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Wall JD, Kim SK, Luca F, Carbone L, Mootnick AR, de Jong PJ, Di Rienzo A. Incomplete lineage sorting is common in extant gibbon genera. PLoS One 2013; 8:e53682. [PMID: 23341974 PMCID: PMC3544895 DOI: 10.1371/journal.pone.0053682] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 12/04/2012] [Indexed: 11/25/2022] Open
Abstract
We sequenced reduced representation libraries by means of Illumina technology to generate over 1.5 Mb of orthologous sequence from a representative of each of the four extant gibbon genera (Nomascus, Hylobates, Symphalangus, and Hoolock). We used these data to assess the evolutionary relationships between the genera by evaluating the likelihoods of all possible bifurcating trees involving the four taxa. Our analyses provide weak support for a tree with Nomascus and Hylobates as sister taxa and with Hoolock and Symphalangus as sister taxa, though bootstrap resampling suggests that other phylogenetic scenarios are also possible. This uncertainty is due to short internal branch lengths and extensive incomplete lineage sorting across taxa. The true phylogenetic relationships among gibbon genera will likely require a more extensive whole-genome sequence analysis.
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Affiliation(s)
- Jeffrey D Wall
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America.
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Mootnick AR, Cunningham C, Baker E. Phylogenetic separation in limb use in captive gibbons (Hylobatidae): a comparison across the primate order. Am J Primatol 2012; 74:1035-43. [PMID: 22847649 DOI: 10.1002/ajp.22057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 06/14/2012] [Accepted: 06/26/2012] [Indexed: 11/07/2022]
Abstract
Although there have been few studies of self-scratching in primates, some have reported distinct differences in whether hands or feet are used, and these variations seem to reflect the evolutionary history of the Order. Monkeys and prosimians use both hands and feet to self-scratch while African great apes use hands almost exclusively. Gibbons represent an evolutionary divergence between monkeys and great apes and incidental observations at the Gibbon Conservation Center pointed to a difference in self-scratching among the four extant gibbon genera (Hoolock, Nomascus, Symphalangus, and Hylobates). To validate and further explore these preliminary observations, we collected systematic data on self-scratching from 32 gibbons, including nine species and all four genera. To supplement gibbon data, we also collected self-scratching information from 18 great apes (four species), five prosimians (two species), 26 New World Monkeys (nine species) and 20 Old World Monkeys (seven species). All monkeys and some prosimians used both hands and feet to self-scratch, whereas one prosimian species used only feet. All African great apes used hands exclusively (orangutans were an exception displaying occasional foot-use). This appears to represent a fundamental difference between monkeys and great apes in limb use. Interestingly, there was a clear difference in self-scratching between the four gibbon genera. Hylobates and Symphalangus self-scratched only with hands (like all African great apes), while Hoolock and Nomascus self-scratched with both hands and feet (like monkeys and prosimians). This difference in gibbon behavior may reflect the evolutionary history of gibbons as Hoolock and Nomascus are thought to have evolved before both Hylobates and Symphalangus. What evolutionary pressures led to this divergent pattern is currently opaque; however, this shift in limb preference may result from niche separation across the order facilitating differences in the behavioral repertoire associated with hind and forelimbs.
