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Kralick AE, Zemel BS, Nolan C, Lin P, Tocheri MW. Relative leg-to-arm skeletal strength proportions in orangutans by species and sex. J Hum Evol 2024; 188:103496. [PMID: 38412694 DOI: 10.1016/j.jhevol.2024.103496] [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: 04/25/2023] [Revised: 01/02/2024] [Accepted: 01/05/2024] [Indexed: 02/29/2024]
Abstract
Among extant great apes, orangutans climb most frequently. However, Bornean orangutans (Pongo pygmaeus) exhibit higher frequencies of terrestrial locomotion than do Sumatran orangutans (Pongo abelii). Variation in long bone cross-sectional geometry is known to reflect differential loading of the limbs. Thus, Bornean orangutans should show greater relative leg-to-arm strength than their Sumatran counterparts. Using skeletal specimens from museum collections, we measured two cross-sectional geometric measures of bone strength: the polar section modulus (Zpol) and the ratio of maximum to minimum area moments of inertia (Imax/Imin), at the midshaft of long bones in Bornean (n = 19) and Sumatran adult orangutans (n = 12) using medical CT and peripheral quantitative CT scans, and compared results to published data of other great apes. Relative leg-to-arm strength was quantified using ratios of femur and tibia over humerus, radius, and ulna, respectively. Differences between orangutan species and between sexes in median ratios were assessed using Wilcoxon rank sum tests. The tibia of Bornean orangutans was stronger relative to the humerus and the ulna than in Sumatran orangutans (p = 0.008 and 0.025, respectively), consistent with behavioral studies that indicate higher frequencies of terrestrial locomotion in the former. In three Zpol ratios, adult female orangutans showed greater leg-to-arm bone strength compared to flanged males, which may relate to females using their legs more during arboreal locomotion than in adult flanged males. A greater amount of habitat discontinuity on Borneo compared to Sumatra has been posited as a possible explanation for observed interspecific differences in locomotor behaviors, but recent camera trap studies has called this into question. Alternatively, greater frequencies of terrestriality in Pongo pygmaeus may be due to the absence of tigers on Borneo. The results of this study are consistent with the latter explanation given that habitat continuity was greater a century ago when our study sample was collected.
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Affiliation(s)
- Alexandra E Kralick
- Studies of Women, Gender, and Sexuality, Harvard University, Cambridge, 02138, USA; Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA.
| | - Babette S Zemel
- Division of Gastroenterology, Hepatology and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Clara Nolan
- Fine Arts Department, University of Pennsylvania, Philadelphia, PA, 19104, USA; Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Phillip Lin
- Stockdale High School, Bakersfield, CA, 93311, USA
| | - Matthew W Tocheri
- Department of Anthropology, Lakehead University, Thunder Bay, Ontario, P7B 5E1, Canada; Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, D.C., 20013, USA; Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, NSW, 2522, Australia
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2
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Shao Y, Zhou L, Li F, Zhao L, Zhang BL, Shao F, Chen JW, Chen CY, Bi X, Zhuang XL, Zhu HL, Hu J, Sun Z, Li X, Wang D, Rivas-González I, Wang S, Wang YM, Chen W, Li G, Lu HM, Liu Y, Kuderna LFK, Farh KKH, Fan PF, Yu L, Li M, Liu ZJ, Tiley GP, Yoder AD, Roos C, Hayakawa T, Marques-Bonet T, Rogers J, Stenson PD, Cooper DN, Schierup MH, Yao YG, Zhang YP, Wang W, Qi XG, Zhang G, Wu DD. Phylogenomic analyses provide insights into primate evolution. Science 2023; 380:913-924. [PMID: 37262173 DOI: 10.1126/science.abn6919] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/26/2023] [Indexed: 06/03/2023]
Abstract
Comparative analysis of primate genomes within a phylogenetic context is essential for understanding the evolution of human genetic architecture and primate diversity. We present such a study of 50 primate species spanning 38 genera and 14 families, including 27 genomes first reported here, with many from previously less well represented groups, the New World monkeys and the Strepsirrhini. Our analyses reveal heterogeneous rates of genomic rearrangement and gene evolution across primate lineages. Thousands of genes under positive selection in different lineages play roles in the nervous, skeletal, and digestive systems and may have contributed to primate innovations and adaptations. Our study reveals that many key genomic innovations occurred in the Simiiformes ancestral node and may have had an impact on the adaptive radiation of the Simiiformes and human evolution.
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Affiliation(s)
- Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Long Zhou
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Fang Li
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Institute of Animal Sex and Development, ZhejiangWanli University, Ningbo 315100, China
| | - Lan Zhao
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China
| | | | - Chun-Yan Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xupeng Bi
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiao-Lin Zhuang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650204, China
| | | | - Jiang Hu
- Grandomics Biosciences, Beijing 102206, China
| | - Zongyi Sun
- Grandomics Biosciences, Beijing 102206, China
| | - Xin Li
- Grandomics Biosciences, Beijing 102206, China
| | - Depeng Wang
- Grandomics Biosciences, Beijing 102206, China
| | | | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Yun-Mei Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Wu Chen
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou 510070, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Hui-Meng Lu
- School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Lukas F K Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA 92122, USA
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA 92122, USA
| | - Peng-Fei Fan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhi-Jin Liu
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - George P Tiley
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Japan Monkey Centre, Inuyama, Aichi 484-0081, Japan
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | | | - Yong-Gang Yao
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650204, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiao-Guang Qi
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650204, China
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3
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Musa F, Darman D. The Contingent Valuation Method contributes solutions for wildlife conservation: A case study at the Sepilok Orangutan Rehabilitation Centre in Borneo, Malaysia. INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT 2022; 18:1174-1186. [PMID: 35765932 DOI: 10.1002/ieam.4655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Deforestation is an alarming issue that is prolific throughout world forests. Endemic fauna, flora, and wildlife habitat loss are serious concerns for world heritage. That is why Goal 15 of the Sustainable Development Goals (SDGs) promotes the conserved use of these natural resources. Sabah, Malaysia is fortunate to have "Orang Hutan" literally "Jungle People" in the Sepilok Forest area. The government had designated the Sepilok Orangutan Rehabilitation Centre as their safeguard. Indeed, this is the world's first Rehabilitation Centre for Orangutans. However, the wildlife conservation of Orangutans needs to be translated into economic values. This study aims to determine the economic valuation of wildlife conservation through visitors' Willingness to Pay (WTP) via applying the Contingent Valuation Method (CVM). A total of 143 questionnaires were distributed randomly to international and local visitors. The Logistic Regression was used to estimate the Mean WTP. Results showed that several significant sociodemographic variables influence the respondents' WTP. Nevertheless, most respondents were willing to pay a maximum of MYR16.73, while the mean was MYR7.27 only. In 2017, the estimated annual economic value of the Rehabilitation Centre was MYR9, 697 074.96 compared to the estimated conservation value of MYR96, 970 749.60. The findings of this study demonstrate the possible beneficial role of economic valuation in assisting not just Orangutan conservation but threatened species conservation elsewhere. The study has assisted the Centre's management in determining the appropriate entrance fees for the future, as they have not been revised in over a decade. Integr Environ Assess Manag 2022;18:1174-1186. © 2022 SETAC.
