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identification of paralogous herv-k ltrs on human chromosomes 3, 4, 7 and 11 in regions containing clusters of olfactory receptor genes.a locus harboring a human endogenous retroviral ltr (long terminal repeat) was mapped on the short arm of human chromosome 7 (7p22), and its evolutionary history was investigated. sequences of two human genome fragments that were homologous to the ltr-flanking sequences were found in human genome databases: (1) an ltr-containing dna fragment from region 3p13 of the human genome, which includes clusters of olfactory receptor genes and pseudogenes; and (2) a fragment of region 21q22.1 lacking ltr ...200111523799
the first discovery of a complete skeleton of a fossil orang-utan in a cave of the hoa binh province, vietnam.here we provide a description of the first complete adult fossil orang-utan skeleton from the asian mainland. this specimen, and remains of a juvenile orang, were collected in a late pleistocene cavern in the hoa binh province of the socialist republic of vietnam. the results confirm the suggestions by hooijer (1948) zool. meded. leiden29, 175-301 and later by schwartz et al. (1995) anthrop. pap. am. mus. nat. hist.76, 1-24, that ancient orang-utans had bigger teeth than those of modern pongo py ...200111535001
rapid detection of the erv-k(c4) retroviral insertion reveals further structural polymorphism of the complement c4 genes in old world primates.the fourth component of complement (c4) is coded for by two tandem-duplicated genes located in the class iii region of the mhc of humans as well as a number of primates. a c4 gene size polymorphism giving rise to two gene variants of 16 and 22.3 kb length can be attributed to a complete endogenous retroviral insertion of 6.3 kb termed erv-k(c4) in intron 9 of the long c4 genes. we developed a simple pcr-based screening assay to detect the presence of this insertion, and tested a number of unrela ...200111549842
a novel, nonclassical mhc class i molecule specific to the common chimpanzee.all expressed human mhc class i genes (hla-a, -b, -c, -e, -f, and -g) have functional orthologues in the mhc of the common chimpanzee (pan troglodytes). in contrast, a nonclassical mhc class i gene discovered in the chimpanzee is not present in humans or the other african ape species. in exons and more so in introns, this patr-al gene is similar to the expressed a locus in the orangutan, popy-a, suggesting they are orthologous. patr-al/popy-a last shared a common ancestor with the classical mhc- ...200111564803
positive selection of a gene family during the emergence of humans and african apes.gene duplication followed by adaptive evolution is one of the primary forces for the emergence of new gene function. here we describe the recent proliferation, transposition and selection of a 20-kilobase (kb) duplicated segment throughout 15 mb of the short arm of human chromosome 16. the dispersal of this segment was accompanied by considerable variation in chromosomal-map location and copy number among hominoid species. in humans, we identified a gene family (morpheus) within the duplicated s ...200111586358
comparative and functional anatomy of the mammalian lumbar spine.as an essential organ of both weight bearing and locomotion, the spine is subject to the conflict of providing maximal stability while maintaining crucial mobility, in addition to maintaining the integrity of the neural structures. comparative morphological adaptation of the lumbar spine of mammals, especially in respect to locomotion, has however received only limited scientific attention. specialised features of the human lumbar spine, have therefore not been adequately highlighted through com ...200111590593
species-specific evolution of repeated dna sequences in great apes.dna sequencing reveals that the genomes of the human, gorilla and chimpanzee share more than 98% homology. comparative chromosome painting and gene mapping have demonstrated that only a few rearrangements of a putative ancestral mammalian genome occurred during great ape and human evolution. however, interspecies representational difference analysis (rda) of the gorilla between human and gorilla revealed gorilla-specific dna sequences. cloning and sequencing of gorilla-specific dna sequences ind ...200111592477
assessing variability by joint sampling of alignments and mutation rates.when two sequences are aligned with a single set of alignment parameters, or when mutation parameters are estimated on the basis of a single "optimal" sequence alignment, the variability of both the alignment and the estimated parameters can be seriously underestimated. to obtain a more realistic impression of the actual uncertainty, we propose sampling sequence alignments and mutation parameters simultaneously from their joint posterior distribution given the two original sequences. we illustra ...200111677626
phylogeny of sine-r retroposons in asian apes.the sine-r retroposon family was derived from the long terminal repeats (ltrs) of human endogenous retrovirus k (herv-k) that had been active during the hominoid evolution. the retroposons and herv-k ltr elements have potential relevance to structural change and genetic variation of the hominoid genome. in our previous study, we found that the sine-r retroposons were hominoid specific. here we identified seventeen new sine-r retroposons (14 from orangutan and 3 from gibbon) from asian apes and p ...200111710532
human-specific duplication and mosaic transcripts: the recent paralogous structure of chromosome 22.in recent decades, comparative chromosomal banding, chromosome painting, and gene-order studies have shown strong conservation of gross chromosome structure and gene order in mammals. however, findings from the human genome sequence suggest an unprecedented degree of recent (<35 million years ago) segmental duplication. this dynamism of segmental duplications has important implications in disease and evolution. here we present a chromosome-wide view of the structure and evolution of the most hig ...200211731936
homosexual behavior in wild sumatran orangutans (pongo pygmaeus abelii).wild male sumatran orangutans at two study sites engaged in homosexual behavior. these observations demonstrate that homosexual behavior is not an artifact of captivity or contact with humans. in separate instances, homosexual behavior was associated with affiliative and agonistic behaviors. these observations add orangutans to the list of primates in which homosexual behavior forms part of the natural repertoire of sexual or sociosexual behavior.200111746281
molecular basis of evolutionary loss of the alpha 1,3-galactosyltransferase gene in higher primates.galactose-alpha1,3-galactose (alphagal) epitopes, the synthesis of which requires the enzyme product of alpha1,3-galactosyltransferase (alpha1,3gt), are sugar chains on the cell surface of most mammalian species. notable exceptions are higher primates including old world monkeys, apes, and humans. the alphagal-negative species as well as mice with deletion of the alpha1,3gt gene produce abundant anti-alphagal antibodies. the evolutionary loss of alphagal epitopes has been attributed to point mut ...200211773054
