Ancient maize samples from San Marcos cave in Tehuacan, Mexico
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PROVIDER: PRJEB16754 | ENA |
REPOSITORIES: ENA
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Project description:The earliest maize from San Marcos cave (Tehuacan, Mexico) is a partial domesticate with genomic evidence of inbreeding
| PRJEB16753 | ENA
Project description:Recent improvements in the analysis ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and past genetic diversity of our species. Here we present a “multi-omics” study, integrating genomic and proteomic analyses of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified “Villabruna cluster”. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analyses of dental calculus using genomics and proteomics showed a similar oral microbiome composition as Neandertals, but distinct from later foragers and farmers, revealing also a diet based on mammals, fish and plants. Our results demonstrate the power of using a multi-omics approach in the study of prehistoric human populations.
2022-10-27 | PXD024346 | Pride
Project description:Caves are populated with a diverse fauna of highly adapted species that tend to exhibit a consistent suite of both regressive and constructive trait modifications. Because molecular studies of cave adaptation have largely concentrated on vertebrate models, our ability to recognize universalities in the genetic trajectories underlying cave adaptation remains limited. We have initiated efforts to elucidate the molecular evolution of the flightless small carrion beetle Ptomaphagus hirtus (Ptomaphagus hirtus), which represents one of the highly endemic signature inhabitants of the Mammoth Cave system of Kentucky. Ptomaphagus hirtus has been considered blind despite the presence of lateral eye rudiments. However, analysis of the Ptomaphagus hirtus adult head transcriptome by deep RNA sequencing reveals the conservation and expression of all essential insect phototransduction genes including a single long wavelength-sensitive opsin. Consistent with the preservation of visual ability, Ptomaphagus hirtus expresses all core members of the clock gene network and exhibits a similar degree of negative phototaxis as does a closely related flight-active species in light-dark choice assays. The structural reduction of the peripheral Ptomaphagus hirtus visual system is reflected by the lack of five eye pigmentation specific genes in the head transcriptome. Taken together our data suggest that wavelength contingent and probably also spatial vision have been lost in Ptomaphagus hirtus, while irradiance vision and contingent behavioral modules have remained preserved. We predict that the adaptive state of Ptomaphagus hirtus is representative for a large number of microphthalmic species adapted to the twilight zone of caves and other subterranean habitats Poly(A)+ transcripts were isolated from a pooled sample of 25 adult Ptomaphagus hirtus heads, reverse transcribed and sequenced on the Illumina GAII
2011-03-19 | E-GEOD-28039 | biostudies-arrayexpress
Project description:Illumina sequencing data of libraries made from DNA extracted from barley grains excavated at Yoram Cave, Israel
| PRJEB12197 | ENA
Project description:The history of maize (Zea mays L.) is one of the most debated topics in New World archaeology. Molecular and genetic studies indicate that maize domestication took place in tropical southwest Mexico. Although archaeological evidence for the evolution of maize from its wild ancestor teosinte has yet to be found in that poorly studied region, other research combining paleoecology and archaeology is documenting the nature and timing of maize domestication and dispersals. Here we report a phytolith analysis of sediments from San Andrés, Tabasco, that confirms the spread of maize cultivation to the tropical Mexican Gulf Coast >7,000 years ago ( approximately 7,300 calendar years before present). We review the different methods used in sampling, identifying, and dating fossil maize remains and compare their strengths and weaknesses. Finally, we examine how San Andrés amplifies the present evidence for widespread maize dispersals into Central and South America. Multiple data sets from many sites indicate that maize was brought under cultivation and domesticated and had spread rapidly out of its domestication cradle in tropical southwest Mexico by the eighth millennium before the present.
| S-EPMC1871877 | biostudies-other