MtDNA sequences from Stajnia S5000 Neanderthal
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB39529 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4369350.fastq.gz | Fastqsanger.gz | |||
| ERR4369360.fastq.gz | Fastqsanger.gz | |||
| ERR4369351.fastq.gz | Fastqsanger.gz | |||
| ERR4369361.fastq.gz | Fastqsanger.gz | |||
| ERR4369352.fastq.gz | Fastqsanger.gz |
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Project description:While Neanderthals are extinct, fragments of their genome still persist in the genomes of contemporary humans. Here, we show that such Neanderthal-like sequences are not distributed randomly in contemporary human genomes. Specifically, while genome-wide frequency of Neanderthal-like sites is close to 6% in all out-of-Africa populations, genes involved in lipid catabolism contain large excess Neanderthal-like sequences in Europeans (24.3%), but not in Asians (12.4%). While lipid catabolism cannot be assayed in Neanderthals, we took advantage of genetic divergence between human populations, chimpanzees and Neanderthals to predict metabolic divergence expected from the observed excess of Neanderthal gene flow into Europeans. We confirmed predicted changes in lipid catabolism using hydrophobic metabolome measurements in the brain tissue and further linked these metabolic changes to gene expression divergence. 14 human and 6 chimpanzee samples were sequenced.
2014-03-31 | E-GEOD-45263 | biostudies-arrayexpress
Project description:While Neanderthals are extinct, fragments of their genome still persist in the genomes of contemporary humans. Here, we show that such Neanderthal-like sequences are not distributed randomly in contemporary human genomes. Specifically, while genome-wide frequency of Neanderthal-like sites is close to 6% in all out-of-Africa populations, genes involved in lipid catabolism contain large excess Neanderthal-like sequences in Europeans (24.3%), but not in Asians (12.4%). While lipid catabolism cannot be assayed in Neanderthals, we took advantage of genetic divergence between human populations, chimpanzees and Neanderthals to predict metabolic divergence expected from the observed excess of Neanderthal gene flow into Europeans. We confirmed predicted changes in lipid catabolism using hydrophobic metabolome measurements in the brain tissue and further linked these metabolic changes to gene expression divergence.
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Project description:For a long time, Neanderthals were considered hunters of large mammals, whereas the diversification of the exploited faunal spectrum to include smaller taxa, including birds, was assumed to be specific to anatomically modern humans. In recent decades, archaeozoological analyses of faunal remains from layers associated with Middle Palaeolithic lithic industries have revealed traces of human manipulation of small taxa, indicating the exploitation of a wider range of animals than previously thought, including small or fast-moving animals such as molluscs, leporids and birds. These new data have challenged the view that Neanderthals did not exploit small animals, thereby narrowing the behavioral gap with anatomically modern humans. Nevertheless, the information currently available comes almost exclusively from southern Europe and the nature of Neanderthal small fauna exploitation in northern Europe remains largely unknown. The present study aims to fill this gap by applying archaeozoological methods, including detailed taphonomic and traceological analyses, to 118 bird remains recovered from levels containing Middle Palaeolithic industries at Scladina cave, southern Belgium. Analyses of proteomics were applied to clarify the taxonomic identity of two morphologically non-diagnostic elements. Compared to mammal remains, bird bones, most of which belong to the order Galliformes, are scarce at Scladina Cave. This is likely due to conservation bias. Traces of non-human predators or scavengers, suggest that mammalian carnivores are responsible for accumulating a considerable portion of the avian assemblage. In total, seven bird bones exhibit anthropogenic traces, and one element presents questionable traces. Various Galliformes and a cormorant were exploited likely for their meat, during MIS 5 and/or 6 and MIS 6. The terminal posterior phalanx (talon) of a raptor of the size of a pomarine eagle displays intense polishing that could be linked to human manipulation of this element (MIS 5 and/or 6), although in the absence of tool marks this remains hypothetical at this stage. On the radius of a Western capercaillie, two deep incisions may indicate bone working, and intense use-wear on one of the fractured ends indicates that the bone has been utilized, potentially on soft organic material (MIS 6). This study provides the first evidence of the exploitation of birds during the Middle Palaeolithic in Belgium and constitutes the only detailed archaeozoological analysis of bird material in northwestern Europe. The likely transformation and use of a bird bone is only the second example recovered from Neanderthal occupations. The novel taxa identified as Neanderthal prey highlight the plasticity of Neanderthal ecological behavior, adapting to different landscapes and climates and exploiting the full spectrum of locally available prey.
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Project description:Some Neanderthal introgressed variation underwent selective sweeps, but little is known about their functional significance. We used a Massively Parallel Reporter Assay (MPRA) to test 5,353 high-frequency introgressed variants for evidence of being in active cis-regulatory elements (CREs) and modulating gene expression in immune cell lines. We identified 2,546 variants in CREs and 292 expression-modulating variants (emVars). These emVars are predicted to regulate genes that are enriched for function in innate immune pathways including interferon signaling, toll like receptor pathways, and anti-viral response; one such emVar is significantly associated with protection against severe COVID-19 response. Using CRISPR-Cas9, we deleted two CREs containing expression-modulation variants linked to immune function, rs11624425 and rs80317430, identifying their primary genic targets as ELMSAN1, and PAN2 and STAT2 respectively, three genes differentially expressed during influenza infection. Overall, we present the first database of directly identified expression-modulating Neanderthal-introgressed alleles contributing to potential immune response in modern humans.
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