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Sariyati NH, Abdul-Latiff MAB, Aifat NR, Mohd-Ridwan AR, Osman NA, Karuppannan KV, Chan E, Md-Zain BM. Molecular phylogeny confirms the subspecies delineation of the Malayan Siamang ( Symphalangussyndactyluscontinentis) and the Sumatran Siamang ( Symphalangussyndactylussyndactylus) based on the hypervariable region of mitochondrial DNA. Biodivers Data J 2024; 12:e120314. [PMID: 38707255 PMCID: PMC11069032 DOI: 10.3897/bdj.12.e120314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/19/2024] [Indexed: 05/07/2024] Open
Abstract
Siamangs (Symphalangussyndactylus) are native to Peninsular Malaysia, Sumatra and southern Thailand and their taxonomical classification at subspecies level remains unclear. Morphologically, two subspecies were proposed as early as 1908 by Thomas namely Symphalangus s.syndactylus and Symphalanguss.continentis. Thus, this study aims to clarify the Siamang subspecies status, based on mtDNA D-loop sequences. Faecal samples were collected from wild Siamang populations at different localities in Peninsular Malaysia. A 600-bp sequence of the mitochondrial D-loop region was amplified from faecal DNA extracts and analysed along with GenBank sequences representing Symphalangus sp., Nomascus sp., Hylobates sp., Hoolock sp. and outgroups (Pongopygmaeus, Macacafascicularis and Papiopapio). The molecular phylogenetic analysis in this study revealed two distinct clades formed by S.s.syndactylus and S.s.continentis which supports the previous morphological delineation of the existence of two subspecies. Biogeographical analysis indicated that the Sumatran population lineage was split from the Peninsular Malaysian population lineage and a diversification occurrred in the Pliocene era (~ 3.12 MYA) through southward expansion. This postulation was supported by the molecular clock, which illustrated that the Peninsular Malaysian population (~ 1.92 MYA) diverged earlier than the Sumatran population (~ 1.85 MYA). This is the first study to use a molecular approach to validate the subspecies statuses of S.s.syndactylus and S.s.continentis. This finding will be useful for conservation management, for example, during Siamang translocation and investigations into illegal pet trade and forensics involving Malayan and Sumatran Siamangs.
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Affiliation(s)
- Nur Hartini Sariyati
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), 84600, Muar, Johor, MalaysiaFaculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus)84600, Muar, JohorMalaysia
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600Bangi, SelangorMalaysia
| | - Muhammad Abu Bakar Abdul-Latiff
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), 84600, Muar, Johor, MalaysiaFaculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus)84600, Muar, JohorMalaysia
| | - Nor Rahman Aifat
- Faculty of Tropical Forestry, Universiti Malaysia Sabah, 88400, Kota Kinabalu, Sabah, MalaysiaFaculty of Tropical Forestry, Universiti Malaysia Sabah, 88400Kota Kinabalu, SabahMalaysia
| | - Abd Rahman Mohd-Ridwan
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, MalaysiaCentre for Pre-University Studies, Universiti Malaysia Sarawak, 94300Kota Samarahan, SarawakMalaysia
| | - Nur Azimah Osman
- Faculty of Applied Sciences, Universiti Teknologi Mara Negeri Sembilan, 72000, Kuala Pilah, Negeri Sembilan, MalaysiaFaculty of Applied Sciences, Universiti Teknologi Mara Negeri Sembilan, 72000Kuala Pilah, Negeri SembilanMalaysia
| | - Kayal Vizi Karuppannan
- National Wildlife Forensic Laboratory (NWFL), Department of Wildlife and National Parks (PERHILITAN), 56100, Kuala Lumpur, MalaysiaNational Wildlife Forensic Laboratory (NWFL), Department of Wildlife and National Parks (PERHILITAN), 56100Kuala LumpurMalaysia
| | - Eddie Chan
- Genting Nature Adventure, Resorts World Awana Hotel, 69000, Genting Highlands, Pahang, MalaysiaGenting Nature Adventure, Resorts World Awana Hotel69000, Genting Highlands, PahangMalaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600Bangi, SelangorMalaysia
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Gani M, Rovie-Ryan JJ, Sitam FT, Kulaimi NAM, Zheng CC, Atiqah AN, Rahim NMA, Mohammed AA. Taxonomic and genetic assessment of captive White-Handed Gibbons ( Hylobateslar) in Peninsular Malaysia with implications towards conservation translocation and reintroduction programmes. Zookeys 2022; 1076:25-41. [PMID: 34975272 PMCID: PMC8674214 DOI: 10.3897/zookeys.1076.73262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/25/2021] [Indexed: 11/29/2022] Open
Abstract
Conservation translocation and reintroduction for the purpose of repopulating and reinforcing extirpated or depleted populations has been recognised as an important conservation tool, particularly for gibbon conservation in the immediate future. Feasibility assessments involving multiple factors, including taxonomic and genetic assessment of rescued and captive gibbons, are imperative prior to translocation and reintroduction programmes. In this study, we attempt to determine the subspecies and origin of captive Hylobateslar, White-handed gibbons, from Peninsular Malaysia to assist in future translocation and reintroduction programmes. A total of 12 captive and rescued H.lar samples were analysed using the control region segment of mitochondrial DNA. Sequence analyses and phylogenetic trees constructed using neighbour-joining, maximum likelihood, Bayesian inference, and network methods congruently differentiate all 12 captive individuals used in this study from other H.lar subspecies suggesting that these individuals belong to the H.larlar subspecies. In addition, two populations of H.l.lar were observed: (1) a southern population consisting of all 12 individuals from Peninsular Malaysia, and (2) a possible northern population represented by three individuals (from previous studies), which might have originated from the region between the Isthmus of Kra, Surat Thani-Krabi depression, and Kangar-Pattani. Our findings suggest that the complete control region segment can be used to determine the subspecies and origin of captive H.lar.
