Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

HuConTest: Testing Human Contamination in Great Ape Samples.

ABSTRACT: Modern human contamination is a common problem in ancient DNA studies. We provide evidence that this issue is also present in studies in great apes, which are our closest living relatives, for example in noninvasive samples. Here, we present a simple method to detect human contamination in short-read sequencing data from different species: HuConTest. We demonstrate its feasibility using blood and tissue samples from these species. This test is particularly useful for more complex samples (such as museum and noninvasive samples) which have smaller amounts of endogenous DNA, as we show here.

SUBMITTER: Kuhlwilm M

PROVIDER: S-EPMC8247554 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

HuConTest: Testing Human Contamination in Great Ape Samples.

Kuhlwilm Martin M Fontsere Claudia C Han Sojung S Alvarez-Estape Marina M Marques-Bonet Tomas T

Genome biology and evolution 20210601 6

Modern human contamination is a common problem in ancient DNA studies. We provide evidence that this issue is also present in studies in great apes, which are our closest living relatives, for example in noninvasive samples. Here, we present a simple method to detect human contamination in short-read sequencing data from different species: HuConTest. We demonstrate its feasibility using blood and tissue samples from these species. This test is particularly useful for more complex samples (such a ...[more]

PMID: 34038549

Similar Datasets

great ape

Project description:Human, Chimpanzee, Bonobo, Gorilla, Sumatran orangutan, Bornean orangutan Raw sequence reads

| PRJNA505331 | ENA

great ape

Project description:Human, Chimpanzee, Bonobo, Gorilla, Sumatran orangutan, Bornean orangutan Raw sequence reads

| PRJNA504650 | ENA

Great Ape Copy Number Variation

2011-08-03 | GSE30559 | GEO

Functional Implications of Human-Specific Changes in Great Ape microRNAs.

Project description:microRNAs are crucial post-transcriptional regulators of gene expression involved in a wide range of biological processes. Although microRNAs are highly conserved among species, the functional implications of existing lineage-specific changes and their role in determining differences between humans and other great apes have not been specifically addressed. We analyzed the recent evolutionary history of 1,595 human microRNAs by looking at their intra- and inter-species variation in great apes using high-coverage sequenced genomes of 82 individuals including gorillas, orangutans, bonobos, chimpanzees and humans. We explored the strength of purifying selection among microRNA regions and found that the seed and mature regions are under similar and stronger constraint than the precursor region. We further constructed a comprehensive catalogue of microRNA species-specific nucleotide substitutions among great apes and, for the first time, investigated the biological relevance that human-specific changes in microRNAs may have had in great ape evolution. Expression and functional analyses of four microRNAs (miR-299-3p, miR-503-3p, miR-508-3p and miR-541-3p) revealed that lineage-specific nucleotide substitutions and changes in the length of these microRNAs alter their expression as well as the repertoires of target genes and regulatory networks. We suggest that the studied molecular changes could have modified crucial microRNA functions shaping phenotypes that, ultimately, became human-specific. Our work provides a frame to study the impact that regulatory changes may have in the recent evolution of our species.

| S-EPMC4841587 | biostudies-literature

Human-Borne Pathogens: Are They Threatening Wild Great Ape Populations?

Project description:Climate change and anthropic activities are the two main factors explaining wild great ape habitat reduction and population decline. The extent to which human-borne infectious diseases are contributing to this trend is still poorly understood. This is due to insufficient or fragmented knowledge on the abundance and distribution of current wild great ape populations, the difficulty obtaining optimal biological samples for diagnostic testing, and the scarcity of pathogen typing data of sufficient quality. This review summarises current information on the most clinically relevant pathogens of viral, bacterial, parasitic, and fungal nature for which transmission from humans to wild great apes is suspected. After appraising the robustness of available epidemiological and/or molecular typing evidence, we attempt to categorise each pathogen according to its likelihood of truly being of human origin. We further discuss those agents for which anthroponotic transmission is more likely. These include two viral (Human Metapneumovirus and Respiratory Syncytial Virus), one bacterial (diarrhoeagenic Escherichia coli), and two parasitic (Cryptosporidium spp. and Giardia duodenalis) pathogens. Finally, we identify the main drawbacks impairing research on anthroponotic pathogen transmission in wild great apes and propose research lines that may contribute to bridging current knowledge gaps.

| S-EPMC9323791 | biostudies-literature

Dynamics of DNA methylation in recent human and great ape evolution.

