Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci collected across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, because few insects have high-quality genome sequences available; assembling new genomes remains a limiting factor; the transcribed portion of the genome is a reasonable, reduced subset of the genome to target; and the data collected from transcribed portions of the genome are similar in composition to the types of data with which biologists have traditionally worked (e.g., exons). However, molecular techniques requiring RNA as a template are limited to using very high quality source materials, which are often unavailable from a large proportion of biologically important insect samples. Recent research suggests that DNA-based target enrichment of conserved genomic elements offers another path to collecting phylogenomic data across insect taxa, provided that conserved elements are present in and can be collected from insect genomes. Here, we identify a large set (n$=$1510) of ultraconserved elements (UCE) shared among the insect order Hymenoptera. We use in silico analyses to show that these loci accurately reconstruct relationships among genome-enabled Hymenoptera, and we design a set of baits for enriching these loci that researchers can use with DNA templates extracted from a variety of sources. We use our UCE bait set to enrich an average of 721 UCE loci from 30 hymenopteran taxa, and we use these UCE loci to reconstruct phylogenetic relationships spanning very old ($\geq$220 MYA) to very young ($\leq$1 MYA) divergences among hymenopteran lineages. In contrast to a recent study addressing hymenopteran phylogeny using transcriptome data, we found ants to be sister to all remaining aculeate lineages with complete support.

💡 Research Summary

This paper presents a novel approach to understanding the genetic relationships among hymenoptera insects using DNA-based target enrichment of ultraconserved elements (UCEs). Traditionally, transcriptome sequencing has been widely used for phylogenetic studies in insects due to the lack of high-quality genome sequences and the complexity of assembling new genomes. However, this method requires very high-quality RNA templates, which are often unavailable from many biologically important insect samples. The authors identified a large set (n=1510) of UCEs shared among hymenoptera insects through in silico analysis, demonstrating that these loci can accurately reconstruct phylogenetic relationships among genome-enabled Hymenoptera species. They designed a bait set to enrich these UCE loci from various DNA templates extracted from different sources. Using their UCE bait set, they enriched an average of 721 UCE loci across 30 hymenopteran taxa and used this data to reconstruct phylogenetic relationships spanning divergences ranging from very old (≥220 million years ago) to very recent (≤1 million years ago). In contrast to a previous study using transcriptome data, which placed ants as sister to all remaining aculeate lineages with complete support. This paper highlights the utility of DNA-based target enrichment methods for overcoming limitations associated with RNA-based approaches in phylogenomic studies across insect taxa.