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Affiliation(s)
- Millawati Gani
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia
| | - Jeffrine J Rovie-Ryan
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia
| | - Frankie Thomas Sitam
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia
| | - Noor Azleen Mohd Kulaimi
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia
| | - Chew Cheah Zheng
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia.,Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi Selangor, Malaysia Universiti Kebangsaan Malaysia Bangi Malaysia
| | - Aida Nur Atiqah
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia.,Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi Selangor, Malaysia Universiti Kebangsaan Malaysia Bangi Malaysia
| | - Nur Maisarah Abd Rahim
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia.,Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia Universiti Putra Malaysia Serdang Malaysia
| | - Ahmad Azhar Mohammed
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia
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Markviriya D, Asensio N, Brockelman WY, Jeratthitikul E, Kongrit C. Genetic analysis of hybridization between white-handed (Hylobates lar) and pileated (Hylobates pileatus) gibbons in a contact zone in Khao Yai National Park, Thailand. Primates 2021; 63:51-63. [PMID: 34716489 DOI: 10.1007/s10329-021-00958-y] [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: 05/23/2021] [Accepted: 10/17/2021] [Indexed: 10/20/2022]
Abstract
Natural hybridization has played various roles in the evolutionary history of primates. Its consequences range from genetic introgression between taxa, formation of hybrid zones, and formation of new lineages. Hylobates lar, the white-handed gibbon, and Hylobates pileatus, the pileated gibbon, are largely allopatric species in Southeast Asia with a narrow contact zone in Khao Yai National Park, Thailand, which contains both parental types and hybrids. Hybrid individuals in the zone are recognizable by their intermediate pelage and vocal patterns, but have not been analyzed genetically. We analyzed mitochondrial and microsatellite DNA of 52 individuals to estimate the relative genetic contributions of the parental species to each individual, and the amount of introgression into the parental species. We obtained fecal samples from 33 H. lar, 15 H. pileatus and four phenotypically intermediate individuals in the contact zone. Both mitochondrial and microsatellite markers confirmed distinct differences between these taxa. Both H. lar and H. pileatus contributed to the maternal lineages of the hybrids based on mitochondrial analysis; hybrids were viable and present in socially normal reproductive pairs. The microsatellite analysis identified ten admixed individuals, four F1 hybrids, which corresponded to phenotypic hybrids, and six H. lar-like backcrosses. All 15 H. pileatus samples were identified as originating from genetically H. pileatus individuals with no H. lar admixture; hence, backcrossing is biased toward H. lar. A relatively low number of phenotypic hybrids and backcrossed individuals along with a high number of parental types indicates a bimodal hybrid zone, which suggests relatively strong bias in mate selection between the species.
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Affiliation(s)
- Darunee Markviriya
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok, 10400, Thailand
| | - Norberto Asensio
- Faculty of Environment and Resource Studies, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand.,Department of Clinical and Health Psychology and Research Methodology, Faculty of Psychology, University of the Basque Country, 20018, Donostia, Gipuzkoa, Spain
| | - Warren Y Brockelman
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand.,National Biobank of Thailand, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Ekgachai Jeratthitikul
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok, 10400, Thailand
| | - Chalita Kongrit
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok, 10400, Thailand.
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Divergence and introgression in small apes, the genus Hylobates, revealed by reduced representation sequencing. Heredity (Edinb) 2021; 127:312-322. [PMID: 34188193 PMCID: PMC8405704 DOI: 10.1038/s41437-021-00452-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/15/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023] Open
Abstract
Gibbons of the genus Hylobates, which inhabit Southeast Asia, show great diversity and comprise seven to nine species. Natural hybridisation has been observed in several species contact zones, but the history and extent of hybridisation and introgression in possibly historical and the current contact zones remain unclear. To uncover Hylobates species phylogeny and the extent of introgression in their evolution, genotyping by random amplicon sequencing-direct (GRAS-Di) was applied to 47 gibbons, representing seven Hylobates species/subspecies and two outgroup gibbon species. Over 200,000 autosomal single-nucleotide variant sites were identified. The autosomal phylogeny supported that divergence from the mainland species began ~3.5 million years ago, and subsequently occurred among the Sundaic island species. Significant introgression signals were detected between H. lar and H. pileatus, H. lar and H. agilis and H. albibarbis and H. muelleri, which all are parapatric and form ongoing hybrid zones. Furthermore, the introgression signals were detected in every analysed individual of these species, indicating a relatively long history of hybridisation, which might have affected the entire gene pool. By contrast, signals of introgression were either not detected or doubtful in other species pairs living on different islands, indicating the rarity of hybridisation and introgression, even though the Sundaic islands were connected during the Pliocene and Pleistocene glacial events.
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Population and genetic structure of a male-dispersing strepsirrhine, Galago moholi (Primates, Galagidae), from northern South Africa, inferred from mitochondrial DNA. Primates 2021; 62:667-675. [PMID: 33909155 DOI: 10.1007/s10329-021-00912-y] [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: 03/06/2020] [Accepted: 04/17/2021] [Indexed: 10/21/2022]
Abstract
The habitats of Galago moholi are suspected to be largely fragmented, while the species is thought to be expanding further into the southernmost fringe of its range, as well as into human settlements. To date, no intraspecific molecular genetic studies have been published on G. moholi. Here we estimate the genetic diversity and connectivity of populations of G. moholi using two mitochondrial gene regions, the cytochrome C oxidase subunit I gene (COI) and the displacement loop of the control region (D-loop). Samples from five localities in northern South Africa were obtained from archived collections. The two mitochondrial DNA gene regions were amplified and sequenced to provide population summary statistics, differentiation [proportion of the total genetic variation in a population relative to the total genetic variance of all the populations (FST), differentiation within populations among regions (ΦST)], genetic distance and structure. There was discernible genetic structure among the individuals, with two COI and six D-loop haplotypes belonging to two genetically different groups. There was population differentiation among regions (FST = 0.670; ΦST = 0.783; P < 0.01). However, there were low levels of differentiation among populations, as haplotypes were shared between distant populations. Adjacent populations were as divergent from each other as from distant populations. The results suggest that genetic introgression, most likely due to past migrations or recent unintentional translocations that include the animal trade, may have led to connectivity among populations.
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Guo Y, Peng D, Han L, Liu T, Li G, Garber PA, Zhou J. Mitochondrial DNA control region sequencing of the critically endangered Hainan gibbon ( Nomascus hainanus) reveals two female origins and extremely low genetic diversity. Mitochondrial DNA B Resour 2021; 6:1355-1359. [PMID: 33889748 PMCID: PMC8032330 DOI: 10.1080/23802359.2021.1909432] [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] [Received: 10/02/2020] [Accepted: 03/22/2021] [Indexed: 11/25/2022] Open
Abstract
The Hainan gibbon (Nomascus hainanus) is endemic to China and is the world's rarest ape. The remaining wild population totals only 33 individuals. In the current study, we sequenced the Mitochondrial DNA control region of 12 wild Hainan gibbons representing three social groups of the five remaining groups. By conducting population genetic analyses, we found that the proportion of four nucleotides (T, C, A and G) were 29.0%, 27.2%, 31.9% and 11.9%, respectively. Hypervariable segments of the mtDNA D-loop region (1005 bp in length), indicated five variable sites (a point mutation), with only two haplotypes present among the 12 samples. We observed that the genetic diversity of Hainan gibbons is lower than that reported in any other wild primate population, and that the two haplotypes detected, represent two ancestral lineages. These findings have important implications for proposing effective conservation strategies to protect this Critically Endangered ape species.
