Revisiting proboscidean phylogeny and evolution through total evidence and palaeogenetic analyses including Notiomastodon ancient DNA

Sina Baleka; Luciano Varela; P Sebastián Tambusso; Johanna L A Paijmans; Dimila Mothé; Thomas W Stafford Jr; Richard A Fariña; Michael Hofreiter

doi:10.1016/j.isci.2021.103559

Revisiting proboscidean phylogeny and evolution through total evidence and palaeogenetic analyses including Notiomastodon ancient DNA

iScience. 2021 Dec 4;25(1):103559. doi: 10.1016/j.isci.2021.103559. eCollection 2022 Jan 21.

Authors

Sina Baleka^{1

2}, Luciano Varela^{3

4}, P Sebastián Tambusso^{3

4}, Johanna L A Paijmans¹, Dimila Mothé^{5

6}, Thomas W Stafford Jr⁷, Richard A Fariña^{3

4}, Michael Hofreiter¹

Affiliations

¹ Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.
² Faculty of Life and Environmental Sciences, University of Iceland, Sæmundargata 2, 102 Reykjavik, Iceland.
³ Departamento de Paleontología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
⁴ Servicio Académico Universitario y Centro de Estudios Paleontológicos (SAUCE-P), Universidad de la República, Santa Isabel s/n, 91500 Sauce, Departamento de Canelones, Uruguay.
⁵ Laboratório de Mastozoologia, Instituto de Biociências, Universidade Federal do Estado do Rio de Janeiro, Av. Pasteur, 458/501, 22290-240 Rio de Janeiro, Brazil.
⁶ Programa de Pós-graduação em Biodiversidade e Biologia Evolutiva, Centro de Ciências da Saúde, Instituto de Biologia, Campus Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
⁷ Stafford Research LLC, 200 Acadia Avenue, Lafayette, CO 80026-1845, USA.

Abstract

The extinct Gomphotheriidae is the only proboscidean family that colonized South America. The phylogenetic position of the endemic taxa has been through several revisions using morphological comparisons. Morphological studies are enhanced by paleogenetic analyses, a powerful tool to resolve phylogenetic relationships; however, ancient DNA (aDNA) preservation decreases in warmer regions. Despite the poor preservation conditions for aDNA in humid, sub-tropical climates, we recovered ∼3,000 bp of mtDNA of Notiomastodon platensis from the Arroyo del Vizcaíno site, Uruguay. Our calibrated phylogeny places Notiomastodon as a sister taxon to Elephantidae, with a divergence time of ∼13.5 Ma. Additionally, a total evidence analysis combining morphological and paleogenetic data shows that the three most diverse clades within Proboscidea diverged during the early Miocene, coinciding with the formation of a land passage between Africa and Eurasia. Our results are a further step toward aDNA analyses on Pleistocene samples from subtropical regions and provide a framework for proboscidean evolution.