Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ancient maize samples from San Marcos cave in Tehuacan, Mexico

ABSTRACT: The earliest maize from San Marcos cave (Tehuacan, Mexico) is a partial domesticate with genomic evidence of inbreeding

PROVIDER: PRJEB16754 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR1709823.fastq.gz	Fastqsanger.gz
	ERR1709824.fastq.gz	Fastqsanger.gz
	ERR1709825.fastq.gz	Fastqsanger.gz

Items per page:

1 - 3 of 3

Similar Datasets

Ancient maize samples from San Marcos cave in Tehuacan, Mexico

Project description:The earliest maize from San Marcos cave (Tehuacan, Mexico) is a partial domesticate with genomic evidence of inbreeding

| PRJEB16753 | ENA

Effects of aging on gene expression in multiple tissues in surface and cave Astyanax mexicanus

Project description:Dysregulation of sleep has widespread health consequences and represents an enormous health burden. Short-sleeping individuals are predisposed to the effects of neurodegeneration, suggesting a critical role for sleep in the maintenance of neuronal health. While the effects of sleep on cellular function are not completely understood, growing evidence has identified an association between sleep loss and DNA damage, raising the possibility that sleep facilitates efficient DNA repair. The Mexican tetra fish, Astyanax mexicanus provides a model to investigate the evolutionary basis for changes in sleep and the consequences of sleep loss. Multiple cave-adapted populations of these fish have evolved to sleep for substantially less time compared to surface populations of the same species without identifiable impacts on healthspan or longevity. To investigate whether the evolved sleep loss is associated with DNA damage and aging, we compared the transcriptional response to aging between surface and cave morphs of A. mexicanus

2024-10-13 | GSE272611 | GEO

Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave (Sicily, Italy)

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

Evolutionary conservation of phototransduction and clock gene expression in the cave beetle Ptomaphagus hirtus (Coleoptera, Leiodidae)

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

cave metagenome

Project description:Cave microbiome

| PRJDB4557 | ENA

cave metagenome

Project description:cave metagenome

| PRJNA340160 | ENA

Ancient barley from Yoram Cave

Project description:Illumina sequencing data of libraries made from DNA extracted from barley grains excavated at Yoram Cave, Israel

| PRJEB12197 | ENA

Microfossil evidence for pre-Columbian maize dispersals in the neotropics from San Andres, Tabasco, Mexico.

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

cave metagenome

Project description:cave Genome sequencing

| PRJNA352141 | ENA

cave metagenome

Project description:cave metagenome Metagenome

| PRJNA325803 | ENA