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Affiliation(s)
- Yanqing Guo
- College of Life Sciences, Northwest University, Xian, China
| | - Dong Peng
- School of Karst Science, Guizhou Normal University, Guiyang, China
| | - Ling Han
- School of Karst Science, Guizhou Normal University, Guiyang, China
| | - Tao Liu
- School of Karst Science, Guizhou Normal University, Guiyang, China
| | - Gang Li
- School of Karst Science, Guizhou Normal University, Guiyang, China
| | - Paul A. Garber
- Department of Anthropology, Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Urbana, IL, USA
- International Centre of Biodiversity and Primate Conservation, Dali University, Dali, Yunnan, China
| | - Jiang Zhou
- College of Life Sciences, Northwest University, Xian, China
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Yao L, Witt K, Li H, Rice J, Salinas NR, Martin RD, Huerta-Sánchez E, Malhi RS. Population genetics of wild Macaca fascicularis with low-coverage shotgun sequencing of museum specimens. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 173:21-33. [PMID: 32643146 DOI: 10.1002/ajpa.24099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 05/10/2020] [Accepted: 05/15/2020] [Indexed: 11/12/2022]
Abstract
OBJECTIVES Long-tailed macaques (Macaca fascicularis) are widely distributed throughout the mainland and islands of Southeast Asia, making them a useful model for understanding the complex biogeographical history resulting from drastic changes in sea levels throughout the Pleistocene. Past studies based on mitochondrial genomes (mitogenomes) of long-tailed macaque museum specimens have traced their colonization patterns throughout the archipelago, but mitogenomes trace only the maternal history. Here, our objectives were to trace phylogeographic patterns of long-tailed macaques using low-coverage nuclear DNA (nDNA) data from museum specimens. METHODS We performed population genetic analyses and phylogenetic reconstruction on nuclear single nucleotide polymorphisms (SNPs) from shotgun sequencing of 75 long-tailed macaque museum specimens from localities throughout Southeast Asia. RESULTS We show that shotgun sequencing of museum specimens yields sufficient genome coverage (average ~1.7%) for reconstructing population relationships using SNP data. Contrary to expectations of divergent results between nuclear and mitochondrial genomes for a female philopatric species, phylogeographical patterns based on nuclear SNPs proved to be closely similar to those found using mitogenomes. In particular, population genetic analyses and phylogenetic reconstruction from the nDNA identify two major clades within M. fascicularis: Clade A includes all individuals from the mainland along with individuals from northern Sumatra, while Clade B consists of the remaining island-living individuals, including those from southern Sumatra. CONCLUSIONS Overall, we demonstrate that low-coverage sequencing of nDNA from museum specimens provides enough data for examining broad phylogeographic patterns, although greater genome coverage and sequencing depth would be needed to distinguish between very closely related populations, such as those throughout the Philippines.
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Affiliation(s)
- Lu Yao
- American Museum of Natural History, New York, New York, USA
| | - Kelsey Witt
- Brown University, Providence, Rhode Island, USA.,University of California Merced, Merced, California, USA
| | - Hongjie Li
- University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan Rice
- University of California Merced, Merced, California, USA
| | - Nelson R Salinas
- American Museum of Natural History, New York, New York, USA.,Instituto de Hidrología, Metereología y Estudios Ambientales IDEAM, Bogotá, Colombia
| | - Robert D Martin
- The Field Museum of Natural History, Chicago, Illinois, USA.,University of Zürich, Zürich, Switzerland
| | | | - Ripan S Malhi
- University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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Yao L, Li H, Martin RD, Moreau CS, Malhi RS. Tracing the phylogeographic history of Southeast Asian long-tailed macaques through mitogenomes of museum specimens. Mol Phylogenet Evol 2017; 116:227-238. [PMID: 28863929 DOI: 10.1016/j.ympev.2017.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 05/23/2017] [Accepted: 08/13/2017] [Indexed: 12/01/2022]
Abstract
The biogeographical history of Southeast Asia is complicated due to the continuous emergences and disappearances of land bridges throughout the Pleistocene. Here, we use long-tailed macaques (Macaca fascicularis), which are widely distributed throughout the mainland and islands of Southeast Asia, asa model for better understanding the biogeographical patterns of diversification in this geographically complex region. A reliable intraspecific phylogeny including individuals from localities on oceanic islands, continental islands, and the mainland is needed to trace relatedness along with the pattern and timing of colonization in this region. We used high-throughput sequencing techniques to sequence mitochondrial genomes (mitogenomes) from 95 Southeast Asian M. fascicularis specimens housed at natural history museums around the world. To achieve a comprehensive picture, we more than tripled the mitogenome sample size for M. fascicularis from previous studies, and for the first time included documented samples from the Philippines and several small Indonesian islands. Confirming the result from a previous, recent intraspecific phylogeny for M. fascicularis, the newly reconstructed phylogeny of 135 specimens divides the samples into two major clades: Clade A includes haplotypes from the mainland and some from northern Sumatra, while Clade B includes all insular haplotypes along with lineages from southern Sumatra. This study resolves a previous disparity by revealing a disjunction in the origin of Sumatran macaques, with separate lineages originating within the two major clades, suggesting that at least two major migrations to Sumatra occurred. However, our dated phylogeny reveals that the two major clades split ∼1.88Ma, which is earlier than in previously published phylogenies. Our new data reveal that most Philippine macaque lineages diverged from the Borneo stock within the last ∼0.06-0.43Ma. Finally, our study provides insight into successful sequencing of DNA across museums and shotgun sequencing of DNA specimens asa method to sequence the mitogenome.
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Affiliation(s)
- Lu Yao
- Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th St., Culver Hall 402, Chicago, IL 60637, USA; Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, IL 60605, USA.
