Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1097058 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:An archaeological bone fragment from Baishiya Karst Cave, China, was identified as stemming from a hominin through ZooMS (Zooarchaeology by Mass Spectrometry). Shotgun palaeoproteomic analyses were thereafter conducted on the specimen to refine the taxonomic identification and perform phylogenetic analyses. The reconstruted proteome shows that the newly described Baishiya Karst Cave individual, Xiahe 2, is most closely related to the high-coverage published genome from a Denisovan individual.
2024-05-22 | PXD047932 | Pride
Project description:Studying how different genotypes respond to environmental variation is essential to understand the genetic basis of adaptation. The Mexican tetra, Astyanax mexicanus, has cave and surface‐dwelling morphotypes that have adapted to entirely different environments in the wild, and are now successfully maintained in lab conditions. While this has enabled the identification of genetic adaptations underlying a variety of physiological processes, few studies have directly compared morphotypes between lab‐reared and natural populations. Such comparative approaches could help dissect the varying effects of environment and morphotype, and determine the extent to which phenomena observed in the lab are generalizable to conditions in the field. To this end, we take a transcriptomic approach to compare the Pachón cavefish and their surface fish counterparts in their natural habitats and the lab environment. We identify key changes in expression of genes implicated in metabolism and physiology between groups of fish, suggesting that morphotype (surface or cave) and environment (natural or lab) both alter gene expression. We find gene expression differences between cave and surface fish in their natural habitats are much larger than differences in expression between morphotypes in the lab environment. However, lab‐raised cave and surface fish still exhibit numerous gene expression changes, supporting genetically encoded changes in livers of this species. From this, we conclude that a controlled laboratory environment may serve as an ideal setting to study the genetic underpinnings of metabolic and physiological differences between the cavefish and surface fish.
2020-02-19 | GSE139490 | GEO
Project description:Genetic and limited palaeoanthropological data suggest that Denisovans, a sister group to Neanderthals, were once widely distributed in eastern Eurasia, likely stretching from high-latitude Siberia, to the high-altitude Tibetan Plateau, to the low-latitude subtropical regions of southeast Asia. This suggests that Denisovans were capable of adapting to a highly diverse range of environments, but archaeological evidence for this is currently limited. As a result, we know little about their behaviours, including subsistence strategies, across the vast areas they likely occupied. Here, we describe the late Middle to Late Pleistocene faunal assemblage from Baishiya Karst Cave on the Tibetan Plateau, where the Xiahe Denisovan mandible and Denisovan sedimentary mtDNA were found, by integrating proteomic screening into traditional zooarchaeological analysis. The results indicate that the faunal assemblage consists of a diverse range of animals, including megafauna, large mammals, small mammals and birds, but is dominated by medium-sized herbivores. Frequent cut marks and percussion traces on bone surfaces throughout the assemblage, even on carnivore bones, indicate that Denisovan activities in Baishiya Karst Cave from at least 190 to 30 thousand years are responsible for the fauna assemblage accumulation. Thorough utilization of acquired animal resources, even perhaps the fur, too, might have helped Denisovans to survive through the last two glacial-interglacial cycles on the cold high-altitude Tibetan Plateau. Our results shed new light on Denisovan behaviours and their adaptations to the diverse and fluctuated environments in the Middle and Late Pleistocene eastern Eurasia.
2024-05-22 | PXD041874 | Pride
Project description:Coding and non-coding mutations in DNA contribute significantly to phenotypic variability during evolution. However, less is known about the role of epigenetics in this process. Although previous studies have identified eye development genes associated with the loss of eyes phenotype in the Pachón blind cave morph of the Mexican tetra Astyanax mexicanus1-6, no inactivating mutations have been found in any of these genes2,3,7-10. Here we show that excess DNA methylation-based epigenetic silencing promotes eye degeneration in blind cave Astyanax mexicanus. By performing parallel analyses in Astyanax mexicanus cave and surface morphs and in the zebrafish Danio rerio, we have discovered that DNA methylation mediates eye-specific gene repression and globally regulates early eye development. The most significantly hypermethylated and down-regulated genes in the cave morph are also linked to human eye disorders, suggesting the function of these genes is conserved across the vertebrates. Our results show that changes in DNA methylation-based gene repression can serve as an important molecular mechanism generating phenotypic diversity during development and evolution.
2018-05-01 | GSE109006 | GEO