Unveiling hidden diversity of Oecomys (Rodentia: Cricetidae) from Brazilian Central Amazonia: description of a new species and new lineages

References

• Aljanabi, S. M., & Martinez, I. (1997). Universal and rapid salt–extraction of high quality genomic DNA for PCR–based techniques. Nucleic Acids Research, 25, 4692–4693. https://doi.org/10.1093/nar/25.22.4692
   PubMed Web of Science ®Google Scholar
• Allen, J. A. (1916). New mammals collected on the Roosevelt Brazilian expedition. Bulletin of American Museum of Natural History, 35, 523–530.
   Google Scholar
• Barber, C. P., Cochrane, M. A., Souza, C. M., & Laurance, W. F. (2014). Roads, deforestation, and the mitigating effect of protected areas in the Amazon. Biological Conservation, 177, 203–209. https://doi.org/10.1016/j.biocon.2014.07.004
   Web of Science ®Google Scholar
• Brandão, M. V., Garbino, G. S. T., Rezende, G. C., Tenório, S. F., & Reis, S. F. (2022). Taxonomic and natural history notes on Oecomys cleberi (Rodentia: Cricetidae) and first records in the Atlantic Forest, Brazil. Studies on Neotropical Fauna and Environment, 1–15. https://doi.org/10.1080/01650521.2022.2046962
   Web of Science ®Google Scholar
• Carleton, M. D., & Musser, G. G. (2015). Genus Oecomys Thomas, 1906. In J. Patton, U. F. J. Pardiñas & G. D’Elía (Eds.), Mammals of South America, vol.2, rodents (pp. 393–417). University of Chicago Press.
   Google Scholar
• Carleton, M. D., Emmons, L. H., & Musser, G. G. (2009). A new species of the rodent genus Oecomys (Cricetidae: Sigmodontinae: Oryzomyini) from eastern Bolivia, with emended definitions of O. concolor and O. mamorae (Thomas). American Museum Novitates, 3661, 1–32. https://doi.org/10.1206/612.1
   Google Scholar
• Cracraft, J. (1985). Historical biogeography and patterns of differentiation within the South American avifauna: Areas of endemism. Ornithological Monographs, 36, 49–84. https://doi.org/10.2307/40168278
   Google Scholar
• Dall’Igna, F., & Maniesi, V. (2022). Spatial and temporary dynamics of heat spots in the amazon ecological corridor conservation unit: The case of intense anthropic pressure in the National Forest of Jamari/RO. Research, Society and Development, 11, e42011629271. https://doi.org/10.33448/rsd-v11i6.29271
   Google Scholar
• Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012). jModelTest 2: More models, new heuristics and parallel computing. Nature Methods, 9, 772–772. https://doi.org/10.1038/nmeth.2109
   PubMed Web of Science ®Google Scholar
• Ferrante, L., & Fearnside, P. M. (2019). Brazil’s new president and ‘ruralists’ threaten Amazonia’s environment, traditional peoples and the global climate. Environmental Conservation, 46, 261–263. https://doi.org/10.1017/S0376892919000213
   Web of Science ®Google Scholar
• Ferrante, L., Andrade, M. B. T., Leite, L., Junior, C. A. S., Lima, M., Junior, G. C., Neto, E. C. S., Campolina, D., Carolino, K., Diele-Viegas, L. M., Pereira, E. J. A. L., & Fearnside, P. M. (2021). Brazil highway BR-319: The road to the collapse of the Amazon and the violation of indigenous rights. Journal of the Geographical Society of Berlin, 152, 1–6. https://doi.org/10.12854/erde-2021-552
   Google Scholar
• Hall, T. A. (1999). BioEdit: A user–friendly biological sequence alignment editor and analisys program for Windows 85/98/NT. Nucleic Acids Symposium Series, 41, 95–98.
   Google Scholar
• Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Meintjes, P., & Drummond, A. (2012). Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics (Oxford, England), 28, 1647–1649. https://doi.org/10.1093/bioinformatics/bts199
   PubMed Web of Science ®Google Scholar
• Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33, 1870–1874. https://doi.org/10.1093/molbev/msw054
   PubMed Web of Science ®Google Scholar
• Matocq, M. D., Shurtliff, Q. R., & Feldman, C. R. (2007). Phylogenetics of the woodrat genus Neotoma (Rodentia: Muridae): Implications for the evolution of phenotypic variation in male external genitalia. Molecular Phylogenetics and Evolution, 42, 637–652. https://doi.org/10.1016/j.ympev.2006.08.011
   PubMed Web of Science ®Google Scholar
• Miller, M. A., Pfeiffer, W., Schwartz, T. (2010). Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Proceedings of the Gateway Computing Environments Workshop (GCE), IEEE, New Orleans, LA, 1–8. https://doi.org/10.1109/GCE.2010.5676129
   Google Scholar
• Musser, G. G., & Carleton, M. D. (2005). Superfamily Muroidea. In D. E. Wilson & D. M. Reeder (Eds.), Mammals species of the world: A taxonomic geographic reference (3rd ed. Vol. 2, pp. 894–1531). The Johns Hopkins University Press.