| | - Hongjie Li
- Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave., 109 Davenport Hall, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 W Gregory Dr., Urbana, IL 61820, USA
| | - Robert D Martin
- Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th St., Culver Hall 402, Chicago, IL 60637, USA; Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, IL 60605, USA; Institute of Evolutionary Medicine, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Corrie S Moreau
- Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th St., Culver Hall 402, Chicago, IL 60637, USA; Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, IL 60605, USA
| | - Ripan S Malhi
- Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave., 109 Davenport Hall, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 W Gregory Dr., Urbana, IL 61820, USA
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10
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Bergman TJ, Cortés-Ortiz L, Dias PAD, Ho L, Adams D, Canales-Espinosa D, Kitchen DM. Striking differences in the loud calls of howler monkey sister species (Alouatta pigra and A. palliata). Am J Primatol 2016; 78:755-66. [PMID: 26950654 DOI: 10.1002/ajp.22539] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 02/08/2016] [Accepted: 02/09/2016] [Indexed: 11/10/2022]
Abstract
Comparing vocalizations across species is useful for understanding acoustic variation at mechanistic and evolutionary levels. Here, we take advantage of the divergent vocalizations of two closely related howler monkey species (Alouatta pigra and A. palliata) to better understand vocal evolution. In addition to comparing multiple acoustic and temporal features of roars and the calling bouts in which they are produced, we tested several predictions. First, A. pigra should have roars with lower fundamental frequency and lower formant dispersion because they are larger than A. palliata and have a larger hyoid apparatus. Second, A. pigra should have faster calling rates, longer roars, longer bouts, and exaggerated call features linked to vocal effort (e.g., nonlinear phenomena and emphasized frequencies) because they are the more aggressive species during intergroup encounters. We found significant interspecific differences supporting our predictions in every tested parameter of roars and bouts, except for roar duration and barking rate. Stepwise discriminant function analyses identified the best features for differentiating roars (acoustic features: formant dispersion followed by highest frequency; temporal features: longest syllable duration followed by number of syllables). Although resembling each other more than they resemble South American howler monkeys, our comparison revealed striking differences in the vocalizations of the two Mesoamerican species. While we cannot completely rule out the influence of body size or the environmental conditions in which the two species evolved, vocal differences were likely influenced by sexual selection. The exaggerated roars and intense calling patterns in A. pigra seem more suitable for intergroup competition, whereas A. palliata calls may be better suited for mate attraction and competition within groups. With interspecific acoustic differences quantified, we will now be able to examine how vocalizations contribute to the evolutionary dynamics of the A. palliata × A. pigra hybrid zone in southern Mexico. Am. J. Primatol. 78:755-766, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Thore J Bergman
- Department of Psychology, University of Michigan, Ann Arbor, Michigan.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Pedro A D Dias
- Laboratorio de Ecología del Comportamiento de Primates, Instituto de Neuroetología, Universidad Veracruzana, Xalapa, Veracruz, Mexico
| | - Lucy Ho
- Department of Psychology, University of Michigan, Ann Arbor, Michigan
| | - Dara Adams
- Department of Anthropology, The Ohio State University, Mansfield, Ohio
| | - Domingo Canales-Espinosa
- Laboratorio de Ecología del Comportamiento de Primates, Instituto de Neuroetología, Universidad Veracruzana, Xalapa, Veracruz, Mexico
| | - Dawn M Kitchen
- Department of Anthropology, The Ohio State University, Mansfield, Ohio.,Department of Anthropology, The Ohio State University, Columbus, Ohio.,Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio
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11
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Roos C. Phylogeny and Classification of Gibbons (Hylobatidae). DEVELOPMENTS IN PRIMATOLOGY: PROGRESS AND PROSPECTS 2016. [DOI: 10.1007/978-1-4939-5614-2_7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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12
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Harrison T. The Fossil Record and Evolutionary History of Hylobatids. DEVELOPMENTS IN PRIMATOLOGY: PROGRESS AND PROSPECTS 2016. [DOI: 10.1007/978-1-4939-5614-2_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Turner TR, Coetzer WG, Schmitt CA, Lorenz JG, Freimer NB, Grobler JP. Localized population divergence of vervet monkeys (Chlorocebus spp.) in South Africa: Evidence from mtDNA. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 159:17-30. [PMID: 26265297 PMCID: PMC4715607 DOI: 10.1002/ajpa.22825] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 02/23/2015] [Accepted: 07/23/2015] [Indexed: 01/22/2023]
Abstract
OBJECTIVE Vervet monkeys are common in most tree-rich areas of South Africa, but their absence from grassland and semi-desert areas of the country suggest potentially restricted and mosaic local population patterns that may have relevance to local phenotype patterns and selection. A portion of the mitochondrial DNA control region was sequenced to study patterns of genetic differentiation. METHODS DNA was extracted, and mitochondrial DNA sequences were obtained from 101 vervet monkeys at 15 localities, which represent both an extensive (widely across the distribution range) and intensive (more than one troop at most of the localities) sampling strategy. Analyses utilized Arlequin 3.1, MEGA 6, BEAST v1.5.2, and Network V3.6.1. RESULTS The dataset contained 26 distinct haplotypes, with six populations fixed for single haplotypes. Pairwise P-distance among population pairs showed significant differentiation among most population pairs, but with nonsignificant differences among populations within some regions. Populations were grouped into three broad clusters in a maximum likelihood phylogenetic tree and a haplotype network. These clusters correspond to i) north-western, northern, and north-eastern parts of the distribution range as well as the northern coastal belt; ii) central areas of the country; and iii) southern part of the Indian Ocean coastal belt and adjacent inland areas. CONCLUSIONS Apparent patterns of genetic structure correspond to current and past distribution of suitable habitat, geographic barriers to gene flow, geographic distance, and female philopatry. However, further work on nuclear markers and other genomic data are necessary to confirm these results.
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Affiliation(s)
- Trudy R. Turner
- Department of Anthropology, University of Wisconsin-Milwaukee, Milwaukee, WI 53201
- Department of Genetics, University of the Free State, Bloemfontein 9300, South Africa
| | - Willem G. Coetzer
- Department of Genetics, University of the Free State, Bloemfontein 9300, South Africa
| | - Christopher A. Schmitt
- Center for Neurobehavioral Genetics, University of California – Los Angeles, Los Angeles, CA, 90095
- Human Evolution Research Center, University of California – Berkeley, Berkeley, CA 94720
| | - Joseph G. Lorenz
- Department of Anthropology & Museum Studies, Central Washington University, Ellensburg, WA 98926
| | - Nelson B. Freimer
- Center for Neurobehavioral Genetics, University of California – Los Angeles, Los Angeles, CA, 90095
| | - J. Paul Grobler
- Department of Genetics, University of the Free State, Bloemfontein 9300, South Africa
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Delezene LK. Modularity of the anthropoid dentition: Implications for the evolution of the hominin canine honing complex. J Hum Evol 2015; 86:1-12. [DOI: 10.1016/j.jhevol.2015.07.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Revised: 03/04/2015] [Accepted: 07/03/2015] [Indexed: 01/12/2023]
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15
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Pampush JD. Selection played a role in the evolution of the human chin. J Hum Evol 2015; 82:127-36. [DOI: 10.1016/j.jhevol.2015.02.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 11/24/2014] [Accepted: 02/05/2015] [Indexed: 11/25/2022]
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Examining phylogenetic relationships among gibbon genera using whole genome sequence data using an approximate bayesian computation approach. Genetics 2015; 200:295-308. [PMID: 25769979 DOI: 10.1534/genetics.115.174425] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/04/2015] [Indexed: 12/30/2022] Open
Abstract
Gibbons are believed to have diverged from the larger great apes ∼16.8 MYA and today reside in the rainforests of Southeast Asia. Based on their diploid chromosome number, the family Hylobatidae is divided into four genera, Nomascus, Symphalangus, Hoolock, and Hylobates. Genetic studies attempting to elucidate the phylogenetic relationships among gibbons using karyotypes, mitochondrial DNA (mtDNA), the Y chromosome, and short autosomal sequences have been inconclusive . To examine the relationships among gibbon genera in more depth, we performed second-generation whole genome sequencing (WGS) to a mean of ∼15× coverage in two individuals from each genus. We developed a coalescent-based approximate Bayesian computation (ABC) method incorporating a model of sequencing error generated by high coverage exome validation to infer the branching order, divergence times, and effective population sizes of gibbon taxa. Although Hoolock and Symphalangus are likely sister taxa, we could not confidently resolve a single bifurcating tree despite the large amount of data analyzed. Instead, our results support the hypothesis that all four gibbon genera diverged at approximately the same time. Assuming an autosomal mutation rate of 1 × 10(-9)/site/year this speciation process occurred ∼5 MYA during a period in the Early Pliocene characterized by climatic shifts and fragmentation of the Sunda shelf forests. Whole genome sequencing of additional individuals will be vital for inferring the extent of gene flow among species after the separation of the gibbon genera.
