Skip to main content
  • Get access
    Check if you have access via personal or institutional login
  • Cited by 5
  • Cited by
    This chapter has been cited by the following publications. This list is generated based on data provided by CrossRef.

    Reyes, Marian C. Ingicco, Thomas Piper, Philip J. Amano, Noel and Pawlik, Alfred F. 2017. First fossil evidence of the extinct Philippine cloud rat Crateromys paulus (Muridae: Murinae: Phloeomyini) from Ilin Island, Mindoro, and insights into its Holocene abundance. Proceedings of the Biological Society of Washington, Vol. 130, Issue. 1, p. 84.

    Candela, Adriana M. Muñoz, Nahuel A. and García-Esponda, César M. 2017. The tarsal-metatarsal complex of caviomorph rodents: Anatomy and functional-adaptive analysis. Journal of Morphology, Vol. 278, Issue. 6, p. 828.

    Marivaux, Laurent Adnet, Sylvain Benammi, Mohamed Tabuce, Rodolphe and Benammi, Mouloud 2017. Anomaluroid rodents from the earliest Oligocene of Dakhla, Morocco, reveal the long-lived and morphologically conservative pattern of the Anomaluridae and Nonanomaluridae during the Tertiary in Africa. Journal of Systematic Palaeontology, Vol. 15, Issue. 7, p. 539.

    Riede, Tobias Borgard, Heather L. and Pasch, Bret 2017. Laryngeal airway reconstruction indicates that rodent ultrasonic vocalizations are produced by an edge-tone mechanism. Royal Society Open Science, Vol. 4, Issue. 11, p. 170976.

    Boivin, Myriam Marivaux, Laurent Candela, Adriana M. Orliac, Maëva J. Pujos, François Salas-Gismondi, Rodolfo Tejada-Lara, Julia V. Antoine, Pierre-Olivier and O'Regan, Hannah 2017. Late Oligocene caviomorph rodents from Contamana, Peruvian Amazonia. Papers in Palaeontology, Vol. 3, Issue. 1, p. 69.

  • Print publication year: 2015
  • Online publication date: August 2015

2 - A synopsis of rodent molecular phylogenetics, systematics and biogeography



Through their taxonomic and phenotypic diversity, rodents constitute a very distinctive placental order. Indeed, with over 2277 described species (Wilson and Reeder, 2005; Fabre et al., 2012), they represent more than 40% of mammalian biodiversity.

In nearly every continent, rodents have colonised all terrestrial ecosystems from tropical deserts to arctic tundra, and from tropical and temperate to boreal forests. They display an astonishing diversity in that they have repeatedly colonised these ecological niches on most continents (Upham and Patterson, 2012; Schenk et al., 2013) and even on isolated archipelagos via the crossing of the Wallace and Lydekker lines to Australia (e.g. Indo-Pacific rats; Rowe et al., 2008; Fabre et al., 2013a). Following these continental dispersals, rodent adaptations converged on a wide array of locomotor repertoires (Samuels and Valkenburgh, 2008) and diets (e.g. vermivory: Musser, 1982; Balete et al., 2007; Samuels, 2009; Charles et al., 2013). Their success has often been connected to their wide-ranging diets, their cranio-dental specialisations (Hunter and Jernvall, 1995; Jernvall, 1995), their small-to-medium size, and their short generation time (Spradling et al., 2001). These recurrent adaptations and striking diversity have created difficulties for inferring their phylogenetic relationships (Luckett and Hartenberger, 1985). Despite some early methodological controversies (Graur et al., 1991), the use of molecular systematics has enabled the rodent tree of life to be deciphered and revealed a broad array of previously unexpected relationships and convergences. Mirroring research progress on Placentalia, the first rodent nuclear gene phylogenies (Huchon et al., 1999; Madsen et al., 2001; DeBry, 2003) have paved the way for understanding the higher-level relationships among rodents and revealed a strong biogeographical footprint (Huchon and Douzery, 2001; Mercer and Roth, 2003; Steppan et al., 2004a; Schenk et al., 2013). Since then, phylogenetic studies on Rodentia (Huchon et al., 1999; DeBry and Sagel, 2001; Montgelard et al., 2008; Blanga-Kanfi et al., 2009) as well as on Placentalia (Meredith et al., 2011) have benefited from the sequencing of mitochondrial DNA, nuclear markers and SINE/retroposons, and provided a large body of multi-locus molecular characters.

Recommend this book

Email your librarian or administrator to recommend adding this book to your organisation's collection.

Evolution of the Rodents
  • Online ISBN: 9781107360150
  • Book DOI:
Please enter your name
Please enter a valid email address
Who would you like to send this to *
Adkins, R. M., Gelke, E. L., Rowe, D. L. and Honeycutt, R. L. (2001). Molecular phylogeny and divergence time estimates for major rodent groups: evidence from multiple genes. Molecular Biology and Evolution, 18, 777–791.
Adkins, R. M., Walton, A. H. and Honeycutt, R. L. (2003). Higher-level systematics of rodents and divergence time estimates based on two congruent nuclear genes. Molecular Phylogenetics and Evolution, 26, 409–420.
Aguilar, J. P. and Michaux, J. (1996). The beginning of the age of Murinae (Mammalia: Rodentia) in southern France. Acta Zoologica Cracoviensia, 39, 35–45.
Antoine, P.-O., Marivaux, L., Croft, D. A., et al. (2012). Middle Eocene rodents from Peruvian Amazonia reveal the pattern and timing of caviomorph origins and biogeography. Proceedings of the Royal Society B – Biological Sciences, 279, 1319–1326.
Aplin, K. P. (2006). Ten million years of rodent evolution in Australasia: phylogenetic evidence and a speculative historical biogeography. In Evolution and Biogeography of Australasian Vertebrates, eds. Merrick, J. R., Archer, M., Hickey, G. M. and Lee, M. S. Y.. Sydney: Auscipub Pty Ltd, pp. 707–744.
