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Published June 19, 2025 | Version v1
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A Multigene Phylogeny for Oecomys (Rodentia: Cricetidae: Sigmodontinae) with Descriptions of New and Revalidated Taxa and a Partial Species-Group Classification

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Voss, Robert S., Giarla, Thomas C., Lim, Burton K., Engstrom, Mark D. (2025): A Multigene Phylogeny for Oecomys (Rodentia: Cricetidae: Sigmodontinae) with Descriptions of New and Revalidated Taxa and a Partial Species-Group Classification. American Museum Novitates 2025 (4038): 1-40, DOI: 10.1206/4038.1, URL: https://bioone.org/journals/american-museum-novitates/volume-2025/issue-4038/4038.1/A-Multigene-Phylogeny-for-Oecomys-Rodentia--Cricetidae--Sigmodontinae/10.1206/4038.1.full

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References

  • Allen, G.M., and T. Barbour. 1923. Mammals from Darien. Bulletin of the Museum of Comparative Zoology 45: 259-274.
  • Ammerman, L.K., D.N. Lee, and T.M. Tipps. 2012. First molecular phylogenetic insights into the evolution of free-tailed bats in the subfamily Molossinae (Molossidae, Chiroptera). Journal of Mammalogy 93: 12-28.
  • Baker, R.J., B.F. Koop, and M.W. Haiduk. 1983. Resolving systematic relationships with G-bands: a study of five genera of South American cricetine rodents. Systematic Zoology 32: 403-416.
  • Bangs, O., and T. Barbour. 1922. Birds from Darien. Bulletin of the Museum of Comparative Zoology 65: 191-229.
  • Barbour, T. 1944. Naturalist at large. Boston: Little, Brown, and Company.
  • Bass, M.S., et al. 2010. Global conservation significance of Ecuador's Yasuni National Park. PLoS ONE 5 (1): e8767.
  • Brandao, M.V., G.S.T. Garbino, G.C. Rezende, S.F. Tenorio, and S.F. Reis. 2024. Taxonomic and natural history notes on Oecomys cleberi (Rodentia: Cricetidae) and first records in the Atlantic Forest, Brazil. Studies on Neotropical Fauna and Environment 59: 59-73.
  • Cabrera, A. 1961. Catalogo de los mamiferos de America del Sur. Revista del Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (Ciencias Zoologicas) 4 (2): 309-732.
  • Calle-Rendon, B.R., M. Peck, S.E. Bennett, C. Morelos-Juarez, and F. Alfonso. 2016. Comparison of forest regeneration in two sites with different primate abundances in northwestern Ecuador. Revista de Biologia Tropical 64: 493-506.
  • Carleton, M.D., and G.G. Musser. 2015. Genus Oecomys Thomas, 1906. In J.L. Patton, U.F.J. Pardinas, and G. D'Elia (editors), Mammals of South America, vol. 2: rodents: 393-417. Chicago: University of Chicago Press.
  • Carleton, M.D., L.H. Emmons, and G.G. Musser. 2009. A new species of the rodent genus Oecomys (Cricetidae: Sigmodontinae: Oryzomyini) from eastern Bolivia, with emended definitions of O. concolor (Wagner), and O. mamorae (Thomas). American Museum Novitates 3661: 1-32.
  • Carstens, B.C., T.A. Pelletier, N.M. Reid, and J.D. Satler. 2013. How to fail at species delimitation. Molecular Ecology 22: 4369-4383.
  • Croat, T.B. 1978. Flora of Barro Colorado Island. Stanford: Stanford University Press.
  • Davalos, L.M., and A.L. Russell. 2014. Sex-biased dispersal produces high error rates in mitochondrial distance-based and tree-based species delimitation. Journal of Mammalogy 95: 781-791.
  • Delacre, M., D. Lakens, and C. Leys. 2017. Why psychologists should by default use Welch's t -test instead of Student's t -test. International Review of Social Psychology 30: 92-101.