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Botero S, Stevenson PR, Di Fiore A. A primer on the phylogeography of Lagothrix lagotricha (sensu Fooden) in northern South America. Mol Phylogenet Evol 2015; 82 Pt B:511-7. [DOI: 10.1016/j.ympev.2014.05.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 04/29/2014] [Accepted: 05/15/2014] [Indexed: 10/25/2022]
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Steinberg ER, Nieves M, Mudry MD. Multiple sex chromosome systems in howler monkeys (Platyrrhini, Alouatta). COMPARATIVE CYTOGENETICS 2014; 8:43-69. [PMID: 24744833 PMCID: PMC3978242 DOI: 10.3897/compcytogen.v8i1.6716] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 01/25/2014] [Indexed: 05/24/2023]
Abstract
In light of the multiple sex chromosome systems observed in howler monkeys (Alouatta Lacépède, 1799) a combined cladistic analysis using chromosomal and molecular characters was applied to discuss the possible origin of these systems. Mesoamerican and South American howlers were karyologically compared. FISH analysis using the chromosome painting probes for the #3 and #15 human chromosomes was applied to corroborate the homeology of the sexual systems. We found that the HSA3/15 syntenic association, present in the sex chromosome systems of South American Howlers, is not present in those of Mesoamerican ones. The autosomes involved in the translocation that formed the sexual systems in the Mesoamerican and South American species are different, thus suggesting an independent origin. Parsimony analysis resolved the phylogenetic relationships among howler species, demonstrating utility of the combined approach. A hypothesis for the origin of the multiple sex chromosome systems for the genus is proposed.
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Affiliation(s)
- Eliana Ruth Steinberg
- Grupo de Investigación en Biología Evolutiva (GIBE) - Departamento de Ecología, Genética y Evolución - Facultad de Ciencias Exactas y Naturales - Universidad de Buenos Aires - IEGEBA (CONICET-UBA) - Ciudad Universitaria - Pab. II -4° piso - Labs 43-46 - (C1428EGA) - Buenos Aires - Argentina
| | - Mariela Nieves
- Grupo de Investigación en Biología Evolutiva (GIBE) - Departamento de Ecología, Genética y Evolución - Facultad de Ciencias Exactas y Naturales - Universidad de Buenos Aires - IEGEBA (CONICET-UBA) - Ciudad Universitaria - Pab. II -4° piso - Labs 43-46 - (C1428EGA) - Buenos Aires - Argentina
| | - Marta Dolores Mudry
- Grupo de Investigación en Biología Evolutiva (GIBE) - Departamento de Ecología, Genética y Evolución - Facultad de Ciencias Exactas y Naturales - Universidad de Buenos Aires - IEGEBA (CONICET-UBA) - Ciudad Universitaria - Pab. II -4° piso - Labs 43-46 - (C1428EGA) - Buenos Aires - Argentina
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Chan YC, Roos C, Inoue-Murayama M, Inoue E, Shih CC, Pei KJC, Vigilant L. Inferring the evolutionary histories of divergences in Hylobates and Nomascus gibbons through multilocus sequence data. BMC Evol Biol 2013; 13:82. [PMID: 23586586 PMCID: PMC3637282 DOI: 10.1186/1471-2148-13-82] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 04/08/2013] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Gibbons (Hylobatidae) are the most diverse group of living apes. They exist as geographically-contiguous species which diverged more rapidly than did their close relatives, the great apes (Hominidae). Of the four extant gibbon genera, the evolutionary histories of two polyspecific genera, Hylobates and Nomascus, have been the particular focus of research but the DNA sequence data used was largely derived from the maternally inherited mitochondrial DNA (mtDNA) locus. RESULTS To investigate the evolutionary relationships and divergence processes of gibbon species, particularly those of the Hylobates genus, we produced and analyzed a total of 11.5 kb DNA of sequence at 14 biparentally inherited autosomal loci. We find that on average gibbon genera have a high average sequence diversity but a lower degree of genetic differentiation as compared to great ape genera. Our multilocus species tree features H. pileatus in a basal position and a grouping of the four Sundaic island species (H. agilis, H. klossii, H. moloch and H. muelleri). We conducted pairwise comparisons based on an isolation-with-migration (IM) model and detect signals of asymmetric gene flow between H. lar and H. moloch, between H. agilis and H. muelleri, and between N. leucogenys and N. siki. CONCLUSIONS Our multilocus analyses provide inferences of gibbon evolutionary histories complementary to those based on single gene data. The results of IM analyses suggest that the divergence processes of gibbons may be accompanied by gene flow. Future studies using analyses of multi-population model with samples of known provenance for Hylobates and Nomascus species would expand the understanding of histories of gene flow during divergences for these two gibbon genera.
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Affiliation(s)
- Yi-Chiao Chan
- Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany.
