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PubMed1994

Sequence divergence of the red and green visual pigments in great apes and humans.

We have determined the coding sequences of red and green visual pigment genes of the chimpanzee, gorilla, and orangutan. The deduced amino acid sequences of these pigments are highly homologous to the equivalent human pigments. None of the amino acid differences occurred at sites that were previously shown to influence pigment absorption characteristics. Therefore, we predict the spectra of red and green pigments of the apes to have wavelengths of maximum absorption that differ by < 2 nm from the equivalent human pigments and that color vision in these nonhuman primates will be very similar, if not identical, to that in humans. A total of 14 within-species polymorphisms (6 involving silent substitutions) were observed in the coding sequences of the red and green pigment genes of the great apes. Remarkably, the polymorphisms at 6 of these sites had been observed in human populations, suggesting that they predated the evolution of higher primates. Alleles at polymorphic sites were often shared between the red and green pigment genes. The average synonymous rate of divergence of red from green sequences was approximately 1/10th that estimated for other proteins of higher primates, indicating the involvement of gene conversion in generating these polymorphisms. The high degree of homology and juxtaposition of these two genes on the X chromosome has promoted unequal recombination and/or gene conversion that led to sequence homogenization. However, natural selection operated to maintain the degree of separation in peak absorbance between the red and green pigments that resulted in optimal chromatic discrimination. This represents a unique case of molecular coevolution between two homologous genes that functionally interact at the behavioral level.

Amino Acid Sequence↗
PubMed1986

Retroviral activation of interleukin 2 gene in a gibbon ape T cell lymphoma line.

The gibbon ape leukemia virus (GaLVSF)-infected T cell line, MLA 144, was established from the lymphoma of a gibbon ape. The cell line constitutively expresses IL-2 and its receptor, implying that an autocrine mechanism could be responsible for or contribute toward its growth. To explore the mechanism of constitutive IL-2 expression in MLA 144, we have isolated and characterized cosmid clones representing a normal and a doubly inserted IL-2 allele in this cell line. The map of the normal MLA 144 IL-2 allele closely resembles that of the normal human IL-2 gene. The abnormal allele contains a 3' insertion that is a GaLVSF provirus with two long terminal repeats (LTR) and an internal 3.25 kb deletion. At the 5' end of the abnormal allele is a second insertion that DNA sequencing showed to be an isolated GaLVSF LTR with a transcriptional orientation opposing that of the IL-2 gene. We demonstrate by Northern blotting analysis that the vast majority of transcripts are from the abnormal allele, implying that one or both retroviral insertions are responsible for constitutive expression of the allele.

Alleles↗
PubMed2006

Are apes really inequity averse?

Brosnan et al. (Brosnan, S. F. Schiff, H. C. & de Waal, F. B. M. 2005 Tolerance for inequity may increase with social closeness in chimpanzees. Proc. R. Soc. B272, 253-258) found that chimpanzees showed increased levels of rejection for less-preferred food when competitors received better food than themselves and postulated as an explanation inequity aversion. In the present study, we extended these findings by adding important control conditions, and we investigated whether inequity aversion could also be found in the other great ape species and whether it would be influenced by subjects' relationship with the competitor. In the present study, subjects showed a pattern of food rejection opposite to the subjects of the above study by Brosnan et al. (2005). Our apes ignored fewer food pieces and stayed longer in front of the experimenter when a conspecific received better food than themselves. Moreover, chimpanzees begged more vigorously when the conspecific got favoured food. The most plausible explanation for these results is the food expectation hypothesis - seeing another individual receive high-quality food creates the expectation of receiving the same food oneself - and not inequity aversion.

Animals↗
PubMed1986

Gibbon ape leukaemia virus RNA in leukaemic T-lymphoid cell lines: expression of a novel RNA transcript.

Fibroblast cell lines infected in vitro with different strains of gibbon ape leukaemia virus or the related woolly monkey virus (SSAV) synthesized two RNA species of approximately 8.4 kb and 2.9 kb. The former, a complete RNA, represents the gag-pol mRNA, while the latter is a spliced transcript lacking gag and pol, and represents the env mRNA. In contrast, RNA from one T-lymphoid cell line derived from a gibbon ape T-lymphocytic leukaemia (UCD-144) expressed a viral mRNA in addition to gag-pol and env mRNA. This RNA is 6.4 kb and lacks at least 3.0 kb of sequences derived from the internal region of the viral genome, including most or all of the pol gene. These data, as well as data from Southern blots of UCD-144 DNA, suggest that the 6.4 kb mRNA could represent a transcript from a defective recombinant provirus and may contain cell-derived sequences.

Animals↗
PubMed2025

Recurrent structural variation and recent turnover at the 17q21.31 locus in humans and great apes.

