Aghova, T. | Search bioRxiv

bioRxiv2023

Phenogenomic resources immortalized in a panel of wild-derived strains of five species of house mice

The house mouse, Mus musculus, is a widely used animal model in biomedical research, with classical laboratory strains (CLS) being the most frequently employed. However, the limited genetic variability in CLS hinders their applicability in evolutionary studies. Wild-derived strains (WDS), on the other hand, provide a suitable resource for such investigations. This study quantifies genetic and phenotypic data of 101 WDS representing 5 species, 3 subspecies, and 8 natural Y consomic strains and compares them with CLS. Genetic variability was estimated using whole mtDNA sequences, the Prdm9 gene, and copy number variation at two sex chromosome-linked genes. WDS exhibit a large natural variation with up to 2173 polymorphic sites in mitogenomes, whereas CLS display 92 sites. Moreover, while CLS have two Prdm9 alleles, WDS harbour 46 different alleles. Although CLS resemble M. m. domesticus and M. m. musculus WDS, they differ from them in 8 and 11 out of 15 phenotypic traits, respectively. The results suggest that WDS can be a useful tool in evolutionary studies and have great potential for medical applications.

evolutionary biology↗

bioRxiv2017

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

Murid rodents (Rodentia: Myomorpha: Muroidea: Muridae) represent the most diverse and abundant mammalian group. In this study, we reconstruct a dated phylogeny of the family using a multilocus dataset (six nuclear and nine mitochondrial gene fragments) encompassing 160 species representing 82 distinct 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 multiple 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, 23.0-16.0 million years ago (Ma), and that most major lineages (i.e. tribes) have started diversifying ca. 10 Ma. Historical biogeography analyses support the Paleotropical origin for the family, with an initial internal split (vicariance event) followed by subsequent migrations between Afrotropical and Indomalayan 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, mostly from the Indomalaya. 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.

zoology↗