Browse
Submit Data
Databases
API
Help

Dataset Information

33 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans.

ABSTRACT: Retroviral infections of the germline have the potential to episodically alter gene function and genome structure during the course of evolution. Horizontal transmissions between species have been proposed, but little evidence exists for such events in the human/great ape lineage of evolution. Based on analysis of finished BAC chimpanzee genome sequence, we characterize a retroviral element (Pan troglodytes endogenous retrovirus 1 [PTERV1]) that has become integrated in the germline of African great ape and Old World monkey species but is absent from humans and Asian ape genomes. We unambiguously map 287 retroviral integration sites and determine that approximately 95.8% of the insertions occur at non-orthologous regions between closely related species. Phylogenetic analysis of the endogenous retrovirus reveals that the gorilla and chimpanzee elements share a monophyletic origin with a subset of the Old World monkey retroviral elements, but that the average sequence divergence exceeds neutral expectation for a strictly nuclear inherited DNA molecule. Within the chimpanzee, there is a significant integration bias against genes, with only 14 of these insertions mapping within intronic regions. Six out of ten of these genes, for which there are expression data, show significant differences in transcript expression between human and chimpanzee. Our data are consistent with a retroviral infection that bombarded the genomes of chimpanzees and gorillas independently and concurrently, 3-4 million years ago. We speculate on the potential impact of such recent events on the evolution of humans and great apes.

SUBMITTER: Yohn CT

PROVIDER: S-EPMC1054887 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Lineage-Specific Changes in Biomarkers in Great Apes and Humans.

Project description:Although human biomedical and physiological information is readily available, such information for great apes is limited. We analyzed clinical chemical biomarkers in serum samples from 277 wild- and captive-born great apes and from 312 healthy human volunteers as well as from 20 rhesus macaques. For each individual, we determined a maximum of 33 markers of heart, liver, kidney, thyroid and pancreas function, hemoglobin and lipid metabolism and one marker of inflammation. We identified biomarkers that show differences between humans and the great apes in their average level or activity. Using the rhesus macaques as an outgroup, we identified human-specific differences in the levels of bilirubin, cholinesterase and lactate dehydrogenase, and bonobo-specific differences in the level of apolipoprotein A-I. For the remaining twenty-nine biomarkers there was no evidence for lineage-specific differences. In fact, we find that many biomarkers show differences between individuals of the same species in different environments. Of the four lineage-specific biomarkers, only bilirubin showed no differences between wild- and captive-born great apes. We show that the major factor explaining the human-specific difference in bilirubin levels may be genetic. There are human-specific changes in the sequence of the promoter and the protein-coding sequence of uridine diphosphoglucuronosyltransferase 1 (UGT1A1), the enzyme that transforms bilirubin and toxic plant compounds into water-soluble, excretable metabolites. Experimental evidence that UGT1A1 is down-regulated in the human liver suggests that changes in the promoter may be responsible for the human-specific increase in bilirubin. We speculate that since cooking reduces toxic plant compounds, consumption of cooked foods, which is specific to humans, may have resulted in relaxed constraint on UGT1A1 which has in turn led to higher serum levels of bilirubin in humans.

| S-EPMC4527672 | biostudies-literature

Threat of mining to African great apes.

Project description:The rapid growth of clean energy technologies is driving a rising demand for critical minerals. In 2022 at the 15th Conference of the Parties to the Convention on Biological Diversity (COP15), seven major economies formed an alliance to enhance the sustainability of mining these essential decarbonization minerals. However, there is a scarcity of studies assessing the threat of mining to global biodiversity. By integrating a global mining dataset with great ape density distribution, we estimated the number of African great apes that spatially coincided with industrial mining projects. We show that up to one-third of Africa's great ape population faces mining-related risks. In West Africa in particular, numerous mining areas overlap with fragmented ape habitats, often in high-density ape regions. For 97% of mining areas, no ape survey data are available, underscoring the importance of increased accessibility to environmental data within the mining sector to facilitate research into the complex interactions between mining, climate, biodiversity, and sustainability.

| S-EPMC10990274 | biostudies-literature

A new Late Miocene great ape from Kenya and its implications for the origins of African great apes and humans.