Project description:DNA methylation is an epigenetic modification involved in regulatory processes such as cell differentiation during development, X-chromosome inactivation, genomic imprinting and susceptibility to complex disease. However, the dynamics of DNA methylation changes between humans and their closest relatives are still poorly understood. We performed a comparative analysis of CpG methylation patterns between 9 humans and 23 primate samples including all species of great apes (chimpanzee, bonobo, gorilla and orangutan) using Illumina Methylation450 bead arrays. Our analysis identified ?800 genes with significantly altered methylation patterns among the great apes, including ?170 genes with a methylation pattern unique to human. Some of these are known to be involved in developmental and neurological features, suggesting that epigenetic changes have been frequent during recent human and primate evolution. We identified a significant positive relationship between the rate of coding variation and alterations of methylation at the promoter level, indicative of co-occurrence between evolution of protein sequence and gene regulation. In contrast, and supporting the idea that many phenotypic differences between humans and great apes are not due to amino acid differences, our analysis also identified 184 genes that are perfectly conserved at protein level between human and chimpanzee, yet show significant epigenetic differences between these two species. We conclude that epigenetic alterations are an important force during primate evolution and have been under-explored in evolutionary comparative genomics.

| S-EPMC3764194 | biostudies-literature

Great Ape Copy Number Variation

Project description:Intra-specific polymorphism in copy number is documented in many organisms, including human and chimpanzee, but very little is known for other great apes. This study aims to provide CNVs data for orangutan, gorilla, bonobo and chimpanzee, and compare the CNV patterns among these species, as well as with human CNVs and segmental duplications from public databases. Each sample is hybridized against a common reference of the same species for two dye combinations (e.g. chimp1_CY5 vs chimpREF_Cy3; chimp1_CY3 vs chimpREF_Cy5; bonobo1_CY5 vs bonoboREF_Cy3; bonobo1_CY3 vs bonoboREF_Cy5;)

2011-08-02 | E-GEOD-30559 | biostudies-arrayexpress

High-resolution comparative analysis of great ape genomes

Project description:We couple long-read sequence assembly, full-length cDNA sequencing, and a multi-platform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies where most genes are complete, gaps are closed, and novel gene models are identified. We further analyzed the overlap between structural variants in the human genome and gene expression differences in human and chimpanzee cells, including iPS-derived organoid radial glia cells.

2018-06-12 | GSE113931 | GEO

Towards a great ape dictionary: Inexperienced humans understand common nonhuman ape gestures.

Project description:In the comparative study of human and nonhuman communication, ape gesturing provided the first demonstrations of flexible, intentional communication outside human language. Rich repertoires of these gestures have been described in all ape species, bar one: us. Given that the majority of great ape gestural signals are shared, and their form appears biologically inherited, this creates a conundrum: Where did the ape gestures go in human communication? Here, we test human recognition and understanding of 10 of the most frequently used ape gestures. We crowdsourced data from 5,656 participants through an online game, which required them to select the meaning of chimpanzee and bonobo gestures in 20 videos. We show that humans may retain an understanding of ape gestural communication (either directly inherited or part of more general cognition), across gesture types and gesture meanings, with information on communicative context providing only a marginal improvement in success. By assessing comprehension, rather than production, we accessed part of the great ape gestural repertoire for the first time in adult humans. Cognitive access to an ancestral system of gesture appears to have been retained after our divergence from other apes, drawing deep evolutionary continuity between their communication and our own.

| S-EPMC9873169 | biostudies-literature

The uniqueness of human vulnerability to brain aging in great ape evolution.

Project description:Aging is associated with progressive gray matter loss in the brain. This spatially specific, morphological change over the life span in humans is also found in chimpanzees, and the comparison between these great ape species provides a unique evolutionary perspective on human brain aging. Here, we present a data-driven, comparative framework to explore the relationship between gray matter atrophy with age and recent cerebral expansion in the phylogeny of chimpanzees and humans. In humans, we show a positive relationship between cerebral aging and cortical expansion, whereas no such relationship was found in chimpanzees. This human-specific association between strong aging effects and large relative cortical expansion is particularly present in higher-order cognitive regions of the ventral prefrontal cortex and supports the "last-in-first-out" hypothesis for brain maturation in recent evolutionary development of human faculties.

| S-EPMC11352902 | 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