Analysis and Visualization of Complex Macroevolutionary Dynamics: An Example from Australian Scincid Lizards

Abstract

The correlation between species diversification and morphological evolution has long been of interest in evolutionary biology. We investigated the relationship between these processes during the radiation of 250+scincid lizards that constitute Australia's most species-rich clade of terrestrial vertebrates. We generated a time-calibrated phylogenetic tree for the group that was more than 85% complete at the species level and collected multivariate morphometric data for 183 species. We reconstructed the dynamics of species diversification and trait evolution using a Bayesian statistical framework (BAMM) that simultaneously accounts for variation in evolutionary rates through time and among lineages. We extended the BAMM model to accommodate time-dependent phenotypic evolution, and we describe several new methods for summarizing and visualizing macroevolutionary rate heterogeneity on phylogenetic trees. Two major clades (Lerista, Ctenotus; >90 spp. each) are associated with high rates of species diversification relative to the background rate across Australian sphenomorphine skinks. The Lerista clade is characterized by relatively high lability of body form and has undergone repeated instances of limb reduction, but Ctenotus is characterized by an extreme deceleration in the rate of body shape evolution. We estimate that rates of phenotypic evolution decreased by more than an order of magnitude in the common ancestor of the Ctenotus clade. These results provide evidence for a modal shift in phenotypic evolutionary dynamics and demonstrate that major axes of morphological variation can be decoupled from species diversification. More generally, the Bayesian framework described here can be used to identify and characterize complex mixtures of dynamic processes on phylogenetic trees. [Bayesian; diversification; evolvability; lizard; macroevolution, punctuated equilibrium, speciation.].

The adaptive radiation of lichen-forming Teloschistaceae is associated with sunscreening pigments and a bark-to-rock substrate shift

“…The difference between the history of the Teloschistaceae and the other families is emphasized by macroevolutionary cohort analysis (Fig. 2B), which summarizes the extent to which any two species share a common macroevolutionary rate dynamic (36). The three tropical families and the family Teloschistaceae behave in general as two separate macroevolutionary cohorts with high probability (a clade within the Xanthorioideae in the Teloschistaceae providing a mild exception to this rule; depicted by red branches in Fig.…”

Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota

“…Even without a firm species concept in prokaryotes (24), comparative phylogenetic methods provide insights into processes of lineage diversification and adaptation because they can test the null hypothesis that diversification occurs at a constant rate under a coalescent model (25,26). For our thaumarchaeotal data, diversification tests based on the γ-statistic reject a rate-constant pure birth model (γ = −4.03; P = 8 × 10 Use of a recently developed Bayesian method, Bayesian Analysis of Mixture Models (BAMM), which explicitly models variation in diversification rates across a tree (13)(14)(15), also provided strong support for heterogeneity in thaumarchaeotal diversification rates ( Fig. 2 and SI Appendix, Fig.…”

“…As pH has a major impact on the ecology of extant Thaumarchaeota (9), we postulated that this environmental variable contributed to the thaumarchaeotal diversification regime. We therefore reconstructed rates of pH adaptation across thaumarchaeotal evolution in the BAMM framework (13)(14)(15). Our reconstructions of adaptation were based on estimates of pH preference of extant Thaumarchaeota, considered as the pH of the soil from which the amoA sequences were isolated.…”

“…In this context, recently developed probabilistic methods geared toward reconstructing the dynamics of species diversification and trait evolution using molecular phylogenies (11)(12)(13) have great potential. A recent Bayesian method that explicitly aims to characterize and quantify heterogeneity in evolutionary rates (13)(14)(15) holds particular promise for modeling prokaryotic evolution, whereby features such as massive population size, frequent lateral gene transfer (LGT), and fast growth all facilitate rapid increases in diversity, suggesting that complex evolutionary regimes may be the norm. Here, we apply these recently developed methods to test a key hypothesis about the ecological drivers of thaumarchaeotal diversification through deep evolutionary time.…”

Historical species losses in bumblebee evolution

“…These methods provide separate estimates for speciation and extinction rates through time and relax the assumption of constant diversification rates by allowing either discrete changes in rates at estimated points in time [16] or continuous changes through time [17]. We also performed Bayesian analysis of macroevolutionary mixtures [19], which allows shifts in rates among/within clades, but has the disadvantage of treating extinction as constant. All of these methods allow for diversification rates to be negative, that is to say periods of declining diversity, and account for undersampled phylogenies.…”