Rates of molecular and morphological evolution are uncoupled across the eukaryote Tree of Life

A vast degree of phenotypic variation can be seen across lineages of eukaryotes. Although at least part of this diversity has a genomic basis, it is unclear whether there are broad-scale links that can be detected between rates of genomic and phenotypic evolution. The presence of a correlation would imply the action of shared drivers, such as mutational or adaptive processes that occur on a genome- and organism-wide scale. We investigated this question by using a phylogenetic approach to test for correlations between molecular and morphological evolutionary rates. We analysed 60 data sets of combined nucleotide sequences and discrete morphological characters, representing a diverse range of eukaryotes that include alveolates, plants, invertebrates, fishes, and tetrapods. Using a maximum-likelihood phylogenetic approach based on sister-pair contrasts, we found very little evidence of any link between rates of molecular and morphological evolution, a striking result given the scale and taxonomic breadth of our analyses. Our results point to contrasting evolutionary dynamics underlying genomes and phenotypic traits, most likely involving differing extents of selection. These processes have also led to greater variation in morphological evolutionary rates across lineages, whereas molecular evolution is more clocklike. Our results have implications for how evolutionary change should be modelled in phylogenetic analyses of combined data sets. Overall, our study reveals the discrepancies in evolutionary drivers that act at the genomic and phenotypic levels across the eukaryotic Tree of Life.