A Phylogenomic Study of Human, Dog, and Mouse

In recent years the phylogenetic relationship of mammalian orders has been addressed in a number of molecular studies. These analyses have frequently yielded inconsistent results with respect to some basal ordinal relationships. For example, the relative placement of primates, rodents, and carnivores has differed in various studies. Here, we attempt to resolve this phylogenetic problem by using data from completely sequenced nuclear genomes to base the analyses on the largest possible amount of data. To minimize the risk of reconstruction artifacts, the trees were reconstructed under different criteria—distance, parsimony, and likelihood. For the distance trees, distance metrics that measure independent phenomena (amino acid replacement, synonymous substitution, and gene reordering) were used, as it is highly improbable that all of the trees would be affected the same way by any reconstruction artifact. In contradiction to the currently favored classification, our results based on full-genome analysis of the phylogenetic relationship between human, dog, and mouse yielded overwhelming support for a primate–carnivore clade with the exclusion of rodents

Low genetic diversity associated with low prevalence of Anaplasma marginale in water buffaloes in Marajó Island, Brazil

The rickettsia Anaplasma marginale is the etiologic agent of bovine anaplasmosis, an important tick-borne disease affecting cattle in tropical and subtropical regions of the world. In endemic regions, the genetic diversity of this pathogen is usually related to the high prevalence of the disease in cattle. The major surface protein 1 alpha (MSP1a) has been used as a marker to characterize the genetic diversity and for geographical identification of A. marginale strains. The present study reports the characterization of A. marginale MSP1a diversity in water buffaloes. Blood samples were collected from 200 water buffaloes on Marajó Island, Brazil where the largest buffalo herd is located in the Western hemisphere. Fifteen buffaloes (7.5%) were positive for A. marginale msp1α by PCR. Four different strains of A. marginale with MSP1a tandem repeat structures (4-63-27), (162-63-27), (78-24-24-25-31) and (τ-10-10-15) were found, being (4-63-27) the most common. MSP1a tandem repeats composition in buffalos and phylogenetic analysis using msp1α gene showed that the A. marginale strains identified in buffaloes are closely related to A. marginale strains from cattle. The results demonstrated low genetic diversity of A. marginale associated with low bacterial prevalence in buffaloes and suggested that buffaloes may be reservoirs of this pathogen for cattle living in the same area. The results also suggested that mechanical transmission and not biological transmission by ticks might be playing the major role for pathogen circulation among water buffaloes in Marajó Island, Brazil.We thank the Coordination for the Improvement of Higher Education Personnel (CAPES) foundation and the National Council for Technological and Scientific Development (CNPq) for their financial support.Peer Reviewe

Duplications and functional divergence of ADP-glucose pyrophosphorylase genes in plants

<p>Abstract</p> <p>Background</p> <p>ADP-glucose pyrophosphorylase (AGPase), which catalyses a rate limiting step in starch synthesis, is a heterotetramer comprised of two identical large and two identical small subunits in plants. Although the large and small subunits are equally sensitive to activity-altering amino acid changes when expressed in a bacterial system, the overall rate of non-synonymous evolution is ~2.7-fold greater for the large subunit than for the small subunit. Herein, we examine the basis for their different rates of evolution, the number of duplications in both large and small subunit genes and document changes in the patterns of AGPase evolution over time.</p> <p>Results</p> <p>We found that the first duplication in the AGPase large subunit family occurred early in the history of land plants, while the earliest small subunit duplication occurred after the divergence of monocots and eudicots. The large subunit also had a larger number of gene duplications than did the small subunit. The ancient duplications in the large subunit family raise concern about the saturation of synonymous substitutions, but estimates of the absolute rate of AGPase evolution were highly correlated with estimates of ω (the non-synonymous to synonymous rate ratio). Both subunits showed evidence for positive selection and relaxation of purifying selection after duplication, but these phenomena could not explain the different evolutionary rates of the two subunits. Instead, evolutionary constraints appear to be permanently relaxed for the large subunit relative to the small subunit. Both subunits exhibit branch-specific patterns of rate variation among sites.</p> <p>Conclusion</p> <p>These analyses indicate that the higher evolutionary rate of the plant AGPase large subunit reflects permanent relaxation of constraints relative to the small subunit and they show that the large subunit genes have undergone more gene duplications than small subunit genes. Candidate sites potentially responsible for functional divergence within each of the AGPase subunits were investigated by examining branch-specific patterns of rate variation. We discuss the phenotypes of mutants that alter some candidate sites and strategies for examining candidate sites of presently unknown function.</p

Phylogenetic assessment of alignments reveals neglected tree signal in gaps

Tree-based tests of alignment methods enable the evaluation of the effect of gap placement on the inference of phylogenetic relationships