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Meyer TJ, McLain AT, Oldenburg JM, Faulk C, Bourgeois MG, Conlin EM, Mootnick AR, de Jong PJ, Roos C, Carbone L, Batzer MA. An Alu-based phylogeny of gibbons (hylobatidae). Mol Biol Evol 2012; 29:3441-50. [PMID: 22683814 DOI: 10.1093/molbev/mss149] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Gibbons (Hylobatidae) are small, arboreal apes indigenous to Southeast Asia that diverged from other apes ∼15-18 Ma. Extant lineages radiated rapidly 6-10 Ma and are organized into four genera (Hylobates, Hoolock, Symphalangus, and Nomascus) consisting of 12-19 species. The use of short interspersed elements (SINEs) as phylogenetic markers has seen recent popularity due to several desirable characteristics: the ancestral state of a locus is known to be the absence of an element, rare potentially homoplasious events are relatively easy to resolve, and samples can be quickly and inexpensively genotyped. During radiation of primates, one particular family of SINEs, the Alu family, has proliferated in primate genomes. Nomascus leucogenys (northern white-cheeked gibbon) sequences were analyzed for repetitive content with RepeatMasker using a custom library. The sequences containing Alu elements identified as members of a gibbon-specific subfamily were then compared with orthologous positions in other primate genomes. A primate phylogenetic panel consisting of 18 primate species, including 13 gibbon species representing all four extant genera, was assayed for all loci, and a total of 125 gibbon-specific Alu insertions were identified. The resulting amplification patterns were used to generate a phylogenetic tree. We demonstrate significant support for Symphalangus as the most basal lineage within the family. Our findings also place Nomascus as a derived lineage, sister to Hoolock, with the Nomascus-Hoolock clade sister to Hylobates. Further, our analysis groups N. leucogenys and Nomascus siki as sister taxa to the exclusion of the other Nomascus species assayed. This study represents the first use of SINEs to determine the genus level phylogenetic relationships within the family Hylobatidae. These relationships have been resolved with robust support at most internal nodes, demonstrating the utility of SINE-based phylogenetic analysis. We postulate that hybridization and rapid radiation may have contributed to the complex and contradictory findings of the previous studies. Our findings will aid in the conservation of these threatened primates and inform future studies of the biogeographical history and distribution of modern gibbon species.
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Affiliation(s)
- Thomas J Meyer
- Department of Biological Sciences, Louisiana State University
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Carbone L, Harris RA, Mootnick AR, Milosavljevic A, Martin DIK, Rocchi M, Capozzi O, Archidiacono N, Konkel MK, Walker JA, Batzer MA, de Jong PJ. Centromere remodeling in Hoolock leuconedys (Hylobatidae) by a new transposable element unique to the gibbons. Genome Biol Evol 2012; 4:648-58. [PMID: 22593550 PMCID: PMC3606032 DOI: 10.1093/gbe/evs048] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Gibbons (Hylobatidae) shared a common ancestor with the other hominoids only 15–18 million years ago. Nevertheless, gibbons show very distinctive features that include heavily rearranged chromosomes. Previous observations indicate that this phenomenon may be linked to the attenuated epigenetic repression of transposable elements (TEs) in gibbon species. Here we describe the massive expansion of a repeat in almost all the centromeres of the eastern hoolock gibbon (Hoolock leuconedys). We discovered that this repeat is a new composite TE originating from the combination of portions of three other elements (L1ME5, AluSz6, and SVA_A) and thus named it LAVA. We determined that this repeat is found in all the gibbons but does not occur in other hominoids. Detailed investigation of 46 different LAVA elements revealed that the majority of them have target site duplications (TSDs) and a poly-A tail, suggesting that they have been retrotransposing in the gibbon genome. Although we did not find a direct correlation between the emergence of LAVA elements and human–gibbon synteny breakpoints, this new composite transposable element is another mark of the great plasticity of the gibbon genome. Moreover, the centromeric expansion of LAVA insertions in the hoolock closely resembles the massive centromeric expansion of the KERV-1 retroelement reported for wallaby (marsupial) interspecific hybrids. The similarity between the two phenomena is consistent with the hypothesis that evolution of the gibbons is characterized by defects in epigenetic repression of TEs, perhaps triggered by interspecific hybridization.
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Affiliation(s)
- Lucia Carbone
- Children's Hospital Oakland Research Institute, Oakland, CA, USA.