Project description:Extant African great apes and humans are thought to have diverged from each other in the Late Miocene. However, few hominoid fossils are known from Africa during this period. Here we describe a new genus of great ape (Nakalipithecus nakayamai gen. et sp. nov.) recently discovered from the early Late Miocene of Nakali, Kenya. The new genus resembles Ouranopithecus macedoniensis (9.6-8.7 Ma, Greece) in size and some features but retains less specialized characters, such as less inflated cusps and better-developed cingula on cheek teeth, and it was recovered from a slightly older age (9.9-9.8 Ma). Although the affinity of Ouranopithecus to the extant African apes and humans has often been inferred, the former is known only from southeastern Europe. The discovery of N. nakayamai in East Africa, therefore, provides new evidence on the origins of African great apes and humans. N. nakayamai could be close to the last common ancestor of the extant African apes and humans. In addition, the associated primate fauna from Nakali shows that hominoids and other non-cercopithecoid catarrhines retained higher diversity into the early Late Miocene in East Africa than previously recognized.

| S-EPMC2148271 | biostudies-literature

Humans and great apes cohabiting the forest ecosystem in central african republic harbour the same hookworms.

Project description:BackgroundHookworms are important pathogens of humans. To date, Necator americanus is the sole, known species of the genus Necator infecting humans. In contrast, several Necator species have been described in African great apes and other primates. It has not yet been determined whether primate-originating Necator species are also parasitic in humans.Methodology/principal findingsThe infective larvae of Necator spp. were developed using modified Harada-Mori filter-paper cultures from faeces of humans and great apes inhabiting Dzanga-Sangha Protected Areas, Central African Republic. The first and second internal transcribed spacers (ITS-1 and ITS-2) of nuclear ribosomal DNA and partial cytochrome c oxidase subunit 1 (cox1) gene of mtDNA obtained from the hookworm larvae were sequenced and compared. Three sequence types (I-III) were recognized in the ITS region, and 34 cox1 haplotypes represented three phylogenetic groups (A-C). The combinations determined were I-A, II-B, II-C, III-B and III-C. Combination I-A, corresponding to N. americanus, was demonstrated in humans and western lowland gorillas; II-B and II-C were observed in humans, western lowland gorillas and chimpanzees; III-B and III-C were found only in humans. Pairwise nucleotide difference in the cox1 haplotypes between the groups was more than 8%, while the difference within each group was less than 2.1%.Conclusions/significanceThe distinctness of ITS sequence variants and high number of pairwise nucleotide differences among cox1 variants indicate the possible presence of several species of Necator in both humans and great apes. We conclude that Necator hookworms are shared by humans and great apes co-habiting the same tropical forest ecosystems.

| S-EPMC3961186 | biostudies-literature

The evolution of laughter in great apes and humans.

Project description:It has long been claimed that human emotional expressions, such as laughter, have evolved from nonhuman displays. The aim of the current study was to test this prediction by conducting acoustic and phylogenetic analyses based on the acoustics of tickle-induced vocalizations of orangutans, gorillas, chimpanzees, bonobos and humans. Results revealed both important similarities and differences among the various species' vocalizations, with the phylogenetic tree reconstructed based on these acoustic data matching the well-established genetic relationships of great apes and humans. These outcomes provide evidence of a common phylogenetic origin of tickle-induced vocalizations in these taxa, which can therefore be termed "laughter" across all five species. Results are consistent with the claims of phylogenetic continuity of emotional expressions. Together with observations made on the use of laughter in great apes and humans, findings of this study further indicate that there were two main periods of selection-driven evolutionary change in laughter within the Hominidae, to a smaller degree, among the great apes and, most distinctively, after the separation of hominins from the last common ancestor with chimpanzees and bonobos.

| S-EPMC2889984 | biostudies-literature

The aorta in humans and African great apes, and cardiac output and metabolic levels in human evolution.

