Factors driving metabolic diversity in the budding yeast subphylum.

BACKGROUND: Associations between traits are prevalent in nature, occurring across a diverse range of taxa and traits. Individual traits may co-evolve with one other, and these correlations can be driven by factors intrinsic or extrinsic to an organism. However, few studies, especially in microbes, have simultaneously investigated both across a broad taxonomic range. Here we quantify pairwise associations among 48 traits across 784 diverse yeast species of the ancient budding yeast subphylum Saccharomycotina, assessing the effects of phylogenetic history, genetics, and ecology. RESULTS: We find extensive negative (traits that tend to not occur together) and positive (traits that tend to co-occur) pairwise associations among traits, as well as between traits and environments. These associations can largely be explained by the biological properties of the traits, such as overlapping biochemical pathways. The isolation environments of the yeasts explain a minor but significant component of the variance, while phylogeny (the retention of ancestral traits in descendant species) plays an even more limited role. Positive correlations are pervasive among carbon utilization traits and track with chemical structures (e.g., glucosides and sugar alcohols) and metabolic pathways, suggesting a molecular basis for the presence of suites of traits. In several cases, characterized genes from model organisms suggest that enzyme promiscuity and overlapping biochemical pathways are likely mechanisms to explain these macroevolutionary trends. Interestingly, fermentation traits are negatively correlated with the utilization of pentose sugars, which are major components of the plant biomass degraded by fungi and present major bottlenecks to the production of cellulosic biofuels. Finally, we show that mammalian pathogenic and commensal yeasts have a suite of traits that includes growth at high temperature and, surprisingly, the utilization of a narrowed panel of carbon sources. CONCLUSIONS: These results demonstrate how both intrinsic physiological factors and extrinsic ecological factors drive the distribution of traits present in diverse organisms across macroevolutionary timescales.

Biological invasions: a field synopsis, systematic review, and database of the literature.

Species introductions of anthropogenic origins are a major aspect of rapid ecological change globally. Research on biological invasions has generated a large literature on many different aspects of this phenomenon. Here, we describe and categorize some aspects of this literature, to better understand what has been studied and what we know, mapping well-studied areas and important gaps. To do so, we employ the techniques of systematic reviewing widely adopted in other scientific disciplines, to further the use of approaches in reviewing the literature that are as scientific, repeatable, and transparent as those employed in a primary study. We identified 2398 relevant studies in a field synopsis of the biological invasions literature. A majority of these studies (58%) were concerned with hypotheses for causes of biological invasions, while studies on impacts of invasions were the next most common (32% of the publications). We examined 1537 papers in greater detail in a systematic review. Superior competitive abilities of invaders, environmental disturbance, and invaded community species richness were the most common hypotheses examined. Most studies examined only a single hypothesis. Almost half of the papers were field observational studies. Studies of terrestrial invasions dominate the literature, with most of these concerning plant invasions. The focus of the literature overall is uneven, with important gaps in areas of theoretical and practical importance.