telomere biology and cellular aging in nonhuman primate cells.to determine how cellular aging is conserved among primates, we analyzed the replicative potential and telomere shortening in skin fibroblasts of anthropoids and prosimians. the average telomere length of the new world primates ateles geoffroyi (spider monkey) and saimiri sciureus (squirrel monkey) and the old world primates macaca mulatta (rhesus monkey), pongo pygmaeus (orangutan), and pan paniscus (pigmy chimpanzee) ranged from 4 to 16 kb. we found that telomere shortening limits the replicat ...200211777339
origin of human bipedalism: the knuckle-walking hypothesis revisited.some of the most long-standing questions in paleoanthropology concern how and why human bipedalism evolved. over the last century, many hypotheses have been offered on the mode of locomotion from which bipedalism originated. candidate ancestral adaptations include monkey-like arboreal or terrestrial quadrupedalism, gibbon- or orangutan-like (or other forms of) climbing and suspension, and knuckle-walking. this paper reviews the history of these hypotheses, outlines their predictions, and assesse ...200111786992
characterization of the mhc class i-related mr1 locus in nonhuman primates.we characterized the mhc-related 1 ( mr1) locus in two nonhuman primates species, pongo pygmaeus and pan troglodytes. mr1 cdna sequences encoding several isoforms generated through alternative splicing were observed in both species. amino acid alignment between the five species in which mr1 has been characterized to date - human, chimpanzee, orangutan, mouse, and rat - reveals a very high degree of conservation specially in the alpha1 and alpha2 domains of the molecule. the main differences conc ...200111797097
the 48 bp centromeric repeat is a functionally conserved motif in great apes and man showing protein-binding properties.the centromere-kinetochore complex is a chromosomal assembly site including repeat motifs and protein binding properties thus mediating chromosome motility and mitotic regulation. next to the alpha-satellite dna family as well as human satellite iii dna, contribution of other repetitive sequences has to be strongly considered in centromere function. here, we report the identification of centromeric 48 bp motifs, isolated from chimpanzee and orang-utan using an orthologous human dna probe. applyi ...200211824617
spontaneous use of magnitude discrimination and ordination by the orangutan (pongo pygmaeus).the ability to discriminate quantity is descriptive of general cognitive ability. in this study, the authors presented 2 orangutans (pongo pygmaeus) with a quantity judgment task. each trial consisted of 2 choices, ranging from 1 to 6 food items in each. the orangutan chose 1 of the quantities, which was removed, and the remaining array was given as a reward. in contrast to chimpanzees previously tested on the same task (s. t. boysen & g. g. berntson, 1995; s. t. boysen, g. g. berntson, m. b. ha ...200111824901
the solitary long terminal repeats of erv-9 endogenous retrovirus are conserved during primate evolution and possess enhancer activities in embryonic and hematopoietic cells.the solitary long terminal repeats (ltrs) of erv-9 endogenous retrovirus contain the u3, r, and u5 regions but no internal viral genes. they are middle repetitive dnas present at 2,000 to 4,000 copies in primate genomes. sequence analyses of the 5" boundary area of the erythroid beta-globin locus control region (beta-lcr) and the intron of the embryonic axin gene show that a solitary erv-9 ltr has been stably integrated in the respective loci for at least 15 million years in the higher primates ...200211836419
geographic and haplotype structure of candidate type 2 diabetes susceptibility variants at the calpain-10 locus.recently, a positional cloning study proposed that haplotypes at the calpain-10 locus (capn10) are associated with increased risk of type 2 diabetes, or non-insulin-dependent diabetes mellitus, in mexican americans, finns, and germans. to inform the interpretation of the original mapping results and to look for evidence for the action of natural selection on capn10, we undertook a population-based genotyping survey of the candidate susceptibility variants. first, we genotyped sites 43, 19, and 6 ...200211891618
human and ape molecular clocks and constraints on paleontological hypotheses.although the relationships of the living hominoid primates (humans and apes) are well known, the relationships of the fossil species, times of divergence of both living and fossil species, and the biogeographic history of hominoids are not well established. divergence times of living species, estimated from molecular clocks, have the potential to constrain hypotheses of the relationships of fossil species. in this study, new dna sequences from nine protein-coding nuclear genes in great apes are ...200111948213
mitochondrial 16s rrna sequence diversity of hominoids.we determined nucleotide sequences of the 16s rrna gene of mitochondrial dna (mtdna) (about 1.6 kb) for 35 chimpanzee, 13 bonobo, 10 gorilla, 16 orangutan, and 23 gibbon individuals. we compared those data with published sequences and estimated nucleotide diversity for each species. all the ape species showed higher diversity than human. we also constructed phylogenetic trees and networks. the two orangutan subspecies were clearly separated from each other, and sumatran orangutans showed much hi ...200111948216
male orangutan subadulthood: a new twist on the relationship between chronic stress and developmental arrest.both in the wild and in captivity, a marked and enduring arrest of secondary sexual developmental occurs in some male orangutans (pongo pygmaeus) (kingsley [1982] the orang-utan: its biology and conservation, the hague: junk; utami [2000]). researchers have hypothesized that chronic stress, perhaps related to aggression from mature males, causes endocrine changes altering growth and maturation rates in these males (maple [1980] orangutan behavior, new york: van nostrand reinhold; graham [1988] o ...200211953942
primate hepatitis b viruses - genetic diversity, geography and evolution.there are six well characterised genotypes (a-f) of human hepatitis b virus that have distinct geographic ranges which generally relate to chronic hbv infection. a seventh human genotype (g) has recently been described, but there is limited information on ethnic and geographic distribution. despite the fact that early studies indicated that hbv antigens were present in other primates, the prevailing dogma that hbv was a human disease precluded alternative explanations. within the past 5 years, h ...200211987138
disturbing behaviors of the orangutan. 200212030092
maintenance of self-imposed delay of gratification by four chimpanzees (pan troglodytes) and an orangutan (pongo pygmaeus).delay maintenance, which is the continuance over time of the choice to forgo an immediate, less preferred reward for a future, more preferred reward, was examined in 4 chimpanzees (pan troglodytes) and 1 orangutan (pongo pygmaeus). in the 1st experiment, the apes were presented with 20 chocolate pieces that were placed, one at a time, into a bowl that was within their reach. the apes could consume the available chocolate pieces at any time during a trial, but no additional pieces would be given. ...200212038494
