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The population genetics of wild chimpanzees in Cameroon and Nigeria suggests a positive role for selection in the evolution of chimpanzee subspecies. BMC Evol Biol 2015; 15:3. [PMID: 25608610 PMCID: PMC4314757 DOI: 10.1186/s12862-014-0276-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 12/15/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chimpanzees (Pan troglodytes) can be divided into four subspecies. Substantial phylogenetic evidence suggests that these subspecies can be grouped into two distinct lineages: a western African group that includes P. t. verus and P. t. ellioti and a central/eastern African group that includes P. t. troglodytes and P. t. schweinfurthii. The geographic division of these two lineages occurs in Cameroon, where the rages of P. t. ellioti and P. t. troglodytes appear to converge at the Sanaga River. Remarkably, few population genetic studies have included wild chimpanzees from this region. RESULTS We analyzed microsatellite genotypes of 187 wild, unrelated chimpanzees, and mitochondrial control region sequencing data from 604 chimpanzees. We found that chimpanzees in Cameroon and eastern Nigeria comprise at least two, and likely three populations. Both the mtDNA and microsatellite data suggest that there is a primary separation of P. t. troglodytes in southern Cameroon from P. t. ellioti north and west of the Sanaga River. These two populations split ~200-250 thousand years ago (kya), but have exchanged one migrant per generation since separating. In addition, P. t. ellioti consists of two populations that split from one another ~4 kya. One population is located in the rainforests of western Cameroon and eastern Nigeria, whereas the second population appears to be confined to a savannah-woodland mosaic in central Cameroon. CONCLUSIONS Our findings suggest that there are as many as three genetically distinct populations of chimpanzees in Cameroon and eastern Nigeria. P. t. troglodytes in southern Cameroon comprises one population that is separated from two populations of P. t. ellioti in western and central Cameroon, respectively. P. t. ellioti and P. t. troglodytes appear to be characterized by a pattern of isolation-with-migration, and thus, we propose that neutral processes alone can not explain the differentiation of P. t. ellioti and P. t. troglodytes.
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OCHIAI T, WATANUKI K, UDONO T, MORIMURA N, HIRATA S, TOMONAGA M, IDANI G, MATSUZAWA T. The History of Captive Chimpanzees ( Pan Troglodytes) in Japan. 1920-1950. ACTA ACUST UNITED AC 2015. [DOI: 10.2354/psj.31.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
| | | | | | | | | | - Masaki TOMONAGA
- Primate Research Institute, Kyoto University
- Wildlife Research Center, Kyoto University
| | - Gen'ichi IDANI
- Wildlife Research Center, Kyoto University
- Japan Monkey Centre
| | - Tetsuro MATSUZAWA
- Primate Research Institute, Kyoto University
- Wildlife Research Center, Kyoto University
- Japan Monkey Centre
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Fünfstück T, Arandjelovic M, Morgan DB, Sanz C, Reed P, Olson SH, Cameron K, Ondzie A, Peeters M, Vigilant L. The sampling scheme matters: Pan troglodytes troglodytes and P. t. schweinfurthii are characterized by clinal genetic variation rather than a strong subspecies break. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2014; 156:181-91. [PMID: 25330245 DOI: 10.1002/ajpa.22638] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 08/15/2014] [Accepted: 10/06/2014] [Indexed: 11/10/2022]
Abstract
Populations of an organism living in marked geographical or evolutionary isolation from other populations of the same species are often termed subspecies and expected to show some degree of genetic distinctiveness. The common chimpanzee (Pan troglodytes) is currently described as four geographically delimited subspecies: the western (P. t. verus), the nigerian-cameroonian (P. t. ellioti), the central (P. t. troglodytes) and the eastern (P. t. schweinfurthii) chimpanzees. Although these taxa would be expected to be reciprocally monophyletic, studies have not always consistently resolved the central and eastern chimpanzee taxa. Most studies, however, used data from individuals of unknown or approximate geographic provenance. Thus, genetic data from samples of known origin may shed light on the evolutionary relationship of these subspecies. We generated microsatellite genotypes from noninvasively collected fecal samples of 185 central chimpanzees that were sampled across large parts of their range and analyzed them together with 283 published eastern chimpanzee genotypes from known localities. We observed a clear signal of isolation by distance across both subspecies. Further, we found that a large proportion of comparisons between groups taken from the same subspecies showed higher genetic differentiation than the least differentiated between-subspecies comparison. This proportion decreased substantially when we simulated a more clumped sampling scheme by including fewer groups. Our results support the general concept that the distribution of the sampled individuals can dramatically affect the inference of genetic population structure. With regard to chimpanzees, our results emphasize the close relationship of equatorial chimpanzees from central and eastern equatorial Africa and the difficult nature of subspecies definitions.