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Chan YC, Roos C, Inoue-Murayama M, Inoue E, Shih CC, Vigilant L. A comparative analysis of Y chromosome and mtDNA phylogenies of the Hylobates gibbons. BMC Evol Biol 2012; 12:150. [PMID: 22909292 PMCID: PMC3444420 DOI: 10.1186/1471-2148-12-150] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 08/15/2012] [Indexed: 01/06/2023] Open
Abstract
Background The evolutionary relationships of closely related species have long been of interest to biologists since these species experienced different evolutionary processes in a relatively short period of time. Comparison of phylogenies inferred from DNA sequences with differing inheritance patterns, such as mitochondrial, autosomal, and X and Y chromosomal loci, can provide more comprehensive inferences of the evolutionary histories of species. Gibbons, especially the genus Hylobates, are particularly intriguing as they consist of multiple closely related species which emerged rapidly and live in close geographic proximity. Our current understanding of relationships among Hylobates species is largely based on data from the maternally-inherited mitochondrial DNAs (mtDNAs). Results To infer the paternal histories of gibbon taxa, we sequenced multiple Y chromosomal loci from 26 gibbons representing 10 species. As expected, we find levels of sequence variation some five times lower than observed for the mitochondrial genome (mtgenome). Although our Y chromosome phylogenetic tree shows relatively low resolution compared to the mtgenome tree, our results are consistent with the monophyly of gibbon genera suggested by the mtgenome tree. In a comparison of the molecular dating of divergences and on the branching patterns of phylogeny trees between mtgenome and Y chromosome data, we found: 1) the inferred divergence estimates were more recent for the Y chromosome than for the mtgenome, 2) the species H. lar and H. pileatus are monophyletic in the mtgenome phylogeny, respectively, but a H. pileatus individual falls into the H. lar Y chromosome clade. Conclusions Based on the ~6.4 kb of Y chromosomal DNA sequence data generated for each of the 26 individuals in this study, we provide molecular inferences on gibbon and particularly on Hylobates evolution complementary to those from mtDNA data. Overall, our results illustrate the utility of comparative studies of loci with different inheritance patterns for investigating potential sex specific processes on the evolutionary histories of closely related taxa, and emphasize the need for further sampling of gibbons of known provenance.
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Affiliation(s)
- Yi-Chiao Chan
- Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany.
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21
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Matsudaira K, Reichard UH, Malaivijitnond S, Ishida T. Molecular evidence for the introgression between Hylobates lar and H. pileatus in the wild. Primates 2012; 54:33-7. [PMID: 22892937 DOI: 10.1007/s10329-012-0323-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 07/24/2012] [Indexed: 10/28/2022]
Abstract
Inter-specific hybrid zones for Hylobates gibbons are known in Southeast Asia. Among these, one hybrid zone between Hylobates lar and H. pileatus is located in Khao Yai National Park, Thailand. To find molecular evidence for the natural hybridization of the gibbons in this region, we studied mitochondrial DNA (mtDNA) of 68 gibbons of the H. lar phenotype living adjacent to the hybrid zone. Nucleotide sequencing of a fragment of mtDNA spanning hyper variable segment I showed that nine gibbons had an mtDNA haplotype of H. pileatus, and that seven of these nine gibbons belonged to a single maternal lineage over three generations. It is thus confirmed that introgression between H. lar and H. pileatus exists and the initial hybridization took place ages ago.
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Affiliation(s)
- Kazunari Matsudaira
- Unit of Human Biology and Genetics, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan.
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22
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Terhune CE. Modeling the biomechanics of articular eminence function in anthropoid primates. J Anat 2011; 219:551-64. [PMID: 21923720 PMCID: PMC3222834 DOI: 10.1111/j.1469-7580.2011.01424.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2011] [Indexed: 10/17/2022] Open
Abstract
One of the most prominent features of the cranial component of the temporomandibular joint (TMJ) is the articular eminence (AE). This bar of bone is the primary surface upon which the condyle translates and rotates during movements of the mandible, and is therefore the primary point at which forces are transmitted from the mandible to the cranium during loading of the masticatory apparatus. The shape of the AE is highly variable across primates, and the raised eminence of humans has often been considered a defining feature of the human TMJ, yet few data exist to address whether this variation is functionally significant. This study used a broad interspecific sample of anthropoid primates to elaborate upon and test the predictions of a previously proposed model of AE function. This model suggests that AE inclination acts to resist non-normal forces at the TMJ, thereby maximizing bite forces (BFs). AE inclination was predicted to covary with two specific features of the masticatory apparatus: height of the TMJ above the occlusal plane; and inclination of the masticatory muscles. A correlate of this model is that taxa utilizing more resistant food objects should also exhibit relatively more inclined AEs. Results of the correlation analyses found that AE inclination is strongly correlated with height of the TMJ above the occlusal plane, but less so with inclination of the masticatory muscles. Furthermore, pairwise comparisons of closely related taxa with documented dietary differences found that the AE is consistently more inclined in taxa that utilize more resistant food items. These data preliminarily suggest that variation in AE morphology across anthropoid primates is functionally related to maximizing BFs, and add to the growing dataset of masticatory morphologies linked to feeding behavior.
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Affiliation(s)
- Claire E Terhune
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC, USA.
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23
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Zihlman AL, Mootnick AR, Underwood CE. Anatomical Contributions to Hylobatid Taxonomy and Adaptation. INT J PRIMATOL 2011; 32:865-877. [PMID: 21892236 PMCID: PMC3139862 DOI: 10.1007/s10764-011-9506-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 11/18/2010] [Indexed: 11/29/2022]
Abstract
Compared with the great apes, the small-bodied hylobatids were treated historically as a relatively uniform group with 2 genera, Hylobates and the larger-bodied Symphalangus. Four genera are now recognized, each with a different chromosome number: Hoolock (hoolock) (38), Hylobates (44), Nomascus (crested gibbon) (52), and Symphalangus (siamang) (50). Previous morphological studies based on relative bone lengths, e.g., intermembral indices; molar tooth sizes; and body masses did not distinguish the 4 genera from each other. We applied quantitative anatomical methods to test the hypothesis that each genus can be differentiated from the others using the relative distribution of body mass to the forelimbs and hind limbs. Based on dissections of 13 hylobatids from captive facilities, our findings demonstrate that each of the 4 genera has a distinct pattern of body mass distribution. For example, the adult Hoolock has limb proportions of nearly equal mass, a pattern that differentiates it from species in the genus Hylobates, e.g., H. lar (lar gibbon), H. moloch (Javan gibbon), H. pileatus (pileated gibbon), Nomascus, and Symphalangus. Hylobates is distinct in having heavy hind limbs. Although Symphalangus has been treated as a scaled up version of Hylobates, its forelimb exceeds its hind limb mass, an unusual primate pattern otherwise found only in orangutans. This research provides new information on whole body anatomy and adds to the genetic, ecological, and behavioral evidence for clarifying the taxonomy of the hylobatids. The research also underscores the important contribution of studies on rare species in captivity.
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Kim SK, Carbone L, Becquet C, Mootnick AR, Li DJ, de Jong PJ, Wall JD. Patterns of genetic variation within and between Gibbon species. Mol Biol Evol 2011; 28:2211-8. [PMID: 21368318 PMCID: PMC3144381 DOI: 10.1093/molbev/msr033] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Gibbons are small, arboreal, highly endangered apes that are understudied compared with other hominoids. At present, there are four recognized genera and approximately 17 species, all likely to have diverged from each other within the last 5-6 My. Although the gibbon phylogeny has been investigated using various approaches (i.e., vocalization, morphology, mitochondrial DNA, karyotype, etc.), the precise taxonomic relationships are still highly debated. Here, we present the first survey of nuclear sequence variation within and between gibbon species with the goal of estimating basic population genetic parameters. We gathered ~60 kb of sequence data from a panel of 19 gibbons representing nine species and all four genera. We observe high levels of nucleotide diversity within species, indicative of large historical population sizes. In addition, we find low levels of genetic differentiation between species within a genus comparable to what has been estimated for human populations. This is likely due to ongoing or episodic gene flow between species, and we estimate a migration rate between Nomascus leucogenys and N. gabriellae of roughly one migrant every two generations. Together, our findings suggest that gibbons have had a complex demographic history involving hybridization or mixing between diverged populations.