human-specific organization of primary visual cortex: alternating compartments of dense cat-301 and calbindin immunoreactivity in layer 4a.there is evidence that the cortical anatomy of the magnocellular (m) visual pathway, which carries information about motion and luminance contrast, was modified in human evolution. recent results indicate that layer 4a of humans contains a meshwork of tissue bands that stain densely for nonphosphorylated neurofilament (npnf), a protein that is preferentially expressed in elements of the m pathway, whereas apes and monkeys lack a comparable pattern. here we examined the distribution of staining f ...200212050080
composition of psoas major muscle fibers compared among humans, orangutans, and monkeys.in primate species the m. psoas major, the only muscle simultaneously controlling the spinal column and lower extremity, is expected to reflect morpho-functional adaptation to diversified locomotor behavior. by using histochemical analysis with sudan black b staining, composition of different types of muscle fibers in the psoas major was compared between 2 japanese macaques, 2 hamadryas baboons, 2 anubis baboons, 2 orangutans, and 17 humans. the comparison has revealed unique features of this mu ...200212050900
the social organisation of a population of sumatran orang-utans.female orang-utans in a sumatran swamp forest live in large, but stable, and widely overlapping home ranges. they preferentially associate with some of their female neighbours, possibly relatives, to form socially distinct clusters that also experience reproductive synchrony. sexually mature males range more widely than females, but among them the dominant adult male has a relatively more limited range. his ranging and that of the subadult males reflect the local abundance of sexually attractive ...200212065937
genetic diversity and evolution of the human leptin locus tetranucleotide repeat.to better understand the evolutionary history of the gene region containing the multifunctional adipose tissue hormone leptin, we genotyped 1,957 individuals from 12 world populations for a highly variable tetranucleotide repeat polymorphism located 476 bp 3' of exon 3 of the leptin gene. common alleles shared among populations, alleles specific to geographically defined populations, and the homologous alleles in the common and pygmy chimpanzee, the gorilla and the orangutan, were sequenced to d ...200212073010
nk cell receptors of the orangutan (pongo pygmaeus): a pivotal species for tracking the coevolution of killer cell ig-like receptors with mhc-c.cd94, nkg2, ly49, and killer cell ig-like receptor (kir) expressed by orangutan peripheral blood cells were examined by cloning and sequencing cdna from a panel of individuals. orthologs of human cd94, nkg2a, d, and f were defined. nkg2c and e are represented by one gene, popy-nkg2ce, that is equidistant from the two human genes. several popy-cd94, nkg2a, and nkg2ce alleles were defined. popy-ly49l is expressed in cultured nk cells and has a sequence consistent with it encoding a functional rece ...200212077248
measuring fruit patch size for three sympatric indonesian primate species.food availability is one of the basic factors affecting primate density and socioecology, but food availability is difficult to assess. two different ways to obtain accurate estimates of food availability have been proposed: using phenology data or using the behaviour of animals. phenology data can be refined by only including trees that are large enough to be used; including (potential) tree species in which by the concerned primate species forage; or including (fruiting) trees of these species ...200212091744
relative placement of the mandibular fossa in great apes and humans.several researchers have investigated, or commented on, the relative placement of the hominin mandibular fossa with regard to brain expansion and masticatory function. two confounding factors are identified in this previous work. first, a number of different measurement techniques have been applied, confusing comparisons between studies. second, the effects of squamous thickening due to temporal bone pneumatization are shown to influence measurements based relative to the ectocranial margin of t ...200212098210
a 76-kb duplicon maps close to the bcr gene on chromosome 22 and the abl gene on chromosome 9: possible involvement in the genesis of the philadelphia chromosome translocation.a patient with a typical form of chronic myeloid leukemia was found to carry a large deletion on the derivative chromosome 9q+ and an unusual bcr-abl transcript characterized by the insertion, between bcr exon 14 and abl exon 2, of 126 bp derived from a region located on chromosome 9, 1.4 mb 5' to abl. this sequence was contained in the bacterial artificial chromosome rp11-65j3, which in fluorescence in situ hybridization experiments on normal metaphases was found to detect, in addition to the p ...200212114534
identification of v1r-like putative pheromone receptor sequences in non-human primates. characterization of v1r pseudogenes in marmoset, a primate species that possesses an intact vomeronasal organ.the vomeronasal organ (vno) is responsible in terrestrial vertebrates for the sensory perception of some pheromones, chemicals that elicit characteristic behaviors among individuals of the same species. two multigene families (v1r, v2r) that encode proteins with seven putative transmembrane domains that are expressed selectively in different neuron subsets of the vno have been described in rodents. pheromone-induced behaviors and a functional vno have been described in a number of mammals, but t ...200212142329
chimeric co-stimulatory molecules that selectively act through cd28 or ctla-4 on human t cells.cd28 and ctla-4 (cd152) play a pivotal role in the regulation of t cell activation. upon ligation by cd80 (b7-1) or cd86 (b7-2), cd28 induces t cell proliferation, cytokine production, and effector functions, whereas ctla-4 signaling inhibits expansion of activated t cells and induces tolerance. therefore, we hypothesized that co-stimulatory molecules that preferentially bind cd28 or ctla-4 would have dramatically altered biological properties. we describe directed molecular evolution of cd80 ge ...200212167647
identification of two novel primate-specific genes in dscr.we recently helped to complete the sequence of human chromosome 21 at a very high level of accuracy. using this sequence we identified two novel genes, designated dscr9 and dscr10, in the so-called down syndrome critical region (dscr) by computational gene prediction and subsequent cdna cloning. both dscr9 and dscr10 are expressed preferentially in testis and encode functionally unknown proteins with 149 and 87 amino acid residues, respectively. zoo blot analysis suggested that both genes are ex ...200212168953
molecular evolution of foxp2, a gene involved in speech and language.language is a uniquely human trait likely to have been a prerequisite for the development of human culture. the ability to develop articulate speech relies on capabilities, such as fine control of the larynx and mouth, that are absent in chimpanzees and other great apes. foxp2 is the first gene relevant to the human ability to develop language. a point mutation in foxp2 co-segregates with a disorder in a family in which half of the members have severe articulation difficulties accompanied by lin ...200212192408
