Phylogenetics and dating

Despite this spectacular diversity, this and many other questions of evolutionary processes have received little formal study because until now the phylogeny of this spececies-rich clade has remained uncertain.Here we reconstruct a phylogeny for Asterophryinae with greatly increased taxon and genetic sampling relative to prior studies.It is sometimes called a gene clock or an evolutionary clock.The notion of the existence of a so-called "molecular clock" was first attributed to Émile Zuckerkandl and Linus Pauling who, in 1962, noticed that the number of amino acid differences in hemoglobin between different lineages changes roughly linearly with time, as estimated from fossil evidence.Asterophryinae is a large monophyletic subfamily of Anurans containing over 300 species distributed across one of the world's most geologically active areas – New Guinea and its satellite islands, Australia and the Philippines.The tremendous ecological and morphological diversity of this clade, with apparent specializations for burrowing, terrestrial, semi-aquatic, and arboreal lifestyle, suggests an evolutionary process of adaptive radiation.We find support for the monophyly of Asterophryinae as well as need for taxonomic reclassification of several genera.

From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.The present study greatly expands phylogenetic analyses of the Pyreae by using a combination of 11 chloroplast regions plus nuclear ribosomal ITS sequences from 486 individuals representing 331 species and 27 genera.Maximum likelihood and Bayesian analyses generally support existing generic boundary, although , as previously circumscribed, is clearly non-monophyletic.Two significant conflicts were detected between the chloroplast and ITS phylogenies, suggesting that hybridization played a role in the origins of .In addition, we provide estimates of the divergence times of the major lineages.We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data.In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme.If this is correct, the cytochrome c of all mammals should be equally different from the cytochrome c of all birds.Since fish diverges from the main stem of vertebrate evolution earlier than either birds or mammals, the cytochrome c of both mammals and birds should be equally different from the cytochrome c of fish.Fortunately, intermediate models employing relaxed molecular clocks have been described.These models open the gate to a new field of "relaxed phylogenetics." Here we introduce a new approach to performing relaxed phylogenetic analysis.


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