Dataset Information

Middle Pleistocene protein sequences from the rhinoceros genus Stephanorhinus and the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae.

ABSTRACT: 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.).

INSTRUMENT(S): Q Exactive

ORGANISM(S): Rhinocerotidae Coelodonta Antiquitatis (woolly Rhinoceros)

TISSUE(S): Bone

SUBMITTER: Frido Welker

LAB HEAD: Frido Welker

PROVIDER: PXD005534 | Pride | 2017-02-02

REPOSITORIES: Pride

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Middle Pleistocene protein sequences from the rhinoceros genus <i>Stephanorhinus</i> and the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae.

Welker Frido F Smith Geoff M GM Hutson Jarod M JM Kindler Lutz L Garcia-Moreno Alejandro A Villaluenga Aritza A Turner Elaine E Gaudzinski-Windheuser Sabine S

PeerJ 20170314

<h4>Background</h4>Ancient protein sequences are increasingly used to elucidate the phylogenetic relationships between extinct and extant mammalian taxa. Here, we apply these recent developments to Middle Pleistocene bone specimens of the rhinoceros genus <i>Stephanorhinus</i>. No biomolecular sequence data is currently available for this genus, leaving phylogenetic hypotheses on its evolutionary relationships to extant and extinct rhinoceroses untested. Furthermore, recent phylogenies based on ...[more]

PMID: 28316883

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Project description:BackgroundAncient protein sequences are increasingly used to elucidate the phylogenetic relationships between extinct and extant mammalian taxa. Here, we apply these recent developments to Middle Pleistocene bone specimens of the rhinoceros genus Stephanorhinus. No biomolecular sequence data is currently available for this genus, leaving phylogenetic hypotheses on its evolutionary relationships to extant and extinct rhinoceroses untested. Furthermore, recent phylogenies based on Rhinocerotidae (partial or complete) mitochondrial DNA sequences differ in the placement of the Sumatran rhinoceros (Dicerorhinus sumatrensis). Therefore, studies utilising ancient protein sequences from Middle Pleistocene contexts have the potential to provide further insights into the phylogenetic relationships between extant and extinct species, including Stephanorhinus and Dicerorhinus.MethodsZooMS screening (zooarchaeology by mass spectrometry) was performed on several Late and Middle Pleistocene specimens from the genus Stephanorhinus, subsequently followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to obtain ancient protein sequences from a Middle Pleistocene Stephanorhinus specimen. We performed parallel analysis on a Late Pleistocene woolly rhinoceros specimen and extant species of rhinoceroses, resulting in the availability of protein sequence data for five extant species and two extinct genera. Phylogenetic analysis additionally included all extant Perissodactyla genera (Equus, Tapirus), and was conducted using Bayesian (MrBayes) and maximum-likelihood (RAxML) methods.ResultsVarious ancient proteins were identified in both the Middle and Late Pleistocene rhinoceros samples. Protein degradation and proteome complexity are consistent with an endogenous origin of the identified proteins. Phylogenetic analysis of informative proteins resolved the Perissodactyla phylogeny in agreement with previous studies in regards to the placement of the families Equidae, Tapiridae, and Rhinocerotidae. Stephanorhinus is shown to be most closely related to the genera Coelodonta and Dicerorhinus. The protein sequence data further places the Sumatran rhino in a clade together with the genus Rhinoceros, opposed to forming a clade with the black and white rhinoceros species.DiscussionThe first biomolecular dataset available for Stephanorhinus places this genus together with the extinct genus Coelodonta and the extant genus Dicerorhinus. This is in agreement with morphological studies, although we are unable to resolve the order of divergence between these genera based on the protein sequences available. Our data supports the placement of the genus Dicerorhinus in a clade together with extant Rhinoceros species. Finally, the availability of protein sequence data for both extinct European rhinoceros genera allows future investigations into their geographic distribution and extinction chronologies.

			Action	DRS
	Coelodonta.mgf	Mgf
	Coelodonta.mzML	Mzml
	Coelodonta.pep.xml	Pepxml
	Stephanorhinus.mgf	Mgf
	Stephanorhinus.mzML	Mzml