Balete, D. S., Rickart, E. A., Rosell-Ambal, R. G. B., et al. (2007). Descriptions of two new species of Rhynchomys Thomas (Rodentia: Muridae: Murinae) from Luzon Island, Philippines. Journal of Mammalogy, 88, 287–301.
Benton, M. J., Donoghue, P. C. J., and Asher, R. J. (2009). Calibrating and constraining molecular clocks. In The Timetree of Life, eds. Hedges, S. B. and Kumar, S.. New York : Oxford University Press, pp. 35–86.
Blainville, H. M. D. (1816). Prodrome d'une nouvelle distribution systématique du règne animal. Bulletin de la Société Philomáthique, Paris, 8, 113–124.
Blanga-Kanfi, S., Miranda, H., Penn, O., et al. (2009). Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades. BMC Evolutionary Biology, 9, 71.
Blanquart, S. and Lartillot, N. (2008). A site- and time-heterogeneous model of amino acid replacement. Molecular Biology and Evolution, 25, 842–858.
Brandt, J. F. (1855). Beiträge zur nähern Kenntniss der Säugethiere Russlands. Buchdruckerei der Kaiserlichen Akademie der Wissenschaften, 6, 1–375.
Bruijn, H. (2009). The Eumyarion (Mammalia, Rodentia, Muridae) assemblage from Sandelzhausen (Miocene, Southern Germany): a test on homogeneity. Paläontologische Zeitschrift, 83, 77–83.
Bryant, J. D. and McKenna, M. C. (1995). Cranial anatomy and phylogenetic position of Tsaganomys altaicus (Mammalia, Rodentia) from the Hsanda Gol Formation (Oligocene), Mongolia. American Museum Novitates, 3156, 1–42.
Bugge, J. (1974). The cephalic arterial system in insectivores, primates, rodents and lagomorphs, with special reference to the systematic classification. Cells Tissues Organs, 101, 45–61.
Bugge, J. (1985). Systematic value of the carotid arterial pattern in Rodents. In Evolutionary Relationships Among Rodents: a Multidisciplinary Analysis, eds. Luckett, W. P. and Hartenberger, J.-L.. New York: Plenum Press, pp. 355–379.
Buzan, E. V., Krystufek, B., Hänfling, B. and Hutchinson, W. F. (2008). Mitochondrial phylogeny of Arvicolinae using comprehensive taxonomic sampling yields new insights. Biological Journal of the Linnean Society, 94, 825–835.
Carleton, M. D. and Musser, G. G. (2005). Order : Rodentia. In Mammal Species of the World Volume 2, eds. Wilson, D. E. and Reeder, D. M.. Baltimore, Maryland: Johns Hopkins University Press, pp. 745–1600.
Carranza-Castañeda, Ó. and Walton, A. H. (1992). Cricetid rodents from the Rancho El Ocote fauna. Late Hemphillian (Miocene), Guanajuato, México. Revista del Instituto de Geología, 10, 71–93.
Carvalho, G. A. and Salles, L. O. (2004). Relationships among extant and fossil echimyids (Rodentia: Hystricognathi). Zoological Journal of the Linnean Society, 142, 445–477.
Charles, C., Solé, F., Rodrigues, H. G. and Viriot, L. (2013). Under pressure? Dental adaptations to termitophagy and vermivory among mammals. Evolution, 67, 1792–1804.
Chevret, P., Denys, C., Jaeger, J.-J., et al. (1993). Molecular evidence that the spiny mouse (Acomys) is more closely related to gerbils (Gerbillinae) than to true mice (Murinae). Proceedings of the National Academy of Sciences of the United States of America, 90, 3433–3436.
Churakov, G., Sadasivuni, M. K., Rosenbloom, K. R., et al. (2010). Rodent evolution: back to the root. Molecular Biology and Evolution, 27, 1315–1326.
D'Erchia, A. M., Saccone, C., Gissi, C., et al (1996). The guinea-pig is not a rodent. Nature, 381, 597–600.
Daams, R. (1999). Family Gliridae. In The Miocene Land Mammals of Europe, eds. Rössner, G. and Heissig, K.. Munich: Verlag Dr. Friedrich Pfeil, pp. 301–318.
Daams, R. and de Bruijn, H. (1995). A classification of the Gliridae (Rodentia) on the basis of dental morphology. Hystrix, 6, 3–50.
Dawson, M. R., Marivaux, L., Li, C-K., et al. (2006). Laonastes and the “Lazarus effect” in recent mammals. Science (New York, N.Y.), 311, 1456–1458.
de Jong, W. W. (1985). Superordinal affinities of Rodentia studied by sequence analysis of Eye Lens Protein. In Evolutionary Relationships Among Rodents: a Multidisciplinary Analysis, eds. Luckett, W. P. and Hartenberger, J.-L.. New York: Plenum Press, pp. 211–226.
DeBry, R. W. (2003). Identifying conflicting signal in a multigene analysis reveals a highly resolved tree: the phylogeny of Rodentia (Mammalia). Systematic Biology, 52, 604–617.
DeBry, R. W. and Sagel, R.M. (2001). Phylogeny of Rodentia (Mammalia) inferred from the nuclear-encoded gene IRBP. Molecular Phylogenetics and Evolution, 19, 290–301.
Delsuc, F., Brinkmann, H. and Philippe, H. E. (2005). Phylogenomics and the reconstruction of the tree of life. Nature Reviews Genetics, 6, 361–375.
dos Reis, M., Inoue, J. G., Hasegawa, M., et al. (2012). Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proceedings of the Royal Society B – Biological Sciences, 279, 3491–3500.
dos Reis, M., Zhu, T. and Yang, Z. (2014). The impact of the rate prior on Bayesian estimation of divergence times with multiple loci. Systematic Biology, doi: 10.1093/sysbio/syu020.
Douzery, E. J. P., Delsuc, F., Stanhope, M. J. and Huchon, D. (2003). Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations. Journal of Molecular Evolution, 57, S201–S213.
Douzery, E. J. P., Scornavacca, C., Romiguier, J., et al. (2014) OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals. Molecular Biology and Evolution,
Drummond, A. J. and Suchard, M. A. (2010). Bayesian random local clocks, or one rate to rule them all. BMC Biology, 8, 114.
