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Schiebelhut LM, Guillaume AS, Kuhn A, Schweizer RM, Armstrong EE, Beaumont MA, Byrne M, Cosart T, Hand BK, Howard L, Mussmann SM, Narum SR, Rasteiro R, Rivera-Colón AG, Saarman N, Sethuraman A, Taylor HR, Thomas GWC, Wellenreuther M, Luikart G. Genomics and conservation: Guidance from training to analyses and applications. Mol Ecol Resour 2024; 24:e13893. [PMID: 37966259 DOI: 10.1111/1755-0998.13893] [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: 06/10/2022] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023]
Abstract
Environmental change is intensifying the biodiversity crisis and threatening species across the tree of life. Conservation genomics can help inform conservation actions and slow biodiversity loss. However, more training, appropriate use of novel genomic methods and communication with managers are needed. Here, we review practical guidance to improve applied conservation genomics. We share insights aimed at ensuring effectiveness of conservation actions around three themes: (1) improving pedagogy and training in conservation genomics including for online global audiences, (2) conducting rigorous population genomic analyses properly considering theory, marker types and data interpretation and (3) facilitating communication and collaboration between managers and researchers. We aim to update students and professionals and expand their conservation toolkit with genomic principles and recent approaches for conserving and managing biodiversity. The biodiversity crisis is a global problem and, as such, requires international involvement, training, collaboration and frequent reviews of the literature and workshops as we do here.
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Affiliation(s)
- Lauren M Schiebelhut
- Life and Environmental Sciences, University of California, Merced, California, USA
| | - Annie S Guillaume
- Geospatial Molecular Epidemiology group (GEOME), Laboratory for Biological Geochemistry (LGB), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Arianna Kuhn
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
- Virginia Museum of Natural History, Martinsville, Virginia, USA
| | - Rena M Schweizer
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | | | - Mark A Beaumont
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Margaret Byrne
- Department of Biodiversity, Conservation and Attractions, Biodiversity and Conservation Science, Perth, Western Australia, Australia
| | - Ted Cosart
- Flathead Lake Biology Station, University of Montana, Missoula, Montana, USA
| | - Brian K Hand
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Leif Howard
- Flathead Lake Biology Station, University of Montana, Missoula, Montana, USA
| | - Steven M Mussmann
- Southwestern Native Aquatic Resources and Recovery Center, U.S. Fish & Wildlife Service, Dexter, New Mexico, USA
| | - Shawn R Narum
- Hagerman Genetics Lab, University of Idaho, Hagerman, Idaho, USA
| | - Rita Rasteiro
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Angel G Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Norah Saarman
- Department of Biology and Ecology Center, Utah State University, Logan, Utah, USA
| | - Arun Sethuraman
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Helen R Taylor
- Royal Zoological Society of Scotland, Edinburgh, Scotland
| | - Gregg W C Thomas
- Informatics Group, Harvard University, Cambridge, Massachusetts, USA
| | - Maren Wellenreuther
- Plant and Food Research, Nelson, New Zealand
- University of Auckland, Auckland, New Zealand
| | - Gordon Luikart
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Flathead Lake Biology Station, University of Montana, Missoula, Montana, USA
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2
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Nie WH, Wang JH, Su WT, Hu Y, He SW, Jiang XL, He K. Species identification of crested gibbons ( Nomascus) in captivity in China using karyotyping- and PCR-based approaches. Zool Res 2018; 39:356-363. [PMID: 29616678 PMCID: PMC6102682 DOI: 10.24272/j.issn.2095-8137.2018.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Gibbons and siamangs (Hylobatidae) are well-known for their rapid chromosomal evolution, which has resulted in high speciation rate within the family. On the other hand, distinct karyotypes do not prevent speciation, allowing interbreeding between individuals in captivity, and the unwanted hybrids are ethically problematic as all gibbon species are endangered or critically endangered. Thus, accurate species identification is crucial for captive breeding, particularly in China where studbooks are unavailable. Identification based on external morphology is difficult, especially for hybrids, because species are usually similar in appearance. In this study, we employed G-banding karyotyping and fluorescence in situ hybridization (FISH) as well as a PCR-based approach to examine karyotypic characteristics and identify crested gibbons of the genus Nomascus from zoos and nature reserves in China. We characterized and identified five karyotypes from 21 individuals of Nomascus. Using karyotypes and mitochondrial and nuclear genes, we identified three purebred species and three hybrids, including one F2 hybrid between N. gabriellae and N. siki. Our results also supported that N. leucogenys and N. siki shared the same inversion on chromosome 7, which resolves arguments from previous studies. Our results demonstrated that both karyotyping and DNA-based approaches were suitable for identifying purebred species, though neither was ideal for hybrid identification. The advantages and disadvantages of both approaches are discussed. Our results further highlight the importance of animal ethics and welfare, which are critical for endangered species in captivity.
