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A hidden Markov model for progressive multiple alignment
A new method for multiple sequence alignment is presented that combines an HMM approach, a progressive alignment algorithm, and a probabilistic evolution model describing the character substitution process, providing an efficient mean by which unreliably aligned columns can be filtered out from a multiple alignment. Expand
Phylogeny and biogeography of a cosmopolitan frog radiation: Late cretaceous diversification resulted in continent-scale endemism in the family ranidae.
A scenario in which the ancestors of several clades 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. Expand
Convergent adaptive radiations in Madagascan and Asian ranid frogs reveal covariation between larval and adult traits.
The phylogenetic analyses of nuclear and mitochondrial DNA sequences here indicate that a major radiation of ranid frogs on Madagascar produced morphological, physiological, and developmental characters that are remarkably similar to those that independently evolved on the Indian subcontinent. Expand
The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation
The metapopulation genetic algorithm, involving several populations of trees that are forced to cooperate in the search for the optimal tree, proves to be both very accurate and vastly faster than existing heuristics, such that data sets comprised of hundreds of taxa can be analyzed in practical computing times under complex models of maximum-likelihood evolution. Expand
Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages.
Using phylogenetic analyses of nucleotide sequences from three mitochondrial and two nuclear genes, it is demonstrated with statistical significance that extant river dolphins are not monophyletic and suggested that they are relict species whose adaptation to riverine habitats incidentally insured their survival against major environmental changes in the marine ecosystem or the emergence of Delphinidae. Expand
Mitochondrial DNA rates and biogeography in European newts (genus Euproctus).
The data suggest that the cladogenic events leading to species formation in Euproctus and Triturus occurred very closely in time, indicating that the two genera may not be monophyletic. Expand
Amphibians as Indicators of Early Tertiary "Out-of-India" Dispersal of Vertebrates
It is shown that multiple lineages of frogs survived Deccan Traps volcanism after millions of years of isolation on drifting India, revealing a zoogeographical pattern that might reconcile paleontological and molecular data in other vertebrate groups. Expand
SOAP, cleaning multiple alignments from unstable blocks
SUMMARY SOAP is a stand-alone, multi-platform program to test the stability of a multiple alignment of molecular sequences.
Molecular Phylogenetic Analyses Indicate a Wide and Ancient Radiation of African Hepatitis Delta Virus, Suggesting a Deltavirus Genus of at Least Seven Major Clades
Phylogenetic reconstructions based on the delta antigen gene and full-length genome sequence data show an extensive and probably ancient radiation of African lineages, suggesting that the genetic variability of HDV is much more complex than was previously thought. Expand
Local Endemism Within the Western Ghats-Sri Lanka Biodiversity Hotspot
It is shown, using molecular phylogenies of two invertebrate and four vertebrate groups, that biotic interchange between these areas has been much more limited than hitherto assumed. Expand