  • Diaz, M.M. 2020. Lista comentada de los pequenos roedores de Iquitos y sus alrededores. Boletim do Museu Paraense Emilio Goeldi Ciencias Naturais Belem 15: 727-766.
  • Dodson, C.H., and A.H. Gentry. 1978. Flora of the Rio Palenque Science Center, Los Rios, Ecuador. Selbyana (Journal of the Marie Selby Botanical Gardens) 4: i -xxx, 1-628.
  • Duellman, W.E., and J.R. Mendelson III. 1995. Amphibians and reptiles from northern Departamento Loreto, Peru: taxonomy and biogeography. University of Kansas Science Bulletin 55: 329-376.
  • Fairchild, G.B., and C.O. Handley Jr. 1966. Gazetteer of collecting localities in Panama. In R.L. Wenzel and V.J. Tipton (editors), Ectoparasites of Panama: 9-22 + folding map.
  • Gardner, A.L., and J.L. Patton. 1976. Karyotypic variation in oryzomyine rodents (Cricetinae) with comments on chromosomal evolution in the Neotropical cricetine complex. Occasional Papers of the Museum of Zoology of Louisiana State University 49: 1-48.
  • Giarla, T.C., and R.S. Voss. 2020. DNA sequence data from the holotype of Marmosa elegans coquimbensis Tate, 1931 (Mammalia: Didelphidae) resolve its disputed relationships. American Museum Novitates 3946: 1-8.
  • Goldman, E.A. 1933. A new climbing mouse from Panama. Journal of the Washington Academy of Sciences 23: 525-526.
  • Gomes,, R.G., Jr., et al. 2016. Intense genomic reorganization in the genus Oecomys (Rodentia, Sigmodontinae): comparison between DNA barcoding and mapping of repetitive elements in three species of the Brazilian Amazon. Comparative Cytogenetics 10: 401-426.
  • Hall, E.R. 1962. Collecting and preparing study specimens of vertebrates. Miscellaneous Publications, University of Kansas Museum of Natural History 30: 1-46.
  • Hall, E.R. 1980. The mammals of North America, 2 vols. New York: John Wiley & Sons.
  • Handley, C.O. Jr. 1976. Mammals of the Smithsonian Venezuelan Project. Brigham Young University Science Bulletin, Biological Series 20 (5): 1-89 + map.
  • Hershkovitz, P. 1960. Mammals of northern Colombia, preliminary report no. 8. Arboreal rice rats, a systematic revision of the subgenus Oecomys, genus Oryzomys. Proceedings of the United States National Museum 110: 513-568 + 12 pls.
  • Hice, C.L., and P.M. Velazco. 2012. The non-volant mammals of the Reserva Nacional Allpahuayo-Mishana, Loreto, Peru. Special Publications of the Museum of Texas Tech University 60: [i, ii], 1-135.
  • Hice, C.L., P.M. Velazco, and M. Willig. 2004. Bats of the Reserva Nacional Allpahuayo-Mishana, northeastern Peru, with notes on community structure. Acta Chiropterologica 6: 319-334.
  • Katoh, K., and D.M. Standley. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30 (4): 772-780.
  • Leigh, E.G. Jr, A.S. Rand, and D.M. Windsor (eds.). 1996. The ecology of a tropical forest, 2nd ed. Washington DC: Smithsonian Institution Press.
  • Lim, B.K., M.D. Engstrom, J.W. Bickham, and J.C. Patton. 2008. Molecular phylogeny of New World sheath-tailed bats (Emballonuridae: Diclidurini) based on loci from the four genetic transmission systems in mammals. Biological Journal of the Linnean Society 93: 189-209.
  • Lira, T. de. 2012. Citogenetica classica e molecular de alguns representantes da tribo Oryzomyini (Rodentia, Cricetidae) da Amazonia Central. Postgraduate thesis, Instituto Nacional de Pesquisas da Amazonia (Manaus).