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5
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Abstract
Compared with the great apes, the small-bodied hylobatids were treated historically as a relatively uniform group with 2 genera, Hylobates and the larger-bodied Symphalangus. Four genera are now recognized, each with a different chromosome number: Hoolock (hoolock) (38), Hylobates (44), Nomascus (crested gibbon) (52), and Symphalangus (siamang) (50). Previous morphological studies based on relative bone lengths, e.g., intermembral indices; molar tooth sizes; and body masses did not distinguish the 4 genera from each other. We applied quantitative anatomical methods to test the hypothesis that each genus can be differentiated from the others using the relative distribution of body mass to the forelimbs and hind limbs. Based on dissections of 13 hylobatids from captive facilities, our findings demonstrate that each of the 4 genera has a distinct pattern of body mass distribution. For example, the adult Hoolock has limb proportions of nearly equal mass, a pattern that differentiates it from species in the genus Hylobates, e.g., H. lar (lar gibbon), H. moloch (Javan gibbon), H. pileatus (pileated gibbon), Nomascus, and Symphalangus. Hylobates is distinct in having heavy hind limbs. Although Symphalangus has been treated as a scaled up version of Hylobates, its forelimb exceeds its hind limb mass, an unusual primate pattern otherwise found only in orangutans. This research provides new information on whole body anatomy and adds to the genetic, ecological, and behavioral evidence for clarifying the taxonomy of the hylobatids. The research also underscores the important contribution of studies on rare species in captivity.
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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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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. J Immunol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Carbone L, Harris RA, Vessere GM, Mootnick AR, Humphray S, Rogers J, Kim SK, Wall JD, Martin D, Jurka J, Milosavljevic A, de Jong PJ. Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution. PLoS Genet 2009; 5:e1000538. [PMID: 19557196 PMCID: PMC2695003 DOI: 10.1371/journal.pgen.1000538] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Accepted: 05/26/2009] [Indexed: 01/30/2023] Open
Abstract
Gibbon species have accumulated an unusually high number of chromosomal changes since diverging from the common hominoid ancestor 15-18 million years ago. The cause of this increased rate of chromosomal rearrangements is not known, nor is it known if genome architecture has a role. To address this question, we analyzed sequences spanning 57 breaks of synteny between northern white-cheeked gibbons (Nomascus l. leucogenys) and humans. We find that the breakpoint regions are enriched in segmental duplications and repeats, with Alu elements being the most abundant. Alus located near the gibbon breakpoints (<150 bp) have a higher CpG content than other Alus. Bisulphite allelic sequencing reveals that these gibbon Alus have a lower average density of methylated cytosine that their human orthologues. The finding of higher CpG content and lower average CpG methylation suggests that the gibbon Alu elements are epigenetically distinct from their human orthologues. The association between undermethylation and chromosomal rearrangement in gibbons suggests a correlation between epigenetic state and structural genome variation in evolution.
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Affiliation(s)
- Lucia Carbone
- Children's Hospital and Research Center Oakland, Oakland, California, United States of America.
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Carbone L, Mootnick AR, Nadler T, Moisson P, Ryder O, Roos C, de Jong PJ. A chromosomal inversion unique to the northern white-cheeked gibbon. PLoS One 2009; 4:e4999. [PMID: 19319194 PMCID: PMC2656618 DOI: 10.1371/journal.pone.0004999] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Accepted: 02/16/2009] [Indexed: 01/03/2023] Open
Abstract
The gibbon family belongs to the superfamily Hominoidea and includes 15 species divided into four genera. Each genus possesses a distinct karyotype with chromosome numbers varying from 38 to 52. This diversity is the result of numerous chromosomal changes that have accumulated during the evolution of the gibbon lineage, a quite unique feature in comparison with other hominoids and most of the other primates. Some gibbon species and subspecies rank among the most endangered primates in the world. Breeding programs can be extremely challenging and hybridization plays an important role within the factors responsible for the decline of captive gibbons. With less than 500 individuals left in the wild, the northern white-cheeked gibbon (Nomascus leucogenys leucogenys, NLE) is the most endangered primate in a successful captive breeding program. We present here the analysis of an inversion that we show being specific for the northern white-cheeked gibbon and can be used as one of the criteria to distinguish this subspecies from other gibbon taxa. The availability of the sequence spanning for one of the breakpoints of the inversion allows detecting it by a simple PCR test also on low quality DNA. Our results demonstrate the important role of genomics in providing tools for conservation efforts.
