Fig. 2: Variation in diversification rate (DR) over time and across strepsirrhine phylogeny.

A A time-calibrated phylogeny of Strepsirrhini, with branches colored according to DR (species per million years) estimated using a three-rate model in MiSSE. Full results of this analysis can be found in Supplementary Fig. 6. Dashed vertical lines distinguish geological epochs (Pal. Paleocene, Pl. Pliocene, Q. Quaternary). Fully detailed time-calibrated phylogenies showing tip labels, node confidence intervals, and outgroups are shown in Supplementary Fig. 4. Three genera with particularly high speciation rates (Eulemur, Lepilemur, and Microcebus) are indicated on the tree and are discussed in the text. B Lineages-through-time plots of lemurs (blue) and lorisiforms (red). Each line represents a distinct tree generated using six different fossil calibration sets and accounting for incomplete taxonomic sampling, which was done by stochastically adding missing taxa to the proper genus 1000 times. The complete set of 6000 trees is available on Figshare (https://doi.org/10.6084/m9.figshare.28699742). Note that the y-axis representing the number of lineages is log-transformed. C Variation in DR between lorisiforms and lemurs is visualized as the distribution of tip DR (λ_DR) values for all species within each taxon. Darker colored distributions represent the empirical λ_DR values across the set of 6000 stochastically resolved trees, while light gray distributions represent simulated λ_DR values, in which trees of the same species richness as each Family were simulated using a rate-constant birth-death model. The empirical and simulated values shown in these plots were calculated using a custom script (TipDr_Calculation.R; see Code Availability statement)¹⁰². D MiSSE results, identical to panel A, but estimated using a two-rate model. See Supplementary Fig. 7 for the full visualization of this analysis, and Supplementary Data 6 for MiSSE model testing results. E Results of our CRABS analysis which estimated ten different diversification models in the congruence class (the set of speciation and extinction functions with equal likelihoods) under three different extinction treatments (left, models where extinction increased over time, center, models where extinction decreased over time, and right, models where extinction fluctuated randomly over time). Each line represents a different model in the congruence class. Across all analyses, an increase in net diversification rate was detected ~5-6 mya (indicated by a yellow vertical bar). Full details of this analysis are provided in Supplementary Fig. 8.