Okladnikov2
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
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Project description:Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides, and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) which died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding twenty-eight chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive-X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth’s death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.
2024-05-22 | GSE268050 | GEO
Project description:Ancient gene flow from modern humans into Siberian Neanderthals
| PRJEB11828 | ENA
Project description:The origins, prevalence and nature of dairying have been long debated by archaeologists. Within the last decade, new advances in high-resolution mass spectrometry have allowed for the direct detection of milk proteins from archaeological remains, including ceramics, dental calculus, and preserved dairy products. Proteins recovered from archaeological remains are susceptible to post-excavation and laboratory contamination, a particular concern for ancient dairying studies as milk proteins are potential laboratory contaminants. Here, we examine how site-specific rates of deamidation can be used to elucidate patterns of peptide degradation, and authenticate ancient milk proteins. First, we characterize site-specific deamidation patterns in modern milk products and experimental samples, confirming that deamidation occurs primarily at low half-time sites. We then compare this to previously published ancient proteomic data from six studies reporting ancient milk peptides. We confirm that site-specific deamidation rates, on average, are more advanced in beta-lactoglobulin recovered from ancient dental calculus and pottery residues. Nevertheless, deamidation rates displayed a high degree of variability, making it challenging to authenticate samples with relatively few milk peptides. We demonstrate that site-specific deamidation is a useful tool for identifying modern contamination but highlight the need for multiple lines of evidence to authenticate ancient protein data.
2021-08-05 | PXD022368 | Pride
Project description:Ancient Siberian wolf sequencing
| PRJEB7788 | ENA
Project description:How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Native Americans diversified into two basal genetic branches around 13 KYA, one in North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians and Australo-Melanesians, the latter possibly through the ancestors of Aleutian Islanders. Putative relict populations in South America, including the historical Pericúes and Fuego-Patagonians, are not directly related to modern Australo-Melanesians.
2015-07-20 | GSE70987 | GEO
Project description:Whole genome sequencing of CTVT, breed dogs, and wild canids reveals pathways that are important in cancer cell survival. Comparison of these mutations with breed dogs shows that the original tumor came from a dog very similar to one of the modern Arctic breeds. DNA was collected from pedigreed dogs of the Alaskan Malamute (AMAL) and Siberian Husky (HUSK) breeds living in North America. SNPs were genotyed using the Illumina CanineHD SNP chip. These SNPs were compared to published data and seqeunced mutations from CTVT by principal component alnalysis to identify the breed of the CTVT originator.
2015-07-30 | E-GEOD-70454 | biostudies-arrayexpress
Project description:Regulatory changes are broadly accepted as key drivers of phenotypic divergence. However, identifying regulatory changes that underlie human-specific traits has proven very challenging. Here, we use 63 DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes affecting the face and vocal tract went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-affecting genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract
2019-09-05 | GSE96833 | GEO
Project description:The ancient preserved molecules in bones offer the opportunity to gain a better knowledge on the biological past. In recent years, bones proteomics has become an attractive method to study extinct species and phylogenetic evolution as an alternative to DNA analysis which is limited by DNA amplification present in ancient samples and its contamination. The analysis of fossils must consume a low quantity of material to avoid damaging the samples. Another difficulty is the absence of genomic data for most of the extinct species. This study applied a proteomic methodology to mammalian bones of 130,000 / 120,000 years old from the last Chibanian and the earlier Upper Pleistocene site of Waziers (France). The presence of lithic artefacts and the traces of butchery observed on the bones indicate the presence of Neanderthal Man on this site. Starting from 5 milligram samples, our results show that most detected peptides match collagen I alpha 1 and alpha 2 proteins with a sequence coverage up to 60 %. Using sequence homology with modern sequences, a biological classification was successfully achieved. Each bone taxonomic rank by proteomics was consistent with the existing osteomorphological studies and palaeoenvironmental and palaeodietary data.
2023-04-20 | PXD039657 | Pride
Project description:The Kashmiri population is an ethno-linguistic group that resides in the Kashmir Valley in northern India. A longstanding hypothesis is that this population derives ancestry from Jewish and/or Greek sources. There is historical and archaeological evidence of ancient Greek presence in India and Kashmir. Further, some historical accounts suggest ancient Hebrew ancestry as well. To date, it has not been determined whether signatures of Greek or Jewish admixture can be detected in the Kashmiri population. Using genome-wide genotyping and admixture detection methods, we determined there are no significant or substantial signs of Greek or Jewish admixture in modern-day Kashmiris. The ancestry of Kashmiri Tibetans was also determined, which showed signs of admixture with populations from northern India and west Eurasia. These results contribute to our understanding of the existing population structure in northern India and its surrounding geographical areas.
2016-08-16 | GSE85594 | GEO
Project description:The evolution of human bipedalism exposed the knee to unique biomechanical challenges, requiring changes in knee anatomy giving rise to the modern-day configuration. In order to better understand the relationship between derived knee morphology and the genetic factors associated with osteoarthritis risk, we performed epigenetic profiling of murine forelimb/hindlimb growth plates to identify regulatory elements shaping formation of specific knee structures, identifying signals of ancient positive selection upon which more recent genetic drift overlaps risk-associated loci. Our functional analyses of an osteoarthritis-risk variant within a reproducibly-associated locus establishes a novel model for studying this degenerative disease.
2020-04-16 | GSE122877 | GEO