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Affiliation(s)
- Lucia Carbone
- BACPAC Resources, Children's Hospital of Oakland Research Institute, Oakland, California, United States of America.
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13
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Baena A, Mootnick AR, Falvo JV, Tsytsykova AV, Ligeiro F, Diop OM, Brieva C, Gagneux P, O'Brien SJ, Ryder OA, Goldfeld AE. Primate TNF promoters reveal markers of phylogeny and evolution of innate immunity. PLoS One 2007; 2:e621. [PMID: 17637837 PMCID: PMC1905939 DOI: 10.1371/journal.pone.0000621] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Accepted: 06/12/2007] [Indexed: 11/18/2022] Open
Abstract
Background Tumor necrosis factor (TNF) is a critical cytokine in the immune response whose transcriptional activation is controlled by a proximal promoter region that is highly conserved in mammals and, in particular, primates. Specific single nucleotide polymorphisms (SNPs) upstream of the proximal human TNF promoter have been identified, which are markers of human ancestry. Methodology/Principal findings Using a comparative genomics approach we show that certain fixed genetic differences in the TNF promoter serve as markers of primate speciation. We also demonstrate that distinct alleles of most human TNF promoter SNPs are identical to fixed nucleotides in primate TNF promoters. Furthermore, we identify fixed genetic differences within the proximal TNF promoters of Asian apes that do not occur in African ape or human TNF promoters. Strikingly, protein-DNA binding assays and gene reporter assays comparing these Asian ape TNF promoters to African ape and human TNF promoters demonstrate that, unlike the fixed differences that we define that are associated with primate phylogeny, these Asian ape-specific fixed differences impair transcription factor binding at an Sp1 site and decrease TNF transcription induced by bacterial stimulation of macrophages. Conclusions/significance Here, we have presented the broadest interspecies comparison of a regulatory region of an innate immune response gene to date. We have characterized nucleotide positions in Asian ape TNF promoters that underlie functional changes in cell type- and stimulus-specific activation of the TNF gene. We have also identified ancestral TNF promoter nucleotide states in the primate lineage that correspond to human SNP alleles. These findings may reflect evolution of Asian and African apes under a distinct set of infectious disease pressures involving the innate immune response and TNF.
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Affiliation(s)
- Andres Baena
- The CBR Institute for Biomedical Research, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alan R. Mootnick
- Gibbon Conservation Center, Santa Clarita, California, United States of America
| | - James V. Falvo
- The CBR Institute for Biomedical Research, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alla V. Tsytsykova
- The CBR Institute for Biomedical Research, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Filipa Ligeiro
- The CBR Institute for Biomedical Research, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ousmane M. Diop
- Laboratoire de Rétrovirologie, Institut Pasteur, Dakar, Senegal
| | - Claudia Brieva
- Unidad de Rescate y Rehabilitación de Animales Silvestres, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Pascal Gagneux
- Project for Explaining the Origin of Humans, Glycobiology Research and Training Center, Department of Medicine and Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California, United States of America
| | - Stephen J. O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, United States of America
| | - Oliver A. Ryder
- Conservation and Research for Endangered Species, Zoological Society of San Diego, San Diego, California, United States of America
- Division of Biological Sciences, University of California at San Diego, La Jolla, California, United States of America
| | - Anne E. Goldfeld
- The CBR Institute for Biomedical Research, Harvard Medical School, Boston, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
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14
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Roberto R, Capozzi O, Wilson RK, Mardis ER, Lomiento M, Tuzun E, Cheng Z, Mootnick AR, Archidiacono N, Rocchi M, Eichler EE. Molecular refinement of gibbon genome rearrangements. Genome Res 2006; 17:249-57. [PMID: 17185643 PMCID: PMC1781357 DOI: 10.1101/gr.6052507] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The gibbon karyotype is known to be extensively rearranged when compared to the human and to the ancestral primate karyotype. By combining a bioinformatics (paired-end sequence analysis) approach and a molecular cytogenetics approach, we have refined the synteny block arrangement of the white-cheeked gibbon (Nomascus leucogenys, NLE) with respect to the human genome. We provide the first detailed clone framework map of the gibbon genome and refine the location of 86 evolutionary breakpoints to <1 Mb resolution. An additional 12 breakpoints, mapping primarily to centromeric and telomeric regions, were mapped to approximately 5 Mb resolution. Our combined FISH and BES analysis indicates that we have effectively subcloned 49 of these breakpoints within NLE gibbon BAC clones, mapped to a median resolution of 79.7 kb. Interestingly, many of the intervals associated with translocations were gene-rich, including some genes associated with normal skeletal development. Comparisons of NLE breakpoints with those of other gibbon species reveal variability in the position, suggesting that chromosomal rearrangement has been a longstanding property of this particular ape lineage. Our data emphasize the synergistic effect of combining computational genomics and cytogenetics and provide a framework for ultimate sequence and assembly of the gibbon genome.