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Affiliation(s)
- Fazilah Musa
- Faculty of Tropical Forestry, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Damri Darman
- Faculty of Tropical Forestry, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
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4
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Ng KKS, Kobayashi MJ, Fawcett JA, Hatakeyama M, Paape T, Ng CH, Ang CC, Tnah LH, Lee CT, Nishiyama T, Sese J, O'Brien MJ, Copetti D, Isa MNM, Ong RC, Putra M, Siregar IZ, Indrioko S, Kosugi Y, Izuno A, Isagi Y, Lee SL, Shimizu KK. The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests. Commun Biol 2021; 4:1166. [PMID: 34620991 PMCID: PMC8497594 DOI: 10.1038/s42003-021-02682-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/17/2021] [Indexed: 02/08/2023] Open
Abstract
Hyperdiverse tropical rainforests, such as the aseasonal forests in Southeast Asia, are supported by high annual rainfall. Its canopy is dominated by the species-rich tree family of Dipterocarpaceae (Asian dipterocarps), which has both ecological (e.g., supports flora and fauna) and economical (e.g., timber production) importance. Recent ecological studies suggested that rare irregular drought events may be an environmental stress and signal for the tropical trees. We assembled the genome of a widespread but near threatened dipterocarp, Shorea leprosula, and analyzed the transcriptome sequences of ten dipterocarp species representing seven genera. Comparative genomic and molecular dating analyses suggested a whole-genome duplication close to the Cretaceous-Paleogene extinction event followed by the diversification of major dipterocarp lineages (i.e. Dipterocarpoideae). Interestingly, the retained duplicated genes were enriched for genes upregulated by no-irrigation treatment. These findings provide molecular support for the relevance of drought for tropical trees despite the lack of an annual dry season.
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Affiliation(s)
- Kevin Kit Siong Ng
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia.
| | - Masaki J Kobayashi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
- Forestry Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Jeffrey A Fawcett
- Department of Evolutionary Studies of Biosystems, SOKENDAI, The Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
- RIKEN iTHEMS, Wako, Saitama, Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
- Functional Genomics Center Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Timothy Paape
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
| | - Chin Hong Ng
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Choon Cheng Ang
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
| | - Lee Hong Tnah
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Chai Ting Lee
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Tomoaki Nishiyama
- Division of Integrated Omics research, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Japan
| | - Jun Sese
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- AIST-Tokyo Tech RWBC-OIL, Meguro-ku, Tokyo, Japan
- Humanome Lab Inc., Chuo-ku, Tokyo, Japan
| | - Michael J O'Brien
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, c/Tulipán s/n., E-28933, Móstoles, Spain
| | - Dario Copetti
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | | | | | - Mahardika Putra
- Faculty of Forestry, Bogor Agricultural University, Bogor, Indonesia
| | | | - Sapto Indrioko
- Faculty of Forestry, Gadjah Mada University, Yogyakarta, Indonesia
| | - Yoshiko Kosugi
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Ayako Izuno
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Forestry and Forest Products Research Institute (FFPRI), Tsukuba, Ibaraki, Japan
| | - Yuji Isagi
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Soon Leong Lee
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia.
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland.
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan.
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5
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Louys J, Roberts P. Environmental drivers of megafauna and hominin extinction in Southeast Asia. Nature 2020; 586:402-406. [PMID: 33029012 DOI: 10.1038/s41586-020-2810-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/14/2020] [Indexed: 11/09/2022]
Abstract
Southeast Asia has emerged as an important region for understanding hominin and mammalian migrations and extinctions. High-profile discoveries have shown that Southeast Asia has been home to at least five members of the genus Homo1-3. Considerable turnover in Pleistocene megafauna has previously been linked with these hominins or with climate change4, although the region is often left out of discussions of megafauna extinctions. In the traditional hominin evolutionary core of Africa, attempts to establish the environmental context of hominin evolution and its association with faunal changes have long been informed by stable isotope methodologies5,6. However, such studies have largely been neglected in Southeast Asia. Here we present a large-scale dataset of stable isotope data for Southeast Asian mammals that spans the Quaternary period. Our results demonstrate that the forests of the Early Pleistocene had given way to savannahs by the Middle Pleistocene, which led to the spread of grazers and extinction of browsers-although geochronological limitations mean that not all samples can be resolved to glacial or interglacial periods. Savannahs retreated by the Late Pleistocene and had completely disappeared by the Holocene epoch, when they were replaced by highly stratified closed-canopy rainforest. This resulted in the ascendency of rainforest-adapted species as well as Homo sapiens-which has a unique adaptive plasticity among hominins-at the expense of savannah and woodland specialists, including Homo erectus. At present, megafauna are restricted to rainforests and are severely threatened by anthropogenic deforestation.
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Affiliation(s)
- Julien Louys
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Brisbane, Queensland, Australia. .,College of Asia and the Pacific, The Australian National University, Canberra, Australia Capital Territory, Australia.
| | - Patrick Roberts
- Max Planck Institute for the Science of Human History, Jena, Germany. .,School of Social Science, The University of Queensland, Brisbane, Queensland, Australia. .,Archaeological Studies Programme, University of the Philippines, Quezon City, The Philippines.
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6
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Bruijnesteijn J, de Groot N, van der Wiel MKH, Otting N, de Vos-Rouweler AJM, de Groot NG, Bontrop RE. Unparalleled Rapid Evolution of KIR Genes in Rhesus and Cynomolgus Macaque Populations. THE JOURNAL OF IMMUNOLOGY 2020; 204:1770-1786. [PMID: 32111732 DOI: 10.4049/jimmunol.1901140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/21/2020] [Indexed: 12/19/2022]
Abstract
The killer cell Ig-like receptors (KIR) modulate immune responses through interactions with MHC class I molecules. The KIR region in large cohorts of rhesus and cynomolgus macaque populations were characterized, and the experimental design enabled the definition of a considerable number of alleles (n = 576) and haplotypes, which are highly variable with regard to architecture. Although high levels of polymorphism were recorded, only a few alleles are shared between species and populations. The rapid evolution of allelic polymorphism, accumulated by point mutations, was further confirmed by the emergence of a novel KIR allele in a rhesus macaque family. In addition to allelic variation, abundant orthologous and species-specific KIR genes were identified, the latter of which are frequently generated by fusion events. The concerted action of both genetic mechanisms, in combination with differential selective pressures at the population level, resulted in the unparalleled rapid evolution of the KIR gene region in two closely related macaque species. The variation of the KIR gene repertoire at the species and population level might have an impact on the outcome of preclinical studies with macaque models.
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Affiliation(s)
- Jesse Bruijnesteijn
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Nanine de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Marit K H van der Wiel
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Nel Otting
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Annemiek J M de Vos-Rouweler
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and .,Theoretical Biology and Bioinformatics Group, Utrecht University, 3527 Utrecht, the Netherlands
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7
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Abstract
China is one of the most dynamic countries of the world and it shelters some amazing levels of biodiversity, including some very special primate species. However, primarily as a result of forest loss, most of which occurred in historical times, approximately 70% of China’s primate species have less than 3 000 individuals. Here I evaluate one road for future conservation/development that could produce very positive gains for China’s primates; namely forest restoration. I argue that for a large scale restoration project to be possible two conditions must be met; the right societal conditions must exist and the right knowledge must be in hand. This evaluation suggests that the restoration of native forest to support many of China’s primates holds great potential to advance conservation goals and to promote primate population recovery.
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Affiliation(s)
- Colin A Chapman
- Department of Anthropology, McGill University, Montréal Québec H3A 2T7, Canada; E-mail: .,Wildlife Conservation Society, Bronx New York 10460, USA.,Section of Social Systems Evolution, Primate Research Institute, Kyoto University, Inuyama 484-8506, Japan
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8
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Karin BR, Das I, Jackman TR, Bauer AM. Ancient divergence time estimates in Eutropis rugifera support the existence of Pleistocene barriers on the exposed Sunda Shelf. PeerJ 2017; 5:e3762. [PMID: 29093993 PMCID: PMC5661453 DOI: 10.7717/peerj.3762] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 08/15/2017] [Indexed: 01/30/2023] Open
Abstract
Episodic sea level changes that repeatedly exposed and inundated the Sunda Shelf characterize the Pleistocene. Available evidence points to a more xeric central Sunda Shelf during periods of low sea levels, and despite the broad land connections that persisted during this time, some organisms are assumed to have faced barriers to dispersal between land-masses on the Sunda Shelf. Eutropis rugifera is a secretive, forest adapted scincid lizard that ranges across the Sunda Shelf. In this study, we sequenced one mitochondrial (ND2) and four nuclear (BRCA1, BRCA2, RAG1, and MC1R) markers and generated a time-calibrated phylogeny in BEAST to test whether divergence times between Sundaic populations of E. rugifera occurred during Pleistocene sea-level changes, or if they predate the Pleistocene. We find that E. rugifera shows pre-Pleistocene divergences between populations on different Sundaic land-masses. The earliest divergence within E. rugifera separates the Philippine samples from the Sundaic samples approximately 16 Ma; the Philippine populations thus cannot be considered conspecific with Sundaic congeners. Sundaic populations diverged approximately 6 Ma, and populations within Borneo from Sabah and Sarawak separated approximately 4.5 Ma in the early Pliocene, followed by further cladogenesis in Sarawak through the Pleistocene. Divergence of peninsular Malaysian populations from the Mentawai Archipelago occurred approximately 5 Ma. Separation among island populations from the Mentawai Archipelago likely dates to the Pliocene/Pleistocene boundary approximately 3.5 Ma, and our samples from peninsular Malaysia appear to coalesce in the middle Pleistocene, about 1 Ma. Coupled with the monophyly of these populations, these divergence times suggest that despite consistent land-connections between these regions throughout the Pleistocene E. rugifera still faced barriers to dispersal, which may be a result of environmental shifts that accompanied the sea-level changes.
