Supplementary material for: Phylogenomic analysis of ultraconserved elements reveals the recent evolutionary radiation of the fairy wrasses (Teleostei: Labridae: Cirrhilabrus)

The fairy wrasses (genus Cirrhilabrus) are among the most captivating and successful of the extant wrasse lineages (Teleostei: Labridae), with their 61 species accounting for nearly 10% of the family. Although species complexes within the genus have been diagnosed on the basis of coloration patterns and synapomorphies, attempts to resolve the evolutionary relationships using molecular and morphological data have largely been unsuccessful. Here we use a phylogenomic analysis of 991 ultraconserved elements (UCEs) and mitochondrial COI to uncover the evolutionary history and patterns of temporal and spatial diversification of the fairy wrasses. We find that analyses of concatenated sequences confidently resolve the major relationships of Cirrhilabrus. Our analyses of phylogenetic signal suggest that extensive gene-tree incongruence is primarily caused by estimation error rather than incomplete lineage sorting, leading to poor phylogenetic resolution in a summary-coalescent analysis of the ...