Drummond, A. J., Ho, S. Y. W., Phillips, M. J. and Rambaut, A. (2006). Relaxed phylogenetics and dating with confidence. PLoS Biology, 4, e88.
Emry, R. J. (2007). The middle Eocene North American myomorph rodent Elymys, her Asian sister Aksyiromys, and other Eocene myomorphs. Bulletin of Carnegie Museum of Natural History, 39, 141–150.
Emry, R. J. and Korth, W. W. (2001). Douglassciurus, new name for Douglassia Emry and Korth, 1996, not Douglassia Bartsch, 1934. Journal of Vertebrate Paleontology, 21, 400.
Engel, S. R., Hogan, K. M., Taylor, J. F. and Davis, S. K. (1998). Molecular systematics and paleobiogeography of the South American sigmodontine rodents. Molecular Biology and Evolution, 15, 35–49.
Esselstyn, J. A., Achmadi, A. S. and Rowe, K. C. (2012). Evolutionary novelty in a rat with no molars. Biology Letters, 8, 990–993.
Fabre, P.-H., Hautier, L., Dimitrov, D. and Douzery, E. J. P. (2012). A glimpse on the pattern of rodent diversification: a phylogenetic approach. BMC Evolutionary Biology, 12, 88.
Fabre, P.-H., Pagès, M., Musser, G. G., et al. (2013a). A new genus of rodent from Wallacea (Rodentia: Muridae: Murinae: Rattini), and its implication for biogeography and Indo-Pacific Rattini systematics. Zoological Journal of the Linnean Society, 169, 408–447.
Fabre, P.-H., Jønsson, K. A. J. and Douzery, E. J. P. (2013b). Jumping and gliding rodents: mitogenomic affinities of Pedetidae and Anomaluridae deduced from an RNA-Seq approach. Gene, 531, 388–397.
Fabre, P-H., Galewski, T., Tilak, M-K. and Douzery, E. J. P. (2013c). Diversification of South American spiny rats (Echimyidae): a multigene phylogenetic approach. Zoologica Scripta, 42, 117–134.
Felsenstein, J. (1978). Cases in which parsimony or compatibility methods will be positively misleading. Systematic Biology, 27, 401–410.
Flynn, J. J. (1995). Cenozoic South American land mammal ages: correlation to global geochronologies. Geochronology Time Scales and Global Stratigraphic Correlation, SEPM Special Publication, 54, 317–333.
Flynn, L. J. (2003). Cenozoic Andean geochronology, paleoenvironments and tectonic history: evidence from South American fossil mammals. Geological Society of America Abstracts with Programs, 35, 58.
Galewski, T., Mauffrey, J.-F., Leite, Y. L. R., et al. (2005). Ecomorphological diversification among South American spiny rats (Rodentia; Echimyidae): a phylogenetic and chronological approach. Molecular Phylogenetics and Evolution, 34, 601–615.
Galewski, T., Tilak, M.-K., Sanchez, S., et al. (2006). The evolutionary radiation of Arvicolinae rodents (voles and lemmings): relative contribution of nuclear and mitochondrial DNA phylogenies. BMC Evolutionary Biology, 6, 80.
Geraads, D. (2001). Plio-Pleistocene mammalian biostratigraphy of Atlantic Morocco. Quaternaire, 13, 43–53.
Graur, D., Hide, W. A. and Li, W. H. (1991). Is the guinea-pig a rodent?Nature, 351, 649–652.
Graur, D., Duret, L. and Gouy, M. (1996). Phylogenetic position of the order Lagomorpha (rabbits, hares and allies). Nature, 379, 333–335.
Hartenberger, J.-L. (1985). The order Rodentia: major questions on their evolutionary origin, relationships and suprafamilial systematics. In Evolutionary Relationships Among Rodents: a Multidisciplinary Analysis, eds. Luckett, W. P. and Hartenberger, J.-L.. New York: Plenum Press, pp. 1–33.
Hartenberger, J.-L. (1994). The evolution of the Gliroidea. In Rodent and Lagomorph Families of Asian Origins and Diversification, eds. Li, C. K., Tomida, Y. and Setoguchi, T.. Tokyo: National Science Museum Monographs, pp. 19–33.
Hartenberger, J.-L. (1998). Description of the radiation of the Rodentia (Mammalia) from the Late Paleocene to the Miocene; phylogenetic consequences. Comptes Rendus de l'Académie des Sciences – Series IIA – Earth and Planetary Science, 326, 439–444.
Hautier, L., Lebrun, R. and Cox, P. G. (2012). Patterns of covariation in the masticatory apparatus of hystricognathous rodents: Implications for evolution and diversification. Journal of Morphology, 273, 1319–1337.
Hautier, L., Bennett, N. C., Viljoen, H., et al. (2013). Patterns of ossification in southern versus northern placental mammals. Evolution, 67, 1994–2010.
Heaney, L. R., Balete, D. S., Rickart, E. A., et al. (2009). A new genus and species of small ‘tree-mouse’ (Rodentia, Muridae) related to the Philippine giant cloud rats. Bulletin of the American Museum of Natural History, 331, 205–229.
Heaney, L. R., Balete, D. S., Rickart, E. A., et al. (2011). Chapter 1: Seven new species and a new subgenus of forest mice (Rodentia: Muridae: Apomys) from Luzon Island. Fieldiana Life and Earth Sciences, 2, 1–60.
Heath, T. A., Huelsenbeck, J. P. and Stadler, T. (2014). The fossilized birth–death process: a coherent model of fossil calibration for divergence time estimation. arXiv, arXiv preprint arXiv:1310.2968, 1–42.
Helgen, L. E., Helgen, K. M., Cole, F. R. and Wilson, D. E. (2009). Generic revision in the Holarctic ground squirrel genus Spermophilus. Journal of Mammalogy, 90, 270–305.
Herron, M. D., Waterman, J. M. and Parkinson, C. L. (2005). Phylogeny and historical biogeography of African ground squirrels: the role of climate change in the evolution of Xerus. Molecular Ecology, 14, 2773–2788.
