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Genetic diversity of Oecomys (Rodentia, Sigmodontinae) from the Tapajós River basin and the role of rivers as barriers for the genus in the region

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Abstract

The genus Oecomys is one of the most speciose within the subfamily Sigmodontinae, with most species found in the Amazon region. Recent studies have shown that the diversity, recognition of specific boundaries and geographical distribution is still imprecise for the genus. Herein, we investigate the genetic diversity of Oecomys in the Tapajós River basin and determine whether its rivers (Tapajós, Teles Pires, and Juruena) act as barriers for some species or populations in this genus based on phylogenetic analyzes with the mitochondrial marker cytochrome b (cytb) and the nuclear marker intron 7 ß-fibrinogen, and on populational analysis with cytb. The phylogenetic relationships showed the presence of seven species in the region, namely O. bicolor, Oecomys aff. catherinae, O. catherinae, O. cleberi, O. paricola, O. roberti, and O. tapajinus. The geographic distributions of O. bicolor and O. cleberi seem to be shaped by the Tapajós and Teles Pires Rivers, with the former species occurring on the right bank and the latter species on the left bank of both rivers. Moreover, O. cleberi was the only Oecomys species to be recorded on the left bank of the Tapajós River. Our results also indicate that gene flow occurs between O. cleberi populations from the west Juruena and Tapajós Rivers and is absent between opposite banks of the Juruena River. The isolation by distance was discarded for this species. No evidence of gene flow was found for O. bicolor populations, and the isolation by distance was positive for this species. The spatial distribution of specimens and hap-lotypes of O. paricola indicates that the Teles Pires River does not act as a barrier for this species. Finally, Fs test significant results for O. cleberi and O. paricola showed that species population expansion cannot be discarded for these species.

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Reference

  • Aljanabi, S.M., Martinez, I., 1997. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res., 25, 4692–4693.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Antonelli, A., Quijada-Mascareñas, A., Crawford, A.J., Bates, J.M., Velazco, P.M., Wüster, W., 2010. Molecular studies and phylogeography of Amazonian tetrapods and their relation to geological and climatic models. In: Hoorn, C., Wesselingh, F.P. (Eds.), Amazônia, Landscape and Species Evolution: A Look into the Past., first ed. Wiley-Blackwell, pp. 386–404.

    Google Scholar 

  • Asfora, P.H., Palma, A.R.T., Astúa, D., Geise, R., 2011. Distribution of Oecomys catherinae Thomas, 1909 (Rodentia: Cricetidae) in northeastern Brazil with karyotypical and morphometrical notes. Biota Neotrop. 11 (2), 415–424.

    Google Scholar 

  • Bandelt, HJ., Forster, P., Röhl, A., 1999. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16(1), 37–48.

    CAS  PubMed  Google Scholar 

  • Bates, J.M., Haffer, J., Grisme, E., 2004. Avian mitochondrial DNA sequence divergence across a headwater stream of the Rio Tapajós, a major Amazonian river. J. Ornithol., 145, 199–205.

    Google Scholar 

  • Bonvicino, C.R., Oliveira, J.A., D’andrea, P.S., 2008. Guia dos roedores do Brasil, com chaves para gêneros baseadas em caracteres externos. Centro Pan-Americano de Febre Aftosa - OPAS/OMS, Rio de Janeiro.

    Google Scholar 

  • Carleton, M.D., Musser, G.G., 2015. Genus Oecomys Thomas., 1906. In: Patton, J., Pardiñas, U.F.J., D’Elía, G. (Eds.), Mammals of South America, Vol.2, Rodents. University of Chicago Press, Chicago, Illinois, pp. 393–417.

    Google Scholar 

  • Excoffier, L., Lischer, H.E.L., 2010. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol., 10, 564–567.

    Google Scholar 

  • Excoffier, L., Smouse, P., Quattro, J., 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131, 479–491.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fu, Y.X., 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915–925.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Haffer, J., 2008. Hypotheses to explain the origin of species in Amazonia. Braz. J. Biol. 68 (4), 917–947.

    CAS  PubMed  Google Scholar 

  • Hall, T.A., 1999. BioEdit: a user-friendly biological sequence alignment editor and analisys program for Windows 85/98/NT. Nucleic Acids Symp. Ser., 41, 95–98.

    CAS  Google Scholar 

  • Harpending, H.C., 1994. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum. Biol., 66, 591–600.

    CAS  PubMed  Google Scholar 

  • Harvey, M.G., Brumfield, R.T., 2014. Genomic variation in a widespread Neotropical bird (Xenops minutus) reveals divergence, population expansion, and gene flow. Mol. Phylogenet. Evol., 38, 305–316.

    Google Scholar 

  • Kumar, S., Stecher, G., Tamura, K., 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol., 33, 1870–1874.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Malcher, M.S., Pieczarka, J.C., Geise, L., Rossi, R.V., Pereira, A.L., O’Brien, P.C.M., Asfora, P.H., Silva, V.F., Sampaio, M.I., Ferguson-Smith, M.A., Nagamachi, C.Y., 2017. Oecomys catherinae (Sigmodontinae, Cricetidae): evidence for chromosomal speciation? PLoS One, https://doi.org/10.1371/journal.pone.0181434.