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Affiliation(s)
- Wen-Hui Nie
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; E-mail:
| | - Jin-Huan Wang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Wei-Ting Su
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Yu Hu
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Shui-Wang He
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Xue-Long Jiang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; E-mail:
| | - Kai He
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; E-mail:.,Kyoto University Museum, Kyoto University, Kyoto 606-8417, Japan
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3
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Lazar NH, Nevonen KA, O'Connell B, McCann C, O'Neill RJ, Green RE, Meyer TJ, Okhovat M, Carbone L. Epigenetic maintenance of topological domains in the highly rearranged gibbon genome. Genome Res 2018; 28:983-997. [PMID: 29914971 PMCID: PMC6028127 DOI: 10.1101/gr.233874.117] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 06/01/2018] [Indexed: 12/27/2022]
Abstract
The relationship between evolutionary genome remodeling and the three-dimensional structure of the genome remain largely unexplored. Here, we use the heavily rearranged gibbon genome to examine how evolutionary chromosomal rearrangements impact genome-wide chromatin interactions, topologically associating domains (TADs), and their epigenetic landscape. We use high-resolution maps of gibbon–human breaks of synteny (BOS), apply Hi-C in gibbon, measure an array of epigenetic features, and perform cross-species comparisons. We find that gibbon rearrangements occur at TAD boundaries, independent of the parameters used to identify TADs. This overlap is supported by a remarkable genetic and epigenetic similarity between BOS and TAD boundaries, namely presence of CpG islands and SINE elements, and enrichment in CTCF and H3K4me3 binding. Cross-species comparisons reveal that regions orthologous to BOS also correspond with boundaries of large (400–600 kb) TADs in human and other mammalian species. The colocalization of rearrangement breakpoints and TAD boundaries may be due to higher chromatin fragility at these locations and/or increased selective pressure against rearrangements that disrupt TAD integrity. We also examine the small portion of BOS that did not overlap with TAD boundaries and gave rise to novel TADs in the gibbon genome. We postulate that these new TADs generally lack deleterious consequences. Last, we show that limited epigenetic homogenization occurs across breakpoints, irrespective of their time of occurrence in the gibbon lineage. Overall, our findings demonstrate remarkable conservation of chromatin interactions and epigenetic landscape in gibbons, in spite of extensive genomic shuffling.
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Affiliation(s)
- Nathan H Lazar
- Bioinformatics and Computational Biology Division, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Kimberly A Nevonen
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Brendan O'Connell
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Christine McCann
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269, USA.,Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Rachel J O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269, USA.,Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Thomas J Meyer
- Bioinformatics and Computational Biology Division, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Mariam Okhovat
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Lucia Carbone
- Bioinformatics and Computational Biology Division, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon 97239, USA.,Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA.,Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA.,Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
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4
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The gastrointestinal tract microbiota of northern white-cheeked gibbons (Nomascus leucogenys) varies with age and captive condition. Sci Rep 2018; 8:3214. [PMID: 29453448 PMCID: PMC5816653 DOI: 10.1038/s41598-018-21117-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/30/2018] [Indexed: 02/08/2023] Open
Abstract
Nutrition and health of northern white-cheeked gibbons (Nomascus leucogenys) are considered to be primarily influenced by the diversity of their gastrointestinal tract (GIT) microbiota. However, the precise composition, structure, and role of the gibbon GIT microbiota remain unclear. Microbial communities from the GITs of gibbons from Nanning (NN, n = 36) and Beijing (BJ, n = 20) Zoos were examined through 16S rRNA sequencing. Gibbon’s GITs microbiomes contained bacteria from 30 phyla, dominated by human-associated microbial signatures: Firmicutes, Bacteroidetes, and Proteobacteria. Microbial species richness was markedly different between adult gibbons (>8 years) under distinct captive conditions. The relative abundance of 14 phyla varied significantly in samples of adults in BJ versus NN. Among the age groups examined in NN, microbiota of adult gibbons had greater species variation and richer community diversity than microbiota of nursing young (<6 months) and juveniles (2–5 years). Age-dependent increases in the relative abundances of Firmicutes and Fibrobacteres were detected, along with simultaneous increases in dietary fiber intake. A few differences were detected between sex cohorts in NN, suggesting a very weak correlation between sex and GIT microbiota. This study is the first to taxonomically identify gibbon’s GITs microbiota confirming that microbiota composition varies with age and captive condition.
