Phylogenomics improves the phylogenetic resolution and provides strong evidence of mito-nuclear discordance in two genera of a New Zealand cicada (Hemiptera: Cicadidae) species radiation

Rapid species radiations present difficulties for phylogenetic
reconstruction due to lack of phylogenetic information and processes such
as deep coalescence/incomplete lineage sorting and hybridization.
Phylogenomic data can overcome some of these difficulties. In this study,
we use Anchored Hybrid Enrichment (AHE) nuclear phylogenomic data and
mitochondrial genomes recovered from AHE bycatch with several concatenated
and coalescent approaches to reconstruct the poorly-resolved radiation of
the New Zealand cicada species in the genera Kikihia Dugdale and
Maoricicada Dugdale. Compared to previous studies using only three to five
Sanger-sequenced genes, we find increased resolution across our
phylogenies, but several branches remain unresolved due to topological
conflict among genes. Some nodes that are strongly supported by
traditional support measures like bootstraps and posterior probabilities
still show significant gene and site concordance conflict. Additionally,
we find strong mito-nuclear discordance; likely the result of
interspecific hybridization events in the evolutionary history
of Kikihia and Maoricicada.