The 17q21.31 locus in humans harbors several complex structural haplotypes including a ~970kb inversion. Different inversion haplotypes have been associated with susceptibility to microdeletions causing Koolen-de Vries syndrome and variation in fecundity and recombination rates. Here, using 210 haplotype-resolved human genome assemblies and pangenome graph-based approaches we characterize 11 distinct structural haplotypes, several of which have not been previously described. Extending our analyses to a set of haplotype-resolved great-ape genomes, we characterize the structure of an independent inversion in chimpanzees which extends an additional 650kb, encompasses 5 additional genes, and is ~2 million years younger than the human inversion. We further determine that gorillas exhibit an independent duplication of the KANSL1 gene which may predispose them to Koolen-de Vries syndrome causing microdeletions. Using short read sequencing data we characterize 17q21.31 haplotype diversity worldwide in ~5174 individuals from 107 populations finding increased frequencies of KANSL1 duplication-containing haplotypes in both European and South Asian populations as well as 8 double recombination events between inverted and non-inverted haplotypes ranging in size from 20-180kb. Finally, using 626 ancient Eurasian human genomes we show the frequency of haplotypes containing KANSL1 duplications has increased ~6-fold over the past 12 thousand years in Europe. Together, our results highlight the dynamics, complexity, and recurrent, independent evolution of a medically relevant locus across humans and great apes.

Journal Article↗
PubMed2003

Recombination has little effect on the rate of sequence divergence in pseudoautosomal boundary 1 among humans and great apes.

Recent studies indicated that recombination is strongly mutagenic. In particular, data from the mouse pseudoautosomal boundary (PAB) suggested that locally intensive recombination increased the nucleotide substitution rate by more than 100-fold and greatly increased the GC content. Here we study the rates of nucleotide substitution in eight introns of the human and great ape XG gene, which spans the boundary between the pseudoautosomal region 1 (PAR1) and the X-specific region. Contrary to what is expected under the above hypothesis, our sequence data from humans and great apes reveal that the PAR1 introns of XG have actually evolved slightly slower than X-specific introns. Only when a New World monkey was compared with hominoids were the rates slightly increased in the PAR1 introns. In terms of base composition, although the intergenic regions of the human PAR1 show a significant increase of G and C nucleotides, the base composition of the surveyed PAR1 introns is similar to that of the X-specific introns. Direct and indirect evidence indicates that the recombination rate is, indeed, much higher in PAR1 introns than in X-specific introns, and that the present PAB has persisted since the common ancestor of hominoids. Therefore, the mutagenic effect of recombination is far weaker than previously proposed, at least in hominoid PABs.

Animals↗
PubMed2006

A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications.

Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence divergence estimates of human duplications have suggested an expansion relatively recently during hominoid evolution. Based on primate comparative sequence analysis of 37 unique duplication-transition regions, we establish a molecular clock for their divergence that shows a significant increase in their effective substitution rate when compared with unique genomic sequence. Fluorescent in situ hybridization (FISH) analyses from 1053 random nonhuman primate BACs indicate that great-ape species have been enriched for interspersed segmental duplications compared with representative Old World and New World monkeys. These findings support computational analyses that show a 12-fold excess of recent (>98%) intrachromosomal duplications when compared with duplications between nonhomologous chromosomes. These architectural shifts in genomic structure and elevated substitution rates have important implications for the emergence of new genes, gene-expression differences, and structural variation among humans and great apes.

Animals↗
PubMedDate not supplied

A nonverbal false belief task: the performance of children and great apes.

A nonverbal task of false belief understanding was given to 4- and 5-year-old children (N = 28) and to two species of great ape: chimpanzees and orangutans (N = 7). The task was embedded in a series of finding games in which an adult (the hider) hid a reward in one of two identical containers, and another adult (the communicator) observed the hiding process and attempted to help the participant by placing a marker on the container that she believed to hold the reward. An initial series of control trials ensured that participants were able to use the marker to locate the reward, follow the reward in both visible and invisible displacements, and ignore the marker when they knew it to be incorrect. In the crucial false belief trials, the communicator watched the hiding process and then left the area, at which time the hider switched the locations of the containers. When the communicator returned, she marked the container at the location where she had seen the reward hidden, which was incorrect. The hider then gave the subject the opportunity to find the sticker. Successful performance required participants to reason as follows: the communicator placed the marker where she saw the reward hidden; the container that was at that location is now at the other location; so the reward is at the other location. Children were also given a verbal false belief task in the context of this same hiding game. The two main results of the study were: (1) children's performance on the verbal and nonverbal false belief tasks were highly correlated (and both fit very closely with age norms from previous studies), and (2) no ape succeeded in the nonverbal false belief task even though they succeeded in all of the control trials indicating mastery of the general task demands.