[a new kiaa1245 gene family with or without herv-k ltrs in their introns].a transcript containing the long terminal repeat (ltr) and the sequence homologous to the kiaa1245 mrna fragment were revealed among the transcribed ltrs of human endogenous viruses of the k family in normal and tumor tissues. ten other sequences with a high level of homology to the kiaa1245 mrna were found in the genbank. the intron-exon structures were determined for all the sequences, and their exon sequences were compared. the comparison showed that they differ both in the extent of the exon ...200212197392
contribution of homoplasy and of ancestral polymorphism to the evolution of genes in anthropoid primates.molecular phylogenies of lineages that split from one another in short succession are often difficult to resolve because different loci and different sites within the same locus yield incongruent relationships. the incongruity is commonly attributed to two causes: differential assortment of ancestral polymorphisms and homoplasy. to assess the relative contribution of these two causes, sequences of 57 segments from 51 loci in six primate lineages (human, chimpanzee, gorilla, orangutan, macaque, a ...200212200478
new tool use by wild sumatran orangutans (pongo pygmaeus abelii).two forms of tool use by wild sumatran orangutans are reported from the agusan monitoring station, a new research site in indonesia. one form, a branch "hook" used in locomotion, has not been reported previously in wild orangutans. the second form, a leaf "pad" used to protect the hands and feet from thorns while feeding, shares similarities in form and function with a tool type used by orangutans at ketambe, a nearby research site. both instances of tool use occurred in areas of disturbance, an ...200212237938
a geometric approach to cranial sexual dimorphism in the orang-utan.adult craniofacial morphology is quantified and compared using euclidean distance matrix analysis (edma), a three-dimensional morphometric method for the comparison of forms, which localizes form differences between comparative groups. results indicate that the number and magnitude of differences between male and female crania are striking. the face, basicranium and neurocranium exhibit the most dimorphism, while the palate shows the least. significant differences also exist between young adult ...200212399656
molecular evolution of igg subclass among nonhuman primates: implication of differences in antigenic determinants among apes.the cross-reactivity of five different rabbit polyclonal antibodies to human igg and igg subclass (igg1, igg2, igg3, and igg4) was determined by competitive elisa with nine nonhuman primate species including five apes, three old world monkeys, and one new world monkey. as similar to those previously reported, the reactivity of anti-human igg antibody with plasma from different primate species was closely related with phylogenic distance from human. every anti-human igg subclass antibody showed l ...200212426468
genetic polymorphism of the major regulatory element hs-40 upstream of the human alpha-globin gene cluster.the highly conserved 350-bp major regulatory element hs-40 (or alphamre) upstream of the human alpha-globin gene cluster is involved in the regulation of alpha-globin gene expression. the study of alphamre differences between human populations and the evolution of alphamre sequences in mammals may lead to a better understanding of the function and importance of this element in the regulation of expression of the downstream alpha-cluster. denaturing gradient gel electrophoresis was used to determ ...200212437670
conservation of the class i beta-tubulin gene in human populations and lack of mutations in lung cancers and paclitaxel-resistant ovarian cancers.the goal of this study was to determine the prevalence of sequence variants in the class i beta-tubulin (clone m40) gene and their occurrence in human tumors and cancer cell lines. dna was isolated from 93 control individuals representing a wide variety of ethnicities, 49 paclitaxel-naive specimens (16 ovarian cancers, 17 non-small cell lung cancers, and 16 ovarian cancer cell lines), and 30 paclitaxel-resistant specimens (9 ovarian cancers, 9 ovarian cancer cell lines, and 12 ovarian cancer xen ...200212467216
three duplicons form a novel chimeric transcription unit in the pericentromeric region of chromosome 22q11.pericentromeric regions of human chromosomes are preferential sites for the integration of duplicated dna, or "duplicons", which often contain gene fragments. although pericentromeric regions appear to be genomic junkyards, they could also be the birthplace of new genes with novel functions. we have characterized a chimeric transcription unit (cat eye syndrome critical region gene 7, cecr7) formed from three duplicons in the pericentromeric region of chromosome 22q. cecr7 exons show similarity t ...200312483300
orangutan cultures and the evolution of material culture.geographic variation in some aspects of chimpanzee behavior has been interpreted as evidence for culture. here we document similar geographic variation in orangutan behaviors. moreover, as expected under a cultural interpretation, we find a correlation between geographic distance and cultural difference, a correlation between the abundance of opportunities for social learning and the size of the local cultural repertoire, and no effect of habitat on the content of culture. hence, great-ape cultu ...200312511649
comparative urinary androstanes in the great apes.urinary androstanes from seven species of male great apes (human, bonobo, chimpanzee, lowland gorilla, mountain gorilla, bornean orangutan, and sumatran orangutan) were separated by hplc and detected by ria using two testosterone antibodies. all animals examined showed the presence of testosterone and six additional immunoreactive peaks. although testosterone was the dominant peak (85%) in human urine, its proportion in urine was much less in the other apes, ranging from a high of 59% in the bon ...200312535626
statistical alignment based on fragment insertion and deletion models.the topic of this paper is the estimation of alignments and mutation rates based on stochastic sequence-evolution models that allow insertions and deletions of subsequences ('fragments') and not just single bases. the model we propose is a variant of a model introduced by thorne et al., (j. mol. evol., 34, 3-16, 1992). the computational tractability of the model depends on certain restrictions in the insertion/deletion process; possible effects we discuss.200312611804
genomic dna insertions and deletions occur frequently between humans and nonhuman primates.comparative dna sequence studies between humans and nonhuman primates will be important for understanding the genetic basis of the phenotypic differences between these species. here we compare approximately 27 mb of human chromosome 21 with chimpanzee dna sequences identifying 57 genomic rearrangements (deletions and insertions ranging in size from 0.2 to 8.0 kb) between the two species. these rearrangements are distributed along the entire length of chromosome 21, with approximately 35% found i ...200312618364
