Chronic bee paralysis virus (CBPV) is an unclassified polymorphic single-stranded RNA virus. Among the viruses infecting honeybees, CBPV is known to induce significant losses in honeybee colonies. In this study, a total number of eighty-nine suspected apiaries from four regions of Iran (including Mazandaran, Khorasan Razavi, Hormozgan, and Kurdistan) were sampled and submitted for molecular ide...

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SUMMARY We have developed an efficient program, the Perfect Phylogeny Haplotyper (PPH) that takes in unphased population genotype data, and determines if that data can be explained by haplotype pairs that could have evolved on a perfect phylogeny.

The development of comparative phylogenetic methods has provided a powerful toolkit for addressing adaptive hypotheses, and researchers have begun to apply these methods to test the role of pollinators in floral evolution and diversification. One approach is to reconstruct the history of both floral traits and pollination systems to determine if floral trait change is spurred by shifts in polli...

It is widely accepted that the rate of evolution (substitution rate) at neutral genes is unaffected by population size fluctuations. This result has implications for the analysis of genetic data in population genetics and phylogenetics, and provides, in particular, a justification for the concept of the molecular clock. Here, we show that the substitution rate at neutral genes does depend on po...

We present an algorithm for determining whether a set of species, described by the characters they exhibit, has a perfect phylogeny, assuming the maximum number of characters is xed. This algorithm is simpler and faster than the known algorithms when the number of characters is at least 4.

The concept of modularity assumes that functionality can be partitioned into a collection of modules. Each module is a discrete entity of elementary components and performs an identifiable task, separable from the functions of other modules [3]. As the modules in the protein 3D structure can be related to molecular functions, the modules in the protein network may be related to cellular functio...

Studying the shape of phylogenetic trees under different random models is an important issue in evolutionary biology. In this paper, we propose a general framework for deriving detailed statistical results for patterns in phylogenetic trees under the Yule-Harding model and the uniform model, two of the most fundamental random models considered in phylogenetics. Our framework will unify several ...

Linguists use phylogenetic methods to build evolutionary trees of languages given lexical, phonological, and morphological data. Perfect phylogeny is too restrictive to explain most data sets. Conservative Dollo phylogeny is more permissive, and has been used in biological applications. We propose the use of conservative Dollo phylogeny as an alternative or complementary approach for linguistic...

Science and society would benefit enormously from detailed and well-supported knowledge of the Tree of Life (TOL). At present, however, we know relatively little about the phylogenetic relationships of most of the species on Earth, or even among many of the major branches of the Tree. Fortunately, we have reached a turning point. Owing to fundamental theoretical advances, to the development of ...