Phylogenomic Analysis of Concatenated Ultraconserved Elements Reveals the Recent Evolutionary Radiation of the Fairy Wrasses (Teleostei: Labridae: Cirrhilabrus)

Abstract

The fairy wrasses (genus Cirrhilabrus) are among the most 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 evolutionary relationships among these groups using molecular and morphological data have largely been unsuccessful. Here we use a phylogenomic approach with a data set comprising 991 ultraconserved elements (UCEs) and mitochondrial COI to uncover the evolutionary history and patterns of temporal and spatial diversification of the fairy wrasses. Our analyses of phylogenetic signal suggest that most gene-tree incongruence is caused by estimation error, leading to poor resolution in a summary-coalescent analysis of the data. In contrast, analyses of concatenated sequences are able to resolve the major relationships of Cirrhilabrus. We determine the placements of species that were previously regarded as incertae sedis and find evidence for the nesting of Conniella, an unusual, monotypic genus, within Cirrhilabrus. Our relaxed-clock dating analysis indicates that the major divergences within the genus occurred around the Miocene-Pliocene boundary, followed by extensive cladogenesis of species complexes in the Pliocene-Pleistocene. Biogeographic reconstruction suggests that the fairy wrasses emerged within the Coral Triangle, with episodic fluctuations of sea levels during glacial cycles coinciding with shallow divergence events but providing few opportunities for more widespread dispersal. Our study demonstrates both the resolving power and limitations of UCEs across shallow timescales where there is substantial estimation error in individual gene trees.

Morphological and genetic divergence supports peripheral endemism and a recent evolutionary history of Chrysiptera demoiselles in the subtropical South Pacific

“…On this basis, we intend to describe the Rangita ¯hua demoiselle as a unique species, endemic to Rangita ¯hua. It is likely that a genomic approach, such as using RAD-seq or Ultra Conserved Elements (described by Smith et al 2014), would provide greater resolution regarding the evolutionary relationships among these taxa (as in DiBattista et al 2018;Stiller et al 2021) and would help to resolve their taxonomy (as in Bernardi et al 2017;Erickson et al 2021;Tea et al 2021).…”

Redescription of Conniella apterygia Allen and its reassignment in the genus Cirrhilabrus Temminck and Schlegel (Teleostei: Labridae), with comments on cirrhilabrin pelvic morphology

“…In addition to morphological similarities between Conniella and Cirrhilabrus, recent phylogenomic studies on cirrhilabrin relationships reveals that Conniella is deeply nested within Cirrhilabrus (Tea et al 2021b). Because the generic recognition of Conniella would result in a non-monophyletic Cirrhilabrus, we propose subsuming it within the synonymy of Cirrhilabrus.…”

“…Owing to the rarity of Conniella, complete representation of the cirrhilabrins has been lacking in both morphological and molecular studies. These relationships have recently been investigated for the first time using a large phylogenomic dataset, revealing Conniella to be deeply nested within Cirrhilabrus (Tea et al 2021b). Due to the current lack of a morphological diagnosis supporting Conniella, and its nested position within Cirrhilabrus in the molecular phylogeny of Tea et al (2021b), we recommend placement of Conniella within the synonymy of Cirrhilabrus.…”

“…Cirrhilabrus apterygia belongs to the Cirrhilabrus jordani complex of fairy wrasses (Tea et al 2021b), a lineage whose species are diagnosed based on the following combination of characters: pelvic fins relatively short (not or barely reaching anal-fin origin; absent in C. apterygia); a pair of stripes on head (in both sexes; strongly evident during male nuptial display); and dorsal and anal fins without obvious stripes or spots. Tea and Gill (2017) previously included C. claire Randall & Pyle, 2001 as a member of the C. jordani complex, though its phylogenetic position remained unclear and was only recently resolved based on a large molecular dataset (as a member of the C. lineatus complex; Tea et al 2021b). The taxonomy of the related C. rubrisquamis Randall & Emery, 1983 from the western Indian Ocean is muddled, and the name is currently applied to several fishes with notable differences in colour pattern and morphology (in prep.…”

“…However, Cirrhilabrus apterygia is readily separated from C. earlei and all congeners in lacking pelvic fins and in having horizontal stripes that run along the isthmus to the anal-fin origin. On the basis of molecular sequence data, C. apterygia is more closely related to C. rubrisquamis sensu lato, C. wakanda, C. sanguineus, and C. blatteus from the western Indian Ocean (Tea et al 2021b). Several species of Pseudocheilinus (in particular P. octotaenia Jenkins, 1901; Fig.…”