A novel, general, and versatile method of diversification of the P1′ position in phosphinic pseudodipeptides, presumable inhibitors of proteolytic enzymes, was elaborated.
The hypothesis that α-IPMS genes were acquired in fungi through horizontal gene transfer events contributes to the growing body of research suggesting the widespread occurrence of HGT as a significant method of diversification for fungal genomes.
Current methods of diversification rate estimates can deal exclusively with primary speciation events (cladogeneses) and the contribution of speciation events via reticulation cannot be assessed.
Rates of secondary speciation cannot be estimated using the established phylogenetic methods of diversification rate analyses because these analyses incorporate only the rate of primary speciation, meaning speciation by lineages splits via cladogenese events.
But for someone who's willing to do a little more work and can grasp the concepts, this strategy offers a prudent method of improving diversification and risk-adjusted returns.' "In other words," he said, "you must be a pretty smart dude to even contemplate our strategy".
Recently there has been a burst in the number of studies that have utilized the BiSSE method to explore rates of diversification in various taxonomic groups for the purpose of testing hypotheses involving key innovations and the evolution of characters [ 8- 19].
The method-of-moments estimator indicated significantly higher diversification rates in the Canarian clade than expected, given their age and the global diversification rate for the entire genus (rG = 0.2673; p < 0.05).
Here we used simulations to test the performance of two widely used methods under complex scenarios of diversification.
In this study, we developed novel bioinformatic methods to study patterns of diversification and neofunctionalization in the rhoptry kinase family, and integrated the results of a systematic, multi-species analysis with the structural context provided by the solved structures.
First, the lack of resolution in our genus-level tree, with low PPs for most nodes within the radiation, leads to many of the genera not being retrieved as monophyletic, thus preventing the use of diversification methods that allow the assignment of unsampled species richness to well-defined tree terminals (e.g. Medusa; Alfaro et al., 2009).
To test whether the evolution of Neotropical Troidini follows a 'museum' or an 'evolutionary cradle' model of diversification, two methods were used: γ-statistics [ 64] and a likelihood-based method [ 42, 65].
