Tempo and mode of evolution of Oryzomyine rodents (Rodentia, Cricetidae, Sigmodontinae): a phylogenomic approach

The tribe Oryzomyini is an impressive group of rodents, comprising 30
extant genera and an estimated 147 species. Recent remarkable advances in
the understanding of the diversity, taxonomy and systematics of the tribe
have mostly derived from analyses of single or few genetic markers.
However, the evolutionary history and biogeography of Oryzomyini, its
origin and diversification across the Neotropics, remain unrevealed. Here
we use a multi-locus dataset (over 400 loci) obtained through anchored
phylogenomics to provide a genome-wide phylogenetic hypothesis for
Oryzomyini and to investigate the tempo and mode of its evolution. Species
tree and supermatrix analyses produced topologies with strong support for
most branches, with all genera confirmed as monophyletic, a
result that previous studies failed to obtain. Our analyses also
corroborated the monophyly and phylogenetic relationship of three main
clades of Oryzomyini (B, C and D). The origin of the
tribe is estimated to be in the Miocene (8.93–5.38 million years ago). The
cladogenetic events leading to the four main clades occurred during the
late Miocene and early Pliocene and most speciation events in the
Pleistocene. Geographic range estimates suggested an east of
Andes origin for the ancestor of oryzomyines, most likely in
the Boreal Brazilian region, which includes the north bank of Rio
Amazonas and the Guiana Shield. Oryzomyini rodents are an autochthonous
South America radiation, that colonized areas and dominions of this
continent mainly by dispersal events. The evolutionary history of the
tribe is deeply associated with the Andean cordillera and the landscape
history of Amazon basin.