of ancestral polymorphism in mtDNA, (2) differences between patterns of ancestral dispersal of matrilines and contemporary dispersal of males, and (3) the fact that female philopatry impedes gene flow of macaque mtDNA.
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Affiliation(s)
- Ben J Evans
- Department of Ecology, Evolution and Environmental Biology and Center for Environmental Research and Conservation, 1200 Amsterdam Avenue, Columbia University, New York 10027, USA.
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KAWAMOTO Y, HAGIHARA K, AIZAWA K. Finding of Hybrid Individuals between Native Japanese Macaques and Introduced Rhesus Macaques in the Bousou Peninsula, Chiba, Japan. ACTA ACUST UNITED AC 2004. [DOI: 10.2354/psj.20.89] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Roos C, Ziegler T, Hodges JK, Zischler H, Abegg C. Molecular phylogeny of Mentawai macaques: taxonomic and biogeographic implications. Mol Phylogenet Evol 2003; 29:139-50. [PMID: 12967615 DOI: 10.1016/s1055-7903(03)00076-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In order to elucidate the evolutionary history and taxonomy of the Mentawai macaques, we sequenced a 567 base pairs (bp) long fragment of the mitochondrial cytochrome b gene from 39 individuals representing pigtailed macaque populations from Siberut, Sipora, South Pagai, and Sumatra. Pairwise difference analyses carried out within and among populations have shown, that: (1) variation within populations is relative low, (2) variation among populations is increased, and (3) pairwise differences within and among the populations from Sipora and South Pagai are in the same range. From phylogenetic tree reconstructions including further macaque species, we detected a paraphyletic origin of Mentawai macaques with the Siberut population more closely related to Macaca nemestrina from Sumatra, than it is to populations from the Southern islands. Based on these results, we favour a scenario in that macaques entered the Mentawai islands by two independent colonisation events. Taking together the paraphyletic origin of Mentawai macaques and the genetic differences detected among pigtailed macaque populations, which are comparable with those observed among the seven Sulawesi macaque species, we propose to separate macaques from Siberut and Sipora, North and South Pagai into two distinct species, Macaca siberu and Macaca pagensis, respectively.
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Affiliation(s)
- Christian Roos
- Primate Genetics, German Primate Centre, Kellnerweg 4, 37077 Göttingen, Germany.
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Blankenburg A, Kaup FJ, Sauermann U. Mhc class II DRB sequences of lion-tailed macaques (Macaca silenus). TISSUE ANTIGENS 2003; 62:267-9. [PMID: 12956883 DOI: 10.1034/j.1399-0039.2003.00094.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The lion-tailed macaque (Macaca silenus) is an endangered species. Research into the genetics of this species is important as a basis for coordinated breeding programs of captive populations. Therefore, we sought to analyze the Mhc class II DRB genes of this species because of it is highly polymorphic in genetically heterogeneous populations of most species. Ten individuals from seven families were evaluated. Nine DRB second exon sequences belonging to eight allelic lineages were identified. These lineages are also present in the best-studied macaque species: the rhesus (Macaca mulatta). Although only these relatively few alleles could be isolated, they display variation on the lineage level. This may be a mechanism for increasing their functional diversity.
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Affiliation(s)
- A Blankenburg
- Department of Virology and Immunology, German Primate Center, Göttingen, Germany
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Zeng Z, McDonald TP, Wang R, Liu Q, Austin CP. Neuropeptide FF receptor 2 (NPFF2) is localized to pain-processing regions in the primate spinal cord and the lower level of the medulla oblongata. J Chem Neuroanat 2003; 25:269-78. [PMID: 12842272 DOI: 10.1016/s0891-0618(03)00038-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Studies have suggested that NPFF-like peptides and their receptors play important roles in physiological and pathological conditions. Here, we show, using multiple expression modalities, that the type 2 NPFF receptor (hNPFF2) is expressed in regions of the primate spinal cord and brainstem mediating pain sensation. In situ hybridization using an NPFF2 riboprobe, and immunohistochemistry using a novel NPFF2 antibody, demonstrated strong NPFF2 expression in the superficial layer of the dorsal horn, and in the spinal trigeminal nucleus of the brainstem of the African green monkey (AGM). In addition, autoradiography using a radiolabeled NPFF analog ([125I]1DMe) revealed dense binding signal in the superficial layer of the dorsal horn in the spinal cord. The distribution pattern of hNPFF2 in the AGM spinal cord and the lower level of the brainstem are consistent with a hypothesized potential role for NPFF peptides in modulation of sensory input, opioid analgesia and morphine tolerance through spinal and supraspinal mechanisms.
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Affiliation(s)
- Zhizhen Zeng
- Department of Neuroscience, Merck Research Laboratories, WP26A-3000, P.O. Box 4, West Point, PA 19486, USA.
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Evans BJ, Supriatna J, Andayani N, Melnick DJ. DIVERSIFICATION OF SULAWESI MACAQUE MONKEYS: DECOUPLED EVOLUTION OF MITOCHONDRIAL AND AUTOSOMAL DNA. Evolution 2003. [DOI: 10.1554/02-476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Affiliation(s)
- Eugene E Harris
- Departamento de Biologia, Instituto de Biociências, Universidade de São Paulo, Brasil.
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