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Affiliation(s)
- Tillmann Fünfstück
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
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Morimoto N, Ponce de León MS, Zollikofer CPE. Phenotypic variation in infants, not adults, reflects genotypic variation among chimpanzees and bonobos. PLoS One 2014; 9:e102074. [PMID: 25013970 PMCID: PMC4094530 DOI: 10.1371/journal.pone.0102074] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 06/13/2014] [Indexed: 11/18/2022] Open
Abstract
Studies comparing phenotypic variation with neutral genetic variation in modern humans have shown that genetic drift is a main factor of evolutionary diversification among populations. The genetic population history of our closest living relatives, the chimpanzees and bonobos, is now equally well documented, but phenotypic variation among these taxa remains relatively unexplored, and phenotype-genotype correlations are not yet documented. Also, while the adult phenotype is typically used as a reference, it remains to be investigated how phenotype-genotye correlations change during development. Here we address these questions by analyzing phenotypic evolutionary and developmental diversification in the species and subspecies of the genus Pan. Our analyses focus on the morphology of the femoral diaphysis, which represents a functionally constrained element of the locomotor system. Results show that during infancy phenotypic distances between taxa are largely congruent with non-coding (neutral) genotypic distances. Later during ontogeny, however, phenotypic distances deviate from genotypic distances, mainly as an effect of heterochronic shifts between taxon-specific developmental programs. Early phenotypic differences between Pan taxa are thus likely brought about by genetic drift while late differences reflect taxon-specific adaptations.
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Affiliation(s)
- Naoki Morimoto
- Laboratory of Physical Anthropology, Graduate School of Science, Kyoto University, Kyoto, Japan
- * E-mail: (NM); (CPEZ)
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55
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The human semicircular canals orientation is more similar to the bonobos than to the chimpanzees. PLoS One 2014; 9:e93824. [PMID: 24710502 PMCID: PMC3978048 DOI: 10.1371/journal.pone.0093824] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Accepted: 03/07/2014] [Indexed: 11/19/2022] Open
Abstract
For some traits, the human genome is more closely related to either the bonobo or the chimpanzee genome than they are to each other. Therefore, it becomes crucial to understand whether and how morphostructural differences between humans, chimpanzees and bonobos reflect the well known phylogeny. Here we comparatively investigated intra and extra labyrinthine semicircular canals orientation using 260 computed tomography scans of extant humans (Homo sapiens), bonobos (Pan paniscus) and chimpanzees (Pan troglodytes). Humans and bonobos proved more similarities between themselves than with chimpanzees. This finding did not fit with the well established chimpanzee – bonobo monophyly. One hypothesis was convergent evolution in which bonobos and humans produce independently similar phenotypes possibly in response to similar selective pressures that may be associated with postural adaptations. Another possibility was convergence following a “random walk” (Brownian motion) evolutionary model. A more parsimonious explanation was that the bonobo-human labyrinthine shared morphology more closely retained the ancestral condition with chimpanzees being subsequently derived. Finally, these results might be a consequence of genetic diversity and incomplete lineage sorting. The remarkable symmetry of the Semicircular Canals was the second major finding of this article with possible applications in taphonomy. It has the potential to investigate altered fossils, inferring the probability of post-mortem deformation which can lead to difficulties in understanding taxonomic variation, phylogenetic relationships, and functional morphology.
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Haslam M. On the tool use behavior of the bonobo-chimpanzee last common ancestor, and the origins of hominine stone tool use. Am J Primatol 2014; 76:910-8. [PMID: 24710771 DOI: 10.1002/ajp.22284] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 03/04/2014] [Accepted: 03/05/2014] [Indexed: 11/08/2022]
Abstract
The last common ancestor (LCA) shared by chimpanzees (Pan troglodytes) and bonobos (P. paniscus) was an Early Pleistocene African ape, which, based on the behavior of modern chimpanzees, may be assumed to be a tool-using animal. However, the character of tool use in the Pan lineage prior to the 20th century is largely unknown. Here, I use available data on wild bonobo tool use and emerging molecular estimates of demography during Pan evolution to hypothesise the plausible tool use behavior of the bonobo-chimpanzee LCA (or "Pancestor") at the start of the Pleistocene, over 2 million years ago. This method indicates that the common ancestor of living Pan apes likely used plant tools for probing, sponging, and display, but it did not use stone tools. Instead, stone tool use appears to have been independently invented by Western African chimpanzees (P. t. verus) during the Middle Pleistocene in the region of modern Liberia-Ivory Coast-Guinea, possibly as recently as 200,000-150,000 years ago. If this is the case, then the LCA of humans and chimpanzees likely also did not use stone tools, and this trait probably first emerged among hominins in Pliocene East Africa. This review also suggests that the consistently higher population sizes of Central African chimpanzees (P. t. troglodytes) over the past million years may have contributed to the increased complexity of wild tool use seen in this sub-species today.