Honeycutt, R. L., Rowe, D. L. and Gallardo, M. H. (2003). Molecular systematics of the South American caviomorph rodents: relationships among species and genera in the family Octodontidae. Molecular Phylogenetics and Evolution, 26, 476–489.
Horn, S., Durka, W., Worf, R., et al. (2011). Mitochondrial genomes reveal slow rates of molecular evolution and the timing of speciation in beavers (Castor), one of the largest rodents. PLoS ONE, 6 (1), e14622.
Horner, D. S., Lefkimmiatis, K., Reyes, A., et al. (2007). Phylogenetic analyses of complete mitochondrial genome sequences suggest a basal divergence of the enigmatic rodent Anomalurus. BMC Evolutionary Biology, 7, 1–12.
Huchon, D. and Catzeflis, F. M. (2000). Phylogénie moléculaire des rongeurs (Mammalia, Rodentia): contribution des gènes nucléaires et confrontation avec les données mitochondriales. PhD dissertation. Montpellier: University Montpellier 2, pp. 1–313.
Huchon, D. and Douzery, E. J. P. (2001). From the Old World to the New World: a molecular chronicle of the phylogeny and biogeography of Hystricognath rodents. Molecular Phylogenetics and Evolution, 20, 238–251.
Huchon, D. and Douzery, E. J. P. (2002). Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes. Molecular Biology and Evolution, 19, 1053–1065.
Huchon, D., Catzeflis, F. M. and Douzery, E. J. P. (1999). Molecular evolution of the nuclear von Willebrand factor gene in mammals and the phylogeny of rodents. Molecular Biology and Evolution, 16, 577–589.
Huchon, D., Catzeflis, F. M. and Douzery, E. J. P. (2000). Variance of molecular datings, evolution of rodents and the phylogenetic affinities between Ctenodactylidae and Hystricognathi. Proceedings of the Royal Society B – Biological Sciences, 267, 393–402.
Huchon, D., Madsen, O., Sibbald, M., et al. (2002). Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes. Molecular Biology and Evolution, 19, 1053–1065.
Huchon, D., Chevret, P., Jordan, U., et al. (2007). Multiple molecular evidences for a living mammalian fossil. Proceedings of the National Academy of Sciences of the United States of America, 104, 7495–7499.
Huelsenbeck, J.P., Larget, B. and Swofford, D. (2000). A compound poisson process for relaxing the molecular clock. Genetics, 154, 1879–1892.
Hunter, J. P. and Jernvall, J. (1995). The hypocone as a key innovation in mammalian evolution. Proceedings of the National Academy of Sciences of the United States of America, 92, 10, 718–10, 722.
Inoue, J. G., Donoghue, P. C. J. and Yang, Z. (2010). The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Systematic Biology, 59, 74–89.
Jacobs, L. and Downs, W. (1994). The evolution of murine rodents in Asia. In Rodent and Lagomorph Families of Asian Origins and their Diversification, ed. Tomida, Y., Setoguschi, L.C.. Tokyo: National Science Museum Monograph, pp. 149–156.
Jacobs, L., Flynn, L., Downs, W. and Barry, J. (1990). Quo Vadis Antemus? The Siwalik muroid record. In European Neogene Mammal Chronology NATO ASI series A: Life Sciences, eds. Lindsay, E. H., Fahlbusch, V. and Mein, P.. New York : Plenum Press, pp. 573–586.
Jaeger, J. J., Coiffait, B., Tong, H. and Denys, C. (1987). Rodent extinctions following Messinian faunal exchanges between Western Europe and Northern Africa. Mémoires de la Société Géologique de France, 150, 153–158.
Janecka, J. E., Miller, W., Pringle, T. H., et al. (2007). Molecular and genomic data identify the closest living relative of Primates. Science, 318, 792–794.
Janke, A., Xu, X. and Arnason, U. (1997). The complete mitochondrial genome of the wallaroo (Macropus robustus) and the phylogenetic relationship among Monotremata, Marsupialia, and Eutheria. Proceedings of the National Academy of Sciences of the United States of America, 94, 1276–1281.
Jansa, S. A., Goodman, S. M. and Tucker, P. K. (1999). Molecular phylogeny and biogeography of the native rodents of Madagascar (Muridae: Nesomyinae): a test of the single-origin hypothesis. Cladistics, 15, 253–270.
Jansa, S. A. and Weksler, M. (2004). Phylogeny of muroid rodents: relationships within and among major lineages as determined by IRBP gene sequences. Molecular Phylogenetics and Evolution, 31, 256–276.
Jansa, S. A., Barker, F. and Heaney, L. R. (2006). The pattern and timing of diversification of Philippine endemic rodents: evidence from mitochondrial and nuclear gene sequences. Systematic Biology, 55, 73–88.
Jansa, S. A., Giarla, T. C. and Lim, B. K. (2009). The phylogenetic position of the rodent genus Typhlomys and the geographic origin of Muroidea. Journal of Mammalogy, 90, 1083–1094.
Jeffroy, O., Brinkmann, H., Delsuc, F. and Philippe, H. E. (2006). Phylogenomics: the beginning of incongruence?Trends in Genetics, 22, 225–231.
Jernvall, J. (1995). Mammalian molar cusp patterns: developmental mechanisms of diversity. Acta Zoologica Fennica, 198, 1–61.
Kim, E. B., Fang, X., Fushan, A. A., et al. (2011). Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature, 479, 223–227.
Kishino, H., Thorne, J. L. and Bruno, W. J. (2001). Performance of a divergence time estimation method under a probabilistic model of rate evolution. Molecular Biology and Evolution, 18, 352–361.
Koenigswald, W. (1985). Evolutionary trends in the enamel of rodent incisors. In Evolutionary Relationships Among Rodents: a Multidisciplinary Analysis, eds. Luckett, W. P. and Hartenberger, J.-L.. New York: Plenum Press, pp. 403–422.
Kramerov, D. A., Vassetzky, N. and Serdobova, I. (1999). The evolutionary position of dormice (Gliridae) in Rodentia determined by a novel short retroposon. Molecular Biology and Evolution, 16, 715–717.