  • Mason, N.A., N.K. Fletcher, B.A. Gill, W.C. Funk, and K.R. Zamudio. 2020. Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance. Systematics and Biodiversity 18: 269-280.
  • Minh, B.Q., M.A.T. Nguyen, and A. von Haesler. 2013. Ultrafast approximation for phylogenetic bootstrap. Molecular Biology and Evolution 30 (5): 1188-1195.
  • Minh, B.Q., et al. 2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution 37 (5): 1530-1534.
  • Musser, G.G., and M.D. Carleton. 1993. Family Muridae. In D.E. Wilson and D.M. Reeder (editors), Mammal species of the world, 2nd ed.: 501-755. Washington DC: Smithsonian Institution Press.
  • Ochoa G., J., F. Garcia, S. Caura, and J. Sanchez H. 2009. Mamiferos de la cuenca del rio Caura, Venezuela: listado taxonomico y distribucion conocida. Memoria de la Fundacion La Salle de Ciencias Naturales 170: 5-80.
  • Pardinas, U.F.J., P. Teta, J. Salazar-Bravo, P. Myers, and C.A. Galliari. 2016. A new species of arboreal rat, genus Oecomys (Rodentia, Cricetidae) from Chaco. Journal of Mammalogy 97: 1177-1196.
  • Patton, J.L. 1967. Chromosome studies of certain pocket mice, genus Perognathus (Rodentia: Heteromyidae). Journal of Mammalogy 48: 27-37.
  • Patton, J.L., and M.N.F. da Silva. 1995. A review of the spiny mouse genus Scolomys (Rodentia: Muridae: Sigmodontinae) with the description of a new species from the western Amazon of Brazil. Proceedings of the Biological Society of Washington 108: 319-337.
  • Patton, J.L., M.N.F. da Silva, and J.R. Malcolm. 2000. Mammals of the Rio Jurua and the evolutionary and ecological diversification of Amazonia. Bulletin of the American Museum of Natural History 244: 1-306.
  • Paynter, R.A. Jr. 1993. Ornithological gazetteer of Ecuador, 2nd ed. Cambridge, MA: Museum of Comparative Zoology.
  • Percequillo, A.R., M. Weksler, and L.P. Costa. 2011. A new genus and species of rodent from the Brazilian Atlantic Forest (Rodentia: Cricetidae: Sigmodontinae: Oryzomyini), with comments on oryzomyine biogeography. Zoological Journal of the Linnean Society 161: 357-390.
  • Pitman, N.C.A. 2000. A large-scale inventory of two Amazonian tree communities. Ph.D. dissertation, Duke University.
  • Prance, G.T. 1979. Notes on the vegetation of Amazonia III. The terminology of Amazonian forest types subject to inundation. Brittonia 31: 26-38.
  • Rambaut, A., A.J. Drummond, D. Xie, G. Baele, and M.A. Suchard. 2018. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Systematic Biology 67 (5): 901-904.
  • Rocha, R.G., et al. 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.
  • Rocha, R.G., C. Fonseca, Z. Zhou, Y.L.R. Leite, and L.P. Costa. 2012. Taxonomic and conservation status of the elusive Oecomys cleberi (Rodentia, Sigmodontinae) from central Brazil. Mammalian Biology 77: 414-419.
  • Rocha, R.G. et al. 2018. Cryptic diversity in the Oecomys roberti complex: revalidation of Oecomys tapajinus (Rodentia: Cricetidae). Journal of Mammalogy 99: 174-186.
  • Ronquist, F., et al. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61 (3): 539-542.
  • Rosa, C.C. et al. 2012. Genetic and morphological variability in South American rodent Oecomys (Sigmodontinae, Rodentia): evidence for a complex of species. Journal of Genetics 91: 265-277.
  • Saldanha, J., and R.V. Rossi. 2021. Integrative analysis supports a new species of the Oecomys catherinae complex (Rodentia, Cricetidae) from Amazonia. Journal of Mammalogy 102: 69-89.
