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

Welker, Frido, Smith, Geoff M., Hutson, Jarod M., Kindler, Lutz, Garcia-Moreno, Alejandro, Villaluenga, Aritza, Turner, Elaine, Gaudzinski-Windheuser, Sabine·2017·PeerJ
DOI 10.7717/peerj.3033PMC PMC5354071
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Abstract

Background: 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 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 . Methods: ZooMS 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. Results: Various 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. Discussion: The 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.

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  • MALDI-TOF-based analyses have been used as a screening tool for LC-MS/MS analysis.

    “For some studies, MALDI-TOF–based analyses have been used as a screening tool for LC-MS/MS analysis”

    From Ancient protein analysis in archaeology (2021) · cites this paper as [174]

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Metadata

Authors
Welker, F., Smith, G. M., Hutson, J. M., Kindler, L., Garcia-Moreno, A., Villaluenga, A., Turner, E., & Gaudzinski-Windheuser, S.
Affiliations
  • Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
  • MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM, Neuwied, Germany
ORCID
Venue
PeerJ
Publisher
PeerJ
Published
2017-03-14
Volume
5
Pages
e3033
ISSN
2167-8359
DOI
10.7717/peerj.3033
PMC
PMC5354071
Cited by
67
References
4
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (unspecified)
Funders
  • Deutsche Forschungsgemeinschaft (GA 683/9-1)
  • Max Planck Society

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