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. 2021 Feb 11;11(1):3564.
doi: 10.1038/s41598-021-82390-2.

The evolutionary history of manatees told by their mitogenomes

Érica Martinha Silva de Souza #  1 , Lucas Freitas #  2 , Elisa Karen da Silva Ramos #  2 , Giovanna Selleghin-Veiga #  2 , Michelle Carneiro Rachid-Ribeiro #  2 , Felipe André Silva  2 , Miriam Marmontel  3 , Fabrício Rodrigues Dos Santos  4 , Anne Laudisoit  5 , Erik Verheyen  6   7 , Daryl P Domning  8   9 , Mariana Freitas Nery #  10
Affiliations

The evolutionary history of manatees told by their mitogenomes

Érica Martinha Silva de Souza et al. Sci Rep. .

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.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Distribution of Trichechus species in the world, map made by EMSS with Rstudio v.1.3 using distribution shapefile from IUCN database, script available at author’s Github webpage (https://github.com/souzaems/scripts/blob/master/map_on_R.r).
Figure 2
Figure 2
Scheme of circular mitochondrial genome of Trichechus species: 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and the putative control region.
Figure 3
Figure 3
A phylogenetic tree for time divergence between the Trichechus species. The purple bars represent the mean age of lineages split.
Figure 4
Figure 4
The alignment of ND4 gene, (a) represents the ND4 domain and the highlighted indicates the amino acid position of positive selection. (b) Modelling protein of ND4 of Trichechus species; the arrow shows the positive selection area.
Figure 5
Figure 5
Schematic figure to show the evolution of the Amazon drainage pattern, based on Albert et al. (2018). (a) Early and Middle Miocene (20.4–9.0 Ma): Potamosiren (P) present in Magdalena basin based on Domning (1982), and fossil described during this period; (b) Late Miocene (9.0–5.3 Ma): Trichechus-like sirenians (T) presumed to be present in the Amazon basin and South America Coast as suggested by Domning (1982), and fossil described by Beatty et al. (2012); (c) Middle Pliocene—Recent (c. 4.5–0 Ma): the possible occurrence of modern Trichechus species T, and a new species of Trichechus described recently by Perini et al. (2020).
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References

    1. Buffrenil, V. de. Mammifères. In Stratotype danien. Muséum national d’histoire naturelle (ed. Montenat, C., Merle, D., de Wever, P., & Cornée, A.) 337–339 (2018).
    1. Berta A, Sumich JL, Kovacs KM. Marine Mammals: Evolutionary Biology Most. Amsterdam: Elsevier; 2005.
    1. Domning DP. Evolution of manatees: a speculative history. J. Paleontol. 1982;56:599–619.
    1. Shoshani J. Order hyracoidea. Mammal Species World Taxon. Geogr. Ref. 2005;1:87–89.
    1. Berta A. Return to the Sea: The Life and Evolutionary Times of Marine Mammals. Berkeley: University of California Press; 2020.

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