Landry, S. O. (1999). A proposal for a new classification and nomenclature for the Glires (Lagomorpha and Rodentia). Zoosystematics and Evolution, 75, 283–316.
Lartillot, N. (2004). A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Molecular Biology and Evolution, 21, 1095–1109.
Lartillot, N. and Philippe, H. E. (2008). Improvement of molecular phylogenetic inference and the phylogeny of Bilateria. Philosophical Transactions: Biological Sciences, 363, 1463–1472.
Lartillot, N. and Poujol, R. (2010). A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters. Molecular Biology and Evolution, 28, 729–744.
Lavocat, R. (1973). Les rongeurs du Miocène d'Afrique Orientale I. Miocène inférieur. Mémoires et Travaux de l'EPHE, 1, 1–284.
Lavocat, R. (1976). Rongeurs Caviomorphes de l'Oligocène de Bolivie; II Rongeurs du bassin Deseadien de Salla-Luribay. Palaeovertebrata, 7, 15–90.
Lavocat, R. and Parent, J.-P. (1985). Phylogenetic analysis of middle ear features in fossil and living rodents. In Evolutionary Relationships Among Rodents: a Multidisciplinary Analysis, ed. Luckett, W.P. and Hartenberger, J.-L.. New York: Plenum Press, pp. 333–354.
Lazzari, V., Charles, C., Vianey-Liaud, M., et al. (2008). Mosaic convergence of rodent dentitions. PLoS ONE, 3, e3607.
Lecompte, E., Denys, C., Aplin, K. P., et al. (2008). Phylogeny and biogeography of African Murinae based on mitochondrial and nuclear gene sequences, with a new tribal classification of the subfamily. BMC Evolutionary Biology, 8, 199.
Leite, Y. L. R. and Patton, J. L. (2002). Evolution of South American spiny rats (Rodentia, Echimyidae): the star-phylogeny hypothesis revisited. Molecular Phylogenetics and Evolution, 25, 455–464.
Lepage, T., Bryant, D., Philippe, H. E. and Lartillot, N. (2007). A general comparison of relaxed molecular clock models. Molecular Biology and Evolution, 24, 2669–2680.
Lessa, E. P. (1989). Morphological evolution of subterranean mammals: integrating structural, functional, and ecological perspectives. Progress in Clinical and Biological Research, 335, 211–230.
Lessa, E. P., Vassallo, A. I., Verzi, D. H. and Mora, M.S. (2008). Evolution of morphological adaptations for digging in living and extinct ctenomyid and octodontid rodents. Biological Journal of the Linnean Society, 95, 267–283.
Li, Q. and Meng, J. (2010). Erlianomys combinatus, a primitive myodont rodent from the Eocene Arshanto Formation, Nuhetingboerhe, Nei Mongol, China. Vertebrata Paleontology Asiatica, 48, 133–144.
Li, Q. and Zheng, S.-H. (2005) Note on four species of dipodids (Dipodidae, Rodentia) from the Late Miocene Bahe Formation, Lantian, Shaanxi. Vertebrata Paleontology Asiatica, 43, 283–296.
Lin, G.-H., Wang, K., Deng, X.-G., et al. (2014). Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia). BMC Genomics, 15, 32.
Linnæus, C. (1758). Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. In Tomus I. Editio decima, reformata. Holmiæ. (Salvius), pp. 1–824.
López Antoñanzas, R., Knoll, F. and Flynn, L. J. (2013). A comprehensive phylogeny of extinct and extant Rhizomyinae (Rodentia): evidence for multiple intercontinental dispersals. Cladistics, 29, 247–273.
Luckett, W. P. and Hartenberger, J.-L. (1985). Evolutionary Relationships Among Rodents: a Multidisciplinary Analysis. New York: Plenum Press, pp. 1–721.
Lundrigan, B. L., Jansa, S. A. and Tucker, P. K. (2002). Phylogenetic relationships in the genus Mus, based on paternally, maternally, and biparentally inherited characters. Systematic Biology, 51, 410–431.
Madsen, O., Scally, M., Douady, C. J., et al. (2001). Parallel adaptive radiations in two major clades of placental mammals. Nature, 409, 610–614.
Maier, W. and Schrerk, F. (1987). The hystricomorphy of the Bathyergidae, as determined from ontogenetic evidence. Zeitschrift füs Säugetierkunde, 52, 156–164.
Maier, W., Klinger, P. and Ruf, I. (2003). Ontogeny of the medial masseter muscle, pseudo-myomorphy, and the systematic position of the Gliridae. Journal of Mammalian Evolution, 9, 253–269.
Marivaux, L., Vianey-Liaud, M., Welcomme, J.-L. and Jaeger, J-J. (2002). The role of Asia in the origin and diversification of hystricognathous rodents. Zoologica Scripta, 31, 225–239.
Marivaux, L., Vianey-Liaud, M. and Jaeger, J.-J. (2004). High-level phylogeny of early Tertiary rodents: dental evidence. Zoological Journal of the Linnean Society, 142, 105–134.
Marshall, L. G., Webb, S. D., Sepkoski, J. J. Jr and Raup, D. M. (1982). Mammalian evolution and the Great American Interchange. Science, 215, 1351–1357.
Martin, T. (1994). African origin of caviomorph rodents is indicated by incisor enamel microstructure. Paleobiology, 20, 5–13.
McKenna, M. C. and Bell, S. K. (1997). Classification of Mammals Above the Species Level. Columbia University Press, New York, pp. 1–631.
Mercer, J. M. and Roth, V. L. (2003). The effects of Cenozoic global change on squirrel phylogeny. Science, 299, 1568–1572.
Meredith, R. W., Janecka, J. E., Gatesy, J., et al. (2011). Impacts of the Cretaceous terrestrial revolution and KPg extinction on mammal diversification. Science, 334, 521–524.
Michaux, J., Aguilar, J.-P., Legendre, S., et al. (1997). Les Murinae (Rodentia, Mammalia) néogènes du sud de la France: evolution et paléoenvironnements. Geobios, 20, 379–385.