  • Saldanha, J., et al. 2023. Unveiling hidden diversity of Oecomys (Rodentia: Cricetidae) from Brazilian central Amazonia: description of a new species and new lineages. Systematics and Biodiversity 21 (1): 2259037.
  • Siegel, D.C., and S.L. Olson. 2008. The birds of the republic of Panama. Part 5. Ornithological gazetteer and bibliography. Shipman, VA: Buteo Books.
  • Silva, W.O. da, et al. 2020. Karyotypic divergence reveals that diversity in the Oecomys paricola complex (Rodentia, Sigmodontinae) from eastern Amazonia is higher than previously thought. PLoS ONE 15(10): e0241495.
  • Silva, W.O. da, et al. 2022. The emergence of a new sex-system (XX/XY1Y2) suggests a species complex in the "monotypic" rodent Oecomys auyantepui (Rodentia, Sigmodontinae). Scientific Reports 12: 8690.
  • Steppan, S.J., and J.J. Schenk. 2017. Muroid rodent phylogenetics: 900-species tree reveals increasing diversification rates. PLoS ONE 12 (8): e0183070.
  • Suarez-Villota, E.Y., A.P. Carmignotto, M.V. Brandao, A.R. Percequillo, and M.J.J. de Silva. 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.
  • Sukumaran, J., and L.L. Knowles. 2017. Multispecies coalescence delimits structure, not species. Proceedings of the National Academy of Sciences of the United States of America 114: 1607-1612.
  • Thomas, O. 1900. Descriptions of new Neotropical mammals. Annals and Magazine of Natural History (ser. 7) 5: 269-274.
  • Thomas, O. 1906. Notes on South American rodents. Annals and Magazine of Natural History (ser. 7) 18: 442-448.
  • Valencia, R., et al. 2004. Tree species distributions and local habitat variation in the Amazon: large forest plot in eastern Ecuador. Journal of Ecology 92: 214-229.
  • Vasquez M., R., and Oliver L. Phillips. 2000. Allpahuayo: floristics, structure, and dynamics of a highdiversity forest in Amazonian Peru. Annals of the Missouri Botanical Garden 87: 499-527.
  • Vormisto, J., O.L. Phillips, K. Ruokolainen, H. Tuomisto, and R. Vasquez. 2000. A comparison of finescale distribution patterns of four plant groups in an Amazonian rainforest. Ecography 23: 349-359.
  • Voss, R.S. 1988. Systematics and ecology of ichthyomyine rodents (Muroidea): patterns of morphological evolution in a small adaptive radiation. Bulletin of the American Museum of Natural History 188 (2): 259-493.
  • Voss, R.S., and A.V. Linzey. 1981. Comparative gross morphology of male accessory glands among Neotropical Muridae (Mammalia: Rodentia) with comments on systematic implications. Miscellaneous Publications of the Museum of Zoology, University of Michigan 159: i -iv, 1-41.
  • Voss, R.S., D.W. Fleck, and T.C. Giarla. 2024. Mammalian diversity and Matses ethnomammalogy in Amazonian Peru. Part 5. Rodents. Bulletin of the American Museum of Natural History 466: 1-179.
  • Wallace, A.R. 1854. On the monkeys of the Amazon. Proceedings of the Zoological Society of London 1852: 107-110.
  • Weksler, M. 2003. Phylogeny of Neotropical oryzomyine rodents (Muridae: Sigmodontinae) based on the nuclear IRBP exon. Molecular Phylogenetics and Evolution 29: 331-349.
  • Weksler, M. 2006. Phylogenetic relationships of oryzomyine rodents (Muroidea: Sigmodontinae): separate and combined analyses of morphological and molecular data. Bulletin of the American Museum of Natural History 296: 1-149.
  • Wuster, W. et al. 2024. How not to describe a species: lessons from a tangle of anacondas. Zoological Journal of the Linnean Society 201: zlae099 (AOP).