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Affiliation(s)
- Michael Haslam
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
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Ferreira Z, Hurle B, Andrés AM, Kretzschmar WW, Mullikin JC, Cherukuri PF, Cruz P, Gonder MK, Stone AC, Tishkoff S, Swanson WJ, Green ED, Clark AG, Seixas S. Sequence diversity of Pan troglodytes subspecies and the impact of WFDC6 selective constraints in reproductive immunity. Genome Biol Evol 2013; 5:2512-23. [PMID: 24356879 PMCID: PMC3879984 DOI: 10.1093/gbe/evt198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Recent efforts have attempted to describe the population structure of common chimpanzee, focusing on four subspecies: Pan troglodytes verus, P. t. ellioti, P. t. troglodytes, and P. t. schweinfurthii. However, few studies have pursued the effects of natural selection in shaping their response to pathogens and reproduction. Whey acidic protein (WAP) four-disulfide core domain (WFDC) genes and neighboring semenogelin (SEMG) genes encode proteins with combined roles in immunity and fertility. They display a strikingly high rate of amino acid replacement (dN/dS), indicative of adaptive pressures during primate evolution. In human populations, three signals of selection at the WFDC locus were described, possibly influencing the proteolytic profile and antimicrobial activities of the male reproductive tract. To evaluate the patterns of genomic variation and selection at the WFDC locus in chimpanzees, we sequenced 17 WFDC genes and 47 autosomal pseudogenes in 68 chimpanzees (15 P. t. troglodytes, 22 P. t. verus, and 31 P. t. ellioti). We found a clear differentiation of P. t. verus and estimated the divergence of P. t. troglodytes and P. t. ellioti subspecies in 0.173 Myr; further, at the WFDC locus we identified a signature of strong selective constraints common to the three subspecies in WFDC6—a recent paralog of the epididymal protease inhibitor EPPIN. Overall, chimpanzees and humans do not display similar footprints of selection across the WFDC locus, possibly due to different selective pressures between the two species related to immune response and reproductive biology.
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Affiliation(s)
- Zélia Ferreira
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
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58
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Genetic diversity at the edge: comparative assessment of Y-chromosome and autosomal diversity in eastern chimpanzees (Pan troglodytes schweinfurthii) of Ugalla, Tanzania. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0556-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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59
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Pilbrow V, Groves C. Evidence for Divergence in Populations of Bonobos (Pan paniscus) in the Lomami-Lualaba and Kasai-Sankuru Regions Based on Preliminary Analysis of Craniodental Variation. INT J PRIMATOL 2013. [DOI: 10.1007/s10764-013-9737-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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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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61
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Templeton AR. Biological races in humans. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:262-71. [PMID: 23684745 PMCID: PMC3737365 DOI: 10.1016/j.shpsc.2013.04.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Races may exist in humans in a cultural sense, but biological concepts of race are needed to access their reality in a non-species-specific manner and to see if cultural categories correspond to biological categories within humans. Modern biological concepts of race can be implemented objectively with molecular genetic data through hypothesis-testing. Genetic data sets are used to see if biological races exist in humans and in our closest evolutionary relative, the chimpanzee. Using the two most commonly used biological concepts of race, chimpanzees are indeed subdivided into races but humans are not. Adaptive traits, such as skin color, have frequently been used to define races in humans, but such adaptive traits reflect the underlying environmental factor to which they are adaptive and not overall genetic differentiation, and different adaptive traits define discordant groups. There are no objective criteria for choosing one adaptive trait over another to define race. As a consequence, adaptive traits do not define races in humans. Much of the recent scientific literature on human evolution portrays human populations as separate branches on an evolutionary tree. A tree-like structure among humans has been falsified whenever tested, so this practice is scientifically indefensible. It is also socially irresponsible as these pictorial representations of human evolution have more impact on the general public than nuanced phrases in the text of a scientific paper. Humans have much genetic diversity, but the vast majority of this diversity reflects individual uniqueness and not race.
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Affiliation(s)
- Alan R Templeton
- Department of Biology, Washington University, St. Louis, MO 63130-4899, USA.