Michaux, J. R. and Catzeflis, F. M. (2000). The bushlike radiation of muroid rodents is exemplified by the molecular phylogeny of the LCAT nuclear gene. Molecular Phylogenetics and Evolution, 17, 280–293.
Michaux, J. R., Pagès, M., Chaval, Y., et al. (2010). Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries. BMC Evolutionary Biology, 10, 184.
Miller, G. S. and Gidley, J. W. (1918). Synopsis of the supergeneric groups of rodents. Journal of the Washington Academy of Sciences, 8, 431–448.
Miller, J. R. and Engstrom, M. D. (2008). The relationships of major lineages within Peromyscine rodents: a molecular phylogenetic hypothesis and systematic reappraisal. Journal of Mammalogy, 89, 1279–1295.
Misawa, K. and Janke, A. (2003). Revisiting the Glires concept–phylogenetic analysis of nuclear sequences. Molecular Phylogenetics and Evolution, 28, 320–327.
Montgelard, C., Bentz, S., Tirard, C., et al. (2002). Molecular systematics of Sciurognathi (Rodentia): the mitochondrial Cytochrome b and 12S rRNA genes support the Anomaluroidea (Pedetidae and Anomaluridae). Molecular Phylogenetics and Evolution, 22, 220–233.
Montgelard, C., Arnal, V., Forty, E. and Matthee, C. A. (2008). Suprafamilial relationships among Rodentia and the phylogenetic effect of removing fast-evolving nucleotides in mitochondrial, exon and intron fragments. BMC Evolutionary Biology, 8, 321.
Murphy, W. J., O'Brien, S. J., Eizirik, E., et al. (2001). Molecular phylogenetics and the origins of placental mammals. Nature, 409, 614–618.
Musser, G. G. (1982). Results of the Archbold expeditions. No. 110. Crunomys and the small-bodied shrew rats native to the Philippine Islands and Sulawesi (Celebes). Bulletin of the American Museum of Natural History, 174, 1–95.
Musser, G. G. and Newcomb, C. (1983). Malaysian murids and the giant rat of Sumatra. Bulletin of the American Museum of Natural History, 174, 327–598.
Nowak, R. M. (1999). Mammals of the World Volume 2. Baltimore, Maryland: Johns Hopkins University Press, pp. 1243–1714.
Nunome, M., Yasuda, S. P., Sato, J. J., et al. (2007). Phylogenetic relationships and divergence times among dormice (Rodentia, Gliridae) based on three nuclear genes. Zoologica Scripta, 36, 537–546.
Olivares, A. I., Verzi, D. H., Vucetich, M. G. and Montalvo, C. I. (2012). Phylogenetic affinities of the late Miocene echimyid †Pampamys and the age of Thrichomys (Rodentia, Hystricognathi). Journal of Mammalogy, 93, 76–86.
Parada, A., Pardiñas, U. F. J., Salazar-Bravo, J., et al. (2013). Dating an impressive Neotropical radiation: molecular time estimates for the Sigmodontinae (Rodentia) provide insights into its historical biogeography. Molecular Phylogenetics and Evolution, 66, 960–968.
Pardiñas, U. F. J. and Tonni, E. P. (1998). Stratigraphic provenance and age of the oldest muroids (Mammalia, Rodentia) in South America. Ameghiniana, 35, 473–475.
Parham, J. F., Donoghue, P. C. J., Bell, C. J., et al. (2012). Best practices for justifying fossil calibrations. Systematic Biology, 61, 346–359.
Patterson, B. and Pascual, R. (1968). Evolution of mammals on southern continents. Quarterly Review of Biology, 43, 409–451.
Patterson, B. and Wood, A.E. (1982). Rodents from the Deseadan Oligocene of Bolivia and the relationships of the Caviomorpha. Bulletin of The Museum of Comparative Zoology, 149, 371–543.
Percequillo, A. R., Weksler, M., and Voss, R. S. (2006). Ten new genera of Oryzomyine rodents (Cricetidae: Sigmodontinae). American Museum Novitates, 3537, 1–29.
Philippe, H. E. (1997). Rodent monophyly: pitfalls of molecular phylogenies. Journal of Molecular Evolution, 45, 712–715.
Poux, C., Madsen, O., Marquard, E., et al. (2005). Asynchronous colonization of Madagascar by the four endemic clades of primates, tenrecs, carnivores, and rodents as inferred from nuclear genes. Systematic Biology, 54, 719–730.
Poux, C., de Jong, W. W., Chevret, P., et al. (2006). Arrival and diversification of caviomorph rodents and platyrrhine primates in South America. Systematic Biology, 55, 228–244.
Prevosti, F. J. and Pardiñas, U. F. J. (2009). Comment on “The oldest South American Cricetidae (Rodentia) and Mustelidae (Carnivora): late Miocene faunal turnover in central Argentina and the Great American Biotic Interchange” by D. H. Verzi and C. I. Montalvo (2008) [Palaeogeography, Palaeoclimatology, Palaeoecology, 267, 284–291].” Palaeogeography, Palaeoclimatology, Palaeoecology, 280, 543–547.
Price, R. D. and Timm, R. M. (1997). A new subgenus and four new species of Gliricola (Phthiraptera: Gyropidae) from Caribbean hutias (Rodentia: Capromyidae). Proceedings of the Royal Society of Washington, 110, 285–300.
Reig, O. A. (1981). Teorίa del origen y desarrollo de la fauna de mamίferos de America del Sur. Museo Municipal de Ciencias Naturales Lorenzo Scaglia, 1, 1–162.
Romiguier, J., Ranwez, V., Douzery, E. J. P. and Galtier, N. (2010). Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes. Genome Research, 20, 1001–1009.
Ronquist, F., Klopfstein, S., Vilhelmsen, L., et al. (2012). A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera. Systematic Biology, 61, 973–999.
Rowe, D. L., Dunn, K. A., Adkins, R. M. and Honeycutt, R. L. (2010). Molecular clocks keep dispersal hypotheses afloat: evidence for trans-Atlantic rafting by rodents. Journal of Biogeography, 37, 305–324.
