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Title: The evolutionary history of manatees told by their mitogenomes
Author: Selleghin-veiga, G.; Magpali, L.; Picorelli, A.; Silva, F. A.; Ramos, E. K. S.; Nery, M. F.
Year: 2024
Is part of: JOURNAL OF MOLECULAR EVOLUTION, v. 92, p. 300 - 316

Citation: Selleghin-veiga, G.; Magpali, L.; Picorelli, A.; Silva, F. A.; Ramos, E. K. S.; Nery, M. F.; The evolutionary history of manatees told by their mitogenomes. JOURNAL OF MOLECULAR EVOLUTION, v.92, p. 300-316, 2024

Abstract: The manatee family encompasses three extant congeneric species: Trichechus senegalensis (African manatee), T. inunguis (Amazonian manatee), and T. manatus (West Indian manatee). The fossil record for manatees is scant, and few phylogenetic studies have focused on their evolutionary history. We use full mitogenomes of all extant manatee species to infer the divergence dates and biogeographical histories of these species and the effect of natural selection on their mitogenomes. The complete mitochondrial genomes of T. inunguis (16,851 bp), T. senegalensis (16,882 bp), and T. manatus (16,882 bp), comprise 13 protein-coding genes, 2 ribosomal RNA genes (rRNA - 12S and 16S), and 22 transfer RNA genes (tRNA), and (D-loop/CR). Our analyses show that the first split within Trichechus occurred during the Late Miocene (posterior mean 6.56 Ma and 95% HPD 3.81-10.66 Ma), followed by a diversification event in the Plio-Pleistocene (posterior mean 1.34 Ma, 95% HPD 0.1-4.23) in the clade composed by T. inunguis and T. manatus; T. senegalensis is the sister group of this clade with higher support values (pp>0.90). The branch-site test identified positive selection on T. inunguis in the 181st position of the ND4 amino acid gene (LRT=6.06, p=0.0069, BEB posterior probability=0.96). The ND4 gene encodes one subunit of the NADH dehydrogenase complex, part of the oxidative phosphorylation machinery. In conclusion, our results provide novel insight into the evolutionary history of the Trichechidae during the Late Miocene, which was influenced by geological events, such as Amazon Basin formation.

Funding: This study is part of EMSS's PhD research at the Universidade Estadual de Campinas (UNICAMP). This work was supported by the Sao Paulo Research Foundation (FAPESP 2015/18269-1), and a scholarship granted to EMSS by CAPES (PROEX-IS/88882.329516/2019-01). AL and EV thank the ICCN for providing CITES certificate 6543 export of the T. senegalensis sample we used, originating from the Park Marin de Mangroves of the DR Congo. Also, we want to thank the Congolese Institute for Nature Conservation (ICCN), and Mr Marcel Collet, Mangrove Marine Park Director, for their administrative, scientific, logistical and financial support in the DRCongo.
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