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63
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Understanding geographic origins and history of admixture among chimpanzees in European zoos, with implications for future breeding programmes. Heredity (Edinb) 2013; 110:586-93. [PMID: 23531981 DOI: 10.1038/hdy.2013.9] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Despite ample focus on this endangered species, conservation planning for chimpanzees residing outside Africa has proven a challenge because of the lack of ancestry information. Here, we analysed the largest number of chimpanzee samples to date, examining microsatellites in >100 chimpanzees from the range of the species in Africa, and 20% of the European zoo population. We applied the knowledge about subspecies differentiation throughout equatorial Africa to assign origin to chimpanzees in the largest conservation management programme globally. A total of 63% of the genotyped chimpanzees from the European zoos could be assigned to one of the recognized subspecies. The majority being of West African origin (40%) will help consolidate the current breeding programme for this subspecies and the identification of individuals belonging to the two other subspecies so far found in European zoos can form the basis for breeding programmes for these. Individuals of various degree of mixed ancestry made up 37% of the genotyped European zoo population and thus highlight the need for appropriate management programmes guided by genetic analysis to preserve maximum genetic diversity and reduce hybridization among subspecies.
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64
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Abstract
Acquired immunodeficiency syndrome (AIDS) of humans is caused by two lentiviruses, human immunodeficiency viruses types 1 and 2 (HIV-1 and HIV-2). Here, we describe the origins and evolution of these viruses, and the circumstances that led to the AIDS pandemic. Both HIVs are the result of multiple cross-species transmissions of simian immunodeficiency viruses (SIVs) naturally infecting African primates. Most of these transfers resulted in viruses that spread in humans to only a limited extent. However, one transmission event, involving SIVcpz from chimpanzees in southeastern Cameroon, gave rise to HIV-1 group M-the principal cause of the AIDS pandemic. We discuss how host restriction factors have shaped the emergence of new SIV zoonoses by imposing adaptive hurdles to cross-species transmission and/or secondary spread. We also show that AIDS has likely afflicted chimpanzees long before the emergence of HIV. Tracing the genetic changes that occurred as SIVs crossed from monkeys to apes and from apes to humans provides a new framework to examine the requirements of successful host switches and to gauge future zoonotic risk.
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Affiliation(s)
- Paul M Sharp
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
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65
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Piel AK, Stewart FA, Pintea L, Li Y, Ramirez MA, Loy DE, Crystal PA, Learn GH, Knapp LA, Sharp PM, Hahn BH. The malagarasi river does not form an absolute barrier to chimpanzee movement in Western Tanzania. PLoS One 2013; 8:e58965. [PMID: 23536841 PMCID: PMC3594223 DOI: 10.1371/journal.pone.0058965] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 02/08/2013] [Indexed: 11/19/2022] Open
Abstract
The Malagarasi River has long been thought to be a barrier to chimpanzee movements in western Tanzania. This potential geographic boundary could affect chimpanzee ranging behavior, population connectivity and pathogen transmission, and thus has implications for conservation strategies and government policy. Indeed, based on mitochondrial DNA sequence comparisons it was recently argued that chimpanzees from communities to the north and to the south of the Malagarasi are surprisingly distantly related, suggesting that the river prevents gene flow. To investigate this, we conducted a survey along the Malagarasi River. We found a ford comprised of rocks that researchers could cross on foot. On a trail leading to this ford, we collected 13 fresh fecal samples containing chimpanzee DNA, two of which tested positive for SIVcpz. We also found chimpanzee feces within the riverbed. Taken together, this evidence suggests that the Malagarasi River is not an absolute barrier to chimpanzee movements and communities from the areas to the north and south should be considered a single population. These results have important consequences for our understanding of gene flow, disease dynamics and conservation management.
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Affiliation(s)
- Alex K Piel
- Department of Anthropology, University of California San Diego, San Diego, California, United States of America.
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Abstract
The genomics era has opened up exciting possibilities in the field of conservation biology by enabling genomic analyses of threatened species that previously were limited to model organisms. Next-generation sequencing (NGS) and the collection of genome-wide data allow for more robust studies of the demographic history of populations and adaptive variation associated with fitness and local adaptation. Genomic analyses can also advance management efforts for threatened wild and captive populations by identifying loci contributing to inbreeding depression and disease susceptibility, and predicting fitness consequences of introgression. However, the development of genomic tools in wild species still carries multiple challenges, particularly those associated with computational and sampling constraints. This review provides an overview of the most significant applications of NGS and the implications and limitations of genomic studies in conservation.