    Google Scholar 

  • Matocq, M.D., Shurtliff, Q.R., Feldman, CR., 2007. Phylogenetics of the woodrat genus Neotoma (Rodentia: Muridae): implications for the evolution of phenotypic variation in male external genitalia. Mol. Phylogenet. Evol., 42, 637–652.

    CAS  PubMed  Google Scholar 

  • Miller, M.P., 2005. Alleles In Space (AIS): computer software for the joint analysis of interindividual spatial and genetic information. J. Hered., 96, 722–724.

    CAS  PubMed  Google Scholar 

  • Moraes, L.J.C.L., Pavan, D., Barros, M.C., Ribas, C.C., 2016. The combined influence of riverine barriers and flooding gradients on biogeographical patterns for amphibians and squamates in south-eastern Amazonia. J. Biogeogr., 43, 2113–2124.

    Google Scholar 

  • Oliveira, J.A., Bonvicino, CR., 2011. Ordem rodentia. In: Reis, N.R., Peracchi, A.L., Pedro, W.A., Lima, I.P. (Eds.), Mamíferos do Brasil., second ed. Londrina (PR), Universidade Estadual de Londrina, pp. 358–415.

    Google Scholar 

  • Oliveira, U., Vasconcelos, M.F., Santos, A.J., 2017. Biogeography of Amazon birds: rivers limit species composition, but not areas of endemism. Sci. Rep. 7, 2992.

    PubMed  PubMed Central  Google Scholar 

  • Paglia, A.P., Fonseca, G.A.B., Rylands, A.B., Herrmann, G., Aguiar, L.M.S., Chiarello, A.G., Leite, Y.L.R., Costa, L.P., Siciliano, S., Kierulff, M.C.M., Mendes, S.L., Tavares, V.C., Mittermeier, RA, Patton, J.L., 2012. Annotated Checklist of Brazilian Mammals, 6., second ed. Occas. Pap. Conserve. Biol., pp. 1–76.

    Google Scholar 

  • Pardiñas, U., Ruelas, D., Brito, J., Bradley, L., Bradley, R., Garza, N.O., Krystufek, B., Cook, J., Soto, E.C., Salazar-Bravo, J., Shenbrot, G., Chiquito, E., Percequillo, A., Prado, J., Haslauer, R., Patton, J., León-Paniagua, L., 2017. Species accounts of cricetidae. In: Wilson, D.E., Lacher, T.E., Mittermeier, RA (Eds.). Handbook of Mammals of the World, vol. 7. Rodents II. Lynx Edicions, Barcelona, Spain}, pp. 281–53

    Google Scholar 

  • Patton, J.L., Da Silva, M.N.F., Malcom, J.R., 2000. Mammals of the Rio Juruá and the evolutionary and ecological diversification of Amazonia. Bull. Am. Mus. Nat. Hist., 244, 1–306.

    Google Scholar 

  • PERH-MDA., 2011. Plano Estratégico de Recursos Hídricos da Bacia Amazônica: Afluentes da margem direita - Volume I: Descrição das bacias e aspectos físicos (accessed 24 April 2018) https://doi.org/margemdireita.ana.gov.br/.

    Google Scholar 

  • Posada, D., 2008. jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 25 (7), 1253–1256, https://doi.org/10.1093/molbev/msn083.

    CAS  PubMed  Google Scholar 

  • Rambaut, A., 2016. FigTree v1.4.3 2006–2016 (Accessed 24 April 2018) https://doi.org/tree.bio.ed.ac.uk/software/figtree/.

    Google Scholar 

  • Ribas, CC., Aleixo, A., Nogueira, A.CR., Miyaki, C.Y., Cracraft, J., 2012. A palaeobiogeographic model for biotic diversification within Amazonia over the past three million years. Proc. R. Soc. B., 279, 681–689.

    PubMed  Google Scholar 

  • Rocha, R.G., Ferreira, E., Costa, B.M.A., Martins, I.C.M., Leite, Y.L.R., Costa, L.P., Fonseca, C., 2011. Small mammals of the mid-Araguaia River in central Brazil, with the description of a new species of climbing rat. Zootaxa, 2789, 1–34.

    Google Scholar 

  • Rocha, R.G., Fonseca, C., Zhou, Z., Leite, Y.L.R., Costa, LP., 2012. Taxonomic and conservation status of the elusive Oecomys cleberi (Rodentia, Sigmodontinae) from central Brazil. Mamm. Biol., 77, 414–419.

    Google Scholar 

  • Rocha, R.G., Ferreira, E., Fonseca, C., Justino, J., Leite, Y.L.R., Costa, L.P., 2014. Seasonal flooding regime and ecological traits influence genetic structure of two small rodents. Ecol. Evol. 4 (24), 4598–4608.

