Data from: Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera
Faircloth, Brant C., Louisiana State University, University of California System
Branstetter, Michael G., Smithsonian Institution
White, Noor D., University of Maryland, College Park, Smithsonian Institution
Brady, Séan G., Smithsonian Institution
Published Sep 19, 2014 on Dryad.
Cite this dataset
Faircloth, Brant C.; Branstetter, Michael G.; White, Noor D.; Brady, Séan G. (2014). Data from: Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera [Dataset]. Dryad. https://doi.org/10.5061/dryad.46195
Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci 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, including transcriptome sequencing, 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 (UCEs) shared among the insect order Hymenoptera. We used in silico analyses to show that these loci accurately reconstruct relationships among genome-enabled hymenoptera, and we designed a set of RNA baits (n = 2749) for enriching these loci that researchers can use with DNA templates extracted from a variety of sources. We used our UCE bait set to enrich an average of 721 UCE loci from 30 hymenopteran taxa, and we used these UCE loci to reconstruct phylogenetic relationships spanning very old (≥220 Ma) to very young (≤1 Ma) 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, although this result could be explained by factors such as taxon sampling. We discuss this approach and our results in the context of elucidating the evolutionary history of one of the most diverse and speciose animal orders.
FASTA file containing target enrichment bait sequences for UCE loci in hymenoptera.
NOTES describing the pipeline steps used to analyze the in silico data.
UCE contigs sliced from available hymenopteran genomes.
LASTZ files showing mapping of UCE probes onto in silico genome slices AND probe.matches.sqlite database.
Archive file containing nested directories of in-silico alignment and analysis data. See overall README or file-specific README.
Top level file defining taxon sets used in analyses (e.g. ABYSS and TRINITY, with and without sawflies.
NOTES describing the pipeline steps used to analyze the ABYSS data.
UCE contigs enriched from hymenopteran taxa and assembled using ABySS.
LASTZ files showing mapping of UCE probes onto in ABySS contigs AND probe.matches.sqlite database.
Log files from ABySS probe alignment.
Archive file containing nested directories of ABySS alignment and analysis data. See overall README or file-specific README.
NOTES describing the pipeline steps used to analyze the TRINITY data.
UCE contigs enriched from hymenopteran taxa and assembled using TRINITY.
LASTZ files showing mapping of UCE probes onto TRINITY contigs AND probe.matches.sqlite database.
Log files from TRINITY probe alignment.
Archive file containing nested directories of TRINITY alignment and analysis data. See overall README or file-specific README.
In silico tree with tips renamed to full species binomial.
ABySS (with sawfly taxa) tree with tips renamed to full species binomial.