large-scale variation among human and great ape genomes determined by array comparative genomic hybridization.large-scale genomic rearrangements are a major force of evolutionary change and the ascertainment of such events between the human and great ape genomes is fundamental to a complete understanding of the genetic history and evolution of our species. here, we present the results of an evolutionary analysis utilizing array comparative genomic hybridization (array cgh), measuring copy-number gains and losses among these species. using an array of 2460 human bacterial artificial chromosomes (bacs) (1 ...200312618365
a middle miocene hominoid from thailand and orangutan origins.the origin of orangutans has long been debated. sivapithecus is considered to be the closest ancestor of orangutans because of its facial-palatal similarities, but its dental characteristics and postcranial skeleton do not confirm this phylogenetic position. here we report a new middle miocene hominoid, cf. lufengpithecus chiangmuanensis n. sp. from northern thailand. its dental morphology relates it to the pongo clade, which includes lufengpithecus, sivapithecus, gigantopithecus, ankarapithecus ...200312621432
microarray analysis of nonhuman primates: validation of experimental models in neurological disorders.nonhuman primates (nhps) have provided robust experimental animal models for many human-related diseases due to their similar physiologies. nonetheless, profound differences remain in the acquisition, progression, and outcome of important diseases such as aids and alzheimer's, for which the underlying basis remains obscure. we explored the utility of human high-density oligonucleotide arrays to survey the transcription profile of nhp genomes. total rna from prefrontal cortices of human (homo sap ...200312626435
estimation of divergence times for major lineages of primate species.although the phylogenetic relationships of major lineages of primate species are relatively well established, the times of divergence of these lineages as estimated by molecular data are still controversial. this controversy has been generated in part because different authors have used different types of molecular data, different statistical methods, and different calibration points. we have therefore examined the effects of these factors on the estimates of divergence times and reached the fol ...200312644563
the impact of ecological conditions on the prevalence of malaria among orangutans.contemporary human land use patterns have led to changes in orangutan ecology, such as the loss of habitat. one management response to orangutan habitat loss is to relocate orangutans into regions of intact, protected habitat. young orangutans are also kept as pets and have at times been a valuable commodity in the illegal pet trade. in response to this situation, government authorities have taken law enforcement action by removing these animals from private hands and attempted to rehabilitate a ...200212653303
molecular phylogeny and evolution of the human endogenous retrovirus herv-w ltr family in hominoid primates.long terminal repeats (ltrs) of human endogenous retrovirus (herv) have contributed to the structural change or genetic variation of primate genome that are connected to speciation and evolution. using genomic dnas that were derived from hominoid primates (chimpanzee, gorilla, orangutan, and gibbon), we performed pcr amplification and identified thirty herv-w ltr elements. these ltr elements showed a 82-98% sequence similarity with herv-w ltr (af072500). specifically, additional sequences (gccac ...200312661771
scoliosis in an orangutan.the first case of scoliosis in an orangutan spine is reported.200312671370
health evaluation of free-ranging and semi-captive orangutans (pongo pygmaeus pygmaeus) in sabah, malaysia.baseline data on health of free-ranging wildlife is essential to evaluate impacts of habitat transformation and wildlife translocation, rehabilitation, and reintroduction programs. health information on many species, especially great apes, is extremely limited. between 1996 and 1998, 84 free-ranging orangutans captured for translocation, underwent a complete health evaluation. analogous data were gathered from 60 semi-captive orangutans in malaysia. baseline hematology and serology; vitamin, min ...200312685070
gorilla ( gorilla gorilla gorilla) and orangutan ( pongo abelii) understanding of first- and second-order relations.four orangutans and one gorilla matched images in a delayed matching-to-sample (dmts) task based on the relationship between items depicted in those images, thus demonstrating understanding of both first- and second-order relations. subjects matched items on the basis of identity, color, or shape (first-order relations, experiment 1) or same shape, same color between items (second-order relations, experiment 2). four of the five subjects performed above chance on the second-order relations dmts ...200312687418
comparative study of urinary reproductive hormones in great apes.urinary estrone conjugates (e(1)c), pregnanediol-3-glucuronide (pdg), and follicle-stimulating hormone (fsh) were determined by enzyme immunoassays (eias) during the normal menstrual cycle in the orangutan, gorilla, chimpanzee, and bonobo. furthermore, the data were compared to those levels in the human and long-tailed macaque. the results showed a typical preovulatory e(1)c surge and postovulatory increase in pdg in all species. the pattern of e(1)c during the menstrual cycle in the great apes ...200312687484
growth and sexual dimorphism in orangutan crania: a three-dimensional approach.new insights may be gleaned by taking an ontogenetic approach to investigations of adult dimorphism. previous work in this area relied on traditional, caliper-based, morphometric methods, and produced conflicting results. this study uses a three-dimensional (3-d) approach for both local and global form comparisons of sex-specific growth and growth patterns. 3-d coordinate data were collected for 20 landmarks on 94 orangutan crania divided into five developmental stages. data were analyzed using ...200312687580
organization of seminiferous epithelium in primates: relationship to spermatogenic efficiency, phylogeny, and mating system.the succession in time and space of specific germ cell associations, denoted as spermatogenic stages, is a typical feature of mammalian spermatogenesis. the arrangement of these stages is either single stage (one spermatogenic stage per tubular cross-section) or multistage (more than one spermatogenic stage per tubular cross-section). it has been proposed that the single-stage versus multistage arrangement is related to spermatogenic efficiency and that the multistage arrangement is typical for ...200312700190
genetic sex identification in orangutans.to date, no established protocol for genetic sex identification in orangutans (pongo pygmaeus) exists. in nearly all apes (gibbons, gorillas, chimpanzees, and humans), genetic sex identification is possible using the amelogenin gene because copies located on x and y chromosomes have different sizes. here we report that orangutan sex identification can be resolved through multiplex polymerase chain reaction (pcr) of the y-linked sry locus and the amelogenin locus. pcr amplifications of orangutan ...200312712768
