Molecular Phylogenetics of Western North American Frogs of the Rana boylii Species Group

Cenozoic biogeography and evolution in direct-developing frogs of Central America (Leptodactylidae: Eleutherodactylus) as inferred from a phylogenetic analysis of nuclear and mitochondrial genes

“…Despite the concordance between previously published rates of evolution and the rates obtained here based on the proto-Antilles model, we still cannot reject the alternative hypothesis that rates of molecular evolution in Eleutherodactylus, particularly in their mtDNA, could be higher than those estimated previously in temperate-zone amphibians, reptiles, and tropical marine fishes (reviewed in Macey et al, 2001). Although no evidence has yet been found to support the hypothesis that tropical organisms in general have higher rates of molecular evolution than temperate-zone species (Bromham and Cardillo, 2003), Eleutherodactylus are unusual in two respects.…”

“…Absolute rates of divergence vary widely among branches for both genes, but the central tendencies are roughly consistent with previous studies (e.g., Macey et al, 2001). Among the 105 branches, the median estimated rate of divergence for ND2-WANCY is 0.8410% per million years (my) (SD = 0.4958%).…”

“…To the contrary, our rates appear to be on the high side of previous estimates of mtDNA divergence. Our resulting mean rate estimate of 0.8410% per lineage per million years is higher than previous estimates for poikilotherms, which range from 0.57% to 0.69% (reviewed in Macey et al, 2001). The absolute level of DNA sequence divergence observed is also particularly high.…”

Phylogeographic Patterns of mtDNA Variation Revealed Multiple Glacial Refugia for the Frog Species Feirana taihangnica Endemic to the Qinling Mountains

“…We ran 50 million generations in two-independent iterations, sampled every 1,000 generations, and discarded the first 10 % as ''burn-in''. Convergence of the chains to the stationary distribution was checked by visual inspection of plotted posterior estimates using the program Tracer v1.5 The mutation rate of the ND2 gene has been found to be fairly constant at 0.57-0.96 % change per lineage per million years across a wide range of vertebrate groups, including fishes, hynobiid salamanders, Laudakia and Teratoscincus lizards, Bufo, Ranid frogs (e.g., Rana boylii), and Eleutherodactylus toads (Bermingham et al 1997;Weisrock et al 2001;Macey et al 1998aMacey et al , b, 1999Macey et al , 2001Crawford 2003). Feirana taihangnica is a close relative of Ranid frogs (Jiang et al 2005), which have a universal substitution rate of 0.65 % change per lineage per million years for the ND2 gene ).…”

A phylogeny of Chinese species in the genus Phrynocephalus (Agamidae) inferred from mitochondrial DNA sequences

“…1-30.6%), are all characteristic of the mitochondrial genome, but not the nuclear genome. Therefore, the DNA sequences analyzed here should represent true mitochondrial genes and not nuclear transpositions (Macey et al, 2001;Zhang and Hewitt, 1996). Table 1 summarizes indices for the MP analyses of the four datasets.…”