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Affiliation(s)
- Cynthia C Steiner
- Institute for Conservation Research, San Diego Zoo Global, Escondido, California 92027; ; ;
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Last C, Muh B. Effects of Human Presence on Chimpanzee Nest Location in the Lebialem-Mone Forest Landscape, Southwest Region, Cameroon. Folia Primatol (Basel) 2013; 84:51-63. [DOI: 10.1159/000346305] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 12/03/2012] [Indexed: 11/19/2022]
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68
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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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Hayakawa T, Sugawara T, Go Y, Udono T, Hirai H, Imai H. Eco-geographical diversification of bitter taste receptor genes (TAS2Rs) among subspecies of chimpanzees (Pan troglodytes). PLoS One 2012; 7:e43277. [PMID: 22916235 PMCID: PMC3420883 DOI: 10.1371/journal.pone.0043277] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 07/18/2012] [Indexed: 12/03/2022] Open
Abstract
Chimpanzees (Pan troglodytes) have region-specific difference in dietary repertoires from East to West across tropical Africa. Such differences may result from different genetic backgrounds in addition to cultural variations. We analyzed the sequences of all bitter taste receptor genes (cTAS2Rs) in a total of 59 chimpanzees, including 4 putative subspecies. We identified genetic variations including single-nucleotide variations (SNVs), insertions and deletions (indels), gene-conversion variations, and copy-number variations (CNVs) in cTAS2Rs. Approximately two-thirds of all cTAS2R haplotypes in the amino acid sequence were unique to each subspecies. We analyzed the evolutionary backgrounds of natural selection behind such diversification. Our previous study concluded that diversification of cTAS2Rs in western chimpanzees (P. t. verus) may have resulted from balancing selection. In contrast, the present study found that purifying selection dominates as the evolutionary form of diversification of the so-called human cluster of cTAS2Rs in eastern chimpanzees (P. t. schweinfurthii) and that the other cTAS2Rs were under no obvious selection as a whole. Such marked diversification of cTAS2Rs with different evolutionary backgrounds among subspecies of chimpanzees probably reflects their subspecies-specific dietary repertoires.
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Affiliation(s)
- Takashi Hayakawa
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
- Japan Society for Promotion of Science, Tokyo, Japan
| | - Tohru Sugawara
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Yasuhiro Go
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Toshifumi Udono
- Kumamoto Sanctuary, Wildlife Research Center of Kyoto University, Uki, Kumamoto, Japan
| | - Hirohisa Hirai
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Hiroo Imai
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
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Pascual-Garrido A, Buba U, Nodza G, Sommer V. Obtaining raw material: plants as tool sources for Nigerian chimpanzees. ACTA ACUST UNITED AC 2012; 83:24-44. [PMID: 22759783 DOI: 10.1159/000338898] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 04/18/2012] [Indexed: 11/19/2022]
Abstract
We investigated the acquisition of plant materials from which Nigerian chimpanzees manufacture wooden tools to harvest insects and honey from nests of army ants, honey bees and stingless bees. Slender trunks of juvenile trees and branches are most commonly used, and bendable vines rarely, probably reflecting the need to work with relatively sturdy tools to extract resources. While several tools are sometimes sourced from the same plant, there is also evidence for a depletion effect, as multiple tool sources at the same site are often spaced several metres apart. Identified tool sources belong to 27 species of at least 13 families. Honey-gathering implements are often chewed upon by chimpanzees. Interestingly, twigs of the most commonly used honey-gathering species possess antibacterial propensities and are favoured by Nigerians as chewing sticks. This suggests that extractive tools might possess associated medicinal or stimulatory properties. We do not know if chimpanzees actively select specific plant parts or species as we cannot compare observed with expected frequencies. Nevertheless, about three quarters of tools are picked from plants more than 6 m away from the extraction site, potentially indicating some degree of forward planning.