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5
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Baicharoen S, Miyabe-Nishiwaki T, Arsaithamkul V, Hirai Y, Duangsa-ard K, Siriaroonrat B, Domae H, Srikulnath K, Koga A, Hirai H. Locational diversity of alpha satellite DNA and intergeneric hybridization aspects in the Nomascus and Hylobates genera of small apes. PLoS One 2014; 9:e109151. [PMID: 25290445 PMCID: PMC4188616 DOI: 10.1371/journal.pone.0109151] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 08/29/2014] [Indexed: 01/05/2023] Open
Abstract
Recently, we discovered that alpha satellite DNA has unique and genus-specific localizations on the chromosomes of small apes. This study describes the details of alpha satellite localization in the genera Nomascus and Hylobates and explores their usefulness in distinguishing parental genome sets in hybrids between these genera. Fluorescence in situ hybridization was used to establish diagnostic criteria of alpha satellite DNA markers in discriminating small ape genomes. In particular we established the genus specificity of alpha satellite distribution in three species of light-cheeked gibbons (Nomascus leucogenys, N. siki, and N. gabriellae) in comparison to that of Hylobates lar. Then we determined the localization of alpha satellite DNA in a hybrid individual which resulted from a cross between these two genera. In Nomascus the alpha satellite DNA blocks were located at the centromere, telomere, and four interstitial regions. In Hylobates detectable amounts of alpha satellite DNA were seen only at centromeric regions. The differences in alpha satellite DNA locations between Nomascus and Hylobates allowed us to easily distinguish the parental chromosomal sets in the genome of intergeneric hybrid individuals found in Thai and Japanese zoos. Our study illustrates how molecular cytogenetic markers can serve as diagnostic tools to identify the origin of individuals. These molecular tools can aid zoos, captive breeding programs and conservation efforts in managing small apes species. Discovering more information on alpha satellite distribution is also an opportunity to examine phylogenetic and evolutionary questions that are still controversial in small apes.
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Affiliation(s)
- Sudarath Baicharoen
- Bioscience Program, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Bangkok, Thailand
- Conservation, Research and Education Division, Zoological Park Organization, Bangkok, Thailand
| | | | - Visit Arsaithamkul
- Conservation, Research and Education Division, Zoological Park Organization, Bangkok, Thailand
| | - Yuriko Hirai
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | | | - Boripat Siriaroonrat
- Conservation, Research and Education Division, Zoological Park Organization, Bangkok, Thailand
| | | | - Kornsorn Srikulnath
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Bangkok, Thailand
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Akihiko Koga
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Hirohisa Hirai
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
- * E-mail:
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6
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Jahan I, Hirai Y, Rahman ZMM, Islam MA, Hirai H. The first finding of chromosome variations in wild-born western hoolock gibbons. Primates 2013; 54:335-40. [DOI: 10.1007/s10329-013-0382-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 08/02/2013] [Indexed: 12/23/2022]
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7
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Kim SK, Carbone L, Becquet C, Mootnick AR, Li DJ, de Jong PJ, Wall JD. Patterns of genetic variation within and between Gibbon species. Mol Biol Evol 2011; 28:2211-8. [PMID: 21368318 PMCID: PMC3144381 DOI: 10.1093/molbev/msr033] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Gibbons are small, arboreal, highly endangered apes that are understudied compared with other hominoids. At present, there are four recognized genera and approximately 17 species, all likely to have diverged from each other within the last 5-6 My. Although the gibbon phylogeny has been investigated using various approaches (i.e., vocalization, morphology, mitochondrial DNA, karyotype, etc.), the precise taxonomic relationships are still highly debated. Here, we present the first survey of nuclear sequence variation within and between gibbon species with the goal of estimating basic population genetic parameters. We gathered ~60 kb of sequence data from a panel of 19 gibbons representing nine species and all four genera. We observe high levels of nucleotide diversity within species, indicative of large historical population sizes. In addition, we find low levels of genetic differentiation between species within a genus comparable to what has been estimated for human populations. This is likely due to ongoing or episodic gene flow between species, and we estimate a migration rate between Nomascus leucogenys and N. gabriellae of roughly one migrant every two generations. Together, our findings suggest that gibbons have had a complex demographic history involving hybridization or mixing between diverged populations.
