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. 2023 Oct 4;18(10):e0291797.
doi: 10.1371/journal.pone.0291797. eCollection 2023.

Genetic diversity analysis in the Brazilian Amazon reveals a new evolutionary lineage and new karyotype for the genus Mesomys (Rodentia, Echimyidae, Eumysopinae)

Leony Dias de Oliveira  1 , Willam Oliveira da Silva  1 , Marlyson Jeremias Rodrigues da Costa  1 , Jeferson Costa Carneiro  2 , Iracilda Sampaio  2 , Juliane Saldanha da Silva  3 , Rogério Vieira Rossi  3 , Ana Cristina Mendes-Oliveira  4 , Julio Cesar Pieczarka  1 , Cleusa Yoshiko Nagamachi  1
Affiliations

Genetic diversity analysis in the Brazilian Amazon reveals a new evolutionary lineage and new karyotype for the genus Mesomys (Rodentia, Echimyidae, Eumysopinae)

Leony Dias de Oliveira et al. PLoS One. .

Abstract

Morphological, molecular and chromosomal studies in the genera Lonchothrix and Mesomys have contributed to a better understanding of taxonomic design, phylogenetic relationships and karyotypic patterns. Recent molecular investigations have shown a yet undescribed diversity, suggesting that these taxa are even more diverse than previously assumed. Furthermore, some authors have questioned the limits of geographic distribution in the Amazon region for the species M. hispidus and M. stimulax. In this sense, the current study sought to understand the karyotypic evolution and geographic limits of the genus Mesomys, based on classical (G- and C-banding) and molecular cytogenetic analysis (FISH using rDNA 18S and telomeric probes) and through the sequencing of mitochondrial genes Cytochrome b (Cytb) and Cytochrome Oxidase-Subunit I (CO using phylogeny, species delimitation and time of divergence, from samples of different locations in the Brazilian Amazon. The species M. stimulax and Mesomys sp. presented 2n = 60/FN = 110, while M. hispidus presented 2n = 60/FN = 112, hitherto unpublished. Molecular dating showed that Mesomys diversification occurred during the Plio-Pleistocene period, with M. occultus diverging at around 5.1 Ma, followed by Mesomys sp. (4.1 Ma) and, more recently, the separation between M. hispidus and M. stimulax (3.5 Ma). The ABGD and ASAP species delimiters support the formation of 7 and 8 potential species of the genus Mesomys, respectively. Furthermore, in both analyzes Mesomys sp. was recovered as a valid species. Our multidisciplinary approach involving karyotypic, molecular and biogeographic analysis is the first performed in Mesomys, with the description of a new karyotype for M. hispidus, a new independent lineage for the genus and new distribution data for M. hispidus and M. stimulax.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Map with the collection points of the samples of the Mesomys genus whose sequences or karyotypes were employed in this study.
Present study: M. hispidus (1 to 10), M. stimulax (4, 11 and 12) and Mesomys sp. (13). Literature and GenBank: M. hispidus (14 to 19), M. stimulax (20 and 21), M. occultus (15). The numbers refer to the locations of each sample. More detailed information can be found in S1 and S2 Tables. Circle: Mesomys sp.; hexagon: M. hispidus; diamond: M. stimulax; and square: M. occultus. This map was made using the free software Quantum-Gis version 2.10.1. The databases were obtained from DIVA-GIS. The files provided by DIVA-GIS are free of charge.
Fig 2
Fig 2. Maximum likelihood tree of the samples from the present study and those available in GenBank for the genus Mesomys, based on sequences of concatenated mitochondrial genes (Cytb and COI).
The numbers near the nodes are bootstrap values for 1,000 replicates. Bootstrap values less than 80% are not shown. The numbers in square brackets precede the locations are referred to in Fig 1.
Fig 3
Fig 3. Time tree and species delimitation of the samples from the present study and those available in GenBank for the genus Mesomys, based on sequences of concatenated mitochondrial genes (Cytb and COI).
Boundaries of 95% confidence intervals: M. occultus node 5.1 Ma (6.5 Ma– 3.5 Ma), Mesomys sp. node 4.1 Ma (5.6 Ma– 2.6 Ma), M. hispidus + M. stimulax node 3.5 Ma (4.9 Ma– 2.2 Ma). The numbers in square brackets precede the locations are referred to in Fig 1.
Fig 4
Fig 4. Mesomys hispidus (2n = 60/FN = 112).
a) G-banding, b) C-banding, c) Telomeric FISH and d) 18S rDNA FISH.
Fig 5
Fig 5. Mesomys stimulax (2n = 60/FN = 110).
a) G-banding, b) C-banding, c) Telomeric FISH and d) 18S rDNA FISH.
Fig 6
Fig 6. Mesomys sp. (2n = 60/FN = 110).
a) G-banding, b) C-banding, c) Telomeric FISH and d) 18S rDNA FISH.
Fig 7
Fig 7. Proposal for expanding the geographic distribution for the species M. hispidus and M. stimulax.
Circle: Mesomys sp., hexagon: M. hispidus, diamond: M. stimulax and square: M. occultus. This map was made using the free software Quantum-Gis version 2.10.1. The databases were obtained from DIVA-GIS. The files provided by DIVA-GIS are free of charge.
See this image and copyright information in PMC

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