Evolution and perspective of the temperate fruit crops in São Paulo state, Brazil

This work was carried out to show the current situation of the temperate fruit crops in São Paulo state, Brazil, with an emphasis on grapes, peaches, apples, plums, nectarines and pears crops. Current economic data of crops, major growing regions, main cultivars produced, as well as the new technologies generated by research are presented. Regarding the grape crop, a decrease in the national production as well as in the major growing states was observed. The main grapes growing centers in São Paulo state are presented, highlighting its peculiarities regarding cultivars, cultural crop management and current researches. A trend has been observed toward increasing Niagara Rosada grape growing area rather than the fine table grape cultivars. It was also observed the adoption of cultural practices, aiming to increase productivity, to improve the fruits quality and to reduce manpower necessity. In terms of stone fruits, peaches are the most widely cultivated in São Paulo state, followed by plums and nectarines. Both for stone fruits crop and for apples and pears crops, statistics and comments are presented on the crops evolution as well as the current researches results and the requirements of these fruit crops in São Paulo state, Brazil.

Family Size Evolution in Drosophila Chemosensory Gene Families: A Comparative Analysis with a Critical Appraisal of Methods

Gene turnover rates and the evolution of gene family sizes are important aspects of genome evolution. Here, we use curated sequence data of the major chemosensory gene families from Drosophila-the gustatory receptor, odorant receptor, ionotropic receptor, and odorant-binding protein families-to conduct a comparative analysis among families, exploring different methods to estimate gene birth and death rates, including an ad hoc simulation study. Remarkably, we found that the state-of-the-art methods may produce very different rate estimates, which may lead to disparate conclusions regarding the evolution of chemosensory gene family sizes in Drosophila. Among biological factors, we found that a peculiarity of D. sechellia's gene turnover rates was a major source of bias in global estimates, whereas gene conversion had negligible effects for the families analyzed herein. Turnover rates vary considerably among families, subfamilies, and ortholog groups although all analyzed families were quite dynamic in terms of gene turnover. Computer simulations showed that the methods that use ortholog group information appear to be the most accurate for the Drosophila chemosensory families. Most importantly, these results reveal the potential of rate heterogeneity among lineages to severely bias some turnover rate estimation methods and the need of further evaluating the performance of these methods in a more diverse sampling of gene families and phylogenetic contexts. Using branch-specific codon substitution models, we find further evidence of positive selection in recently duplicated genes, which attests to a nonneutral aspect of the gene birth-and-death process.