neutral substitutions occur at a faster rate in exons than in noncoding dna in primate genomes.point mutation rates in exons (synonymous sites) and noncoding (introns and intergenic) regions are generally assumed to be the same. however, comparative sequence analyses of synonymous substitutions in exons (81 genes) and that of long intergenic fragments (141.3 kbp) of human and chimpanzee genomes reveal a 30%-60% higher mutation rate in exons than in noncoding dna. we propose a differential cpg content hypothesis to explain this fundamental, and seemingly unintuitive, pattern. we find that ...200312727904
pollical oblique ligament in humans and non-human primates.a morphological study of the oblique ligament in the thumb is presented. the ligament was consistently described in human specimens and compared with dissections of non-human primates from different species. the oblique ligament was found in some, but not all, specimens in each of the following species examined: chimpanzee, orangutan, gibbon, anubis baboon, hamadryas baboon, squirrel monkey, lemur and marmoset. a revised identity of the oblique ligament is proposed as a reinforced distal border ...200312739617
implications of natural selection in shaping 99.4% nonsynonymous dna identity between humans and chimpanzees: enlarging genus homo.what do functionally important dna sites, those scrutinized and shaped by natural selection, tell us about the place of humans in evolution? here we compare approximately 90 kb of coding dna nucleotide sequence from 97 human genes to their sequenced chimpanzee counterparts and to available sequenced gorilla, orangutan, and old world monkey counterparts, and, on a more limited basis, to mouse. the nonsynonymous changes (functionally important), like synonymous changes (functionally much less impo ...200312766228
new approaches in hominoid taxonomy: morphometrics.we report here on new cranial data relevant to hominoid taxonomic analyses, based on a study of 438 skulls belonging to 13 nonhuman living hominoid taxa. nineteen landmarks were selected to describe the overall shape of the maxillofacial complex, in order to investigate its discriminative power in taxonomic analyses. we used a geometric morphometrics approach to depict morphological variation from the genus down to the subspecific level, and we evaluated whether our morphologic criteria are rele ...200312772209
divergence of the genes on human chromosome 21 between human and other hominoids and variation of substitution rates among transcription units.the study of genomic divergence between humans and primates may provide insight into the origins of human beings and the genetic basis of unique human traits and diseases. chromosome 21 is the smallest chromosome in the human genome, and some of its regions have been implicated in mental retardation and other diseases. in this study, we sequenced the coding and regulatory regions of 127 known genes on human chromosome 21 in dna samples from human and chimpanzees and a part of the corresponding g ...200312826612
structural and evolutionary analysis of an orangutan foamy virus.the full-length proviral genome of a foamy virus infecting a bornean orangutan was amplified, and its sequence was analyzed. although the genome showed a clear resemblance to other published foamy virus genomes from apes and monkeys, phylogenetic analysis revealed that simian foamy virus sfvora was evolutionarily equidistant from foamy viruses from other hominoids and from those from old world monkeys. this finding suggests an independent evolution within its host over a long period of time.200312857929
polymorphism of human and primate rantes, cx3cr1, ccr2 and cxcr4 genes with regard to hiv/siv infection.among genes that influence human susceptibility to hiv (human immunodeficiency virus) infection or aids (acquired immunodeficiency syndrome) progression, chemokine-receptor and chemokine genes were extensively studied because of their role as hiv co-receptors or co-receptor competitors, respectively. we have studied in non-human primates (chimpanzee, gorilla, gibbon, orang-utan, crab-eating and rhesus macaque, baboon and marmoset) the rantes, ccr2 and cx3cr1 gene sequences in regions surrounding ...200312879309
characterization of the low-copy herv-fc family: evidence for recent integrations in primates of elements with coding envelope genes.in a previous search based on the envelope gene, we had identified two related proviral elements that could not be included in identified erv families. an in silico database screening associated with an in vivo polymerase chain reaction search using primers in the reverse transcriptase domain, now allowed identification of a series of related elements, found at a limited number in simians. a phylogenetic analysis led to their inclusion in a new family of endogenous retroviruses with limited expa ...200312890629
natural selection on the olfactory receptor gene family in humans and chimpanzees.the olfactory receptor (or) genes constitute the largest gene family in mammalian genomes. humans have >1,000 or genes, of which only approximately 40% have an intact coding region and are therefore putatively functional. in contrast, the fraction of intact or genes in the genomes of the great apes is significantly greater (68%-72%), suggesting that selective pressures on the or repertoire vary among these species. we have examined the evolutionary forces that shaped the or gene family in humans ...200312908129
the 200-kb segmental duplication on human chromosome 21 originates from a pericentromeric dissemination involving human chromosomes 2, 18 and 13.regions close to human centromeres contain dna fragments spanning hundreds of kilobases that exhibit a high degree of sequence identity (>95%). here we report the genomic structure and evolution of a family of four paralogous regions related to a 220-kb genomic fragment present on the long arm of human chromosome 21 (21q22.1). phylogenetic classification of the paralogous sequences obtained from the draft of the human genome project are in agreement with results from comparative fluorescence in ...200312909340
spatial rotations and transpositions in orangutans ( pongo pygmaeus) and chimpanzees ( pan troglodytes).this study investigated the ability of three chimpanzees and three orangutans to track the position of a reward after a series of displacements. the reward was placed under one of two opaque containers resting on a platform. experiment 1 investigated rotational displacements in which the platform was rotated 0 degrees, 180 degrees, or 360 degrees. experiment 2 investigated transpositional displacements in which the platform remained stationary while the containers either remained stationary, or ...200312937996
cranial capacity of oreopithecus bambolii.from a plaster reconstruction of the skull of the august 1958 skeleton, the cranial capacity of oreopithecus bambolii has been estimated as fallingbetween 276 and 529 cubic centimeters, thus within the ranges of variation of both orangutan and chimpanzee. in cranial capacity, therefore, and probably in body-brain ratio as well, oreopithecus is a hominoid.196013835142