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Affiliation(s)
- Sung K Kim
- Institute for Human Genetics, University of California San Francisco, CA, USA
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25
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Nater A, Nietlisbach P, Arora N, van Schaik CP, van Noordwijk MA, Willems EP, Singleton I, Wich SA, Goossens B, Warren KS, Verschoor EJ, Perwitasari-Farajallah D, Pamungkas J, Krützen M. Sex-Biased Dispersal and Volcanic Activities Shaped Phylogeographic Patterns of Extant Orangutans (genus: Pongo). Mol Biol Evol 2011; 28:2275-88. [DOI: 10.1093/molbev/msr042] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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26
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Chan YC, Roos C, Inoue-Murayama M, Inoue E, Shih CC, Pei KJC, Vigilant L. Mitochondrial genome sequences effectively reveal the phylogeny of Hylobates gibbons. PLoS One 2010; 5:e14419. [PMID: 21203450 PMCID: PMC3009715 DOI: 10.1371/journal.pone.0014419] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 11/29/2010] [Indexed: 11/18/2022] Open
Abstract
Background Uniquely among hominoids, gibbons exist as multiple geographically contiguous taxa exhibiting distinctive behavioral, morphological, and karyotypic characteristics. However, our understanding of the evolutionary relationships of the various gibbons, especially among Hylobates species, is still limited because previous studies used limited taxon sampling or short mitochondrial DNA (mtDNA) sequences. Here we use mtDNA genome sequences to reconstruct gibbon phylogenetic relationships and reveal the pattern and timing of divergence events in gibbon evolutionary history. Methodology/Principal Findings We sequenced the mitochondrial genomes of 51 individuals representing 11 species belonging to three genera (Hylobates, Nomascus and Symphalangus) using the high-throughput 454 sequencing system with the parallel tagged sequencing approach. Three phylogenetic analyses (maximum likelihood, Bayesian analysis and neighbor-joining) depicted the gibbon phylogenetic relationships congruently and with strong support values. Most notably, we recover a well-supported phylogeny of the Hylobates gibbons. The estimation of divergence times using Bayesian analysis with relaxed clock model suggests a much more rapid speciation process in Hylobates than in Nomascus. Conclusions/Significance Use of more than 15 kb sequences of the mitochondrial genome provided more informative and robust data than previous studies of short mitochondrial segments (e.g., control region or cytochrome b) as shown by the reliable reconstruction of divergence patterns among Hylobates gibbons. Moreover, molecular dating of the mitogenomic divergence times implied that biogeographic change during the last five million years may be a factor promoting the speciation of Sundaland animals, including Hylobates species.
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Affiliation(s)
- Yi-Chiao Chan
- Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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27
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Israfil H, Zehr SM, Mootnick AR, Ruvolo M, Steiper ME. Unresolved molecular phylogenies of gibbons and siamangs (Family: Hylobatidae) based on mitochondrial, Y-linked, and X-linked loci indicate a rapid Miocene radiation or sudden vicariance event. Mol Phylogenet Evol 2010; 58:447-55. [PMID: 21074627 DOI: 10.1016/j.ympev.2010.11.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 10/19/2010] [Accepted: 11/03/2010] [Indexed: 11/28/2022]
Abstract
According to recent taxonomic reclassification, the primate family Hylobatidae contains four genera (Hoolock, Nomascus, Symphalangus, and Hylobates) and between 14 and 18 species, making it by far the most species-rich group of extant hominoids. Known as the "small apes", these small arboreal primates are distributed throughout Southeast, South and East Asia. Considerable uncertainty surrounds the phylogeny of extant hylobatids, particularly the relationships among the genera and the species within the Hylobates genus. In this paper we use parsimony, likelihood, and Bayesian methods to analyze a dataset containing nearly 14 kilobase pairs, which includes newly collected sequences from X-linked, Y-linked, and mitochondrial loci together with data from previous mitochondrial studies. Parsimony, likelihood, and Bayesian analyses largely failed to find a significant difference among phylogenies with any of the four genera as the most basal taxon. All analyses, however, support a tree with Hylobates and Symphalangus as most closely related genera. One strongly supported phylogenetic result within the Hylobates genus is that Hylobates pileatus is the most basal taxon. Multiple analyses failed to find significant support for any singular genus-level phylogeny. While it is natural to suspect that there might not be sufficient data for phylogenetic resolution (whenever that situation occurs), an alternative hypothesis relating to the nature of gibbon speciation exists. This lack of resolution may be the result of a rapid radiation or a sudden vicariance event of the hylobatid genera, and it is likely that a similarly rapid radiation occurred within the Hylobates genus. Additional molecular and paleontological evidence are necessary to better test among these, and other, hypotheses of hylobatid evolution.
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Affiliation(s)
- H Israfil
- Department of Anthropology, Hunter College of the City University of New York, New York, NY 10065, USA.