   Google Scholar
• Pardiñas, U. F. J., Teta, P., Salazar-Bravo, J., Myers, P., & Galliari, C. A. (2016). A new species of arboreal rat, genus Oecomys (Rodentia, Cricetidae) from Chaco. Journal of Mammalogy, 97, 1177–1196. https://doi.org/10.1093/jmammal/gyw070
   Web of Science ®Google Scholar
• Pardiñas, U., Ruelas, D., Brito, J., Bradley, L., Bradley, R., Garza, N. O., Kryštufek, 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 D. E. Wilson, T. E. Lacher & R. A. Mittermeier (Eds.), Handbook of mammals of the world, Vol.7, Rodents II (pp. 281–535). Lynx Edicions.
   Google Scholar
• Pires, C., Gudinho, F., & Weksler, M. (2016). Morfologia dentária de gêneros de Sigmodontinae (Rodentia: Cricetidae) com ocorrência no Cerrado brasileiro. Boletim da Sociedade Brasileira de Mastozoologia, 75, 1–32.
   Google Scholar
• Reig, O. A. (1977). A proposed unified nomenclature for the enamelled components of the molar teeth of the Cricetidae (Rodentia). Journal of Zoology, 181, 227–241. https://doi.org/10.1111/j.1469-7998.1977.tb03238.x
   Web of Science ®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). Journal of Mammalogy, 99, 174–186. https://doi.org/10.1093/jmammal/gyx149
   Web of Science ®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. Ecology and Evolution, 4, 4598–4608. https://doi.org/10.1002/ece3.1336
   PubMed Web of Science ®Google Scholar
• Rocha, R. G., Fonseca, C., Zhou, Z., Leite, Y. L. R., & Costa, L. P. (2012). Taxonomic and conservation status of the elusive Oecomys cleberi (Rodentia, Sigmodontinae) from central Brazil. Mammalian Biology, 77, 414–419. https://doi.org/10.1016/j.mambio.2012.02.004
   Web of Science ®Google Scholar
• Ronquist, F., Teslenko, M., Van Der Mark, P., Ayres, D. L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M. A., & Huelsenbeck, J. P. (2012). MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61, 539–542. https://doi.org/10.1093/sysbio/sys029
   PubMed Web of Science ®Google Scholar
• Rosa, C. C., 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. Journal of Genetics, 91, 265–277. https://doi.org/10.1007/s12041-012-0182-2
   PubMed Web of Science ®Google Scholar
• Saldanha, J., & Rossi, R. V. (2021). Integrative analysis supports a new species of the Oecomys catherinae complex (Rodentia, Cricetidae) from Amazonia. Journal of Mammalogy, 102, 69–89. https://doi.org/10.1093/jmammal/gyaa145
   Web of Science ®Google Scholar
• Saldanha, J., Ferreira, D. C., da Silva, V. F., Santos–Filho, M., Mendes–Oliveira, A. C., & Rossi, R. V. (2019). Genetic diversity of Oecomys (Rodentia, Sigmodontinae) from the Tapajós River basin and the role of rivers as barriers for the genus in the region. Mammalian Biology, 97, 41–49. https://doi.org/10.1016/j.mambio.2019.04.009
   Web of Science ®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. Biological Journal of the Linnean Society, 50, 149–177. https://doi.org/10.1111/j.1095-8312.1993.tb00924.x
   Web of Science ®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. Zoological Journal of the Linnean Society, 184, 182–210. https://doi.org/10.1093/zoolinnean/zlx095
   Web of Science ®Google Scholar
• Sukumaran, J., & Holder, M. T. (2010). DendroPy: A Python library for phylogenetic computing. Bioinformatics (Oxford, England), 26, 1569–1571. https://doi.org/10.1093/bioinformatics/btq228
   PubMed Web of Science ®Google Scholar
• Voss, R. S., & Carleton, M. D. (1993). A new genus for Hesperomys molitor Winge and Holochilus magnus Hershkovitz (Mammalia, Muridae) with an analysis of its phylogenetic relationships. American Museum of Natural History, 3085, 1–39. http://hdl.handle.net/2246/4982 (Accessed 16 Jul. 2021)
   Google Scholar
• Voss, R. S. (1988). Systematics and ecology of ichthyomyine rodents (Muroidea): Patterns of morphological evolution in a small adaptative radiation. Bulletin of the American Museum of Natural History, 188, 259–493. http://hdl.handle.net/2246/927 (Accessed 16 Jul. 2021)
   Web of Science ®Google Scholar
• Voss, R. S. (1991). An introduction to the neotropical muroid rodent genus Zygodontomys. Bulletin of the American Museum of Natural History, 210, 1–113.
   Google Scholar
• Weksler, M. (2006). Phylogenetic relationships of Oryzomine rodents (Muroidea: Sigmodontinae): Separate and combined analyses of morphological and molecular data. Bulletin of the American Museum of Natural History, 296, 1–149. https://doi.org/10.1206/0003-0090(2006)296[0001:PROORM]2.0.CO;22.0.CO;2]
   Google Scholar
• Zwickl, D. J. (2006). Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion [Ph.D. dissertation]. The University of Texas at Austin. Retrieved July 16, 2021, from http://hdl.handle.net/2152/2666
   Google Scholar