The ever growing availability of phylogenomic data makes it increasingly possible to study and analyze phylogenetic relationships across a wide range of species. Indeed, current phylogenetic analyses are now producing enormous collections of trees that vary greatly in size. Our proposed research addresses the challenges posed by storing, querying, and analyzing such phylogenetic databases. Our ...

Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is that of identifiability, which essentially asks under what circumstances can we reliably identify the phylogenetic network that gave rise to the observed data?...

Gene expression patterns (motivation) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Transcription factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Experimental discovery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 Computational discovery . . . . . . . . . . . . . . . . . . . . . . . . ...

There is an urgent need to reduce drastically the rate at which biodiversity is declining worldwide. Phylogenetic methods are increasingly being recognised as providing a useful framework for predicting future losses, and guiding efforts for pre-emptive conservation actions. In this study, we used a reconstructed phylogenetic tree of angiosperm species of the Eastern Arc Mountains - an importan...

The internal transcribed spacers of the nuclear ribosomal RNA gene cluster, termed ITS1 and ITS2, are the most frequently used nuclear markers for phylogenetic analyses across many eukaryotic groups including most plant families. The reasons for the popularity of these markers include: 1.) Ease of amplification due to high copy number of the gene clusters, 2.) Available cost-effective methods a...

Although substantial uncertainty typically surrounds the choice of the best model in most phylogenetic analyses, little is known about how accommodating this uncertainty affects phylogenetic inference. Here we explore the influence of Bayesian model averaging on the phylogenetic inference of the triggerfishes (Family: Balistidae), a charismatic group of reef fishes. We focus on clade support as...

The genus Crocodylus consists of 11 species including the largest living reptile, Crocodylus porosus. The current understanding of the intrageneric relationships between the members of the genus Crocodylus is sparse. Even though members of this genus have been included in many phylogenetic analyses, different molecular approaches have resulted in incongruent trees leaving the phylogenetic relat...

The chordate proteome history database (http://ioda.univ-provence.fr) comprises some 20,000 evolutionary analyses of proteins from chordate species. Our main objective was to characterize and study the evolutionary histories of the chordate proteome, and in particular to detect genomic events and automatic functional searches. Firstly, phylogenetic analyses based on high quality multiple sequen...

The slight perversion of the original title of this piece (The Future of the Bayesian Brain) reflects my attempt to write prospectively about 'Science and Stories' over the past 20 years. I will meet this challenge by dealing with the future and then turning to its history. The future of the Bayesian brain (in neuroimaging) is clear: it is the application of dynamic causal modeling to understan...

barley belongs to the poaceae which is the largest monocotyledon family. plastid single-copy gene acetyl-coa carboxylase (accase) is the first step in the biosynthesis of fatty acids and therefore, it is used to study the phylogenetic relationships, evolutionary and systematic of grasses. in this study, for the first time, phylogenetic relationship of eight species of hordeum genus from iran in...