Ontology highlight
ABSTRACT:
PROVIDER: PRJNA650542 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12440010_1.fastq.gz | Fastqsanger.gz | |||
| SRR12440010_2.fastq.gz | Fastqsanger.gz | |||
| SRR12440011_1.fastq.gz | Fastqsanger.gz | |||
| SRR12440011_2.fastq.gz | Fastqsanger.gz | |||
| SRR12440012_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 35 |
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Project description:<p>The biogeography of tropical Andean plants and the effects of altitudinal barriers as evolutionary constraints have been the focus of great debate. Although genetic markers have provided evidence for the geographic isolation of Andean-endemic groups, even highly variable molecular markers commonly used to assess biogeography do not have the resolving power needed for a fine geographic discrimination in some Andean taxa. We present a metabolomics approach based on ultrahigh-performance liquid chromatography-mass spectrometry combined with multivariate statistical methods and machine learning algorithms of multiple species and populations of Espeletiinae (Asteraceae) to provide metabolomic evidence for biogeographic segregation in this Andean-endemic subtribe. Our approach allows the discrimination of Espeletiinae taxa at different geographic scales with characteristic metabolic fingerprints related to their country of origin on a global scale, to their páramo massifs on a regional scale and to their páramo complexes on a local scale, revealing inter- and intraspecific metabolic variations. Our results, together with previous studies, suggest that Andean geography and Pleistocene glacial cycles not only shaped the evolutionary history of Espeletiinae but also its metabolic fingerprints, demonstrating the potential of metabolomics for understanding biogeographic patterns in recently diversified plant groups where genetic divergence is still at an early stage.</p><p><br></p><p><strong>Intraspecific chemical variability assay</strong> protocols and data are reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS943' rel='noopener noreferrer' target='_blank'><strong>MTBLS943</strong></a>.</p><p>I<strong>nterspecific chemical variability assay</strong> protocols and data are reported in study <a href='https://www.ebi.ac.uk/metabolights/MTBLS944' rel='noopener noreferrer' target='_blank'><strong>MTBLS944</strong></a>.</p>
2020-03-24 | MTBLS943 | MetaboLights
Project description:<p>The biogeography of tropical Andean plants and the effects of altitudinal barriers as evolutionary constraints have been the focus of great debate. Although genetic markers have provided evidence for the geographic isolation of Andean-endemic groups, even highly variable molecular markers commonly used to assess biogeography do not have the resolving power needed for a fine geographic discrimination in some Andean taxa. We present a metabolomics approach based on ultrahigh-performance liquid chromatography-mass spectrometry combined with multivariate statistical methods and machine learning algorithms of multiple species and populations of Espeletiinae (Asteraceae) to provide metabolomic evidence for biogeographic segregation in this Andean-endemic subtribe. Our approach allows the discrimination of Espeletiinae taxa at different geographic scales with characteristic metabolic fingerprints related to their country of origin on a global scale, to their páramo massifs on a regional scale and to their páramo complexes on a local scale, revealing inter- and intraspecific metabolic variations. Our results, together with previous studies, suggest that Andean geography and Pleistocene glacial cycles not only shaped the evolutionary history of Espeletiinae but also its metabolic fingerprints, demonstrating the potential of metabolomics for understanding biogeographic patterns in recently diversified plant groups where genetic divergence is still at an early stage.</p><p><br></p><p><strong>Interspecific chemical variability assay</strong> protocols and data are reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS944' rel='noopener noreferrer' target='_blank'><strong>MTBLS944</strong></a>.</p><p><strong>Intraspecific chemical variability assay</strong> protocols and data are reported in study <a href='https://www.ebi.ac.uk/metabolights/MTBLS943' rel='noopener noreferrer' target='_blank'><strong>MTBLS943</strong></a>.</p>
2020-03-24 | MTBLS944 | MetaboLights
Project description:Here we show the potential of proteins preserved in Pleistocene eggshell for addressing a longstanding controversy in human and evolution: the identity of the extinct bird that laid the eggs which were exploited by Australia’s first inhabitants. The eggs had been originally attributed to the iconic extinct flightless Genyornis newtoni, and subsequently dated to before 50 ±5 ka by Miller et al. (2016). This was taken to represent the extinction date for this endemic megafaunal species and thus implied a role of humans in its demise. A contrasting hypothesis, according to which the eggshell was laid by a large megapode (mound-builder), would therefore acquit humans of their responsibility in the extinction of Genyornis. Ancient protein sequences were reconstructed and used to assess the evolutionary proximity of the undetermined eggshell to extant birds, rejecting the megapode hypothesis. Ancient DNA could not be retrieved from these highly degraded samples, but morphometric data supported the attribution of the eggshell to Genyornis. When used in triangulation to address well-defined hypotheses, palaeoproteomics is a precious tool for reconstructing the evolutionary history of extinct and extant species. Here we show that the identification of Genyornis eggshell implies a more nuanced understanding of the modes of interactions between humans and their environment.
2022-07-19 | PXD027713 | Pride
Project description:Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears
| PRJEB42442 | ENA
Project description:Gigantopithecus blacki was a giant hominid that inhabited Southeast Asia during the Pleistocene. Its evolutionary relationship to other great ape species, and their divergence during the Middle and Late Miocene (16-5.3 Mya), remains disputed. In part, this is due to the absence of cranial and postcranial remains and size-induced allometry. Proposed hypothesis on the phylogenetic positions of Gigantopithecus have therefore been wide-ranging among hominoids, but none has received independent validation based on molecular evidence. To clarify the phylogenetic placement of Gigantopithecus blacki, we retrieved enamel proteome sequences from a 1.9 million years (Mya) old molar found in Chuifeng Cave, China. We demonstrate that Gigantopithecus is most closely related to orangutans (genus Pongo). We also estimate the Gigantopithecus-Pongo divergence to about 10-12 Mya, implying its speciation is part of the Miocene radiation of great apes. These sequences are approximately 6 times older, in a normalized thermal context, than any previously published mammalian proteome or genome. The survival of an Early Pleistocene dental enamel proteome in the subtropics further expands the scope of palaeoproteomic analysis into geographic areas and time periods previously considered incompatible with biomolecular preservation.
2019-11-12 | PXD013838 | Pride