title: Mitogenomic Phylogeny, Diversification, and Biogeography of South American Spiny Rats.
abstract: Echimyidae is one of the most speciose and ecologically diverse rodent families in the world, occupying a wide range of habitats in the Neotropics. However, a resolved phylogeny at the genus-level is still lacking for these 22 genera of South American spiny rats, including the coypu (Myocastorinae), and 5 genera of West Indian hutias (Capromyidae) relatives. Here, we used Illumina shotgun sequencing to assemble 38 new complete mitogenomes, establishing Echimyidae, and Capromyidae as the first major rodent families to be completely sequenced at the genus-level for their mitochondrial DNA. Combining mitogenomes and nuclear exons, we inferred a robust phylogenetic framework that reveals several newly supported nodes as well as the tempo of the higher level diversification of these rodents. Incorporating the full generic diversity of extant echimyids leads us to propose a new higher level classification of two subfamilies: Euryzygomatomyinae and Echimyinae. Of note, the enigmatic Carterodon displays fast-evolving mitochondrial and nuclear sequences, with a long branch that destabilizes the deepest divergences of the echimyid tree, thereby challenging the sister-group relationship between Capromyidae and Euryzygomatomyinae. Biogeographical analyses involving higher level taxa show that several vicariant and dispersal events impacted the evolutionary history of echimyids. The diversification history of Echimyidae seems to have been influenced by two major historical factors, namely (1) recurrent connections between Atlantic and Amazonian Forests and (2) the Northern uplift of the Andes.
authors.affiliation: Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS-IRD-UM), Université de Montpellier, Montpellier, France.|National Museum of Natural History, Smithsonian Institution, Washington, DC.
authors.forename: Pierre-Henri
authors.initials: PH
authors.lastname: Fabre
authors.affiliation: Ecology and Evolutionary Biology, Yale University, New Haven, CT.|Integrative Research Center, Field Museum of Natural History, Chicago, IL.
authors.forename: Nathan S
authors.initials: NS
authors.lastname: Upham
authors.affiliation: National Museum of Natural History, Smithsonian Institution, Washington, DC.
authors.forename: Louise H
authors.initials: LH
authors.lastname: Emmons
authors.affiliation: Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS-IRD-UM), Université de Montpellier, Montpellier, France.
authors.forename: Fabienne
authors.initials: F
authors.lastname: Justy
authors.affiliation: Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil.
authors.forename: Yuri L R
authors.initials: YL
authors.lastname: Leite
authors.affiliation: Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil.
authors.forename: Ana
authors.initials: A
authors.lastname: Carolina Loss
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.|Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, Université de Toulouse, University Paul Sabatier, Toulouse, France.
authors.forename: Ludovic
authors.initials: L
authors.lastname: Orlando
authors.affiliation: Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS-IRD-UM), Université de Montpellier, Montpellier, France.
authors.forename: Marie-Ka
authors.initials: MK
authors.lastname: Tilak
authors.affiliation: Integrative Research Center, Field Museum of Natural History, Chicago, IL.
authors.forename: Bruce D
authors.initials: BD
authors.lastname: Patterson
authors.affiliation: Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS-IRD-UM), Université de Montpellier, Montpellier, France.
authors.forename: Emmanuel J P
authors.initials: EJ
authors.lastname: Douzery
mesh_terms: D000818:Animals; D001483:Base Sequence; D001499:Bayes Theorem; D005075:Biological Evolution; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D014644:Genetic Variation; D054629:Genome, Mitochondrial; D008928:Mitochondria / Q000235:genetics*; D010802:Phylogeny; D058974:Phylogeography / Q000379:methods; D051381:Rats; D012377:Rodentia / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D013020:South America
chemical_list: D004272:DNA, Mitochondrial
keywords: Carterodon.; Echimyidae; Neotropics; biogeography; diversification; fast-evolving gene; mitogenomics; nuclear DNA