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Affiliation(s)
- Benjamin R Karin
- Department of Biology, Villanova University, Villanova, PA, United States of America.,Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Todd R Jackman
- Department of Biology, Villanova University, Villanova, PA, United States of America
| | - Aaron M Bauer
- Department of Biology, Villanova University, Villanova, PA, United States of America
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9
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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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Reid MJC, Switzer WM, Schillaci MA, Klegarth AR, Campbell E, Ragonnet-Cronin M, Joanisse I, Caminiti K, Lowenberger CA, Galdikas BMF, Hollocher H, Sandstrom PA, Brooks JI. Bayesian inference reveals ancient origin of simian foamy virus in orangutans. INFECTION GENETICS AND EVOLUTION 2017; 51:54-66. [PMID: 28274887 DOI: 10.1016/j.meegid.2017.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 02/25/2017] [Accepted: 03/03/2017] [Indexed: 02/08/2023]
Abstract
Simian foamy viruses (SFVs) infect most nonhuman primate species and appears to co-evolve with its hosts. This co-evolutionary signal is particularly strong among great apes, including orangutans (genus Pongo). Previous studies have identified three distinct orangutan SFV clades. The first of these three clades is composed of SFV from P. abelii from Sumatra, the second consists of SFV from P. pygmaeus from Borneo, while the third clade is mixed, comprising an SFV strain found in both species of orangutan. The existence of the mixed clade has been attributed to an expansion of P. pygmaeus into Sumatra following the Mount Toba super-volcanic eruption about 73,000years ago. Divergence dating, however, has yet to be performed to establish a temporal association with the Toba eruption. Here, we use a Bayesian framework and a relaxed molecular clock model with fossil calibrations to test the Toba hypothesis and to gain a more complete understanding of the evolutionary history of orangutan SFV. As with previous studies, our results show a similar three-clade orangutan SFV phylogeny, along with strong statistical support for SFV-host co-evolution in orangutans. Using Bayesian inference, we date the origin of orangutan SFV to >4.7 million years ago (mya), while the mixed species clade dates to approximately 1.7mya, >1.6 million years older than the Toba super-eruption. These results, combined with fossil and paleogeographic evidence, suggest that the origin of SFV in Sumatran and Bornean orangutans, including the mixed species clade, likely occurred on the mainland of Indo-China during the Late Pliocene and Calabrian stage of the Pleistocene, respectively.
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Affiliation(s)
- Michael J C Reid
- Department of Anthropology, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada; Department of Anthropology, University of Toronto, 19 Russell Street, Toronto, Ontario M5S 2S2, Canada.
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, GA 30329, USA.
| | - Michael A Schillaci
- Department of Anthropology, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada.
| | - Amy R Klegarth
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA; Department of Anthropology, University of Washington, Seattle, WA 98105, USA.
| | - Ellsworth Campbell
- Laboratory Branch, Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, GA 30329, USA.
| | - Manon Ragonnet-Cronin
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, West Mains Road, Edinburgh EH9 3JT, United Kingdom
| | - Isabelle Joanisse
- National HIV & Retrovirology Laboratories, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Kyna Caminiti
- Centre for Biosecurity, Public Health Agency of Canada, 100 Colonnade Road, Ottawa, Ontario, Canada.
| | - Carl A Lowenberger
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.
| | - Birute Mary F Galdikas
- Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada; Orangutan Foundation International, 824 S. Wellesley Ave., Los Angeles, CA 90049, USA
| | - Hope Hollocher
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Paul A Sandstrom
- National HIV & Retrovirology Laboratories, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Ontario, Canada.
| | - James I Brooks
- National HIV & Retrovirology Laboratories, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; The Ottawa Hospital, Division of Infectious Diseases, Department of Medicine, University of Ottawa, 1053 Carling Ave., Ottawa, ONK1Y 4E9, Canada
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11
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Manawatthana S, Laosinchai P, Onparn N, Brockelman WY, Round PD. Phylogeography of bulbuls in the genus Iole (Aves: Pycnonotidae). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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12
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Muangkram Y, Wajjwalku W, Amano A, Sukmak M. The novel primers for mammal species identification-based mitochondrial cytochrome b sequence: implication for reserved wild animals in Thailand and endangered mammal species in Southeast Asia. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:62-72. [PMID: 27758125 DOI: 10.1080/24701394.2016.1238902] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We presented the powerful techniques for species identification using the short amplicon of mitochondrial cytochrome b gene sequence. Two faecal samples and one single hair sample of the Asian tapir were tested using the new cytochrome b primers. The results showed a high sequence similarity with the mainland Asian tapir group. The comparative sequence analysis of the reserved wild mammals in Thailand and the other endangered mammal species from Southeast Asia comprehensibly verified the potential of our novel primers. The forward and reverse primers were 94.2 and 93.2%, respectively, by the average value of the sequence identity among 77 species sequences, and the overall mean distance was 35.9%. This development technique could provide rapid, simple, and reliable tools for species confirmation. Especially, it could recognize the problematic biological specimens contained less DNA material from illegal products and assist with wildlife crime investigation of threatened species and related forensic casework.
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Affiliation(s)
- Yuttamol Muangkram
- a Graduate School of Life Sciences , Ritsumeikan University , Kusatsu , Shiga , Japan.,b Faculty of Veterinary Medicine , Kasetsart University , Kamphaeng Saen , Nakhon Pathom , Thailand
| | - Worawidh Wajjwalku
- b Faculty of Veterinary Medicine , Kasetsart University , Kamphaeng Saen , Nakhon Pathom , Thailand
| | - Akira Amano
- a Graduate School of Life Sciences , Ritsumeikan University , Kusatsu , Shiga , Japan
| | - Manakorn Sukmak
- b Faculty of Veterinary Medicine , Kasetsart University , Kamphaeng Saen , Nakhon Pathom , Thailand
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13
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Kuhlwilm M, de Manuel M, Nater A, Greminger MP, Krützen M, Marques-Bonet T. Evolution and demography of the great apes. Curr Opin Genet Dev 2016; 41:124-129. [PMID: 27716526 DOI: 10.1016/j.gde.2016.09.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 09/03/2016] [Accepted: 09/12/2016] [Indexed: 01/27/2023]
Abstract
The great apes are the closest living relatives of humans. Chimpanzees and bonobos group together with humans, while gorillas and orangutans are more divergent from humans. Here, we review insights into their evolution pertaining to the topology of species and subspecies and the reconstruction of their demography based on genome-wide variation. These advances have only become possible recently through next-generation sequencing technologies. Given the close relationship to humans, they provide an important evolutionary context for human genetics.
