Protein‐encoding ultraconserved elements provide a new phylogenomic perspective of Oestroidea flies (Diptera: Calyptratae)

Abstract

The diverse superfamily Oestroidea with more than 15 000 known species includes among others blow flies, flesh flies, bot flies and the diverse tachinid flies. Oestroidea exhibit strikingly divergent morphological and ecological traits, but even with a variety of data sources and inferences there is no consensus on the relationships among major Oestroidea lineages. Phylogenomic inferences derived from targeted enrichment of ultraconserved elements or UCEs have emerged as a promising method for resolving difficult phylogenetic problems at varying timescales. To reconstruct phylogenetic relationships among families of Oestroidea, we obtained UCE loci exclusively derived from the transcribed portion of the genome, making them suitable for larger and more integrative phylogenomic studies using other genomic and transcriptomic resources. We analysed datasets containing 37–2077 UCE loci from 98 representatives of all oestroid families (except Ulurumyiidae and Mystacinobiidae) and seven calyptrate outgroups, with a total concatenated aligned length between 10 and 550 Mb. About 35% of the sampled taxa consisted of museum specimens (2–92 years old), of which 85% resulted in successful UCE enrichment. Our maximum likelihood and coalescent‐based analyses produced well‐resolved and highly supported topologies. With the exception of Calliphoridae and Oestridae all included families were recovered as monophyletic with the following conclusions: Oestroidea is monophyletic with Mesembrinellidae as sister to the remaining oestroid families; Oestridae is paraphyletic with respect to Sarcophagidae; Polleniidae is sister to Tachinidae; Rhinophoridae sister to (Luciliinae (Toxotarsinae (Melanomyinae + Calliphorinae))); Phumosiinae is sister to Chrysomyinae and Bengaliinae is sister to Rhiniidae. These results support the ranking of most calliphorid subfamilies as separate families.

The limits of Quediini at last (Staphylinidae: Staphylininae): a rove beetle mega‐radiation resolved by comprehensive sampling and anchored phylogenomics

“…In corroboration with previous studies (e.g. St. Laurent et al, 2018; Buenaventura et al, 2020), we showed that target capture datasets heavily derived from pinned insect specimens (up to 46%) can recover well‐resolved phylogenies. The combination of low‐input lab protocols, target enrichment and next‐generation sequencing allowed for extensive sampling of Quediini and incertae sedis Staphylininae through the inclusion of pinned museum specimens, which formed nearly half of the taxon sample.…”

“…Next‐generation sequencing uses massively parallel short‐read technologies to read these short DNA library fragments that are then assembled into longer target gene regions using bioinformatics pipelines. These advances can be combined with sequence capture methods, which target hundreds to thousands of single‐copy loci using a set of short probe sequences, to attain comprehensively sampled phylogenomic datasets (St. Laurent et al, 2018; Hamilton et al, 2019; Buenaventura et al, 2020).…”

Ultraconserved elements help resolve the phylogeny of an ancient radiation of venomous flies (Diptera: Asilidae)

“…It is now understood that many arthropod UCE loci occur in protein-coding regions, to a greater degree than UCEs found in vertebrates (Blaimer et al, 2019, Buenaventura et al 2020Hedin et al, 2019). The high number of UCE loci recovered here from asilid transcriptome assemblies, and the fact that they were recovered in phylogenetic positions with high support, lends further evidence to the idea that transcriptomes can be effectively combined with UCEs in phylogenomic analyses (Blaimer et al, 2019).…”

“…It is now understood that many arthropod UCE loci occur in protein-coding regions, to a greater degree than UCEs found in vertebrates (Blaimer et al ., 2019, Buenaventura et al . 2020; Hedin et al ., 2019).…”

“…For example, Ultraconserved elements (UCEs) provide orders of magnitude more data at lower costs per-specimen -and data with better phylogenetic signalthan traditional sanger-based datasets (e.g., Blaimer et al, 2015;Gilbert et al, 2015;Zhang et al, 2019), are much cheaper per-specimen than transcriptome-based methods, and are capable of recovering phylogenetic loci from museum specimens (Blaimer et al, 2016;Van Dam et al, 2017). UCEs are useful for recovering both deep (Faircloth et al, 2012;Starrett et al, 2016;Branstetter et al, 2017;Baca et al, 2017;Buenaventura et al 2020) and shallow relationships (Smith et al, 2014;Harvey et al, 2016;Manthey et al, 2016). The recently developed Dipterawide UCE baitset (2.7kv1; Faircloth, 2017) was successfully tested in a group of closely related genera in the Empididae (Rhodén & Wahlberg 2020).…”