    PubMed  PubMed Central  Google Scholar 

  • Rocha, R.G., Ferreira, E., Loss, A.C., Heller, R., Fonseca, C., Costa, L.P., 2015. The Araguaia Riveras an important biogeographical divide for Didelphid Marsupials in Central Brazil. J. Hered. 106 (5), 593–607.

    CAS  PubMed  Google Scholar 

  • Rocha, R.G., Duda, R., Flores, T., Rossi, R., Sampaio, I., Mendes-Oliveira, A.C., Leite, Y.L.R., Costa, L.P., 2018. Cryptic diversity in the Oecomys roberti complex: revalidation of Oecomys tapajinus (Rodentia, Cricetidae). J. Mammal., 99, 174–186.

    Google Scholar 

  • Ronquist, F., Huelsenbeck, J.F., 2003. MrBayes: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (12), 1572–1574.

    CAS  PubMed  Google Scholar 

  • Rosa, CC., Flores, T., Pieczarka, J.C., Rossi, R.V., Sampaio, M.I.C., Rissino, J.D., Amaral, P.J.S., Nagamachi, C.Y., 2012. Genetic and morphological variability in South American rodent Oecomys (Sigmodontinae, Rodentia): evidence for a complex of species. J. Genet. 91 (3), 265–277.

    CAS  PubMed  Google Scholar 

  • Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J.C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S.E., Sánchez-Gracia, A., 2017. DnaSP v6: DNA sequence polymorphism analyses of large datasets. Mol. Biol., 34, 3299–3302.

    CAS  Google Scholar 

  • Silva, J.M.C., Rylands, A.B., Fonseca, GAB., 2005. The fate of the Amazonian areas of endemism. Conserv. Biol. 19 (3), 689–694.

    Google Scholar 

  • Silva, CR., Martins, A.C.M., Castro, I.J., Bernard, E., Cardoso, E.M., Lima, D.S., Gregorin, R., Rossi, R.V., Percequillo, A.R., Castro, K.C., 2013. Mammals of Amapá State, Eastern Brazilian Amazonia: a revised taxonomic list withcomments on species distributions. Mammals, 77, 409–424.

    Google Scholar 

  • Smith, M.F., Patton, J.L., 1993. The diversification of South American murid rodents: evidence from mitochondrial DNA sequence data for Akodontine tribe. Biol. J. Linn. Soc., 50, 149–177.

    Google Scholar 

  • Suárez-Villota, E.Y., Carmignotto, A.P., Brandão, M.V., Percequillo, A.R., Silva, M.J.J., 2018. Systematics of the genus Oecomys(Sigmodontinae: Oryzomyini): molecular phylogenetic, cytogenetic and morphological approaches reveal cryptic species. Zool. J. Linn. Soc., 184, 182–210.

    Google Scholar 

  • Tajima, F., 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genet., 123, 585–595.

    CAS  Google Scholar 

  • Voss, R.S., Lunde, D.P., Limmons, N.B., 2001. The mammals of paracou, french guiana: a neotropical lowland rainforest fauna part 2. Nonvolant species. Bull. Am. Mus. Nat. Hist., 263, 1–236.

    Google Scholar 

  • Wallace, A.R., 1852. On the monkeys of the Amazon. Proc. Zool. Soc. Lond., 20, 107–110.

    Google Scholar 

  • Weir, B.S., Cockerham, C.C., 1984. Estimating F-statistics forthe analysis of population structure. Evolution 38 (6), 1358–1370.

    CAS  PubMed  Google Scholar 

  • Xia, X., 2013. DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution. Mol. Biol. Evol. 30(7), 1720–1728.

    Google Scholar 

  • Zwickl, D.J., 2006. Genetic Algorithm Approaches forthe Phylogenetic Analysis of Large Biological Sequence Datasets Under the Maximum Likelihood Criterion. Ph.D. Dissertation. The University of Texas at Austin, pp. 1–125

    Google Scholar 

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Authors and Affiliations

  1. Laboratório de Mastozoologia, Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, Mato Grosso, Brazil

    Juliane Saldanha, Victor Fonsêca da Silva & Rogério Vieira Rossi

  2. Laboratório de Citogenética e Genética Animal, Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, Mato Grosso, Brazil

    Juliane Saldanha & Daniela Cristina Ferreira

  3. Laboratório de Mastozoologia, Universidade do Estado de Mato Grosso, Cáceres, Mato Grosso, Brazil

    Manoel Santos-Filho

  4. Laboratório de Ecologia e Zoologia de Vertebrados - Mastozoologia, ICB, Universidade Federal do Pará, Belém, Pará, Brazil

    Ana Cristina Mendes-Oliveira

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  1. Juliane Saldanha
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Saldanha, J., Ferreira, D.C., da Silva, V.F. et al. Genetic diversity of Oecomys (Rodentia, Sigmodontinae) from the Tapajós River basin and the role of rivers as barriers for the genus in the region. Mamm Biol 97, 41–49 (2019). https://doi.org/10.1016/j.mambio.2019.04.009

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