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Affiliation(s)
- Martin Kuhlwilm
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Marc de Manuel
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Alexander Nater
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Maja P Greminger
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Michael Krützen
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
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14
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Brandon-Jones D, Groves CP, Jenkins PD. The type specimens and type localities of the orangutans, genus Pongo Lacépède, 1799 (Primates: Hominidae). J NAT HIST 2016. [DOI: 10.1080/00222933.2016.1190414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
| | - Colin P. Groves
- School of Archaeology & Anthropology, Australian National University, Canberra, ACT, Australia
| | - Paulina D. Jenkins
- Department of Life Sciences, Mammal Group, The Natural History Museum, London, UK
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15
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Smith TM. Dental development in living and fossil orangutans. J Hum Evol 2016; 94:92-105. [DOI: 10.1016/j.jhevol.2016.02.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 12/29/2015] [Accepted: 02/25/2016] [Indexed: 10/22/2022]
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16
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17
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Larick R, Ciochon RL. Retracted: Early hominin biogeography in Island Southeast Asia. Evol Anthropol 2015; 24:185-213. [DOI: 10.1002/evan.21460] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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18
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Identification of Diagnostic Mitochondrial DNA Single Nucleotide Polymorphisms Specific to Sumatran Orangutan (Pongo abelii) Populations. HAYATI JOURNAL OF BIOSCIENCES 2015. [DOI: 10.1016/j.hjb.2015.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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19
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Abstract
The world of primate genomics is expanding rapidly in new and exciting ways owing to lowered costs and new technologies in molecular methods and bioinformatics. The primate order is composed of 78 genera and 478 species, including human. Taxonomic inferences are complex and likely a consequence of ongoing hybridization, introgression, and reticulate evolution among closely related taxa. Recently, we applied large-scale sequencing methods and extensive taxon sampling to generate a highly resolved phylogeny that affirms, reforms, and extends previous depictions of primate speciation. The next stage of research uses this phylogeny as a foundation for investigating genome content, structure, and evolution across primates. Ongoing and future applications of a robust primate phylogeny are discussed, highlighting advancements in adaptive evolution of genes and genomes, taxonomy and conservation management of endangered species, next-generation genomic technologies, and biomedicine.
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Affiliation(s)
- Jill Pecon-Slattery
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702; Current Affiliation: Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, Virginia 22630;
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20
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Nater A, Greminger MP, Arora N, van Schaik CP, Goossens B, Singleton I, Verschoor EJ, Warren KS, Krützen M. Reconstructing the demographic history of orang-utans using Approximate Bayesian Computation. Mol Ecol 2015; 24:310-27. [PMID: 25439562 DOI: 10.1111/mec.13027] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 11/24/2014] [Accepted: 11/27/2014] [Indexed: 11/27/2022]
Abstract
Investigating how different evolutionary forces have shaped patterns of DNA variation within and among species requires detailed knowledge of their demographic history. Orang-utans, whose distribution is currently restricted to the South-East Asian islands of Borneo (Pongo pygmaeus) and Sumatra (Pongo abelii), have likely experienced a complex demographic history, influenced by recurrent changes in climate and sea levels, volcanic activities and anthropogenic pressures. Using the most extensive sample set of wild orang-utans to date, we employed an Approximate Bayesian Computation (ABC) approach to test the fit of 12 different demographic scenarios to the observed patterns of variation in autosomal, X-chromosomal, mitochondrial and Y-chromosomal markers. In the best-fitting model, Sumatran orang-utans exhibit a deep split of populations north and south of Lake Toba, probably caused by multiple eruptions of the Toba volcano. In addition, we found signals for a strong decline in all Sumatran populations ~24 ka, probably associated with hunting by human colonizers. In contrast, Bornean orang-utans experienced a severe bottleneck ~135 ka, followed by a population expansion and substructuring starting ~82 ka, which we link to an expansion from a glacial refugium. We showed that orang-utans went through drastic changes in population size and connectedness, caused by recurrent contraction and expansion of rainforest habitat during Pleistocene glaciations and probably hunting by early humans. Our findings emphasize the fact that important aspects of the evolutionary past of species with complex demographic histories might remain obscured when applying overly simplified models.
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Affiliation(s)
- Alexander Nater
- Anthropological Institute & Museum, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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21
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Greminger MP, Stölting KN, Nater A, Goossens B, Arora N, Bruggmann R, Patrignani A, Nussberger B, Sharma R, Kraus RHS, Ambu LN, Singleton I, Chikhi L, van Schaik CP, Krützen M. Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms. BMC Genomics 2014; 15:16. [PMID: 24405840 PMCID: PMC3897891 DOI: 10.1186/1471-2164-15-16] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 12/21/2013] [Indexed: 12/30/2022] Open
Abstract
Background High-throughput sequencing has opened up exciting possibilities in population and conservation genetics by enabling the assessment of genetic variation at genome-wide scales. One approach to reduce genome complexity, i.e. investigating only parts of the genome, is reduced-representation library (RRL) sequencing. Like similar approaches, RRL sequencing reduces ascertainment bias due to simultaneous discovery and genotyping of single-nucleotide polymorphisms (SNPs) and does not require reference genomes. Yet, generating such datasets remains challenging due to laboratory and bioinformatical issues. In the laboratory, current protocols require improvements with regards to sequencing homologous fragments to reduce the number of missing genotypes. From the bioinformatical perspective, the reliance of most studies on a single SNP caller disregards the possibility that different algorithms may produce disparate SNP datasets. Results We present an improved RRL (iRRL) protocol that maximizes the generation of homologous DNA sequences, thus achieving improved genotyping-by-sequencing efficiency. Our modifications facilitate generation of single-sample libraries, enabling individual genotype assignments instead of pooled-sample analysis. We sequenced ~1% of the orangutan genome with 41-fold median coverage in 31 wild-born individuals from two populations. SNPs and genotypes were called using three different algorithms. We obtained substantially different SNP datasets depending on the SNP caller. Genotype validations revealed that the Unified Genotyper of the Genome Analysis Toolkit and SAMtools performed significantly better than a caller from CLC Genomics Workbench (CLC). Of all conflicting genotype calls, CLC was only correct in 17% of the cases. Furthermore, conflicting genotypes between two algorithms showed a systematic bias in that one caller almost exclusively assigned heterozygotes, while the other one almost exclusively assigned homozygotes. Conclusions Our enhanced iRRL approach greatly facilitates genotyping-by-sequencing and thus direct estimates of allele frequencies. Our direct comparison of three commonly used SNP callers emphasizes the need to question the accuracy of SNP and genotype calling, as we obtained considerably different SNP datasets depending on caller algorithms, sequencing depths and filtering criteria. These differences affected scans for signatures of natural selection, but will also exert undue influences on demographic inferences. This study presents the first effort to generate a population genomic dataset for wild-born orangutans with known population provenance.
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Affiliation(s)
- Maja P Greminger
- Evolutionary Genetics Group, Anthropological Institute and Museum, University of Zurich, Zurich, Switzerland.
