Anchored phylogenomics unravels the evolution of spider flies (Diptera, Acroceridae) and reveals discordance between nucleotides and amino acids

Abstract

The onset of phylogenomics has contributed to the resolution of numerous challenging evolutionary questions while offering new perspectives regarding biodiversity. However, in some instances, analyses of large genomic datasets can also result in conflicting estimates of phylogeny. Here, we present the first phylogenomic scale study of a dipteran parasitoid family, built upon anchored hybrid enrichment and transcriptomic data of 240 loci of 43 ingroup acrocerid taxa. A new hypothesis for the timing of spider fly evolution is proposed, wielding recent advances in divergence time dating, including the fossilized birth-death process to show that the origin of Acroceridae is younger than previously proposed. To test the robustness of our phylogenetic inferences, we analyzed our datasets using different phylogenetic estimation criteria, including supermatrix and coalescent-based approaches, maximum-likelihood and Bayesian methods, combined with other approaches such as permutations of the data, homogeneous versus heterogeneous models, and alternative data and taxon sets. Resulting topologies based on amino acids and nucleotides are both strongly supported but critically discordant, primarily in terms of the monophyly of Panopinae. Conflict was not resolved by controlling for compositional heterogeneity and saturation in third codon positions, which highlights the need for a better understanding of how different biases affect different data sources. In our study, results based on nucleotides were both more robust to alterations of the data and different analytical methods and more compatible with our current understanding of acrocerid morphology and patterns of host usage.

Evolution of fossil and living spider flies based on morphological and molecular data (Diptera, Acroceridae)

“…However, Gillung et al . () indicated that species in the genus Ogcodes represent yet a fourth independent lineage of Acrocerinae, in contrast to the close association of Ogcodes with Pterodontia as recovered in the topologies of Winterton et al . ().…”

“…() using Sanger sequencing data, and by Gillung et al . () using phylogenomic data. Winterton et al .…”

“…(); and a 2058‐bp region obtained via anchored hybrid enrichment from Gillung et al . () (Table S1). CAD sequences were inspected by eye and no introns were identified (i.e.…”

“…Each clade was strongly supported statistically in the analyses of nucleotides performed by Gillung et al . (), with posterior probabilities (PPs) of 1.0 for each node. We follow the phylogeny based on nucleotides, as opposed to the alternative topology based on amino acids, because the results based on nucleotides were both more robust to alterations of the data and different analytical methods and more compatible with biological (i.e.…”

“…() and Gillung et al . () to include 12 additional genera of spider flies, further increasing our confidence in the estimated relationships. The classification of Acroceridae is revised, resulting in a new framework for the comparative study of parasitoid flies.…”