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Vallo P, Petrželková KJ, Profousová I, Petrášová J, Pomajbíková K, Leendertz F, Hashimoto C, Simmons N, Babweteera F, Machanda Z, Piel A, Robbins MM, Boesch C, Sanz C, Morgan D, Sommer V, Furuichi T, Fujita S, Matsuzawa T, Kaur T, Huffman MA, Modrý D. Molecular diversity of entodiniomorphid ciliateTroglodytella abrassartiand its coevolution with chimpanzees. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 148:525-33. [DOI: 10.1002/ajpa.22067] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 03/07/2012] [Indexed: 11/07/2022]
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The relative congruence of cranial and genetic estimates of hominoid taxon relationships: implications for the reconstruction of hominin phylogeny. J Hum Evol 2012; 62:640-53. [PMID: 22513382 DOI: 10.1016/j.jhevol.2012.02.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 02/27/2012] [Accepted: 02/27/2012] [Indexed: 01/02/2023]
Abstract
Previous analyses of extant catarrhine craniodental morphology have often failed to recover their molecular relationships, casting doubt on the accuracy of hominin phylogenies based on anatomical data. However, on the basis of genetic, morphometric and environmental affinity patterns, a growing body of literature has demonstrated that particular aspects of cranial morphology are remarkably reliable proxies for neutral modern human population history. Hence, it is important to test whether these intra-specific patterns can be extrapolated to a broader primate taxon level such that inference rules for understanding the morphological evolution of the extinct hominins may be devised. Here, we use a matrix of molecular distances between 15 hominoid taxa to test the genetic congruence of 14 craniomandibular regions, defined and morphometrically delineated on the basis of previous modern human analyses. This methodology allowed us to test directly whether the cranial regions found to be reliable indicators of population history were also more reliable proxies for hominoid genetic relationships. Cranial regions were defined on the basis of three criteria: developmental-functional units, individual bones, and regions differentially affected by masticatory stress. The results found that all regions tested were significantly and strongly correlated with the molecular matrix. However, the modern human predictions regarding the relative congruence of particular regions did not hold true, as the face was statistically the most reliable indicator of hominoid genetic distances, as opposed to the vault or basicranium. Moreover, when modern humans were removed from the analysis, all cranial regions improved in their genetic congruence, suggesting that it is the inclusion of morphologically-derived humans that has the largest effect on incongruence between morphological and molecular estimates of hominoid relationships. Therefore, it may be necessary to focus on smaller intra-generic taxonomic levels to more fully understand the effects of neutral and selective evolutionary processes in generating morphological diversity patterns.
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Species association of hepatitis B virus (HBV) in non-human apes; evidence for recombination between gorilla and chimpanzee variants. PLoS One 2012; 7:e33430. [PMID: 22432021 PMCID: PMC3303819 DOI: 10.1371/journal.pone.0033430] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 02/08/2012] [Indexed: 01/28/2023] Open
Abstract
Hepatitis B virus (HBV) infections are widely distributed in humans, infecting approximately one third of the world's population. HBV variants have also been detected and genetically characterised from Old World apes; Gorilla gorilla (gorilla), Pan troglodytes (chimpanzee), Pongo pygmaeus (orang-utan), Nomascus nastusus and Hylobates pileatus (gibbons) and from the New World monkey, Lagothrix lagotricha (woolly monkey). To investigate species-specificity and potential for cross species transmission of HBV between sympatric species of apes (such as gorillas and chimpanzees in Central Africa) or between humans and chimpanzees or gorillas, variants of HBV infecting captive wild-born non-human primates were genetically characterised. 9 of 62 chimpanzees (11.3%) and two from 11 gorillas (18%) were HBV-infected (15% combined frequency), while other Old world monkey species were negative. Complete genome sequences were obtained from six of the infected chimpanzee and both gorillas; those from P. t .ellioti grouped with previously characterised variants from this subspecies. However, variants recovered from P. t. troglodytes HBV variants also grouped within this clade, indicative of transmission between sub-species, forming a paraphyletic clade. The two gorilla viruses were phylogenetically distinct from chimpanzee and human variants although one showed evidence for a recombination event with a P.t.e.-derived HBV variant in the partial X and core gene region. Both of these observations provide evidence for circulation of HBV between different species and sub-species of non-human primates, a conclusion that differs from the hypothesis if of strict host specificity of HBV genotypes.