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28
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Mootnick AR, Fan PF. A comparative study of crested gibbons (Nomascus). Am J Primatol 2010; 73:135-54. [DOI: 10.1002/ajp.20880] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 07/29/2010] [Accepted: 07/29/2010] [Indexed: 11/11/2022]
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Phylogenetic relationships and divergence dates of the whole mitochondrial genome sequences among three gibbon genera. Mol Phylogenet Evol 2010; 55:454-9. [DOI: 10.1016/j.ympev.2010.01.032] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2009] [Revised: 01/22/2010] [Accepted: 01/29/2010] [Indexed: 11/17/2022]
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30
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Thinh VN, Mootnick AR, Geissmann T, Li M, Ziegler T, Agil M, Moisson P, Nadler T, Walter L, Roos C. Mitochondrial evidence for multiple radiations in the evolutionary history of small apes. BMC Evol Biol 2010; 10:74. [PMID: 20226039 PMCID: PMC2841658 DOI: 10.1186/1471-2148-10-74] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 03/12/2010] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Gibbons or small apes inhabit tropical and subtropical rain forests in Southeast Asia and adjacent regions, and are, next to great apes, our closest living relatives. With up to 16 species, gibbons form the most diverse group of living hominoids, but the number of taxa, their phylogenetic relationships and their phylogeography is controversial. To further the discussion of these issues we analyzed the complete mitochondrial cytochrome b gene from 85 individuals representing all gibbon species, including most subspecies. RESULTS Based on phylogenetic tree reconstructions, several monophyletic clades were detected, corresponding to genera, species and subspecies. A significantly supported branching pattern was obtained for members of the genus Nomascus but not for the genus Hylobates. The phylogenetic relationships among the four genera were also not well resolved. Nevertheless, the new data permitted the estimation of divergence ages for all taxa for the first time and showed that most lineages emerged during four short time periods. In the first, between approximately 6.7 and approximately 8.3 mya, the four gibbon genera diverged from each other. In the second (approximately 3.0 - approximately 3.9 mya) and in the third period (approximately 1.3 - approximately 1.8 mya), Hylobates and Hoolock differentiated. Finally, between approximately 0.5 and approximately 1.1 mya, Hylobates lar diverged into subspecies. In contrast, differentiation of Nomascus into species and subspecies was a continuous and prolonged process lasting from approximately 4.2 until approximately 0.4 mya. CONCLUSIONS Although relationships among gibbon taxa on various levels remain unresolved, the present study provides a more complete view of the evolutionary and biogeographic history of the hylobatid family, and a more solid genetic basis for the taxonomic classification of the surviving taxa. We also show that mtDNA constitutes a useful marker for the accurate identification of individual gibbons, a tool which is urgently required to locate hunting hotspots and select individuals for captive breeding programs. Further studies including nuclear sequence data are necessary to completely understand the phylogeny and phylogeography of gibbons.
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Affiliation(s)
- Van Ngoc Thinh
- Primate Genetics Laboratory, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | - Alan R Mootnick
- Gibbon Conservation Center, PO Box 800249, Santa Clarita, CA 91380, USA
| | - Thomas Geissmann
- Anthropological Institute, University Zurich-Irchel, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Ming Li
- Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, PR China
| | - Thomas Ziegler
- Siberut Conservation Programme, Reproductive Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | - Muhammad Agil
- Department of Clinic, Reproduction and Pathology, Faculty of Veterinary Medicine, Bogor Agricultural University, Jl. Agatis, Kampus IPB Darmaga, 16680 Bogor, Indonesia
| | - Pierre Moisson
- Parc Zoologique et Botanique de Mulhouse, 51, rue du Jardin Zoologique, 68100 Mulhouse, France
| | - Tilo Nadler
- Frankfurt Zoological Society, Endangered Primate Rescue Center, Cuc Phuong National Park, Nho Quan District, Ninh Binh Province, Vietnam
| | - Lutz Walter
- Primate Genetics Laboratory, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
- Gene Bank of Primates, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
- Gene Bank of Primates, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
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Heller R, Sander AF, Wang CW, Usman F, Dabelsteen T. Macrogeographical variability in the great call of Hylobates agilis: assessing the applicability of vocal analysis in studies of fine-scale taxonomy of gibbons. Am J Primatol 2009; 72:142-51. [PMID: 19937738 DOI: 10.1002/ajp.20762] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Vocal characteristics have been used extensively to distinguish different taxonomic units of gibbons (family Hylobatidae). The agile gibbon (Hylobates agilis) has a disjunct distribution range in the Southeast Asian archipelago (remnants of the former Sunda landmass), and populations on different islands are currently recognized as distinct subspecies or even species. We recorded great calls from female agile gibbons from two populations on Sumatra and two populations on Borneo and examined the vocal variability on four levels: within-individuals, between-individuals, between-populations and between-islands. The primary objective was to evaluate the effect of geographical isolation on variability in song pattern and to test whether proposed island-specific song characteristics exist, reflecting evolutionary divergence between Sumatran and Bornean agile gibbons. One hundred great calls were recorded from 20 females and analyzed for 18 spectral and temporal acoustic parameters. Principal component analysis followed by a nested ANOVA on components revealed a complex pattern of song variability not likely to reflect taxonomic or evolutionary relationship. We found no evidence that Sumatran and Bornean agile gibbons have evolved different vocal characteristics, refuting a distinction between them based on vocal characteristics. A high level of plasticity was found in great calls from the same individual, and generally the inferred pattern of variability suggested that ecological or social factors may confound any genetically based island dialects.
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Affiliation(s)
- R Heller
- Section of Evolution and Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark.
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Kawashima T, Thorington RW, Kunimatsu Y, Whatton JF. Systematic Morphology and Evolutionary Anatomy of the Autonomic Cardiac Nervous System in the Lesser Apes, Gibbons (Hylobatidae). Anat Rec (Hoboken) 2008; 291:939-59. [DOI: 10.1002/ar.20700] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Misceo D, Capozzi O, Roberto R, Dell'oglio MP, Rocchi M, Stanyon R, Archidiacono N. Tracking the complex flow of chromosome rearrangements from the Hominoidea Ancestor to extant Hylobates and Nomascus Gibbons by high-resolution synteny mapping. Genome Res 2008; 18:1530-7. [PMID: 18552313 DOI: 10.1101/gr.078295.108] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In this study we characterized the extension, reciprocal arrangement, and orientation of syntenic chromosomal segments in the lar gibbon (Hylobates lar, HLA) by hybridization of a panel of approximately 1000 human BAC clones. Each lar gibbon rearrangement was defined by a splitting BAC clone or by two overlapping clones flanking the breakpoint. A reconstruction of the synteny arrangement of the last common ancestor of all living lesser apes was made by combining these data with previous results in Nomascus leucogenys, Hoolock hoolock, and Symphalangus syndactylus. The definition of the ancestral synteny organization facilitated tracking the cascade of chromosomal changes from the Hominoidea ancestor to the present day karyotype of Hylobates and Nomascus. Each chromosomal rearrangement could be placed within an approximate phylogenetic and temporal framework. We identified 12 lar-specific rearrangements and five previously undescribed rearrangements that occurred in the Hylobatidae ancestor. The majority of the chromosomal differences between lar gibbons and humans are due to rearrangements that occurred in the Hylobatidae ancestor (38 events), consistent with the hypothesis that the genus Hylobates is the most recently evolved lesser ape genus. The rates of rearrangements in gibbons are 10 to 20 times higher than the mammalian default rate. Segmental duplication may be a driving force in gibbon chromosome evolution, because a consistent number of rearrangements involves pericentromeric regions (10 events) and centromere inactivation (seven events). Both phenomena can be reasonably supposed to have strongly contributed to the euchromatic dispersal of segmental duplications typical of pericentromeric regions. This hypothesis can be more fully tested when the sequence of this gibbon species becomes available. The detailed synteny map provided here will, in turn, substantially facilitate sequence assembly efforts.
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Affiliation(s)
- Doriana Misceo
- Department of Genetics and Microbiology, University of Bari, 70126 Bari, Italy
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