chromosomes of the orang-utan (pongo pygmaeus). 196113878899
[the lamination of the masseter muscle of the crab-eating monkey, the orang-utan, and the gorilla]. 196214002709
cutaneous sensory end organs of some anthropoid apes.the organized end organs of nerves in glabrous skin of the chimpanzee, orangutan, and gibbon are similar to those of man in form and distribution but are more numerous on the soles of the feet than in man. i found cholinesterase in all the end organs of all these animals and, in the gibbon, alkaline phosphatase as well.196214007521
social learning by orangutans (pongo abelii and pongo pygmaeus) in a simulated food-processing task.increasing evidence for behavioral differences between populations of primates has created a resurgence of interest in examining mechanisms of information transfer between individuals. the authors examined the social transmission of information in 15 captive orangutans (pongo abelii and pongo pygmaeus) using a simulated food-processing task. experimental subjects were shown 1 of 2 methods for removing a suite of defenses on an "artificial fruit." control subjects were given no prior exposure bef ...200314498803
development and validation of the y-plex 5, a y-chromosome str genotyping system, for forensic casework.a genotyping system, y-plex 5, has been developed for use in human identification. the y-plex 5 enables simultaneous amplification of five polymorphic short tandem repeat (str) loci residing on the y-chromosome, which are dys389i, dys389ii, dys439, dys438, and dys392. as little as 0.1 ng of template dna can be used for analysis. the specificity of the amplification reaction enabled analysis of male dna in a male: female dna mixture at a ratio of 1:600. mean stutter values ranged from 3.60-10.97% ...200314535662
gait parameters in vertical climbing of captive, rehabilitant and wild sumatran orang-utans (pongo pygmaeus abelii).vertical climbing is central to the locomotor and foraging strategies of the great apes and, indeed, to theories about the evolution of locomotor specialisations of hominoid primates. nevertheless, its kinematics have yet to be fully evaluated. here, we present spatio-temporal parameters of 80 climbing sequences containing 560 limb cycles obtained from video recordings of captive, rehabilitant and wild sumatran orang-utans (pongo pygmaeus abelii). gait parameters such as cycle duration, duty fac ...200314555748
chromosomal phylogeny and evolution of gibbons (hylobatidae).although human and gibbons are classified in the same primate superfamily (hominoidae), their karyotypes differ by extensive chromosome reshuffling. to date, there is still limited understanding of the events that shaped extant gibbon karyotypes. further, the phylogeny and evolution of the twelve or more extant gibbon species (lesser apes, hylobatidae) is poorly understood, and conflicting phylogenies have been published. we present a comprehensive analysis of gibbon chromosome rearrangements an ...200314569461
mixed-model reanalysis of primate data suggests tissue and species biases in oligonucleotide-based gene expression profiles.an emerging issue in evolutionary genetics is whether it is possible to use gene expression profiling to identify genes that are associated with morphological, physiological, or behavioral divergence between species and whether these genes have undergone positive selection. some of these questions were addressed in a recent study (enard et al. 2002) of the difference in gene expression among human, chimp, and orangutan, which suggested an accelerated rate of divergence in gene expression in the ...200314573485
is somnambulism a distinct disorder of humans and not seen in non-human primates?though somnambulism (sleepwalking) is a well-recognized sleep disorder in humans, a biomedical literature search in medline and primate literature bibliographic databases showed no publications on sleepwalking in non-human primates. from this finding, two inferences can be made. first is that somnambulism may be present in non-human primates; but due to limitations in expertise and methodological resources as well as narrow focus of research interest, until now researchers have not detected it i ...200314592779
high mutation rates in human and ape pseudoautosomal genes.it has been suggested that recombination may be mutagenic, which, if true, would inflate intraspecies diversity and interspecies silent divergence in regions of high recombination. here, we test this hypothesis comparing human/orangutan genome-wide non-coding divergence (k) to that in the pseudoautosomal genes which were reported to recombine much more frequently than the rest of the genome. we demonstrate that, compared to the average human/orangutan non-coding divergence (k=3%), the substituti ...200314604793
gene arrangement at the rhesus blood group locus of chimpanzees detected by fiber-fish.the rhesus (rh) blood group system in humans is encoded by two genes with high sequence homology. these two genes, namely, rhce and rhd, have been implied to be duplicated during evolution. however, the genomic organization of rh genes in chimpanzees and other nonhuman primates has not been precisely studied. we analyzed the arrangement of the rh genes of chimpanzees (pan troglodytes) by two-color fluorescence in situ hybridization on chromatin dna fibers (fiber-fish) using two genomic dna probe ...200314610358
homology of primate dna fragments for estrous-associated oviductal glycoprotein.in this study, the dna fragments encoded for oviduct egp were amplified by pcr method. corresponding sequences from chimpanzee, orangutan and human were similarly amplified, but we failed to amplify the corresponding dna sequences from: spider monkey, salmon and several different species of rodents, bandicoot, sheep and pig. through analyzing the restriction enzyme map and the dna sequence of the amplified fragments from primates, the data suggest that monkey and human dna encoded for egp are ge ...200314641477
victorian spectacle: julia pastrana, the bearded and hairy female.julia pastrana toured europe in the late 1850s advertising herself as the 'bearded and hairy lady' or 'nonedescript'. she suffered from a rare inherited disorder, not understood until the late 20th century, which manifested itself in facial distortion and considerable facial hair in the male pattern. doctors, as well as sensation seekers, were very keen to examine her. her story is unusual, not least because she was mummified after death by her husband-manager and continued to tour as a mounted ...200314652038
a gradient of silent substitution rate in the human pseudoautosomal region.it has been demonstrated that recombination in the human p-arm pseudoautosomal region (p-par) is at least twenty times more frequent than the genomic average of approximately 1 cm/mb, which may affect substitution patterns and rates in this region. here i report the analysis of substitution patterns and rates in 10 human, chimpanzee, gorilla, and orangutan genes across the p-par. between species silent divergence in the p-par forms a gradient, increasing toward the telomere. the correlation of s ...200414660686