Analysis of Variance↗
PubMed2006

Apes' and children's understanding of cooperative and competitive motives in a communicative situation.

Chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) (Study 1) and 18- and 24-month-old human children (Study 2) participated in a novel communicative task. A human experimenter (E) hid food or a toy in one of two opaque containers before gesturing towards the reward's location in one of two ways. In the Informing condition, she attempted to help the subject find the hidden object by simply pointing to the correct container. In the Prohibiting condition, E held out her arm toward the correct container (palm out) and told the subject firmly 'Don't take this one.' As in previous studies, the apes were at chance in the Informing condition. However, they were above chance in the new Prohibiting condition. Human 18-month-olds showed this same pattern of results, whereas 24-month-olds showed the opposite pattern: they were better in the Informing condition than in the Prohibiting condition. In our interpretation, success in the Prohibiting condition requires subjects to understand E's goal toward them and their behavior, and then to make an inference (she would only prohibit if there were something good in there). Success in the Informing condition requires subjects to understand a cooperative communicative motive - which apparently apes and young infants find difficult.

Animal Communication↗
PubMed2004

The mentality of crows: convergent evolution of intelligence in corvids and apes.

Discussions of the evolution of intelligence have focused on monkeys and apes because of their close evolutionary relationship to humans. Other large-brained social animals, such as corvids, also understand their physical and social worlds. Here we review recent studies of tool manufacture, mental time travel, and social cognition in corvids, and suggest that complex cognition depends on a "tool kit" consisting of causal reasoning, flexibility, imagination, and prospection. Because corvids and apes share these cognitive tools, we argue that complex cognitive abilities evolved multiple times in distantly related species with vastly different brain structures in order to solve similar socioecological problems.

Animals↗
PubMed2006

Apes save tools for future use.

Planning for future needs, not just current ones, is one of the most formidable human cognitive achievements. Whether this skill is a uniquely human adaptation is a controversial issue. In a study we conducted, bonobos and orangutans selected, transported, and saved appropriate tools above baseline levels to use them 1 hour later (experiment 1). Experiment 2 extended these results to a 14-hour delay between collecting and using the tools. Experiment 3 showed that seeing the apparatus during tool selection was not necessary to succeed. These findings suggest that the precursor skills for planning for the future evolved in great apes before 14 million years ago, when all extant great ape species shared a common ancestor.

Animals↗
PubMed1987

Phylogenetic relations of humans and African apes from DNA sequences in the psi eta-globin region.

Sequences from the upstream and downstream flanking DNA regions of the psi eta-globin locus in Pan troglodytes (common chimpanzee), Gorilla gorilla (gorilla), and Pongo pygmaeus (orangutan, the closest living relative to Homo, Pan, and Gorilla) provided further data for evaluating the phylogenetic relations of humans and African apes. These newly sequenced orthologs [an additional 4.9 kilobase pairs (kbp) for each species] were combined with published psi eta-gene sequences and then compared to the same orthologous stretch (a continuous 7.1-kbp region) available for humans. Phylogenetic analysis of these nucleotide sequences by the parsimony method indicated (i) that human and chimpanzee are more closely related to each other than either is to gorilla and (ii) that the slowdown in the rate of sequence evolution evident in higher primates is especially pronounced in humans. These results indicate that features (for example, knuckle-walking) unique to African apes (but not to humans) are primitive and that even local molecular clocks should be applied with caution.

Animals↗
PubMed1980

Relationship of retroviruses isolated from human leukemia tissues to the woolly monkey-gibbon ape leukemia viruses.

Retroviruses have been isolated from the tissues of human leukemia patients. Previous studies have shown that these isolates share some antigenic determinants with the family of viruses isolated from the woolly monkey and gibbon ape and that they exhibit partial nuclei acid homology with this same group of viruses. We have compared the RNAs of the viruses by two-dimensional polyacrylamide gel electrophoresis of the large RNase T1-resistant oligonucleotides. The degree of sequence identity between the RNAs was determined by the similarity of their RNase T1-resistant oligonucleotide pattern on gels, fingerprints, and in some cases by partial sequence analysis of individual oligonucleotides. This technique permits us to determine the degree of sequence identity among related RNA species. From our studies we conclude that viruses isolated from the tissues of two human leukemia patients, A1476 and SKA 21-3, as well as some subcultures of a virus isolated from the leukemic tissues of a third patient, HL23V, are closely related to the wooly monkey virus. However, the fingerprints of other HL23 viral isolates are very similar to that of GaLVSF, a gibbon ape leukemia virus isolated from a lymphosarcoma.

Animals↗
PubMed1982

Molecular cloning of circular unintegrated DNA of two types of the SEATO strain of gibbon ape leukemia virus.

