Genetic diversity and ecological success of Staphylococcus aureus strains colonizing humans

The genetic determinants and phenotypic traits which make a Staphylococcus aureus strain a successful colonizer are largely unknown. The genetic diversity and population structure of 133 S. aureus isolates from healthy, generally risk-free adult carriers were investigated using four different typing methods: multilocus sequence typing (MLST), amplified fragment length polymorphism analysis (AFLP), double-locus sequence typing (DLST), and spa typing were compared. Carriage isolates displayed great genetic diversity which could only be revealed fully by DLST. Results of AFLP and MLST were highly concordant in the delineation of genotypic clusters of closely related isolates, roughly equivalent to clonal complexes. spa typing and DLST provided considerably less phylogenetic information. The resolution of spa typing was similar to that of AFLP and inferior to that of DLST. AFLP proved to be the most universal method, combining a phylogeny-building capacity similar to that of MLST with a much higher resolution. However, it had a lower reproducibility than sequencing-based MLST, DLST, and spa typing. We found two cases of methicillin-resistant S. aureus colonization, both of which were most likely associated with employment at a health service. Of 21 genotypic clusters detected, 2 were most prevalent: cluster 45 and cluster 30 each colonized 24% of the carrier population. The number of bacteria found in nasal samples varied significantly among the clusters, but the most prevalent clusters were not particularly numerous in the nasal samples. We did not find much evidence that genotypic clusters were associated with different carrier characteristics, such as age, sex, medical conditions, or antibiotic use. This may provide empirical support for the idea that genetic clusters in bacteria are maintained in the absence of adaptation to different niches. Alternatively, carrier characteristics other than those evaluated here or factors other than human hosts may exert selective pressure maintaining genotypic clusters.

Diversity versus disparity and the role of ecological opportunity in a continental bird radiation

Aim The Neotropical parrots (Arini) are an unusually diverse group which colonized South America in the Oligocene. The newly invaded Neotropics may have functioned as an underused adaptive zone and provided novel ecological opportunities that facilitated diversification. Alternatively, diversification may have been driven by ecological changes caused by Andean uplift and/or climate change from the Miocene onwards. Our aim was to find out whether Arini diversified in a classical adaptive radiation after their colonization of South America, or whether their diversification occurred later and was influenced by more recent environmental change. Location Neotropics. Methods We generated a time-calibrated phylogeny of more than 80% of all Arini species in order to analyse lineage diversification. This chronogram was also used as the basis for the reconstruction of morphological evolution within Arini using a multivariate ratio analysis of three size measurements. Results We found a concentration of size evolution and partitioning of size niches in the early history of Arini consistent with the process of adaptive radia- tion, but there were no signs of an early burst of speciation or a decrease in speci- ation rates through time. Although we detected no overall temporal shifts in diversification rates, we discovered two young, unexpectedly species-rich clades. Main conclusions Arini show signs of an early adaptive radiation, but we found no evidence of the slowdown in speciation rate generally considered a feature of island or lake radiations. Historical processes and environmental change from the Miocene onwards may have kept diversification rates roughly constant ever since the colonization of the Neotropics. Thus, Arini may not yet have reached equilibrium diversity. The lack of diversity-dependent speciation might be a general feature of adaptive radiations on a continental scale, and diversification processes on continents might therefore not be as ecologically limited as in isolated lakes or on oceanic islands.