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22
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Gordon AD, Marcus E, Wood B. Great ape skeletal collections: Making the most of scarce and irreplaceable resources in the digital age. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 152 Suppl 57:2-32. [DOI: 10.1002/ajpa.22391] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Adam D. Gordon
- Department of Anthropology; University at Albany; SUNY Albany NY 12222
| | - Emily Marcus
- Honors Program; George Washington University; Washington, DC 20052
- Center for the Advanced Study of Hominid Paleobiology, Department of Anthropology; George Washington University; Washington, DC 20052
| | - Bernard Wood
- Center for the Advanced Study of Hominid Paleobiology, Department of Anthropology; George Washington University; Washington, DC 20052
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23
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Dunkel LP, Arora N, van Noordwijk MA, Atmoko SSU, Putra AP, Krützen M, van Schaik CP. Variation in developmental arrest among male orangutans: a comparison between a Sumatran and a Bornean population. Front Zool 2013; 10:12. [PMID: 23510027 PMCID: PMC3607856 DOI: 10.1186/1742-9994-10-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 03/13/2013] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION The presence of two sexually active male morphs with different reproductive tactics in a single species is rare among mammals. The most striking case of bimaturism among primates is exhibited by the orangutan (Pongo spp), in which one adult morph, the unflanged male, irreversibly develops into another one, the flanged form, but may remain arrested in the unflanged state for many years. However, it has been suggested that such arrest is less common among Bornean orangutans (Pongo pygmaeus) compared to Sumatrans (Pongo abelii). To investigate this possible inter-specific difference we compared both the number of developing males and the ratios of the two male morphs at two long-term study sites, Suaq Balimbing on Sumatra and Tuanan on Borneo. RESULTS First, we observed a significantly greater number of flanged than unflanged males per month in the Tuanan study area, whereas the opposite pattern held at Suaq. Second, the same contrast held for the total number of identified individuals over the study, with more flanged than unflanged males at Tuanan and the opposite at Suaq. These differences were mainly due to transient males. For Tuanan, the identification results were confirmed by detailed genetic analyses. Finally, we recorded a higher proportion of unflanged males that became flanged during any given year at Tuanan than at Suaq. CONCLUSION These results show that developmental arrest is far more common at Suaq than at Tuanan. Preliminary comparisons suggest that this is a general contrast between the island taxa of orangutans and should help efforts to identify the function and proximate control of developmental arrest in orangutan males.
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Affiliation(s)
- Lynda P Dunkel
- Anthropological Institute & Museum, University of Zurich, Winterthurerstrasse 190, Zürich, CH-8057, Switzerland
| | - Natasha Arora
- Anthropological Institute & Museum, University of Zurich, Winterthurerstrasse 190, Zürich, CH-8057, Switzerland
| | - Maria A van Noordwijk
- Anthropological Institute & Museum, University of Zurich, Winterthurerstrasse 190, Zürich, CH-8057, Switzerland
| | - Sri Suci Utami Atmoko
- Faculty of Biology, Universitas Nasional, Jalan Sawo Manila, Pejaten Pasar Minggu, Jakarta, 12520, Indonesia
| | - Angga Prathama Putra
- Faculty of Mathematics and Science, Universitas Indonesia, Depok, 16424, Indonesia
| | - Michael Krützen
- Anthropological Institute & Museum, University of Zurich, Winterthurerstrasse 190, Zürich, CH-8057, Switzerland
| | - Carel P van Schaik
- Anthropological Institute & Museum, University of Zurich, Winterthurerstrasse 190, Zürich, CH-8057, Switzerland
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24
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Ohtani M, Kondo T, Tani N, Ueno S, Lee LS, Ng KKS, Muhammad N, Finkeldey R, Na'iem M, Indrioko S, Kamiya K, Harada K, Diway B, Khoo E, Kawamura K, Tsumura Y. Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in South-East Asia. Mol Ecol 2013; 22:2264-79. [PMID: 23432376 DOI: 10.1111/mec.12243] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 12/26/2012] [Accepted: 01/05/2013] [Indexed: 11/29/2022]
Abstract
Tropical rainforests in South-East Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag-based simple sequence repeats and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear genetic differentiation between populations in Borneo and those in the Malay Peninsula and Sumatra (Malay/Sumatra). However, in the south-western part of Borneo, genetic admixture of the lineages was observed in the two marker types. Coalescent simulation based on cpDNA sequence variation suggested that the two lineages arose 0.28-0.09 million years before present and that following their divergence migration from Malay/Sumatra to Borneo strongly exceeded migration in the opposite direction. We conclude that the genetic structure of S. leprosula was largely formed during the middle Pleistocene and was subsequently modified by eastward migration across the subaerially exposed Sunda Shelf.
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Affiliation(s)
- Masato Ohtani
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
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25
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Mailund T, Halager AE, Westergaard M, Dutheil JY, Munch K, Andersen LN, Lunter G, Prüfer K, Scally A, Hobolth A, Schierup MH. A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. PLoS Genet 2012; 8:e1003125. [PMID: 23284294 PMCID: PMC3527290 DOI: 10.1371/journal.pgen.1003125] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 10/14/2012] [Indexed: 11/18/2022] Open
Abstract
We present a hidden Markov model (HMM) for inferring gradual isolation between two populations during speciation, modelled as a time interval with restricted gene flow. The HMM describes the history of adjacent nucleotides in two genomic sequences, such that the nucleotides can be separated by recombination, can migrate between populations, or can coalesce at variable time points, all dependent on the parameters of the model, which are the effective population sizes, splitting times, recombination rate, and migration rate. We show by extensive simulations that the HMM can accurately infer all parameters except the recombination rate, which is biased downwards. Inference is robust to variation in the mutation rate and the recombination rate over the sequence and also robust to unknown phase of genomes unless they are very closely related. We provide a test for whether divergence is gradual or instantaneous, and we apply the model to three key divergence processes in great apes: (a) the bonobo and common chimpanzee, (b) the eastern and western gorilla, and (c) the Sumatran and Bornean orang-utan. We find that the bonobo and chimpanzee appear to have undergone a clear split, whereas the divergence processes of the gorilla and orang-utan species occurred over several hundred thousands years with gene flow stopping quite recently. We also apply the model to the Homo/Pan speciation event and find that the most likely scenario involves an extended period of gene flow during speciation.
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Affiliation(s)
- Thomas Mailund
- Bioinformatics Research Center, Aarhus University, Aarhus, Denmark.
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Sharma R, Arora N, Goossens B, Nater A, Morf N, Salmona J, Bruford MW, Van Schaik CP, Krützen M, Chikhi L. Effective population size dynamics and the demographic collapse of Bornean orang-utans. PLoS One 2012; 7:e49429. [PMID: 23166666 PMCID: PMC3499548 DOI: 10.1371/journal.pone.0049429] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Accepted: 10/07/2012] [Indexed: 11/30/2022] Open
Abstract
Bornean orang-utans experienced a major demographic decline and local extirpations during the Pleistocene and Holocene due to climate change, the arrival of modern humans, of farmers and recent commercially-driven habitat loss and fragmentation. The recent loss of habitat and its dramatic fragmentation has affected the patterns of genetic variability and differentiation among the remaining populations and increased the extinction risk of the most isolated ones. However, the contribution of recent demographic events to such genetic patterns is still not fully clear. Indeed, it can be difficult to separate the effects of recent anthropogenic fragmentation from the genetic signature of prehistoric demographic events. Here, we investigated the genetic structure and population size dynamics of orang-utans from different sites. Altogether 126 individuals were analyzed and a full-likelihood Bayesian approach was applied. All sites exhibited clear signals of population decline. Population structure is known to generate spurious bottleneck signals and we found that it does indeed contribute to the signals observed. However, population structure alone does not easily explain the observed patterns. The dating of the population decline varied across sites but was always within the 200–2000 years period. This suggests that in some sites at least, orang-utan populations were affected by demographic events that started before the recent anthropogenic effects that occurred in Borneo. These results do not mean that the recent forest exploitation did not leave its genetic mark on orang-utans but suggests that the genetic pool of orang-utans is also impacted by more ancient events. While we cannot identify the main cause for this decline, our results suggests that the decline may be related to the arrival of the first farmers or climatic events, and that more theoretical work is needed to understand how multiple demographic events impact the genome of species and how we can assess their relative contributions.
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Affiliation(s)
- Reeta Sharma
- Population and Conservation Genetics, Instituto Gulbenkian de Ciência, Oeiras, Portugal.
