GenFamClust: an accurate, synteny-aware and reliable homology inference algorithm

BACKGROUND: Homology inference is pivotal to evolutionary biology and is primarily based on significant sequence similarity, which, in general, is a good indicator of homology. Algorithms have also been designed to utilize conservation in gene order as an indication of homologous regions. We have developed GenFamClust, a method based on quantification of both gene order conservation and sequence similarity. RESULTS: In this study, we validate GenFamClust by comparing it to well known homology inference algorithms on a synthetic dataset. We applied several popular clustering algorithms on homologs inferred by GenFamClust and other algorithms on a metazoan dataset and studied the outcomes. Accuracy, similarity, dependence, and other characteristics were investigated for gene families yielded by the clustering algorithms. GenFamClust was also applied to genes from a set of complete fungal genomes and gene families were inferred using clustering. The resulting gene families were compared with a manually curated gold standard of pillars from the Yeast Gene Order Browser. We found that the gene-order component of GenFamClust is simple, yet biologically realistic, and captures local synteny information for homologs. CONCLUSIONS: The study shows that GenFamClust is a more accurate, informed, and comprehensive pipeline to infer homologs and gene families than other commonly used homology and gene-family inference methods. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12862-016-0684-2) contains supplementary material, which is available to authorized users

Plasticity in the diet of Astyanax taeniatus in a coastal stream from south-east Brazil

In this work we aimed to characterise the diet of Astyanax taeniatus (Jenyns 1842) (Characiformes, Characidae) along the Mato Grosso stream and we hypothesised that the diet of this species would vary according to spatial, seasonal and ontogenetic differences. Specimens were collected every second month at three sites with different physical attributes. The feeding habits of 651 specimens were analysed using the Alimentary Index (IAi). Analysis of the diet showed an effect of spatial, temporal and ontogenetic factors. Vegetal allochthonous items were more important in the diet of Astyanax taeniatus in upstream sites while animal autochthonous items were more important downstream. Ontogenetic differences in the diet were significant only in upstream sites, where adults consumed a greater amount of vegetal matter than juveniles. These results reinforce the idea that Astyanax species are opportunistic and show trophic plasticity