What affects power to estimate speciation rate shifts?

The development of methods to estimate rates of speciation and extinction from time-calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal factors. A growing number of researchers are interested in testing whether the evolution of a trait or a trait variant has influenced speciation rate, and three modelling methods—BiSSE, MEDUSA and BAMM—have been widely used in such studies. We simulated phylogenies with a single speciation rate shift each, and evaluated the power of the three methods to detect these shifts. We varied the degree of increase in speciation rate (speciation rate asymmetry), the number of tips, the tip-ratio bias (ratio of number of tips with each character state) and the relative age in relation to overall tree age when the rate shift occurred. All methods had good power to detect rate shifts when the rate asymmetry was strong and the sizes of the two lineages with the distinct speciation rates were large. Even when lineage size was small, power was good when rate asymmetry was high. In our simulated scenarios, small lineage sizes appear to affect BAMM most strongly. Tip-ratio influenced the accuracy of speciation rate estimation but did not have a strong effect on power to detect rate shifts. Based on our results, we provide suggestions to users of these methods.

Polyploidy and elevation contribute to opposing latitudinal gradients in diversification and species richness in lady ferns (Athyriaceae)

In ferns, the temperate-tropical sister clades Athyrium and Diplazium present an opportunity to study a latitudinal contrast in diversification dynamics. We generated a taxonomically expanded molecular chronogram and used macroevolutionary models to analyze how diversification rates have changed through time, across lineages, and in concert with changes in elevation and ploidy. We tested a novel model of cladogenetic state-change in which polyploidy can arise as an infraspecific polymorphism, with diversification parameters distinct from those of pure diploids and polyploids. Both Athyrium and Diplazium accelerated their diversification near the Oligocene-Miocene transition. In Diplazium, the rate shift is older, with subsequent net diversification somewhat slower and suggestive of diversity-dependence. In Athyrium, diversification is faster and associated with higher elevations. In both clades, polyploids have the highest rate of net accumulation but lowest (negative) net diversification, while the converse is true for polymorphic species; diploids have low rates of both net accumulation and diversification. Diversification in Athyrium may have responded to ecological opportunities in expanding temperate habitats during the Neogene, especially in mountains, while the pattern in Diplazium suggests saturation in the tropics. Neopolyploids are generated rapidly, primarily through accelerated cladogenesis in polymorphic species, but are evolutionary dead ends.

What affects power to estimate speciation rate shifts?

The development of methods to estimate rates of speciation and extinction from time- calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal ecological factors. A growing number of researchers are interested in testing whether the evolution of a trait or a trait variant has influenced speciation rates, and three modelling methods – BiSSE, MEDUSA and BAMM – have been widely used in such studies. We simulated phylogenies with a single speciation rate shift each, and evaluated the power of the three methods to detect these shifts. We varied the degree of increase in speciation rate (rate asymmetry), the number of tips, the tip-ratio bias (ratio of number of tips with each character state) and the relative age in relation to overall tree age when the rate shift occurred. All methods had good power to detect rate shifts when the rate asymmetry was strong and the sizes of the two lineages with the distinct speciation rates were large. Even when lineage size was small, power was good when rate asymmetry was high. In our simulated scenarios, small lineage sizes appear to affect BAMM most strongly. Tip-ratio influenced the accuracy of speciation rate estimation but did not have a strong effect on power to detect rate shifts. Based on our results, we provide some suggestions to users of these methods.

What affects power to estimate speciation rate shifts?

The development of methods to estimate rates of speciation and extinction from time- calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal ecological factors. A growing number of researchers are interested in testing whether the evolution of a trait or a trait variant has influenced speciation rates, and three modelling methods – BiSSE, MEDUSA and BAMM – have been widely used in such studies. We simulated phylogenies with a single speciation rate shift each, and evaluated the power of the three methods to detect these shifts. We varied the degree of increase in speciation rate (rate asymmetry), the number of tips, the tip-ratio bias (ratio of number of tips with each character state) and the relative age in relation to overall tree age when the rate shift occurred. All methods had good power to detect rate shifts when the rate asymmetry was strong and the sizes of the two lineages with the distinct speciation rates were large. Even when lineage size was small, power was good when rate asymmetry was high. In our simulated scenarios, small lineage sizes appear to affect BAMM most strongly. Tip-ratio influenced the accuracy of speciation rate estimation but did not have a strong effect on power to detect rate shifts. Based on our results, we provide some suggestions to users of these methods.

Tree size and relative clade age influence estimation of speciation rate shifts

The development of methods to estimate rates of speciation and extinction from time-calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal ecological factors. We use rigorous simulations to evaluate the statistical performance of three widely used modelling approaches - BiSSE, BAMM and MEDUSA - in relation to detection of speciation rates shifts. We simulated sets of trees with each tree having a single increase in speciation rate. We varied the location of shifts, the degree of increase in speciation rate and the total age of the tree. We then used BiSSE, BAMM and MEDUSA to estimate rate shifts. For BiSSE, we assigned different character states for the lineages with different simulated speciation rates. We show that all methods are better at detecting rate shifts when the change in speciation rate is higher, but had high Type II errors (non-detection of rate shifts). While the algorithms more accurately identified rate shifts close to the root of the tree, both perform poorly when the rate shift occurred more recently. All methods performed better with increase in the overall number of tips and the number of tips in the clade with rate shift, both of which are correlated with tree age and speciation rate asymmetry. We discuss the implications of this study for the use and development of methods for hypothesis testing based on diversification rate shifts.