Project description:Characterization of Middle Pleistocene rhinoceros proteins and the phylogenetic relationships between extinct and extanct rhinoceros was investigated by obtaining ancient protein data for two extinct rhinoceros genera (Coelodonta antiquitatis and Stephanorhinus sp.).
2017-02-02 | PXD005534 | Pride
Project description:Whole genome sequencing of Galapagos giant tortoises
Project description:The living tree sloths Choloepus and Bradypus are the only remaining members of Folivora, a major xenarthran radiation that occupied a wide range of habitats in many parts of the western hemisphere during the Cenozoic, including both continents and the West Indies (Antilles). To date, molecular evidence has played only a minor role in folivoran systematics, as most recently-extinct species lived in places not conducive to DNA preservation. Here we utilize collagen sequence information to assess the relationships of tree sloths to a large sample (13 species) of extinct Quaternary folivorans.
Project description:Studies of ancient DNA have revolutionized our understanding of extinct organisms, but thus far the maximum estimated age of sequenced DNA is two million years. However, evidence for endogenous biomolecules, including proteins, lipids, and pigments have been found in much older fossils, dating to up to 195 million years. Amino acid sequence data consistent with ancient, endogenous biomolecules have been derived from specimens of the theropod Tyrannosaurus rex (MOR 1125) and the hadrosaur Brachylophosaurus canadensis (MOR 2598). Histochemical and immunological studies also identified a molecule consistent with DNA in these two ancient specimens, localized to a single point within preserved osteocytes. Here we report the sequencing and analysis of DNA extracted from osteocytes and blood vessels of T. rex and B. canadensis, liberated after demineralization of dense cortical bone. Usable sequence reads were obtained at a low recovery rate. After the removal of high-quality reads that mapped to the human genome, the remaining reads were highly fragmented, with similarities to multiple animal species including reptilian and avian genomes. Our findings support the hypothesis that DNA and histone signal from imaging, mass spectrometry, and DNA sequencing of dinosaur osteocytes are endogenously preserved biomolecules.
Project description:High resolution Mass Spectrometry and Peptides identification uncovered ancestral giant insect viruses motifs within Histone-4 peptides in human liver cells. These peptides did not match any human sequence. This finding consolidates the dogma that molecular patterns are universal and suggests that metazoan cellular structures possibly share an evolutionary link with ancient giant viruses.
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.
