The fossil record of modern amphibians (frogs, salamanders, and caecilians) provides no evidence for major extinction or radiation episodes throughout most of the Mesozoic and early Tertiary. However, long-term gradual diversification is difficult to reconcile with the sensitivity of present-day amphibian faunas to rapid ecological changes and the incidence of similar environmental perturbations in the past that have been associated with high turnover rates in other land vertebrates. To provide a comprehensive overview of the history of amphibian diversification, we constructed a phylogenetic timetree based on a multigene data set of 3.75 kb for 171 species. Our analyses reveal several episodes of accelerated amphibian diversification, which do not fit models of gradual lineage accumulation. Global turning points in the phylogenetic and ecological diversification occurred after the end-Permian mass extinction and in the late Cretaceous. Fluctuations in amphibian diversification show strong temporal correlation with turnover rates in amniotes and the rise of angiosperm-dominated forests. Approximately 86% of modern frog species and >81% of salamander species descended from only five ancestral lineages that produced major radiations in the late Cretaceous and early Tertiary. This proportionally late accumulation of extant lineage diversity contrasts with the long evolutionary history of amphibians but is in line with the Tertiary increase in fossil abundance toward the present.

The apparent biotic affinities between the mainland and the island in the Western Ghats–Sri Lanka biodiversity hotspot have been interpreted as the result of frequent migrations during recent periods of low sea level. We show, using molecular phylogenies of two invertebrate and four vertebrate groups, that biotic interchange between these areas has been much more limited than hitherto assumed. Despite several extended periods of land connection during the past 500,000 years, Sri Lanka has maintained a fauna that is largely distinct from that of the Indian mainland. Future conservation programs for the subcontinent should take into account such patterns of local endemism at the finest scale at which they may occur.

Evolutionary Hops: In order for animals to colonize new environments and disperse, specific traits may be required. Toads form a large and ecologically diverse group and have achieved extremely wide distribution in a very short time frame. To test what traits may be associated with species range in modern toads, Van Bocxlaer et al. (p. 679 ; see the news story by Pennisi ) phylogenetically reconstructed the evolutionary history of morphological and physiological traits linked to the toads' geographic ranges. Toads have evolved an optimal dispersal phenotype comprising many traits, including those affecting reproductive choices and water retention, which preceded their expansion and radiation.

Ranidae is a large anuran group with a nearly cosmopolitan distribution. We investigated the phylogenetic relationships and early biogeographic history of ranid frogs, using 104 representatives of all subfamilies and families, sampled from throughout their distribution. Analyses of ∼ 1570 bp of nuclear gene fragments (Rag-1, rhod, Tyr) and ∼ 2100 bp of the mitochondrial genome (12S rRNA, tRNA^VAL, 16S rRNA) indicate that the monophyly of several taxa can be rejected with high confidence. Our tree is characterized by a clear historical association of each major clade with one Gondwanan plate. This prevalence of continent-scale endemism suggests that plate tectonics has played a major role in the distribution of ranid frogs. We performed dispersal-vicariance analyses, as well as analyses constrained by paleogeographic data, to estimate ancestral distributions during early ranid diversification. Additionally, we used molecular clock analyses to evaluate whether these scenarios fit the temporal framework of continental breakup. Our analyses suggest that a scenario in which the ancestors of several clades (Rhacophorinae, Dicroglossinae, Raninae) reached Eurasia via the Indian subcontinent, and the ancestor of Ceratobatrachinae entered via the Australia–New Guinea plate, best fits the paleogeographic models and requires the fewest number of dispersal/vicariance events. However, several alternatives, in which part of the ranid fauna colonized Laurasia from Africa, are not significantly worse. Most importantly, all hypotheses make clear predictions as to where to expect key fossils and where to sample other living ranids, and thus constitute a strong basis for further research.

High taxonomic level endemism in the Western Ghats-Sri Lanka biodiversity hotspot has been typically attributed to the subcontinent's geological history of long-term isolation. Subsequent out of – and into India dispersal of species after accretion to the Eurasian mainland is therefore often seen as a biogeographic factor that 'diluted' the composition of previously isolated Indian biota. However, few molecular studies have focussed on into-India dispersal as a possible source of endemism on the subcontinent. Using c. 6000 base pairs of mitochondrial and nuclear DNA, we investigated the evolutionary history and biogeography of true toads (Bufonidae), a group that colonized the Indian Subcontinent after the Indo-Asia collision.

Current models for the early diversification of living frogs inferred from morphological, ontogenetic, or DNA sequence data invoke very different scenarios of character evolution and biogeography. To explore central controversies on the phylogeny of Anura, we analyzed nearly 4000 base pairs of mitochondrial and nuclear DNA for the major frog lineages. Likelihood-based analyses of this data set are congruent with morphological evidence in supporting a paraphyletic arrangement of archaeobatrachian frogs, with an (Ascaphus + Leiopelma) clade as the sister-group of all other living anurans. The stability of this outcome is reinforced by screening for phylogenetic bias resulting from site-specific rate variation, homoplasy, or the obligatory use of distantly related outgroups. Twenty-one alternative branching and rooting hypotheses were evaluated using a nonparametric multicomparison test and parametric bootstrapping. Relaxed molecular clock estimates situate the emergence of crown-group anurans in the Triassic, approximately 55 million years prior to their first appearance in the fossil record. The existence of at least four extant frog lineages on the supercontinent Pangaea before its breakup gains support from the estimation that three early splits between Laurasia- and Gondwana-associated families coincide with the initial rifting of these landmasses. This observation outlines the potential significance of this breakup event in the formation of separate Mesozoic faunal assemblages in both hemispheres.