plasticity of human chromosome 3 during primate evolution.comparative mapping of more than 100 region-specific clones from human chromosome 3 in bornean and sumatran orangutans, siamang gibbon, and old and new world monkeys allowed us to reconstruct ancestral simian and hominoid chromosomes. a single paracentric inversion derives chromosome 1 of the old world monkey presbytis cristata from the simian ancestor. in the new world monkey callithrix geoffroyi and siamang, the ancestor diverged on multiple chromosomes, through utilizing different breakpoints ...200414706448
hepatitis b virus genotypes: comparison of genotyping methods.there are eight genotypes of hbv designated a to h based on greater than 8% nucleotide variation over the entire genome. hepadnaviruses infecting primates like the chimpanzee, orangutan and gibbon are very similar and can be regarded as genotypes of hbv. the eight genotypes of hbv show a distinct geographical distribution and influence the course of disease and the prognosis of treatment. due to the variability of hbv, diagnostic procedures risk giving false-negative results or reporting an inac ...200414716688
referential understanding of videos in chimpanzees (pan troglodytes), orangutans (pongo pygmaeus), and children (homo sapiens).performance on identical search tasks based on cues directly perceived or indirectly perceived through video were compared among a group of 4 adult chimpanzees (pan troglodytes), a group of 2 adult orangutans (pongo pygmaeus), and a group of 36 children (between 2 and 3 years of age). children comprehended directly perceived cues but had difficulty with video cues. in contrast, chimpanzees and 1 orangutan were successful in using video to guide their search for a hidden object. two follow-up stu ...200314717644
tool-use and tool-making by captive, group-living orangutans (pongo pygmaeus abelii) at an artificial termite mound.the present study examined the use and making of tools to obtain foodstuffs in artificial-mound holes by five captive, group-living sumatran orangutans (pongo pygmaeus abelii). three adult orangutans frequently stripped leaves and twigs from a branch provided (tool-making), and then inserted the tool into a hole to obtain foodstuffs (tool-using). a 5-year-old female juvenile usually used the tools that adult orangutans had previously used, but rarely made tools herself. a 2-year-old male infant ...200414744550
lineage-specific homogenization of the polyubiquitin gene among human and great apes.ubiquitin is a highly conserved protein, and is encoded by a multigene family among eukaryote species. the polyubiquitin genes, ubb and ubc, comprise tandem multiple ubiquitin coding units without a spacer region or intron. we determined nucleotide sequences for the ubb and ubc of human, chimpanzee, gorilla, and orangutan. the ubiquitin repeat number of ubb was constant (3) in human and great apes, while that of ubc varied: 6 to 11 for human, 10 to 12 for chimpanzee, 8 for gorilla, and 10 for or ...200314745543
phylogenetic relationships in the lymphocryptovirus genus of the gammaherpesvirinae.complete dna sequences were determined for the glycoprotein b (gb) genes of four viruses from the genus lymphocryptovirus, whose hosts had been assigned as baboon, orangutan, chimpanzee and gorilla. together with published sequences for the gb genes of three lymphocryptoviruses, namely the human pathogen epstein-barr virus (ebv), a rhesus monkey virus and a marmoset virus, the sequences were used to investigate evolutionary relationships in the genus. the chimpanzee and orangutan viruses' sequen ...200414749184
a new orang-utan relative from the late miocene of thailand.the fossil record of the living great apes is poor. new fossils from undocumented areas, particularly the equatorial forested habitats of extant hominoids, are therefore crucial for understanding their origins and evolution. two main competing hypotheses have been proposed for orang-utan origins: dental similarities support an origin from lufengpithecus, a south chinese and thai middle miocene hominoid; facial and palatal similarities support an origin from sivapithecus, a miocene hominoid from ...200414749830
the endogenous retroviral locus ervwe1 is a bona fide gene involved in hominoid placental physiology.the definitive demonstration of a role for a recently acquired gene is a difficult task, requiring exhaustive genetic investigations and functional analysis. the situation is indeed much more complicated when facing multicopy gene families, because most or portions of the gene are conserved among the hundred copies of the family. this is the case for the ervwe1 locus of the human endogenous retrovirus w family (herv-w), which encodes an envelope glycoprotein (syncytin) likely involved in trophob ...200414757826
amino-acid changes acquired during evolution by olfactory receptor 912-93 modify the specificity of odorant recognition.the sense of smell in mammals can perceive and discriminate a wide variety of volatile odorants. odorants bind to specific olfactory receptors (ors) to initiate an action potential that transduces olfactory information to the olfactory cortex. we previously identified the structural motifs of odorant molecules (aliphatic 2- or 3-ketones) required to activate mouse or912-93 by detection of the odorant response using calcium measurement in transfected cells. in order to study changes in the specif ...200414962981
hypothesis for the causes and periodicity of repetitive linear enamel hypoplasia in large, wild african (pan troglodytes and gorilla gorilla) and asian (pongo pygmaeus) apes.repetitive linear enamel hypoplasia (rleh) is often observed in recent large-bodied apes from africa and asia as well as mid- to late miocene sites from spain to china. the ubiquity and periodicity of rleh are not understood. its potential as an ontogenetic marker of developmental stress in threatened species (as well as their ancient relatives) makes rleh an important if enigmatic problem. we report research designed to show the periodicity of rleh among west african pan troglodytes (12 male, 3 ...200414968420
interactions of decay-accelerating factor (daf) with haemagglutinating human enteroviruses: utilizing variation in primate daf to map virus binding sites.a cellular receptor for the haemagglutinating enteroviruses (hev), and the protein that mediates haemagglutination, is the membrane complement regulatory protein decay accelerating factor (daf; cd55). although primate daf is highly conserved, significant differences exist to enable cell lines derived from primates to be utilized for the characterization of the daf binding phenotype of human enteroviruses. thus, several distinct daf-binding phenotypes of a selection of hevs (viz. coxsackievirus a ...200414993659
levels of abstraction in orangutan (pongo abelii) categorization.levels of abstraction have rarely been manipulated in studies of natural concept formation in nonhumans. isolated examples have indicated that animals, relative to humans, may learn concepts at varying levels of abstraction with differential ease. the ability of 6 orangutans (pongo abelii) of various ages to make natural concept discriminations at 3 levels of abstraction was therefore investigated. the orangutans were rewarded for selecting photos of orangutans instead of humans and other primat ...200415008667
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