MICRORNAS AND VERTEBRATE PHYLOGENETICS

Understanding the evolution of a clade, either from a morphologic or genomic perspective requires a correct topology, allowing for the polarization of traits and the ability to distinguish between homologies from homoplasies. Although great advances have been made in unraveling the tree of life, primarily based on the incorporation of molecular data and the discovery of new fossils, nonetheless, some areas of the tree still remain largely unknown. Two contentious areas in the vertebrate tree, in particular, are the interrelationships of the jawless fishes (hagfish and lamprey) with respect to the jawed fishes, and the interrelationships among the amniotes. Here, we propose that microRNAs, small non-coding regulatory genes, may be a new dataset that can resolve many relationships as they show three properties that make them excellent phylogenetic markers: 1) new microRNA families are continually being incorporated into metazoan genomes through time; 2) they show very low homoplasy, with only rare instances of secondary loss, and only rare instances of substitutions occurring in the mature gene sequence; and 3) they are almost impossible to evolve convergently. Sequencing small RNA libraries coupled with genomic searches reveals the cyclostomes to be monophyletic, as hagfish and lamprey share several novel miRNA families not found in gnathostomes or in any other metazoan taxa, and the possession of several novel miRNA families supports a sister group relationship between testudines and lepidosaurs. Because of these three properties, we propose that miRNAs are a novel type of data that can be applied to virtually any area of the metazoan tree, including the vertebrate tree, to test among competing hypotheses or to forge new ones.