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Affiliation(s)
- Sung K Kim
- Institute for Human Genetics, University of California San Francisco, CA, USA
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8
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Mootnick AR, Fan PF. A comparative study of crested gibbons (Nomascus). Am J Primatol 2010; 73:135-54. [DOI: 10.1002/ajp.20880] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 07/29/2010] [Accepted: 07/29/2010] [Indexed: 11/11/2022]
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9
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Thinh VN, Mootnick AR, Geissmann T, Li M, Ziegler T, Agil M, Moisson P, Nadler T, Walter L, Roos C. Mitochondrial evidence for multiple radiations in the evolutionary history of small apes. BMC Evol Biol 2010; 10:74. [PMID: 20226039 PMCID: PMC2841658 DOI: 10.1186/1471-2148-10-74] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 03/12/2010] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Gibbons or small apes inhabit tropical and subtropical rain forests in Southeast Asia and adjacent regions, and are, next to great apes, our closest living relatives. With up to 16 species, gibbons form the most diverse group of living hominoids, but the number of taxa, their phylogenetic relationships and their phylogeography is controversial. To further the discussion of these issues we analyzed the complete mitochondrial cytochrome b gene from 85 individuals representing all gibbon species, including most subspecies. RESULTS Based on phylogenetic tree reconstructions, several monophyletic clades were detected, corresponding to genera, species and subspecies. A significantly supported branching pattern was obtained for members of the genus Nomascus but not for the genus Hylobates. The phylogenetic relationships among the four genera were also not well resolved. Nevertheless, the new data permitted the estimation of divergence ages for all taxa for the first time and showed that most lineages emerged during four short time periods. In the first, between approximately 6.7 and approximately 8.3 mya, the four gibbon genera diverged from each other. In the second (approximately 3.0 - approximately 3.9 mya) and in the third period (approximately 1.3 - approximately 1.8 mya), Hylobates and Hoolock differentiated. Finally, between approximately 0.5 and approximately 1.1 mya, Hylobates lar diverged into subspecies. In contrast, differentiation of Nomascus into species and subspecies was a continuous and prolonged process lasting from approximately 4.2 until approximately 0.4 mya. CONCLUSIONS Although relationships among gibbon taxa on various levels remain unresolved, the present study provides a more complete view of the evolutionary and biogeographic history of the hylobatid family, and a more solid genetic basis for the taxonomic classification of the surviving taxa. We also show that mtDNA constitutes a useful marker for the accurate identification of individual gibbons, a tool which is urgently required to locate hunting hotspots and select individuals for captive breeding programs. Further studies including nuclear sequence data are necessary to completely understand the phylogeny and phylogeography of gibbons.
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Affiliation(s)
- Van Ngoc Thinh
- Primate Genetics Laboratory, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | - Alan R Mootnick
- Gibbon Conservation Center, PO Box 800249, Santa Clarita, CA 91380, USA
| | - Thomas Geissmann
- Anthropological Institute, University Zurich-Irchel, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Ming Li
- Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, PR China
| | - Thomas Ziegler
- Siberut Conservation Programme, Reproductive Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | - Muhammad Agil
- Department of Clinic, Reproduction and Pathology, Faculty of Veterinary Medicine, Bogor Agricultural University, Jl. Agatis, Kampus IPB Darmaga, 16680 Bogor, Indonesia
| | - Pierre Moisson
- Parc Zoologique et Botanique de Mulhouse, 51, rue du Jardin Zoologique, 68100 Mulhouse, France
| | - Tilo Nadler
- Frankfurt Zoological Society, Endangered Primate Rescue Center, Cuc Phuong National Park, Nho Quan District, Ninh Binh Province, Vietnam
| | - Lutz Walter
- Primate Genetics Laboratory, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
- Gene Bank of Primates, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
- Gene Bank of Primates, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
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Abi-Rached L, Kuhl H, Roos C, ten Hallers B, Zhu B, Carbone L, de Jong PJ, Mootnick AR, Knaust F, Reinhardt R, Parham P, Walter L. A small, variable, and irregular killer cell Ig-like receptor locus accompanies the absence of MHC-C and MHC-G in gibbons. THE JOURNAL OF IMMUNOLOGY 2009; 184:1379-91. [PMID: 20026738 DOI: 10.4049/jimmunol.0903016] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The killer cell Ig-like receptors (KIRs) of NK cells recognize MHC class I ligands and function in placental reproduction and immune defense against pathogens. During the evolution of monkeys, great apes, and humans, an ancestral KIR3DL gene expanded to become a diverse and rapidly evolving gene family of four KIR lineages. Characterizing the KIR locus are three framework regions, defining two intervals of variable gene content. By analysis of four KIR haplotypes from two species of gibbon, we find that the smaller apes do not conform to these rules. Although diverse and irregular in structure, the gibbon haplotypes are unusually small, containing only two to five functional genes. Comparison with the predicted ancestral hominoid KIR haplotype indicates that modern gibbon KIR haplotypes were formed by a series of deletion events, which created new hybrid genes as well as eliminating ancestral genes. Of the three framework regions, only KIR3DL3 (lineage V), defining the 5' end of the KIR locus, is present and intact on all gibbon KIR haplotypes. KIR2DL4 (lineage I) defining the central framework region has been a major target for elimination or inactivation, correlating with the absence of its putative ligand, MHC-G, in gibbons. Similarly, the MHC-C-driven expansion of lineage III KIR genes in great apes has not occurred in gibbons because they lack MHC-C. Our results indicate that the selective forces shaping the size and organization of the gibbon KIR locus differed from those acting upon the KIR of other hominoid species.
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Affiliation(s)
- Laurent Abi-Rached
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
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