Phylotranscriptomics reveals discordance in the phylogeny of Hawaiian Drosophila and Scaptomyza (Diptera: Drosophilidae)

Abstract

Island radiations present natural laboratories for studying the evolutionary process. The Hawaiian Drosophil-idae are one such radiation, with nearly 600 described species and substantial morphological and ecological diversification. These species are largely divided into a few major clades, but the relationship between these clades remains uncertain. Here we present 12 new assembled transcriptomes from across these clades, and use these transcriptomes to resolve the base of the evolutionary radiation. We recover a new hypothesis for the relationship between clades, and demonstrate its support over previously published hypotheses. We then use the evolutionary radiation to explore dynamics of concordance in phylogenetic support, by analyzing the gene and site concordance factors for every possible topological combination of major groups. We show that high bootstrap values mask low evolutionary concordance, and we demonstrate that the most likely topology is distinct from the topology with the highest support across gene trees and from the topology with highest support across sites. We then combine all previously published genetic data for the group to estimate a time-calibrated tree for over 300 species of drosophilids. Finally, we digitize dozens of published Hawaiian Drosophilidae descriptions, and use this to pinpoint probable evolutionary shifts in reproductive ecology as well as body, wing, and egg size. We show that by examining the entire landscape of tree and trait space, we can gain a more complete understanding of how evolutionary dynamics play out across an island radiation.

The evolution of ovary-biased gene expression in Hawaiian Drosophila

“…The phylogenetic methods for inferring homology, orthology, and estimating gene and species trees are the same as those described in our previous manuscript 44 . Genetrees were additionally annotated with the software Phyldog 65 .…”

“…We reconstructed the evolutionary history of tissue bias for each homology group using the species tree published in Church and Extavour, 2021 44 , based on the same reference transcriptome data (Fig. S2C).…”

“…For the twelve reference transcriptomes, reads from separate rounds of sequencing were concatenated and inserted into the agalma catalog. Further details of transcriptome assembly and homology assessment are included in our previous manuscript 44 .…”

“…We subsequently performed the same transformation steps described above, averaging over ratios from the same homology group and across biological replicates, to calculate average expression bias per homology group per library. To avoid division by zero, we added a pseudocount We reconstructed the evolutionary history of tissue bias for each homology group using the species tree published in Church and Extavour, 2021 44 , based on the same reference transcriptome data (Fig. S2C).…”

“…A, Twelve species of Hawaiian Drosophilidae flies were collected in the wild and processed for RNA sequencing. The twelve reference transcriptomes assembled from these species were combined with twelve published genomes to generate the phylogeny shown here (originally published in Church and Extavour, 2021 44 ). Three clades within the group are highlighted: the genus Scaptomyza , nested within the paraphyletic genus Drosophila ; the Hawaiian Drosophila , which, along with Scaptomyza , make up the Hawaiian Drosophilidae; and the well-known picture-wing clade.…”