Data from: Anchored phylogenomics of burrowing mayflies (Ephemeroptera) and the evolution of tusks

Miller, Dustin B., Brigham Young University, Utah Valley University

Bartlett, Stephanie, Utah Valley University

Sartori, Michel, Utah Valley University

Breinholt, Jesse W., RAPiD Genomics; Gainesville FL U.S.A.

Ogden, T. Heath, Utah Valley University

Published Mar 16, 2019 on Dryad. https://doi.org/10.5061/dryad.cj262df

Cite this dataset

Miller, Dustin B. et al. (2019). Data from: Anchored phylogenomics of burrowing mayflies (Ephemeroptera) and the evolution of tusks [Dataset]. Dryad. https://doi.org/10.5061/dryad.cj262df

Abstract

This study investigated the phylogenetic relationships among seven burrowing mayfly families. Genetic data from four ribosomal DNA genes (12S, 16S, 18S, and 28S) generated with sanger sequencing, 448 protein coding loci generated using a novel hybrid enrichment probe set and available RNAseq and genome assembly for 19 ingroup taxa and 4 outgroup taxa. Maximum Likelihood, and Bayesian analyses were carried out to estimate phylogenetic relationships. The results indicated that Potamanthidae, Euthyplociidae, Behningiidae, and Palingeniidae were recovered as monophyletic. Ephemeridae was not monophyletic. Mandibular tusks evolved in the common ancestor of burrowing mayflies and were lost in the lineage leading to Behningiidae.

Usage notes

README

README File containing list of files contained in this dryad package

MAYFLY_ref

Folder containing the reference sequences by each loci used to make the Mayfly_1 probe kit as well as used as a set of references in IBA assembly

Mayfly_1_Probes

Mayfly_1 probe kit

Miller_et_al_Alignments

Folder containing the alignments used for analyses. DN12_rDNA_ML.fas was used in IQ-TREE for the DNA1&2 ML analysis (code used is included at top of file). DN12_rDNA_MrBayes.nex was used in the DNA1&2+rDNA MrBayes analysis (code is at bottom of file). AA_for_ML.phy and rDNA_for_ML.phy were used in IQ-TREE for the AA+rDNA ML analysis (code is contained in the AA_rDNA_ML.nex file). AA_rDNA_Bayes.nex was used in the AA+rDNA MrBayes analysis (code included at the bottom).

Miller_et_al_Loci

Folder contains alignments of each loci used in the study.

Miller_et_al_ST1-ST2

Supplementary tables for Miller_et_al 2017 that include genbank accessions.

Miller_et_al_SF1

Supplementary figures. Bayesian and Maximum Likelihood trees for AA+rDNA and DNA1&2+rDNA datasets.

ML_Bayes_Con

Trees in newick format, in the following order: AA+rDNA Bayesian, AA+rDNA ML, DNA1&2+rDNA Bayesian, DNA1&2+rDNA ML, Constraint.

Funding

National Science Foundation, Award: NSF EAGER 1545281