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Bowden R, MacFie TS, Myers S, Hellenthal G, Nerrienet E, Bontrop RE, Freeman C, Donnelly P, Mundy NI. Genomic tools for evolution and conservation in the chimpanzee: Pan troglodytes ellioti is a genetically distinct population. PLoS Genet 2012; 8:e1002504. [PMID: 22396655 PMCID: PMC3291532 DOI: 10.1371/journal.pgen.1002504] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 11/09/2011] [Indexed: 11/23/2022] Open
Abstract
In spite of its evolutionary significance and conservation importance, the population structure of the common chimpanzee, Pan troglodytes, is still poorly understood. An issue of particular controversy is whether the proposed fourth subspecies of chimpanzee, Pan troglodytes ellioti, from parts of Nigeria and Cameroon, is genetically distinct. Although modern high-throughput SNP genotyping has had a major impact on our understanding of human population structure and demographic history, its application to ecological, demographic, or conservation questions in non-human species has been extremely limited. Here we apply these tools to chimpanzee population structure, using ∼700 autosomal SNPs derived from chimpanzee genomic data and a further ∼100 SNPs from targeted re-sequencing. We demonstrate conclusively the existence of P. t. ellioti as a genetically distinct subgroup. We show that there is clear differentiation between the verus, troglodytes, and ellioti populations at the SNP and haplotype level, on a scale that is greater than that separating continental human populations. Further, we show that only a small set of SNPs (10–20) is needed to successfully assign individuals to these populations. Tellingly, use of only mitochondrial DNA variation to classify individuals is erroneous in 4 of 54 cases, reinforcing the dangers of basing demographic inference on a single locus and implying that the demographic history of the species is more complicated than that suggested analyses based solely on mtDNA. In this study we demonstrate the feasibility of developing economical and robust tests of individual chimpanzee origin as well as in-depth studies of population structure. These findings have important implications for conservation strategies and our understanding of the evolution of chimpanzees. They also act as a proof-of-principle for the use of cheap high-throughput genomic methods for ecological questions. Chimpanzees are viewed with fondness as our closest animal relatives and are valued by scientists for the biological and evolutionary insights they provide. In spite of this, the relationships between different populations of common chimpanzees are still relatively poorly understood, a situation that potentially threatens conservation efforts. Here we have used information gathered in the Chimpanzee Genome Project to design comprehensive tests of genetic variability that show unambiguously the existence of four genetically distinct groups (or populations) of common chimpanzee. We demonstrate that previous methods based on mitochondrial DNA sequences alone are not always accurate and show the feasibility of cheap new genetic tests of individuals' origins that could play an important role in conservation.
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Affiliation(s)
- Rory Bowden
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tammie S. MacFie
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Simon Myers
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Broad Institute, Boston, Massachusetts, United States of America
| | - Garrett Hellenthal
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | | | - Colin Freeman
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Peter Donnelly
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail:
| | - Nicholas I. Mundy
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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Comparison of the endocranial ontogenies between chimpanzees and bonobos via temporal regression and spatiotemporal registration. J Hum Evol 2012; 62:74-88. [PMID: 22137587 DOI: 10.1016/j.jhevol.2011.10.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 10/05/2011] [Accepted: 10/09/2011] [Indexed: 12/21/2022]
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Greve G, Alechine E, Pasantes JJ, Hodler C, Rietschel W, Robinson TJ, Schempp W. Y-Chromosome variation in hominids: intraspecific variation is limited to the polygamous chimpanzee. PLoS One 2011; 6:e29311. [PMID: 22216243 PMCID: PMC3246485 DOI: 10.1371/journal.pone.0029311] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 11/25/2011] [Indexed: 11/23/2022] Open
Abstract
Background We have previously demonstrated that the Y-specific ampliconic fertility genes DAZ (deleted in azoospermia) and CDY (chromodomain protein Y) varied with respect to copy number and position among chimpanzees (Pan troglodytes). In comparison, seven Y-chromosomal lineages of the bonobo (Pan paniscus), the chimpanzee's closest living relative, showed no variation. We extend our earlier comparative investigation to include an analysis of the intraspecific variation of these genes in gorillas (Gorilla gorilla) and orangutans (Pongo pygmaeus), and examine the resulting patterns in the light of the species' markedly different social and mating behaviors. Methodology/Principal Findings Fluorescence in situ hybridization analysis (FISH) of DAZ and CDY in 12 Y-chromosomal lineages of western lowland gorilla (G. gorilla gorilla) and a single lineage of the eastern lowland gorilla (G. beringei graueri) showed no variation among lineages. Similar findings were noted for the 10 Y-chromosomal lineages examined in the Bornean orangutan (Pongo pygmaeus), and 11 Y-chromosomal lineages of the Sumatran orangutan (P. abelii). We validated the contrasting DAZ and CDY patterns using quantitative real-time polymerase chain reaction (qPCR) in chimpanzee and bonobo. Conclusion/Significance High intraspecific variation in copy number and position of the DAZ and CDY genes is seen only in the chimpanzee. We hypothesize that this is best explained by sperm competition that results in the variant DAZ and CDY haplotypes detected in this species. In contrast, bonobos, gorillas and orangutans—species that are not subject to sperm competition—showed no intraspecific variation in DAZ and CDY suggesting that monoandry in gorillas, and preferential female mate choice in bonobos and orangutans, probably permitted the fixation of a single Y variant in each taxon. These data support the notion that the evolutionary history of a primate Y chromosome is not simply encrypted in its DNA sequences, but is also shaped by the social and behavioral circumstances under which the specific species has evolved.
