Fossils know it best: Using a new set of fossil calibrations to improve the temporal phylogenetic framework of murid rodents (Rodentia: Muridae)

Abstract

Murid rodents (Rodentia: Muridae) represent the most diverse and abundant mammalian family. In this study, we provide a refined set of fossil calibrations which is used to reconstruct a dated phylogeny of the family using a multilocus dataset (six nuclear and nine mitochondrial gene fragments) encompassing 161 species representing 82 murid genera from four extant subfamilies (Deomyinae, Gerbillinae, Lophiomyinae and Murinae). In comparison with previous studies on murid or muroid rodents, our work stands out for the implementation of nine robust fossil constraints within the Muridae thanks to a thorough review of the fossil record. Before being assigned to specific nodes of the phylogeny, all potential fossil constraints were carefully assessed; they were also subjected to several cross-validation analyses. The resulting phylogeny is consistent with previous phylogenetic studies on murids, and recovers the monophyly of all sampled murid subfamilies and tribes. Based on nine controlled fossil calibrations, our inferred temporal timeframe indicates that the murid family likely originated in the course of the Early Miocene, 22.0-17.0 million years ago (Ma), and that most major lineages (i.e. tribes) started diversifying ca. 10 Ma. Historical biogeography analyses support the tropical origin for the family, with an initial internal split (vicariance event) between Afrotropical and Oriental (Indomalaya and Philippines) lineages. During the course of their diversification, the biogeographic pattern of murids is marked by several dispersal events toward the Australasian and the Palearctic regions. The Afrotropical region was also secondarily colonized at least three times from the Indomalaya, indicating that the latter region has acted as a major centre of diversification for the family.

Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on RAD-seq

“…Considering a divergence time between A. flavicollis and A. sylvaticus estimated from archeological data of 4 Mya [38], the evolutionary rate is 0.0019 substitutions per site per million of years. While this estimate of sequence divergence level is in broad agreement with calculations based on mitochondrial 12S rRNA, IRBP and Cytochrome b genes [39], we note that Aghova et al (2018) [1] provided an updated timing of a split between A. sylvaemus and A. mystacinus, which, at 9.6Mya, is 2Mya older than previously suggested by Michaux et al (2002) [39]. If we use that date as a reference and move the presumed split between A. flavicollis and A. sylvaticus by 2.6Mya, the estimated evolutionary rate from our data would be 0.0011.…”

Genetic variation of the most abundant forest‐dwelling rodents in Central Africa (Praomys jacksoni complex): Evidence for Pleistocene refugia in both montane and lowland forests

“…Because Praomys has a poor fossil record, it is not possible to calibrate the molecular clock using ingroup fossils. We therefore performed a secondary calibration using the time to most recent common ancestor (TMRCA) of the P. jacksoni complex estimated by Aghová et al (2018). More details about specification of priors and evaluation of outputs can be found in Appendix S3.…”

Biogeography and ecology in a pantropical family, the Meliaceae

“…The standard view on evolutionary chronology was expressed in a recent study: "fossils know best" (Aghová et al, 2018). But it is only possible to know whether or not fossil-based methods are 'best' by comparing them with others.…”