Closed circular unintegrated DNA of the SEATO strain of gibbon ape leukemia virus (GaLV-S) was isolated from canine thymus fibroblasts after cocultivation with chronically infected bat lung fibroblasts. Restriction endonuclease HindIII cleaves GaLV-S DNA once, thus allowing isolation and cloning of HindIII-digested unintegrated DNA in a permitted form. Two clones isolated in the vector, Charon 21A, were nearly identical by restriction enzyme mapping to each of the two types of GaLV-S previously observed. These two types differ at a single SalI site. Unlike previous maps of GaLV-S proviral DNA, however, both clones lack SstI sites in the long-terminal-repeat units. Both the GaLV-S clones and the major species of GaLV-S proviral DNA contain an EcoRI site in the long-terminal-repeat units. The presence of this EcoRI site and the absence of an SstI site in the GaLV-S long-terminal-repeat units differentiate it from all other known GaLV strains and from the closely related nononcogenic simian sarcoma-associated virus. Heteroduplex comparisons of each of the two clones to clones of simian sarcoma-associated virus show no obvious deletion or substitution loops. This suggests that the ability of GaLV-S to induce myeloid leukemia in gibbon apes in not due to an acquired onc gene.

Animals↗
PubMed1991

Construction and properties of retrovirus packaging cells based on gibbon ape leukemia virus.

We have constructed hybrid retrovirus packaging cell lines that express the gibbon ape leukemia virus env and the Moloney murine leukemia virus gag-pol proteins. These cells were used to produce a retrovirus vector at over 10(6) CFU/ml, with a host range that included rat, hamster, bovine, cat, dog, monkey, and human cells. The gag-pol and env expression plasmids were separately transfected to reduce the potential for helper virus production, which was not observed. The NIH 3T3 mouse cells from which the packaging lines were made are not infectable by gibbon ape leukemia virus; thus, the generation and spread of possible recombinant viruses in the packaging cells is greatly reduced. These simian virus-based packaging cells extend the host range of currently available murine and avian packaging cells and should be useful for efficient gene transfer into higher mammals.

Animals↗
PubMed1992

GLVR1, a receptor for gibbon ape leukemia virus, is homologous to a phosphate permease of Neurospora crassa and is expressed at high levels in the brain and thymus.

The human gene GLVR1 has been shown to render mouse cells sensitive to infection by gibbon ape leukemia virus. This indication that the GLVR1 protein acts as a virus receptor does not reveal the protein's normal physiological role. We now report that GLVR1 is homologous to pho-4+, a phosphate permease of Neurospora crassa, at a level sufficiently high to predict that GLVR1 is also a transport protein, although the substrate transported remains unknown. To characterize the gene further, we have cloned cDNA for the mouse homolog of the gene, Glvr-1. The sequence of the murine protein differs from that of the human protein in 10% of residues, and it may be presumed that some of these differences are responsible for the inability of gibbon ape leukemia virus to infect mouse fibroblasts. Glvr-1 RNA is most abundant in mouse brain and thymus, although it is present in all tissues examined. The pattern of RNA expression found in mouse tissues was also found in rat tissues, in which the RNA was expressed at high levels in all compartments of the brain except the caudate nucleus and was expressed most abundantly early in embryogenesis. Thus, high-level expression of Glvr-1 appears to be restricted to specific tissues and may have developmental consequences.

Amino Acid Sequence↗
PubMed2003

Cortical orofacial motor representation in Old World monkeys, great apes, and humans. I. Quantitative analysis of cytoarchitecture.

Social life in anthropoid primates is mediated by interindividual communication, involving movements of the orofacial muscles for the production of vocalization and gestural expression. Although phylogenetic diversity has been reported in the auditory and visual communication systems of primates, little is known about the comparative neuroanatomy that subserves orofacial movement. The current study reports results from quantitative image analysis of the region corresponding to orofacial representation of primary motor cortex (Brodmann's area 4) in several catarrhine primate species (Macaca fascicularis, Papio anubis, Pongo pygmaeus, Gorilla gorilla, Pan troglodytes, and Homo sapiens) using the Grey Level Index method. This cortical region has been implicated in the execution of skilled motor activities such as voluntary facial expression and human speech. Density profiles of the laminar distribution of Nissl-stained neuronal somata were acquired from high-resolution images to quantify cytoarchitectural patterns. Despite general similarity in these profiles across catarrhines, multivariate analysis showed that cytoarchitectural patterns of individuals were more similar within-species versus between-species. Compared to Old World monkeys, the orofacial representation of area 4 in great apes and humans was characterized by an increased relative thickness of layer III and overall lower cell volume densities, providing more neuropil space for interconnections. These phylogenetic differences in microstructure might provide an anatomical substrate for the evolution of greater volitional fine motor control of facial expressions in great apes and humans.

Aged↗