Positive phenotypic selection inferred from phylogenies

Abstract

Rates of phenotypic evolution vary widely in nature and these rates may often reflect the intensity of natural selection. Here we outline an approach for detecting exceptional shifts in the rate of phenotypic evolution across phylogenies. We introduce a simple new branch-specific metric Δ V /Δ B that divides observed phenotypic change along a branch into two components: (1) that attributable to the background rate (Δ B ), and (2) that attributable to departures from the background rate (Δ V ). Where the amount of expected change derived from variation in the rate of morphological evolution doubles that explained by to the background rate (Δ V /Δ B > 2), we identify this as positive phenotypic selection. We apply our approach to six datasets, finding multiple instances of positive selection in each. Our results support the growing appreciation that the traditional gradual view of phenotypic evolution is rarely upheld, with a more episodic view taking its place. This moves focus away from viewing phenotypic evolution as a simple homogeneous process and facilitates reconciliation with macroevolutionary interpretations from a genetic perspective, paving the way to novel insights into the link between genotype and phenotype. The ability to detect positive selection when genetic data are unavailable or unobtainable represents an attractive prospect for extant species, but when applied to fossil data it can reveal patterns of natural selection in deep time that would otherwise be impossible.

Selection towards larger body size in both herbivorous and carnivorous synapsids during the Carboniferous

“…Different selective pressures acting on different lineages will lead to deviations from a "Brownian motion" (random walk) model of evolution. Recently, Baker et al (2015) proposed a method of identifying lineages along which "positive phenotypic selection" occurred. The concept of positive selection was defined as change beyond what would be expected under Brownian motion.…”

“…A Markov Chain Monte Carlo reversible-jump framework was used to generate posterior distributions of scalars for each branch and to deduce what pattern of rate variation best fits the morphological data observed. Baker et al (2015) proposed (somewhat arbitrarily) that positive phenotypic selection could be deemed to have occurred along a branch if the amount of morphological change occurring along that branch was more than double that which would be expected under Brownian motion. All the time-calibrated trees described above were analysed using the method proposed by Baker et al (2015).…”

“…Baker et al (2015) proposed (somewhat arbitrarily) that positive phenotypic selection could be deemed to have occurred along a branch if the amount of morphological change occurring along that branch was more than double that which would be expected under Brownian motion. All the time-calibrated trees described above were analysed using the method proposed by Baker et al (2015). The analyses were performed in BayesTraits V2.0.…”

Tempo and mode in the evolution of morphological disparity in the Neotropical fern genusPleopeltis

“…Future analyses may explore phenotypic selection using the approach recently developed (Baker et al, 2015) respectively on models describing the rates of morphological changes as used in other studies (see Yu et al, 2014). These observations are notable because these results indicate a widespread discordance of SD and MD in land plants.…”

Directional selection in the evolution of elongated upper canines in clouded leopards and sabre‐toothed cats

“…Hunt () modelled a directional evolutionary trend in a specific lineage using ancestral fossil data. Another approach to address lineage‐ or branch‐specific selection is to use the Brownian motion model with varying rates across branches of a tree (Venditti et al ., ; Baker et al ., ). This can show an exceptional shift in the rate of nondirectional evolution, which could be attributable to directional selection along a branch.…”