Molecular Phylogeny and Divergence Time Estimates for Major Rodent Groups: Evidence from Multiple Genes

Abstract

The order Rodentia contains half of all extant mammal species, and from an evolutionary standpoint, there are persistent controversies surrounding the monophyly of the order, divergence dates for major lineages, and relationships among families. Exons of growth hormone receptor (GHR) and breast cancer susceptibility (BRCA1) genes were sequenced for a wide diversity of rodents and other mammals and combined with sequences of the mitochondrial 12S rRNA gene and previously published sequences of von Willebrand factor (vWF). Rodents exhibit rates of amino acid replacement twice those observed for nonrodents, and this rapid rate of evolution influences estimates of divergence dates. Based on GHR sequences, monophyly is supported, with the estimated divergence between hystricognaths and most sciurognaths dating to about 75 MYA. Most estimated dates of divergence are consistent with the fossil record, including a date of 23 MYA for Mus-Rattus divergence. These dates are considerably later than those derived from some other molecular studies. Among combined and separate analyses of the various gene sequences, moderate to strong support was found for several clades. GHR appears to have greater resolving power than do 12S or vWF. Despite its complete unresponsiveness to growth hormone, Cavia (and other hystricognaths) exhibits a conservative rate of change in the intracellular domain of GHR.

Causes and evolutionary consequences of primordial germ-cell specification mode in metazoans

“…It was also suggested that the faster evolution reported for mouse gene sequences (based on analysis of substitutions of amino acids and each of three codon positions for three protein-coding genes, and of a ribosomal RNA; ref. 33) compared with other mammals concurs with the deterministicstochastic hypothesis (32). However, rapid sequence evolution in the mouse lineage is well known, and need not indicate a release of selection, but, rather, is likely an effect of their short generation time (34,35).…”

Loss of LINE-1 Activity in the Megabats

“…The range recognizes that L1 extinction could have occurred as recently as the divergence time of megabat species from each other or as far back as the divergence of the megabat lineage from the rest of the Yinpterochiroptera (Figure 1). This rate can be compared to the neutral substitution rates in human, mouse, and rat (Rat Genome Sequencing Project Consortium 2004), if the divergence of human from these rodent lineages is assumed to be 87 MYA and the divergence of mouse from rat is assumed to be 9-23 MYA (Adkins et al 2001(Adkins et al , 2003Springer et al 2003;Steppan et al 2004). These divergence times give a relatively slow human rate of 0.15%/MY, and faster mouse and rat rates of 0.36-0.92%/MY, and 0.40-1.01%/MY, respectively.…”

Genetic similarity of Puumala viruses found in Finland and western Siberia and of the mitochondrial DNA of their rodent hosts suggests a common evolutionary origin

“…The BRCA1 gene was selected for analysis because it had given robust resolution of relationships at varying levels of divergence in previous studies (Adkins et al, 2001) and was easily amplified. C. glareolus and C. rufocanus samples from Omsk (CG/AF1946, CG191, CG193, CG324, CRF179, CRF302 and CRF443) were randomly selected and 497 nt fragments of their BRCA1 genes were compared.…”