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Affiliation(s)
- Roberta Roberto
- Department of Genetics and Microbiology, University of Bari, 70126 Bari, Italy
| | - Oronzo Capozzi
- Department of Genetics and Microbiology, University of Bari, 70126 Bari, Italy
| | - Richard K. Wilson
- Washington University Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Elaine R. Mardis
- Washington University Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Mariana Lomiento
- Department of Genetics and Microbiology, University of Bari, 70126 Bari, Italy
| | - Eray Tuzun
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Ze Cheng
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Alan R. Mootnick
- Gibbon Conservation Center, Santa Clarita, California 91380, USA
| | | | - Mariano Rocchi
- Department of Genetics and Microbiology, University of Bari, 70126 Bari, Italy
- Corresponding authors.E-mail ; fax 39-080-544-3386.E-mail ; fax (206) 221-5795
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
- Howard Hughes Medical Institute, Seattle, Washington 98195, USA
- Corresponding authors.E-mail ; fax 39-080-544-3386.E-mail ; fax (206) 221-5795
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Hirai H, Wijayanto H, Tanaka H, Mootnick AR, Hayano A, Perwitasari-Farajallah D, Iskandriati D, Sajuthi D. A whole-arm translocation (WAT8/9) separating Sumatran and Bornean agile gibbons, and its evolutionary features. Chromosome Res 2005; 13:123-33. [PMID: 15861302 DOI: 10.1007/s10577-005-7475-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2004] [Revised: 11/01/2004] [Accepted: 11/28/2004] [Indexed: 11/25/2022]
Abstract
Gibbons, like orangutans, are a group of threatened Asian apes, so that genetic monitoring of each species or subspecies is a pressing need for conservation programmes. We conducted a project to take, as far as possible, samples of known origin from wild-born animals from Sumatra and Borneo (Central Kalimantan) for genetic monitoring of agile gibbons. As a result, we found a whole arm translocation between chromosomes 8 and 9 (WAT8/9) specific to Sumatran agile gibbons. Furthermore, population surveys suggested that the form with the WAT8/9 seems to be incompatible with an ancestral form, suggesting that the former might have extinguished the latter from Sumatran populations by competition. In any case, this translocation is a useful chromosomal marker for identifying Sumatran agile gibbons. Population genetic analyses with DNA showed that the molecular genetic distance between Sumatran and Bornean agile gibbons is the smallest, although the chromosomal difference is the largest. Thus, it is postulated that WAT8/9 occurred and fixed in a small population of Sumatra after migration and geographical isolation at the last glacial period, and afterwards dispersed rapidly to other populations in Sumatra as a result of the bottleneck effect and a chromosomal isolating mechanism.
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Affiliation(s)
- Hirohisa Hirai
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan.