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Nater A, Arora N, Greminger MP, van Schaik CP, Singleton I, Wich SA, Fredriksson G, Perwitasari-Farajallah D, Pamungkas J, Krützen M. Marked Population Structure and Recent Migration in the Critically Endangered Sumatran Orangutan (Pongo abelii). J Hered 2012; 104:2-13. [DOI: 10.1093/jhered/ess065] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Grine FE, Jacobs RL, Reed KE, Plavcan JM. The enigmatic molar from Gondolin, South Africa: Implications for Paranthropus paleobiology. J Hum Evol 2012; 63:597-609. [DOI: 10.1016/j.jhevol.2012.06.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 04/11/2012] [Accepted: 06/28/2012] [Indexed: 11/24/2022]
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Variation in the Social Systems of Extant Hominoids: Comparative Insight into the Social Behavior of Early Hominins. INT J PRIMATOL 2012. [DOI: 10.1007/s10764-012-9617-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Meijaard E, Wich S, Ancrenaz M, Marshall AJ. Not by science alone: why orangutan conservationists must think outside the box. Ann N Y Acad Sci 2011; 1249:29-44. [PMID: 22175247 DOI: 10.1111/j.1749-6632.2011.06288.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Orangutan survival is threatened by habitat loss and illegal killing. Most wild populations will disappear over the next few decades unless threats are abated. Saving orangutans is ultimately in the hands of the governments and people of Indonesia and Malaysia, which need to ensure that habitats of viable orangutan populations are protected from deforestation and well managed to ensure no hunting takes place. Companies working in orangutan habitat also have to play a much bigger role in habitat management. Although the major problems and the direct actions required to solve them-reducing forest loss and hunting-have been known for decades, orangutan populations continue to decline. Orangutan populations in Sumatra and Borneo have declined by between 2,280 and 5,250 orangutans annually over the past 25 years. As the total current population for the two species is some 60,000 animals in an area of about 90,000 km(2) , there is not much time left to make conservation efforts truly effective. Our review discusses what has and has not worked in conservation to guide future conservation efforts.
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Affiliation(s)
- Erik Meijaard
- People and Nature Consulting International, Kerobokan, Bali, Indonesia.
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31
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Abstract
The evolutionary history of chromosomes can be tracked by the comparative hybridization of large panels of bacterial artificial chromosome clones. This approach has disclosed an unprecedented phenomenon: 'centromere repositioning', that is, the movement of the centromere along the chromosome without marker order variation. The occurrence of evolutionary new centromeres (ENCs) is relatively frequent. In macaque, for instance, 9 out of 20 autosomal centromeres are evolutionarily new; in donkey at least 5 such neocentromeres originated after divergence from the zebra, in less than 1 million years. Recently, orangutan chromosome 9, considered to be heterozygous for a complex rearrangement, was discovered to be an ENC. In humans, in addition to neocentromeres that arise in acentric fragments and result in clinical phenotypes, 8 centromere-repositioning events have been reported. These 'real-time' repositioned centromere-seeding events provide clues to ENC birth and progression. In the present paper, we provide a review of the centromere repositioning. We add new data on the population genetics of the ENC of the orangutan, and describe for the first time an ENC on the X chromosome of squirrel monkeys. Next-generation sequencing technologies have started an unprecedented, flourishing period of rapid whole-genome sequencing. In this context, it is worth noting that these technologies, uncoupled from cytogenetics, would miss all the biological data on evolutionary centromere repositioning. Therefore, we can anticipate that classical and molecular cytogenetics will continue to have a crucial role in the identification of centromere movements. Indeed, all ENCs and human neocentromeres were found following classical and molecular cytogenetic investigations.
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Lim HC, Sheldon FH. Multilocus analysis of the evolutionary dynamics of rainforest bird populations in Southeast Asia. Mol Ecol 2011; 20:3414-38. [PMID: 21777318 DOI: 10.1111/j.1365-294x.2011.05190.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Sundaland has a dynamic geographic history because its landmasses were periodically interconnected when sea levels fell during glacial periods. Superimposed on this geographic dynamism were environmental changes related to climatic oscillations. To investigate how tropical taxa responded to such changes, we studied the divergence and demographic history of two co-distributed rainforest passerine species, Arachnothera longirostra and Malacocincla malaccensis. We sampled birds primarily from Borneo and the Malay Peninsula, which straddle the now-submerged Sunda shelf, and analysed multilocus DNA data with a variety of coalescent and gene genealogy methods. Cross-shelf divergence in both species occurred well before the last glacial maximum, i.e., before the most recent land connection. However, post-divergence gene flow occurred, and it was more pronounced in A. longirostra (a highly vagile nectarivore/insectivore) than in M. malaccensis (an understory insectivore). Despite current habitat continuity on Borneo, the population of M. malaccensis in northeastern Borneo is substantially divergent from that on the rest of the island. The NE population experienced dramatic demographic fluctuations, probably because of competition with the other population, which expanded from western Borneo after the mid-Pleistocene. In contrast, the Borneo population of A. longirostra has little structure and appears to have experienced demographic expansion 16 kya, long after it had diverged from the Malay Peninsula population (630-690 kya). Malay Peninsula populations of both species have remained relatively stable. Overall, the most recent glacial period was not the chief determinant of the evolutionary dynamics of our study species, and in this respect, they are different from temperate species.
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Affiliation(s)
- Haw Chuan Lim
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA.
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Perelman P, Johnson WE, Roos C, Seuánez HN, Horvath JE, Moreira MAM, Kessing B, Pontius J, Roelke M, Rumpler Y, Schneider MPC, Silva A, O'Brien SJ, Pecon-Slattery J. A molecular phylogeny of living primates. PLoS Genet 2011; 7:e1001342. [PMID: 21436896 PMCID: PMC3060065 DOI: 10.1371/journal.pgen.1001342] [Citation(s) in RCA: 879] [Impact Index Per Article: 67.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 02/16/2011] [Indexed: 12/13/2022] Open
Abstract
Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (∼8 Mb) from 186 primates representing 61 (∼90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species. Advances in human biomedicine, including those focused on changes in genes triggered or disrupted in development, resistance/susceptibility to infectious disease, cancers, mechanisms of recombination, and genome plasticity, cannot be adequately interpreted in the absence of a precise evolutionary context or hierarchy. However, little is known about the genomes of other primate species, a situation exacerbated by a paucity of nuclear molecular sequence data necessary to resolve the complexities of primate divergence over time. We overcome this deficiency by sequencing 54 nuclear gene regions from DNA samples representing ∼90% of the diversity present in living primates. We conduct a phylogenetic analysis to determine the origin, evolution, patterns of speciation, and unique features in genome divergence among primate lineages. The resultant phylogenetic tree is remarkably robust and unambiguously resolves many long-standing issues in primate taxonomy. Our data provide a strong foundation for illuminating those genomic differences that are uniquely human and provide new insights on the breadth and richness of gene evolution across all primate lineages.
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Affiliation(s)
- Polina Perelman
- Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Warren E. Johnson
- Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Göttingen, Germany
| | - Hector N. Seuánez
- Division of Genetics, Instituto Nacional de Câncer and Department of Genetics, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Julie E. Horvath
- Department of Evolutionary Anthropology and Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
| | - Miguel A. M. Moreira
- Division of Genetics, Instituto Nacional de Câncer and Department of Genetics, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bailey Kessing
- SAIC–Frederick, Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Joan Pontius
- SAIC–Frederick, Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Melody Roelke
- SAIC–Frederick, Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Yves Rumpler
- Physiopathologie et Médecine Translationnelle, Faculté de Médecine, Université Louis Pasteur, Strasbourg, France
| | | | | | - Stephen J. O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Jill Pecon-Slattery
- Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
- * E-mail:
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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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35
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Effects of Pleistocene glaciations and rivers on the population structure of Bornean orangutans (Pongo pygmaeus). Proc Natl Acad Sci U S A 2010; 107:21376-81. [PMID: 21098261 DOI: 10.1073/pnas.1010169107] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sundaland, a tropical hotspot of biodiversity comprising Borneo and Sumatra among other islands, the Malay Peninsula, and a shallow sea, has been subject to dramatic environmental processes. Thus, it presents an ideal opportunity to investigate the role of environmental mechanisms in shaping species distribution and diversity. We investigated the population structure and underlying mechanisms of an insular endemic, the Bornean orangutan (Pongo pygmaeus). Phylogenetic reconstructions based on mtDNA sequences from 211 wild orangutans covering the entire range of the species indicate an unexpectedly recent common ancestor of Bornean orangutans 176 ka (95% highest posterior density, 72-322 ka), pointing to a Pleistocene refugium. High mtDNA differentiation among populations and rare haplotype sharing is consistent with a pattern of strong female philopatry. This is corroborated by isolation by distance tests, which show a significant correlation between mtDNA divergence and distance and a strong effect of rivers as barriers for female movement. Both frequency-based and Bayesian clustering analyses using as many as 25 nuclear microsatellite loci revealed a significant separation among all populations, as well as a small degree of male-mediated gene flow. This study highlights the unique effects of environmental and biological features on the evolutionary history of Bornean orangutans, a highly endangered species particularly vulnerable to future climate and anthropogenic change as an insular endemic.
