TY - JOUR
T1 - Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny
AU - Cappellini, Enrico
AU - Welker, Frido
AU - Pandolfi, Luca
AU - Ramos-Madrigal, Jazmín
AU - Samodova, Diana
AU - Rüther, Patrick L.
AU - Fotakis, Anna K.
AU - Lyon, David
AU - Moreno-Mayar, J. Víctor
AU - Bukhsianidze, Maia
AU - Rakownikow Jersie-Christensen, Rosa
AU - Mackie, Meaghan
AU - Ginolhac, Aurélien
AU - Ferring, Reid
AU - Tappen, Martha
AU - Palkopoulou, Eleftheria
AU - Dickinson, Marc R.
AU - Stafford, Thomas W.
AU - Chan, Yvonne L.
AU - Götherström, Anders
AU - Nathan, Senthilvel K.S.S.
AU - Heintzman, Peter D.
AU - Kapp, Joshua D.
AU - Kirillova, Irina
AU - Moodley, Yoshan
AU - Agusti, Jordi
AU - Kahlke, Ralf Dietrich
AU - Kiladze, Gocha
AU - Martínez-Navarro, Bienvenido
AU - Liu, Shanlin
AU - Sandoval Velasco, Marcela
AU - Sinding, Mikkel Holger S.
AU - Kelstrup, Christian D.
AU - Allentoft, Morten E.
AU - Orlando, Ludovic
AU - Penkman, Kirsty
AU - Shapiro, Beth
AU - Rook, Lorenzo
AU - Dalén, Love
AU - Gilbert, M. Thomas P.
AU - Olsen, Jesper V.
AU - Lordkipanidze, David
AU - Willerslev, Eske
N1 - This is an author-produced version of the published paper. Uploaded in accordance with the publisher’s self-archiving policy. Further copying may not be permitted; contact the publisher for details.
PY - 2019/10/3
Y1 - 2019/10/3
N2 - The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa. However, the irreversible post-mortem degradation2 of ancient DNA has so far limited its recovery—outside permafrost areas—to specimens that are not older than approximately 0.5 million years (Myr). By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I, and suggested the presence of protein residues in fossils of the Cretaceous period—although with limited phylogenetic use. In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch, using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia). Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the clade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck’s rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel—which is the hardest tissue in vertebrates, and is highly abundant in the fossil record—can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation.
AB - The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa. However, the irreversible post-mortem degradation2 of ancient DNA has so far limited its recovery—outside permafrost areas—to specimens that are not older than approximately 0.5 million years (Myr). By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I, and suggested the presence of protein residues in fossils of the Cretaceous period—although with limited phylogenetic use. In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch, using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia). Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the clade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck’s rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel—which is the hardest tissue in vertebrates, and is highly abundant in the fossil record—can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation.
UR - http://www.scopus.com/inward/record.url?scp=85072903285&partnerID=8YFLogxK
U2 - 10.1038/s41586-019-1555-y
DO - 10.1038/s41586-019-1555-y
M3 - Article
C2 - 31511700
AN - SCOPUS:85072903285
SN - 0028-0836
VL - 574
SP - 103
EP - 107
JO - Nature
JF - Nature
IS - 7776
ER -