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Hirai H, Mootnick AR, Takenaka O, Suryobroto B, Mouri T, Kamanaka Y, Katoh A, Kimura N, Katoh A, Maeda N. Genetic mechanism and property of a whole-arm translocation (WAT) between chromosomes 8 and 9 of agile gibbons (Hylobates agilis). Chromosome Res 2003; 11:37-50. [PMID: 12675304 DOI: 10.1023/a:1022006015379] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
C-banding analysis with 47 gibbons of the subgenus Hylobates (Hylobates) (44-chromosome gibbons) uncovered that the gibbons had a characteristic complicated C-banding pattern. The C-band pattern also revealed that a whole-arm translocation (WAT) between chromosomes 8 and 9 existed only in the species H. agilis (agile gibbon). Comprehensive consideration allows postulation that the translocation seemed to be restricted to two subspecies: H. agilis agilis (mountain agile gibbon) and H. agilis unko (lowland agile gibbon), found in Sumatra and part of the Malay Peninsula. Moreover, combined intensive analyses of C-banding and chromosome painting provided strong evidence for a plausible evolutionary pathway of chromosome differentiation of chromosomes 8 and 9. The C-banded morph 8M(t/c) seemed to be the primary type of chromosome 8 in the subgenus and to have altered into the three morphs through three pericentric inversions. The newest morph (8A(M/ci)) produced by the third inversion exchanged the long arm for chromosome 9, and subsequently constructed the WAT morphs of 8/9A(Mc/ct) and 9/8M(i/ci).
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Affiliation(s)
- Hirohisa Hirai
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan.
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Van Tuinen P, Mootnick AR, Kingswood SC, Hale DW, Kumamoto AT. Complex, compound inversion/translocation polymorphism in an ape: presumptive intermediate stage in the karyotypic evolution of the agile gibbon Hylobates agilis. Am J Phys Anthropol 1999; 110:129-42. [PMID: 10502239 DOI: 10.1002/(sici)1096-8644(199910)110:2<129::aid-ajpa2>3.0.co;2-m] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Karyotypic variation in five gibbon species of the subgenus Hylobates (2n = 44) was assessed in 63 animals, 23 of them wild born. Acquisition of key specimens of Hylobates agilis (agile gibbon), whose karyotype had been problematic due to unresolved structural polymorphisms, led to disclosure of a compound inversion/translocation polymorphism. A polymorphic region of chromosome 8 harboring two pericentric inversions, one nested within the other, was in turn bissected by one breakpoint of a reciprocal translocation. In double-inversion + translocation heterozygotes, the theoretical meiotic pairing configuration is a double inversion loop, with four arms of a translocation quadrivalent radiating from the loop. Electron-microscopic analysis of synaptonemal complex configurations consistently revealed translocation quadrivalents but no inversion loops. Rather, nonhomologous pairing was evident in the inverted region, a condition that should preclude crossing over and the subsequent production of duplication-deficiency gametes. This is corroborated by the existence of normal offspring of compound heterozygotes, indicating that fertility may not be reduced despite the topological complexity of this polymorphic system. The distribution of inversion and translocation morphs in these taxa suggests application of cytogenetics in identifying gibbon specimens and avoiding undesirable hybridization in captive breeding efforts.
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Affiliation(s)
- P Van Tuinen
- Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA.
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Mootnick AR, Ostrowski SR. Procedures utilized for primate import quarantine at the International Center for Gibbon Studies. J Zoo Wildl Med 1999; 30:201-7. [PMID: 10484134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023] Open
Abstract
The intent of the Foreign Quarantine requirements (42 CFR 71.53) for nonhuman primates (NHPs) is to prevent the importation of potentially serious infectious diseases that are not endemic to the United States. In 1990, prompted by an outbreak of Ebola (Reston) hemorrhagic fever at an (NHP) quarantine facility, the Centers for Disease Control and Prevention (CDC) initiated unannounced inspections of all NHP importers' quarantine facilities. During the inspections, the majority did not meet the required infection control and containment standards. Numerous discrepancies were identified in infection control and NHP quarantine protocols. Zoos should have knowledge of CDC requirements and recommendations for the importation of NHPs into the United States. Zoos planning to import NHPs should register with the CDC and have their NHP quarantine facility and protocols inspected and approved by CDC's Division of Quarantine. Specific areas addressed must include protocols for in-transit shipping and handling, transport to the quarantine facility, biocontainment procedures (transfer of NHPs from shipping containers to quarantine cages, entering/exiting the quarantine room, routine daily and emergency procedures, protective clothing, infection control, infectious waste disposal), occupational health, and employee training. Here, we provide information on the approved protocols used for import quarantine at a single registered importer facility specializing in importation of gibbons (Hylobatidae) for species conservation purposes. These procedures are site specific and are not intended to be applicable to the needs of all NHP import facilities.