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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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Lim HC, Rahman MA, Lim SLH, Moyle RG, Sheldon FH. Revisiting Wallace's haunt: coalescent simulations and comparative niche modeling reveal historical mechanisms that promoted avian population divergence in the Malay Archipelago. Evolution 2010; 65:321-34. [PMID: 20796023 DOI: 10.1111/j.1558-5646.2010.01105.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sundaland, a biogeographic region of Southeast Asia, is a major biodiversity hotspot. However, little is known about the relative importance of Pleistocene habitat barriers and rivers in structuring populations and promoting diversification here. We sampled 16 lowland rainforest bird species primarily from peninsular Malaysia and Borneo to test the long-standing hypothesis that animals on different Sundaic landmasses intermixed extensively when lower sea-levels during the Last Glacial Maximum (LGM) exposed land-bridges. This hypothesis was rejected in all but five species through coalescent simulations. Furthermore, we detected a range of phylogeographic patterns; Bornean populations are often genetically distinct from each other, despite their current habitat connectivity. Environmental niche modeling showed that the presence of unsuitable habitats between western and eastern Sundaland during the LGM coincided with deeper interpopulation genetic divergences. The location of this habitat barrier had been hypothesized previously based on other evidence. Paleo-riverine barriers are unlikely to have produced such a pattern, but we cannot rule out that they acted with habitat changes to impede population exchanges across the Sunda shelf. The distinctiveness of northeastern Borneo populations may be underlied by a combination of factors such as rivers, LGM expansion of montane forests and other aspects of regional physiography.
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Affiliation(s)
- Haw Chuan Lim
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
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38
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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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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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40
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Pouyaud L, Sudarto, Paradis E. The phylogenetic structure of habitat shift and morphological convergence in AsianClarias(Teleostei, Siluriformes: Clariidae). J ZOOL SYST EVOL RES 2009. [DOI: 10.1111/j.1439-0469.2008.00507.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Marques-Bonet T, Ryder OA, Eichler EE. Sequencing primate genomes: what have we learned? Annu Rev Genomics Hum Genet 2009; 10:355-86. [PMID: 19630567 DOI: 10.1146/annurev.genom.9.081307.164420] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We summarize the progress in whole-genome sequencing and analyses of primate genomes. These emerging genome datasets have broadened our understanding of primate genome evolution revealing unexpected and complex patterns of evolutionary change. This includes the characterization of genome structural variation, episodic changes in the repeat landscape, differences in gene expression, new models regarding speciation, and the ephemeral nature of the recombination landscape. The functional characterization of genomic differences important in primate speciation and adaptation remains a significant challenge. Limited access to biological materials, the lack of detailed phenotypic data and the endangered status of many critical primate species have significantly attenuated research into the genetic basis of primate evolution. Next-generation sequencing technologies promise to greatly expand the number of available primate genome sequences; however, such draft genome sequences will likely miss critical genetic differences within complex genomic regions unless dedicated efforts are put forward to understand the full spectrum of genetic variation.
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Affiliation(s)
- Tomas Marques-Bonet
- Department of Genome Sciences, University of Washington and the Howard Hughes Medical Institute, Seattle, Washington 98105, USA.
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The current refugial rainforests of Sundaland are unrepresentative of their biogeographic past and highly vulnerable to disturbance. Proc Natl Acad Sci U S A 2009; 106:11188-93. [PMID: 19549829 DOI: 10.1073/pnas.0809865106] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding the historical dynamics of forest communities is a critical element for accurate prediction of their response to future change. Here, we examine evergreen rainforest distribution in the Sunda Shelf region at the last glacial maximum (LGM), using a spatially explicit model incorporating geographic, paleoclimatic, and geologic evidence. Results indicate that at the LGM, Sundaland rainforests covered a substantially larger area than currently present. Extrapolation of the model over the past million years demonstrates that the current "island archipelago" setting in Sundaland is extremely unusual given the majority of its history and the dramatic biogeographic transitions caused by global deglaciation were rapid and brief. Compared with dominant glacial conditions, lowland forests were probably reduced from approximately 1.3 to 0.8 x 10(6) km(2) while upland forests were probably reduced by half, from approximately 2.0 to 1.0 x 10(5) km(2). Coastal mangrove and swamp forests experienced the most dramatic change during deglaciations, going through a complete and major biogeographic relocation. The Sundaland forest dynamics of fragmentation and contraction and subsequent expansion, driven by glacial cycles, occur in the opposite phase as those in the northern hemisphere and equatorial Africa, indicating that Sundaland evergreen rainforest communities are currently in a refugial stage. Widespread human-mediated reduction and conversion of these forests in their refugial stage, when most species are passing through significant population bottlenecks, strongly emphasizes the urgency of conservation and management efforts. Further research into the natural process of fragmentation and contraction during deglaciation is necessary to understand the long-term effect of human activity on forest species.
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Kirsch S, Münch C, Jiang Z, Cheng Z, Chen L, Batz C, Eichler EE, Schempp W. Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions. Genome Res 2008; 18:1030-42. [PMID: 18445620 DOI: 10.1101/gr.076711.108] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Human chromosomal regions enriched in segmental duplications are subject to extensive genomic reorganization. Such regions are particularly informative for illuminating the evolutionary history of a given chromosome. We have analyzed 866 kb of Y-chromosomal non-palindromic segmental duplications delineating four euchromatin/heterochromatin transition regions (Yp11.2/Yp11.1, Yq11.1/Yq11.21, Yq11.23/Yq12, and Yq12/PAR2). Several computational methods were applied to decipher the segmental duplication architecture and identify the ancestral origin of the 41 different duplicons. Combining computational and comparative FISH analysis, we reconstruct the evolutionary history of these regions. Our analysis indicates a continuous process of transposition of duplicated sequences onto the evolving higher primate Y chromosome, providing unique insights into the development of species-specific Y-chromosomal and autosomal duplicons. Phylogenetic sequence comparisons show that duplicons of the human Yp11.2/Yp11.1 region were already present in the macaque-human ancestor as multiple paralogs located predominantly in subtelomeric regions. In contrast, duplicons from the Yq11.1/Yq11.21, Yq11.23/Yq12, and Yq12/PAR2 regions show no evidence of duplication in rhesus macaque, but map to the pericentromeric regions in chimpanzee and human. This suggests an evolutionary shift in the direction of duplicative transposition events from subtelomeric in Old World monkeys to pericentromeric in the human/ape lineage. Extensive chromosomal relocation of autosomal-duplicated sequences from euchromatin/heterochromatin transition regions to interstitial regions as demonstrated on the pygmy chimpanzee Y chromosome support a model in which substantial reorganization and amplification of duplicated sequences may contribute to speciation.
