Muroid rodent phylogenetics: 900-species tree reveals increasing diversification rates

Abstract

We combined new sequence data for more than 300 muroid rodent species with our previously published sequences for up to five nuclear and one mitochondrial genes to generate the most widely and densely sampled hypothesis of evolutionary relationships across Muroidea. An exhaustive screening procedure for publically available sequences was implemented to avoid the propagation of taxonomic errors that are common to supermatrix studies. The combined data set of carefully screened sequences derived from all available sequences on GenBank with our new data resulted in a robust maximum likelihood phylogeny for 900 of the approximately 1,620 muroids. Several regions that were equivocally resolved in previous studies are now more decisively resolved, and we estimated a chronogram using 28 fossil calibrations for the most integrated age and topological estimates to date. The results were used to update muroid classification and highlight questions needing additional data. We also compared the results of multigene supermatrix studies like this one with the principal published supertrees and concluded that the latter are unreliable for any comparative study in muroids. In addition, we explored diversification patterns as an explanation for why muroid rodents represent one of the most species-rich groups of mammals by detecting evidence for increasing net diversification rates through time across the muroid tree. We suggest the observation of increasing rates may be due to a combination of parallel increases in rate across clades and high average extinction rates. Five increased diversification-rate-shifts were inferred, suggesting that multiple, but perhaps not independent, events have led to the remarkable species diversity in the superfamily. Our results provide a phylogenetic framework for comparative studies that is not highly dependent upon the signal from any one gene.

Diversification rates of the “Old Endemic” murine rodents of Luzon Island, Philippines are inconsistent with incumbency effects and ecological opportunity

“…Our study corroborates previous molecular studies that fail to find the suggested alliance of Vandeleuria oleracea with Chiropodomys that has been postulated based on dental characters (Musser and Carleton ) and instead strongly supports a sister‐taxon relationship between Chiropodomys and the clade containing Chrotomyini + SOE murines (Schenk et al. ; Steppan and Schenk ). Otherwise, the phylogenetic position of Vandeleuria is not secure in any molecular analysis to date (Schenk et al.…”

“…Sequences from additional murid species were chosen primarily from publicly available sources obtained from previous studies (Steppan et al 2005;Rowe et al 2008;Benson et al 2013;Schenk et al 2013;Pagès et al 2016;Rowe et al 2016;P.-H. Fabre, Université Montpellier II, personal communication, August 2017) and were included to place the Philippine murine radiations in the context of murid phylogeny and to provide the best possible divergence date estimates given available fossil data. We selected taxa from subfamilies Gerbillinae, Deomyinae, and Lophiomyinae as outgroups based on their close phylogenetic proximity to Murinae (Schenk et al 2013;Pagès et al 2016;Steppan and Schenk 2017).…”

Evolutionary patterns of major urinary protein scent signals in house mice and relatives

“…Species tree for muroid rodents examined in this study. Modified from (Steppan & Schenk, ). The scale bar measures substitutions per site…”

Social but lonely: Species delimitation of social voles and the evolutionary history of the onlyMicrotusspecies living in Africa

“…This family includes more than 600 species divided into several subfamilies (Carleton & Musser, ). Voles and lemmings represent a well‐defined, monophyletic subfamily (Arvicolinae), although phylogenetic relationships among and within the genera of this subfamily are not yet fully resolved (Bužan, Kryštufek, Hänfling, & Hutchinson, ; Steppan & Schenk, ). Approximately 60 species of voles found in North America, Europe, and northern Asia are placed in the genus Microtus (Carleton & Musser, ) together with the only representative of the entire Cricetidae family distributed in the African continent, the Cyrenaican vole.…”