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Affiliation(s)
- A R Mootnick
- International Center for Gibbon Studies, Santa Clarita, California 91380, USA
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Mootnick AR, Reingold M, Holshuh HJ, Mirkovic RR. Isolation of a herpes simplex virus type 1-like agent from the brain of a mountain agile gibbon (Hylobates agilis agilis) with encephalitis. J Zoo Wildl Med 1998; 29:61-4. [PMID: 9638628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A captive-born 2-yr-old male mountain agile gibbon (Hylobates agilis agilis) that died of encephalitis harbored a herpes simplex virus type 1 (HSV1)-like agent in the brain. A complete necropsy revealed intensive meningeal congestion with nonsuppurative encephalitis. The virus was recovered from frozen brain tissue in Vero cells. The isolate was very similar but not identical to human HSV1. Both western blot assay and virus neutralization tests were done with sera from 15 gibbons. Antibodies against HSV1 and herpes simplex virus type 2 (HSV2) were detected in four healthy gibbons, which included four species in three subgenera.
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Affiliation(s)
- A R Mootnick
- International Center for Gibbon Studies, Santa Clarita, California 91380, USA
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Mootnick AR, Nadler RD. Sexual behavior of maternally separated gibbons (Hylobates). Dev Psychobiol 1997; 31:149-61. [PMID: 9298641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The effect of early maternal separation on the sexual behavior of captive gibbons was investigated because (a) maternal separation compromises sexual behavior of some nonhuman primates and (b) adequate sexual behavior is essential to species propagation. Most of the maternally separated gibbons (24/31) were sexually proficient. Sexual behavior overall did not differ significantly in relation to species, sex, origin (wild-vs. captive-born), or type of rearing facility (home vs. zoo). Sexual proficiency was not related to the age at separation from the mother, but it was associated with introduction within 19 months of age to a conspecific of less than 3 years of age and an absolute age difference of less than 2 years. Sexual proficiency was associated with rearing and adult housing in relatively large enclosures. Gibbons that were isolated from conspecifics between 6 months and 2 years of age were strongly attached to humans, but this did not prevent sexual proficiency. A greater proportion of males than females were adversely affected sexually by prolonged early social isolation. Inadequate sexual behavior was associated with fearfulness of conspecifics, which probably interfered with compatible social relationships, including duetting. Inadequate sexual behavior was but one aspect of a more general behavioral deficiency resulting from inadequate early socialization. Early maternal separation in gibbons is compatible with species-typical sexual behavior under the conditions described above. It is not necessary for gibbons to learn sexual and parental behavior by observing experienced adult conspecifics.
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Affiliation(s)
- A R Mootnick
- International Center for Gibbon Studies, Santa Clarita, CA 91380, USA
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Prouty LA, Buchanan PD, Pollitzer WS, Mootnick AR. Taxonomic note:Bunopithecus: A genus-level taxon for the hoolock gibbon (Hylobates hoolock). Am J Primatol 1983; 5:83-87. [DOI: 10.1002/ajp.1350050110] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/1982] [Accepted: 03/18/1983] [Indexed: 11/10/2022]
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Prouty LA, Buchanan PD, Pollitzer WS, Mootnick AR. A presumptive new hylobatid subgenus with 38 chromosomes. Cytogenet Cell Genet 1983; 35:141-2. [PMID: 6851671 DOI: 10.1159/000131856] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The gibbon <i>Hylobates hoolock </i>has been found to possess a karyotype different in diploid number and banding pattern from that of any other hylobatid. We propose that the hoolock gibbon occupy its own subgenus in the genus <i>Hylobates.</i>
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