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Affiliation(s)
- Stefan Kirsch
- Institute of Human Genetics, University of Freiburg, 79106 Freiburg, Germany
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Fertility and mortality patterns of captive Bornean and Sumatran orangutans: is there a species difference in life history? J Hum Evol 2007; 54:34-42. [PMID: 17804037 DOI: 10.1016/j.jhevol.2007.05.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2006] [Revised: 03/24/2007] [Accepted: 05/22/2007] [Indexed: 11/24/2022]
Abstract
Across broad taxonomic groups, life history models predict that increased ecological predictability will lead to conservative investment in reproductive effort. Within species, however, organisms are predicted to have increased reproductive rates under improved environmental conditions. It is not clear how these models apply to closely-related species. In this paper, we examine predictions from these models as applied to variability in reproductive rates between the two species of orangutans, Pongo pygmaeus (Bornean) and Pongo abelii (Sumatran). Orangutans exhibit characteristics of a "slow" life history strategy with large bodies, late age at maturity, low reproductive rates, and long lifespan. Recently, researchers proposed that Sumatran orangutans may have an even slower life history than Bornean orangutans as a result of ecological and genetic differences (Wich et al., 2004). We examined this hypothesis by studying important aspects of life history of both species under conditions of relative ecological stability, in captivity. In this large dataset, there were no significant species differences in age of first or last reproduction, completed fertility, perinatal and postnatal mortality, or female longevity. Bornean orangutans in captivity did have significantly longer interbirth intervals, and male Bornean orangutans had higher survival past maturity. Our results do not support the hypothesis that selection has led to decreased reproductive effort under conditions of increased habitat quality in Sumatra (Wich et al., 2004), and instead suggest that phenotypic flexibility may be particularly important in explaining differences between closely related species.
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Terhune CE, Kimbel WH, Lockwood CA. Variation and diversity in Homo erectus: a 3D geometric morphometric analysis of the temporal bone. J Hum Evol 2007; 53:41-60. [PMID: 17512034 DOI: 10.1016/j.jhevol.2007.01.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Revised: 11/30/2006] [Accepted: 01/29/2007] [Indexed: 11/25/2022]
Abstract
Although the level of taxonomic diversity within the fossil hominin species Homo erectus (sensu lato) is continually debated, there have been relatively few studies aiming to quantify the morphology of this species. Instead, most researchers have relied on qualitative descriptions or the evaluation of nonmetric characters, which in many cases display continuous variation. Also, only a few studies have used quantitative data to formally test hypotheses regarding the taxonomic composition of the "erectus" hypodigm. Despite these previous analyses, however, and perhaps in part due to these varied approaches for assessing variation within specimens typically referred to H. erectus (sensu lato) and the general lack of rigorous statistical testing of how variation within this taxon is partitioned, there is currently little consensus regarding whether this group is a single species, or whether it should instead be split into separate temporal or geographically delimited taxa. In order to evaluate possible explanations for variation within H. erectus, we tested the general hypothesis that variation within the temporal bone morphology of H. erectus is consistent with that of a single species, using great apes and humans as comparative taxa. Eighteen three-dimensional (3D) landmarks of the temporal bone were digitized on a total of 520 extant and fossil hominid crania. Landmarks were registered by Generalized Procrustes Analysis, and Procrustes distances were calculated for comparisons of individuals within and between the extant taxa. Distances between fossil specimens and between a priori groupings of fossils were then compared to the distances calculated within the extant taxa to assess the variation within the H. erectus sample relative to that of known species, subspecies, and populations. Results of these analyses indicate that shape variation within the entire H. erectus sample is generally higher than extant hominid intraspecific variation, and putative H. ergaster specimens are significantly different from other specimens in H. erectus (sensu lato). However, shape distances within geographical groups of H. erectus are also high, and OH 9 and Dmanisi 2280 are morphologically distinct from the Koobi Fora specimens that are sometimes classified as H. ergaster. These findings suggest that, although H. erectus may be composed of multiple species, the differentiation is complex, and specimens cannot easily be grouped geographically or chronologically. Consequently, more complicated scenarios seeking to explain the observed variation within H. erectus must be considered.
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Affiliation(s)
- Claire E Terhune
- Institute of Human Origins, School of Human Evolution and Social Change, Arizona State University, Box 872402, Tempe, AZ 85287-2402, USA.
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Wilting A, Buckley-Beason VA, Feldhaar H, Gadau J, O'Brien SJ, Linsenmair KE. Clouded leopard phylogeny revisited: support for species recognition and population division between Borneo and Sumatra. Front Zool 2007; 4:15. [PMID: 17535420 PMCID: PMC1904214 DOI: 10.1186/1742-9994-4-15] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2007] [Accepted: 05/29/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The clouded leopard (Neofelis nebulosa) is one of the least known cat species and depletion of their forested habitats puts it under heavy pressure. Recently reclassification of Bornean clouded leopards (N. nebulosa diardi) to species level (N.diardi) was suggested based on molecular and morphological evidence. Since the genetic results were based solely on three Bornean samples we re-evaluated this partition using additional samples of Bornean clouded leopards (N = 7) and we were also able to include specimens from Sumatra (N = 3), which were lacking in previous analysis. RESULTS We found strong support for the distinction between N. nebulosa and N. diardi based on three fragments of mtDNA (900 bp) and 18 microsatellites. Forty-one fixed mitochondrial nucleotide differences and non-overlapping allele sizes in 8 of 18 microsatellite loci distinguished N. nebulosa and N. diardi. This is equivalent to the genetic divergence among recognized species in the genus Panthera. Sumatran clouded leopards clustered with specimens from Borneo, suggesting that Sumatran individuals also belong to N. diardi. Additionally, a significant population subdivision was apparent among N. diardi from Sumatra and Borneo based on mtDNA and microsatellite data. CONCLUSION Referring to their origin on two Sunda Islands we propose to give N. diardi the common name "Sundaland clouded leopard". The reduced gene flow between Borneo and Sumatra might suggest the recognition of two subspecies of N. diardi. Based on this reclassification of clouded leopards not only species, but also the populations on Borneo and Sumatra should be managed separately and a higher priority should be placed to protect the different populations from extinction.
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Affiliation(s)
- Andreas Wilting
- University of Würzburg, Biocentre, Department of Animal Ecology and Tropical Biology, 97074 Würzburg, Germany
| | | | - Heike Feldhaar
- University of Würzburg, Biocentre, Department of Behavioural Physiology and Sociobiology, 97074 Würzburg, Germany
| | - Jürgen Gadau
- School of Life Science, Arizona State University, Tempe, AZ 85287, USA
| | - Stephen J O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, USA
| | - K Eduard Linsenmair
- University of Würzburg, Biocentre, Department of Animal Ecology and Tropical Biology, 97074 Würzburg, Germany
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Abstract
The observation of monophyly for a specified set of genealogical lineages is often used to place the lineages into a distinctive taxonomic entity. However, it is sometimes possible that monophyly of the lineages can occur by chance as an outcome of the random branching of lineages within a single taxon. Thus, especially for small samples, an observation of monophyly for a set of lineages--even if strongly supported statistically--does not necessarily indicate that the lineages are from a distinctive group. Here I develop a test of the null hypothesis that monophyly is a chance outcome of random branching. I also compute the sample size required so that the probability of chance occurrence of monophyly of a specified set of lineages lies below a prescribed tolerance. Under the null model of random branching, the probability that monophyly of the lineages in an index group occurs by chance is substantial if the sample is highly asymmetric, that is, if only a few of the sampled lineages are from the index group, or if only a few lineages are external to the group. If sample sizes are similar inside and outside the group of interest, however, chance occurrence of monophyly can be rejected at stringent significance levels (P < 10(-5)) even for quite small samples (approximately 20 total lineages). For a fixed total sample size, rejection of the null hypothesis of random branching in a single taxon occurs at the most stringent level if samples of nearly equal size inside and outside the index group--with a slightly greater size within the index group--are used. Similar results apply, with smaller sample sizes needed, when reciprocal monophyly of two groups, rather than monophyly of a single group, is of interest. The results suggest minimal sample sizes required for inferences to be made about taxonomic distinctiveness from observations of monophyly.
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Affiliation(s)
- Noah A Rosenberg
- Department of Human Genetics, Bioinformatics Program, and the Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109-2218, USA.
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Focusing on comparative ape population genetics in the post-genomic age. Curr Opin Genet Dev 2006; 16:586-91. [DOI: 10.1016/j.gde.2006.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2006] [Accepted: 09/15/2006] [Indexed: 01/19/2023]
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