Rowe, K. C., Reno, M. L., Richmond, D. M., et al. (2008). Pliocene colonization and adaptive radiations in Australia and New Guinea (Sahul): multilocus systematics of the old endemic rodents (Muroidea: Murinae). Molecular Phylogenetics and Evolution, 47, 84–101.
Rowe, K. C., Aplin, K. P., Baverstock, P. R. and Moritz, C. (2011a). Recent and rapid speciation with limited morphological disparity in the genus Rattus. Systematic Biology, 60, 188–203.
Rowe, K. C., Singhal, S., Macmanes, M. D., et al. (2011b). Museum genomics: low-cost and high-accuracy genetic data from historical specimens. Molecular Ecology Resources, 11, 1082–1092.
Ruf, I., Frahnert, S. and Maier, W. (2009). The chorda tympani and its significance for rodent phylogeny. Mammalian Biology, 74, 100–113.
Sallam, H. M., Seiffert, E. R., Steiper, M. E., and Simons, E. L. (2009). Fossil and molecular evidence constrain scenarios for the early evolutionary and biogeographic history of hystricognathous rodents. Proceedings of the National Academy of SciencesUSA, 106, 16 722–16, 727.
Samuels, J. X. (2009). Cranial morphology and dietary habits of rodents. Zoological Journal of the Linnean Society, 156, 864–888.
Samuels, J. X. and Valkenburgh, B. (2008). Skeletal indicators of locomotor adaptations in living and extinct rodents. Journal of Morphology, 269, 1387–1411.
Sanderson, M. J. (1997). A nonparametric approach to estimating divergence times in the absence of rate constancy. Molecular Biology and Evolution, 14, 1218–1231.
Schenk, J. J., Rowe, K. C. and Steppan, S. J. (2013). Ecological opportunity and incumbency in the diversification of repeated continental colonizations by muroid rodents. Systematic Biology, 62, 837–864.
Shedlock, A. M., Milinkovitch, M. C. and Okada, N. (2000). SINE evolution, missing data, and the origin of whales. Systematic Biology, 49, 808–817.
Simpson, G. G. (1945). The principles of classification and a classification of mammals. Bulletin of the American Museum of Natural History, 85, 1–350.
Spradling, T. A., Hafner, M. S. and Demastes, J.W. (2001), Differences in rate of cytochrome-b evolution among species of rodents. Journal of Mammalogy, 82, 65–80.
Springer, M. S. (2004). Molecules consolidate the placental mammal tree. Trends in Ecology and Evolution, 19, 430–438.
Springer, M. S., Eizirik, E., Murphy, W. J. and O'Brien, S.J. (2003). Placental mammal diversification and the Cretaceous–Tertiary boundary. Proceedings of the National Academy of Sciences of the United States of America, 100, 1056–1061.
Steppan, S. J. (1996). A new species of Holochilus (Rodentia: Sigmodontinae) from the middle Pleistocene of Bolivia and its phylogenetic significance. Journal of Vertebrate Paleontology, 16, 522–530.
Steppan, S. J., Akhverdyan, M. R., Lyapunova, E. A., et al. (1999). Molecular phylogeny of the marmots (Rodentia: Sciuridae): tests of evolutionary and biogeographic hypotheses. Systematic Biology, 48, 715–734.
Steppan, S. J., Adkins, R. M. and Anderson, J. (2004a). Phylogeny and divergence-date estimates of rapid radiations in muroid rodents based on multiple nuclear genes. Systematic Biology, 53, 533–553.
Steppan, S. J., Storz, B. L. and Hoffmann, R. S. (2004b). Nuclear DNA phylogeny of the squirrels (Mammalia: Rodentia) and the evolution of arboreality from c-myc and RAG1. Molecular Phylogenetics and Evolution, 30, 703–719.
Steppan, S. J., Adkins, R. M., Spinks, P. Q. and Hale, C. (2005). Multigene phylogeny of the Old World mice, Murinae, reveals distinct geographic lineages and the declining utility of mitochondrial genes compared to nuclear genes. Molecular Phylogenetics and Evolution, 37, 370–388.
Suarez, E. M. and Mein, P. (1998). Revision of the genera Parapodemus, Apodemus, Rhagamys and Rhagapodemus (Rodentia, Mammalia). Geobios, 31, 87–97.
Sun, J.-M., Ye, J., Wu, al. (2010). Late Oligocene–Miocene mid-latitude aridification and wind patterns in Asian interior. Geology, 38, 515–518.
Tedford, R. H., Wells, R. T. and Barghoorn, S. F. (1992). Tirari formation and contained faunas, Pliocene of Lake Eyre Basin, South Australia. Beagle. Records of the Northern Territory Museum of Arts and Sciences, 9, 173–194.
Tomasco, I. H. and Lessa, E. P. (2011). The evolution of mitochondrial genomes in subterranean caviomorph rodents: adaptation against a background of purifying selection. Molecular Phylogenetics and Evolution, 61, 64–70.
Tong, Y.-S. (1992 ). Papporicetodon, a pre-Oligocene cricetid genus (Rodentia) from central China. Vertebrata Paleontology Asiatica, 30, 1–16.
Tong, Y.-S. (1997). Middle Eocene small mammals from Liguanqiao Basin of Henan Province and Yuanqu Basin of Shanxi Province, central China. Paleontologica Sinica, 26, 1–68.
Tullberg, T. (1899). Ueber das system der nagetiere: ein phylogenetische studie. Nova Acta Regiae Societatis Scientarium Upsaliersis, 18, 1–514.
Upham, N. S. and Patterson, B. D. (2012). Diversification and biogeography of the Neotropical caviomorph lineage Octodonkoidea (Rodentia: Hystricognathi). Molecular Phylogenetics and Evolution, 63, 417–429.
Upham, N. S., Ojala-Barbour, R., Brito, M. J., et al. (2013). Transitions between Andean and Amazonian centers of endemism in the radiation of some arboreal rodents. BMC Evolutionary Biology, 13, 191.