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Affiliation(s)
- Gabriele Greve
- Institute of Human Genetics, University of Freiburg, Freiburg, Germany
| | - Evguenia Alechine
- Institute of Human Genetics, University of Freiburg, Freiburg, Germany
- Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, University of Buenos Aires, Buenos Aires, Argentina
| | - Juan J. Pasantes
- Institute of Human Genetics, University of Freiburg, Freiburg, Germany
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
| | - Christine Hodler
- Institute of Human Genetics, University of Freiburg, Freiburg, Germany
| | | | - Terence J. Robinson
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
| | - Werner Schempp
- Institute of Human Genetics, University of Freiburg, Freiburg, Germany
- * E-mail:
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Rudicell RS, Piel AK, Stewart F, Moore DL, Learn GH, Li Y, Takehisa J, Pintea L, Shaw GM, Moore J, Sharp PM, Hahn BH. High prevalence of simian immunodeficiency virus infection in a community of savanna chimpanzees. J Virol 2011; 85:9918-28. [PMID: 21775446 PMCID: PMC3196395 DOI: 10.1128/jvi.05475-11] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 07/13/2011] [Indexed: 12/27/2022] Open
Abstract
Simian immunodeficiency virus of chimpanzees (SIVcpz) has a significant negative impact on the health, reproduction, and life span of chimpanzees, yet the prevalence and distribution of this virus in wild-living populations are still only poorly understood. Here, we show that savanna chimpanzees, who live in ecologically marginal habitats at 10- to 50-fold lower population densities than forest chimpanzees, can be infected with SIVcpz at high prevalence rates. Fecal samples were collected from nonhabituated eastern chimpanzees (Pan troglodytes schweinfurthii) in the Issa Valley (n = 375) and Shangwa River (n = 6) areas of the Masito-Ugalla region in western Tanzania, genotyped to determine the number of sampled individuals, and tested for SIVcpz-specific antibodies and nucleic acids. None of 5 Shangwa River apes tested positive for SIVcpz; however, 21 of 67 Issa Valley chimpanzees were SIVcpz infected, indicating a prevalence rate of 31% (95% confidence interval, 21% to 44%). Two individuals became infected during the 14-month observation period, documenting continuing virus spread in this community. To characterize the newly identified SIVcpz strains, partial and full-length viral sequences were amplified from fecal RNA of 10 infected chimpanzees. Phylogenetic analyses showed that the Ugalla viruses formed a monophyletic lineage most closely related to viruses endemic in Gombe National Park, also located in Tanzania, indicating a connection between these now separated communities at some time in the past. These findings document that SIVcpz is more widespread in Tanzania than previously thought and that even very low-density chimpanzee populations can be infected with SIVcpz at high prevalence rates. Determining whether savanna chimpanzees, who face much more extreme environmental conditions than forest chimpanzees, are more susceptible to SIVcpz-associated morbidity and mortality will have important scientific and conservation implications.
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Affiliation(s)
| | - Alex K. Piel
- Department of Anthropology, University of California at San Diego, La Jolla, California 92093
| | - Fiona Stewart
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge CB2 1QH, United Kingdom
| | - Deborah L. Moore
- Department of Anthropology, University of Texas at San Antonio, San Antonio, Texas 78249
| | - Gerald H. Learn
- Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Yingying Li
- Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Jun Takehisa
- Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Lilian Pintea
- The Jane Goodall Institute, Arlington, Virginia 22203
| | - George M. Shaw
- Departments of Microbiology
- Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Jim Moore
- Department of Anthropology, University of California at San Diego, La Jolla, California 92093
| | - Paul M. Sharp
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - Beatrice H. Hahn
- Departments of Microbiology
- Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294
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Fischer A, Prüfer K, Good JM, Halbwax M, Wiebe V, André C, Atencia R, Mugisha L, Ptak SE, Pääbo S. Bonobos fall within the genomic variation of chimpanzees. PLoS One 2011; 6:e21605. [PMID: 21747915 PMCID: PMC3126833 DOI: 10.1371/journal.pone.0021605] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 06/06/2011] [Indexed: 11/19/2022] Open
Abstract
To gain insight into the patterns of genetic variation and evolutionary relationships within and between bonobos and chimpanzees, we sequenced 150,000 base pairs of nuclear DNA divided among 15 autosomal regions as well as the complete mitochondrial genomes from 20 bonobos and 58 chimpanzees. Except for western chimpanzees, we found poor genetic separation of chimpanzees based on sample locality. In contrast, bonobos consistently cluster together but fall as a group within the variation of chimpanzees for many of the regions. Thus, while chimpanzees retain genomic variation that predates bonobo-chimpanzee speciation, extensive lineage sorting has occurred within bonobos such that much of their genome traces its ancestry back to a single common ancestor that postdates their origin as a group separate from chimpanzees.
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Affiliation(s)
- Anne Fischer
- Max Plank Institute for Evolutionary Anthropology, Leipzig, Germany.
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