Project description:Humans have a larger energy budget than great apes, allowing the combination of the metabolically expensive traits that define our life history. This budget is ultimately related to the cardiac output, the product of the blood pumped from the ventricle and the number of heart beats per minute, a measure of the blood available for the whole organism physiological activity. To show the relationship between cardiac output and energy expenditure in hominid evolution, we study a surrogate measure of cardiac output, the aortic root diameter, in humans and great apes. When compared to gorillas and chimpanzees, humans present an increased body mass adjusted aortic root diameter. We also use data from the literature to show that over the human lifespan, cardiac output and total energy expenditure follow almost identical trajectories, with a marked increase during the period of brain growth, and a plateau during most of the adult life. The limited variation of adjusted cardiac output with sex, age and physical activity supports the compensation model of energy expenditure in humans. Finally, we present a first study of cardiac output in the skeleton through the study of the aortic impression in the vertebral bodies of the spine. It is absent in great apes, and present in humans and Neanderthals, large-brained hominins with an extended life cycle. An increased adjusted cardiac output, underlying higher total energy expenditure, would have been a key process in human evolution.

| S-EPMC10133235 | biostudies-literature

The influence of life history and sexual dimorphism on entheseal changes in modern humans and African great apes.

Project description:Entheseal changes have been widely studied with regard to their correlation to biomechanical stress and their usefulness for biocultural reconstructions. However, anthropological and medical studies have demonstrated the marked influence of both age and sex on the development of these features. Studies of entheseal changes are mostly aimed in testing functional hypotheses and are mostly focused on modern humans, with few data available for non-human primates. The lack of comparative studies on the effect of age and sex on entheseal changes represent a gap in our understanding of the evolutionary basis of both development and degeneration of the human musculoskeletal system. The aim of the present work is to compare age trajectories and patterns of sexual dimorphism in entheseal changes between modern humans and African great apes. To this end we analyzed 23 postcranial entheses in a human contemporary identified skeletal collection (N = 484) and compared the results with those obtained from the analysis of Pan (N = 50) and Gorilla (N = 47) skeletal specimens. Results highlight taxon-specific age trajectories possibly linked to differences in life history schedules and phyletic relationships. Robusticity trajectories separate Pan and modern humans from Gorilla, whereas enthesopathic patterns are unique in modern humans and possibly linked to their extended potential lifespan. Comparisons between sexes evidence a decreasing dimorphism in robusticity from Gorilla, to modern humans to Pan, which is likely linked to the role played by size, lifespan and physical activity on robusticity development. The present study confirms previous hypotheses on the possible relevance of EC in the study of life history, pointing moreover to their usefulness in evolutionary studies.

| S-EPMC4175998 | biostudies-literature

Diversity of Entamoeba spp. in African Great Apes and Humans

Project description:Diversity of Entamoeba spp. in African Great Apes and Humans

| PRJEB23126 | ENA

Sound symbolic congruency detection in humans but not in great apes.

Project description:Theories on the evolution of language highlight iconicity as one of the unique features of human language. One important manifestation of iconicity is sound symbolism, the intrinsic relationship between meaningless speech sounds and visual shapes, as exemplified by the famous correspondences between the pseudowords 'maluma' vs. 'takete' and abstract curved and angular shapes. Although sound symbolism has been studied extensively in humans including young children and infants, it has never been investigated in non-human primates lacking language. In the present study, we administered the classic "takete-maluma" paradigm in both humans (N = 24 and N = 31) and great apes (N = 8). In a forced choice matching task, humans but not great apes, showed crossmodal sound symbolic congruency effects, whereby effects were more pronounced for shape selections following round-sounding primes than following edgy-sounding primes. These results suggest that the ability to detect sound symbolic correspondences is the outcome of a phylogenetic process, whose underlying emerging mechanism may be relevant to symbolic ability more generally.

| S-EPMC6722092 | biostudies-literature

Common Visual Preference for Curved Contours in Humans and Great Apes.

Project description:Among the visual preferences that guide many everyday activities and decisions, from consumer choices to social judgment, preference for curved over sharp-angled contours is commonly thought to have played an adaptive role throughout human evolution, favoring the avoidance of potentially harmful objects. However, because nonhuman primates also exhibit preferences for certain visual qualities, it is conceivable that humans' preference for curved contours is grounded on perceptual and cognitive mechanisms shared with extant nonhuman primate species. Here we aimed to determine whether nonhuman great apes and humans share a visual preference for curved over sharp-angled contours using a 2-alternative forced choice experimental paradigm under comparable conditions. Our results revealed that the human group and the great ape group indeed share a common preference for curved over sharp-angled contours, but that they differ in the manner and magnitude with which this preference is expressed behaviorally. These results suggest that humans' visual preference for curved objects evolved from earlier primate species' visual preferences, and that during this process it became stronger, but also more susceptible to the influence of higher cognitive processes and preference for other visual features.

| S-EPMC4641621 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data