What affects power to estimate speciation rate shifts?

Abstract

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.

Clade-age-dependent diversification under high species turnover shapes species richness disparities among tropical rainforest lineages of Bulbophyllum (Orchidaceae)

“…Also, we caution that failure of our modelling methods (RPANDA, BAMM) to detect diversification-rate shifts does not imply that the null hypothesis of constant-rate evolution is ‘true’, but only that there is insufficient evidence to reject this hypothesis, as probably best achieved with larger-sized lineages (≥ 300 taxa; cf. [81]).…”

Geo-Climatic Changes and Apomixis as Major Drivers of Diversification in the Mediterranean Sea Lavenders (Limonium Mill.)

“…Woodiness on oceanic islands has been regarded as a key innovation linked to higher diversification rates when it is associated with disparity in growth forms (e.g., arborescent shrubs, subshrubs, trees, cushion forms, woody lianas, and giant rosette plants), because it enables the exploration of a broader niche space (Nürk et al, 2019). However, our results suggest that insular woodiness in the Canarian Nobiles clade of Limonium is either not linked to accelerated diversification (Figure 6; Supplementary Tables S14, S5) or a shift in rates for woody vs. herbaceous taxa is too moderate for the SSE methods to detect it, considering their limited power in analyses of small-size clades (Gamisch, 2016;Kodandaramaiah and Murali, 2018). A possible explanation for the result that the evolution of woodiness on the Canary Islands did not trigger a significant shift to much higher diversification rates may be that, in Canarian Limonium, woodiness is not associated with a diversity of woody growth forms (as found by Nürk et al, 2019), since all species in Nobiles clade have similar subshrub suffruticose habit.…”

“…(e.g., Gamisch, 2016), their power in detecting state-dependent diversification depends on the strength of speciation rate asymmetry in the tree. If state-dependent diversification were detected, this would mean that speciation rate asymmetry between woody and herbaceous taxa is sufficiently high (i.e., >2.5-fold) to be detected despite small clade size, as demonstrated by simulations (Gamisch, 2016;Kodandaramaiah and Murali, 2018). Conversely, if state-independent diversification were supported, this would not automatically exclude the existence of moderate levels of speciation rate asymmetry (i.e., <2.5-fold), but might simply mean that such levels are insufficient to be recovered by the SSE methods in small clades.…”

Live fast, diversify non-adaptively: evolutionary diversification of exceptionally short-lived annual killifishes

“…We find no evidence of diversification rate heterogeneity, which again supports gradual access to suitable niche space for diversification in allopatry. However, the power to detect rate heterogeneity in a phylogeny of this size is low [84], especially when only few species may be diversifying under a different macroevolutionary regime [85, 86]. The savannah pools replicate the insular biogeographic conditions of archipelago systems and thus, impose dispersal limitations, and so diversification is due to extrinsic factors that promote allopatry (i.e.…”