Quantifying phenotypic evolutionary rates and their variation across phylogenetic trees is a major issue in evolutionary biology. A number of phylogenetic comparative methods (PCMs) currently perform such task. However, available PCMs can locate rate shifts pertaining to entire portions of the phylogeny, but not those expected to occur at the level of individual species and lineages, such as with the idea that body size changes more rapidly in insular vertebrates. Still, most PCMs cannot deal with fossil phylogenies, albeit fossils provide highly desirable information when it comes to understand trait variation and evolution. We developed a PCM based on phylogenetic ridge regression, which we named RRphylo, which assigns an evolutionary rate to each branch of the phylogeny, and is designed to locate rate shifts relating to entire clades, as well as to unrelated tree tips. We tested RRphylo on simulated trees and data to assess its performance under different conditions. Then, we repeated its application with two real case scenarios, the evolution of flight in ornithodirans and mammals and body size evolution in insular mammals, which are usually subsumed to evolve under different range regimes than terrestrial and continental species respectively. RRphylo performs well across all different conditions. The simulation experiments demonstrated it has low Type I and Type II error rate. We found significant evidence that flight accelerates the rate of body size evolution in vertebrates, and that the acquisition of very large body size slows down the rate. Still, insular mammals body size evolution is not faster than in continental species. RRphylo is a new PCM ideal to estimate variation and shift in the rate of phenotypic evolution with fossil data. In addition to testing evolutionary rate variation, it is open to a variety of further questions, such as the evolution of rates in time, the estimation of ancestral states and the estimation of phenotypic trends over time.

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Toothed whales (Odontoceti, Cetacea) are well-known for their ability to produce complex vocalizations, to use tools, to possess self-recognition, and for their extreme behavioural plasticity. The toothed whale intelligence is said to compete with that of primates, so does their extremely large brain to body size ratio. Common explanations for the acquisition of such large brains over the evolutionary time (encephalization) in toothed whales range from their demanding, complex social lives, to their feeding habits, to echolocation. Yet, several studies found no macroevolutionary trend in Odontoceti encephalization, which casts doubts on its selective advantage. We applied a recently developed phylogenetic comparative method to study macroevolutionary trends in relative brain size (RBS) and brain size evolutionary rates in cetaceans, comparing toothed whales to the other cetaceans and contrasting groups of species as ascribed to different feeding categories. We found that cetaceans as a whole followed a trend for increased encephalization over time, starting from small-brained archaeocete ancestors. Toothed whales do not show this same trend in RBS but have possessed larger RBS than any other cetacean ever since the beginning of their existence. The rate of RBS evolution in Odontoceti is significantly slower than in other Cetacea and slower than the rate of Odontoceti body size evolution. These results suggest that toothed whales' history is characterized by high and conservative relative encephalization. Feeding lifestyle does not explain these patterns, while the appearance of echolocation within stem group Odontoceti remains a viable candidate for them.

The ability to develop complex social bonds and an increased capacity for behavioural flexibility in novel environments have both been forwarded as selective forces favouring the evolution of a large brain in mammals. However, large brains are energetically expensive, and in circumstances in which selective pressures are relaxed, e.g. on islands, smaller brains are selected for. Similar reasoning has been offered to explain the reduction of brain size in domestic species relative to their wild relatives. Herein, we assess the effect of domestication, insularity and sociality on brain size evolution at the macroevolutionary scale. Our results are based on analyses of a 426-taxon tree, including both wild species and domestic breeds. We further develop the phylogenetic ridge regression comparative method (RRphylo) to work with discrete variables and compare the rates (tempo) and direction (mode) of brain size evolution among categories within each of three factors (sociality, insularity and domestication). The common assertion that domestication increases the rate of brain size evolution holds true. The same does not apply to insularity. We also find support for the suggested but previously untested hypothesis that species living in medium-sized groups exhibit faster rates of brain size evolution than either solitary or herding taxa.