Vangegeim, E. A., Lungu, A. N. and Tesakov, A. S. (2006). Age of Vallesian lower boundary (continental Miocene of Europe). Stratigraphy and Geological Correlation, 14, 655–667.
Veniaminova, N. A., Vassetzky, N. S., Lavrenchenko, L. A., et al. (2007). Phylogeny of the order Rodentia inferred from structural analysis of short retroposon B1. Russian Journal of Genetics, 43, 757–768.
Verzi, D. H. 2008. Phylogeny and adaptive diversity of rodents of the family Ctenomyidae (Caviomorpha): delimiting lineages and genera in the fossil record. Journal of Zoology, 274, 386–394.
Verzi, D. H. and Montalvo, C. I. (2008). The oldest South American Cricetidae (Rodentia) and Mustelidae (Carnivora): late Miocene faunal turnover in central Argentina and the Great American Biotic Interchange. Palaeogeography, Palaeoclimatology, Palaeoecology, 267, 284–291.
Verzi, D. H., Vieytes, E. C. and Montalvo, C. I. (2004). Dental evolution in Xenodontomys and first notice on secondary acquisition of radial enamel in rodents (Rodentia, Caviomorpha, Octodontidae). Geobios, 37, 795–806.
Verzi, D. H., Olivares, A. I. and Morgan, C. C. (2014). Phylogeny, evolutionary patterns and timescale of South American octodontoid rodents: the importance of recognising morphological differentiation in the fossil record. Acta Palaeontologica Polonica, 59, 757–769.
Vianey-Liaud, M. (1979). Evolution des rongeurs à l’ Oligocène en Europe Occidentale. Paleontographica, 166, 136–236.
Vianey-Liaud, M. (1985). Possible evolutionary relationships among Eocene and lower Oligocene rodents of Asia, Europe and North America. In Evolutionary Relationships Among Rodents: a Multidisciplinary Analysis, eds. Luckett, W. P. and Hartenberger, J.-L.. New York: Plenum Press, pp. 277–309.
Vianey-Liaud, M. (1989). Parallelism among gliridae (rodentia): the genus Gliravus Stehlin and Schaub. Historical Biology, 2, 213–226.
Vianey-Liaud, M. (1994). La radiation des Gliridae (Rodentia) à l'Eocène Supérieur en Europe Occidentale, et sa descendance Oligocène. Münchner geowissenschaftliche Abhandlungen: Geologie und Paläontologie, 26, 1–44.
Vianey-Liaud, M. and Jaeger, J-J. (1996). A new hypothesis for the origin of African Anomaluridae and Graphiuridae (Rodentia). Palaeovertebrata, 25, 349–358.
Vilela, R. V., Machado, T., Ventura, K., et al. (2009). The taxonomic status of the endangered thin-spined porcupine, Chaetomys subspinosus (Olfers, 1818), based on molecular and karyologic data. BMC Evolutionary Biology, 9, 29.
Voss, R. S., Hubbard, C. and Jansa, S. A. (2013). Phylogenetic relationships of New World porcupines (Rodentia, Erethizontidae): implications for taxonomy, morphological evolution, and biogeography. American Museum Novitates, 3769, 1–36.
Vucetich, G. M., Verzi, H. D. and Hartenberger, J. L. (1999). Review and analysis of the radiation of the South American Hystricognathi (Mammalia, Rodentia). Comptes Rendus de l'Académie des Sciences-Series IIA – Earth and Planetary Science, 329, 763–769.
Vucetich, M. G., Vieytes, E. C., Perez, M. E. and Carlini, A. A. (2010). 13. The rodents from La Cantera and the early evolution of caviomorphs in South America. In The Paleontology of Gran Barranca: Evolution and Environmental Change Through the Middle Cenozoic of Patagonia, eds. Madden, R. H., Carlini, A. A., Vucetich, M. G., and Kay, R. F., Cambridge: Cambridge University Press, pp. 193–205.
Waterhouse, G. R. (1839). Observations on the Rodentia with a view to point out groups as indicated by the structure of the crania in this order of mammals. Magazine of Natural History, 3, 90–96.
Weksler, M. (2003). Phylogeny of Neotropical oryzomyine rodents (Muridae: Sigmodontinae) based on the nuclear IRBP exon. Molecular Phylogenetics and Evolution, 29, 331–349.
Wessels, W. (2009). Miocene rodent evolution and migration. Muroidea from Pakistan, Turkey and Northern Africa. Geologica Ultraiectina, 307, 1–290.
Wilson, D. E. and Reeder, D.M. (2005). Mammal Species of the World Volume 2. Johns Hopkins University Press, Baltimore, Maryland, pp. 1–2142.
Winkler, A. J. (2002). Neogene paleobiogeography and East African paleoenvironments: contributions from the Tugen Hills rodents and lagomorphs. Journal of Human Evolution, 42, 237–256.
Wood, A. E. (1955). A revised classification of the rodents. Journal of Mammalogy, 36, 165–187.
Woods, C. A. and Hermanson, J. W. (1985). Myology of Hystricognath Rodents: an analysis of form, function, and phylogeny. In Evolutionary Relationships Among Rodents: a Multidisciplinary Analysis, eds. Luckett, W. P. and Hartenberger, J.-L.. New York: Plenum Press, pp. 515–548.
Wu, S., Wu, W., Zhang, al. (2012). Molecular and paleontological evidence for a post-Cretaceous origin of rodents. PLoS ONE, 7, e46445.
Xijun, N. and Zhuding, Q. (2002). The micromammalian fauna from the Leilao, Yuanmou hominoid locality: implications for biochronology and paleoecology. Journal of Human Evolution, 42, 535–546.
Yang, Z. and Rannala, B. (2006). Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Molecular Biology and Evolution, 23, 212–226.
Yoder, J. B., Clancey, E., Roches, S., et al. (2010). Ecological opportunity and the origin of adaptive radiations. Journal of Evolutionary Biology, 23, 1581–1596.
Zuckerkandl, E. and Pauling, L. (1965). Molecules as documents of evolutionary history. Journal of Theoretical Biology, 8, 357–366.