DOI: 10.5061/dryad.612jm647k
title: Phylogenomics resolves the higher-level phylogeny of herbivorous eriophyoid mites (Acariformes: Eriophyoidea)

description: Eriophyoid mites (Eriophyoidea) are among the largest groups in the Acari;
 their higher-level phylogeny, however, remains unresolved due to the
 availability of limited number of morphological characters, some of which
 are suspected as homoplasy. Nevertheless, the eriophyoid mites sequenced
 to date showed highly variable mitochondrial (mt) gene orders, which could
 potentially be useful for resolving the higher-level phylogenetic
 relationships. Here, we sequenced and compared the complete mt genomes of
 153 eriophyoid mite species, which showed 54 patterns of rearranged mt
 gene orders relative to that of the hypothetical ancestor of arthropods.
 The shared derived mt gene clusters support the monophyly of eriophyoid
 mites (Eriophyoidea) as a whole and the monophylies of six clades within
 the Eriophyoidea. These monophyletic groups and their relationships were
 largely supported in the phylogenetic trees inferred from mt genome
 sequences as well. Our molecular dating results showed that the
 Eriophyoidea originated in the Triassic and diversified in the Cretaceous,
 coinciding with the diversification of angiosperms. This study
 demonstrates the use of derived mt gene clusters in unveiling the
 higher-level phylogeny of eriophyoid mites, and underlines the origin of
 these mites and their co-diversification with angiosperms.
description: See our manuscript titled "Phylogenomics resolves the
 higher-level phylogeny of herbivorous eriophyoid mites (Acariformes:
 Eriophyoidea)"
description: # Phylogenomics resolves the higher-level phylogeny of herbivorous
 eriophyoid mites (Acariformes: Eriophyoidea)
 This data package
 accompanies the above publication. This manuscript has been submitted to
 BMC Biology. ## Description of the data and file structure This dataset
 includes three parts. 1\. Alignment file folder: This folder includes
 three files in fasta format which are the alignment for (1) Amino acid
 alignment (2268AA), (2) Nucleotide sequence alignment without the third
 codon positions of PCGs (7153Nu), and (3) Nucleotide sequence alignment
 (10071Nu). One file in zip format is the original alignment without
 removing large gaps. We provided the original alignment for nucleotide
 sequences and amino acid sequences (28 fasta files). These alignments are
 named by genes. 2\. Tree file folder: Includes 22 tree files for
 supplement trees. 3\. Supplementary folder: Includes six supplementary
 tables and 22 figures. Abbreviations Mt Mitochondrial PCGs Protein coding
 genes rRNAs Ribosomal RNA genes tRNAs Transfer RNA genes rrnS 12S
 ribosomal RNA rrnL 16S ribosomal RNA nad2 NADH dehydrogenase subunits 2
 nad4 NADH dehydrogenase subunits 4 nad4L NADH dehydrogenase subunits 4L
 nad5 NADH dehydrogenase subunits 5 nad6 NADH dehydrogenase subunits 6 cox1
 cytochrome oxidase subunits 1 cob cytochrome b ML Maximum likelihood
 methods BI Bayesian methods BPP Bayesian posterior probabilities BSP
 Maximum likelihood bootstrap proportion HPD Highest posterior density Ka
 Number of nonsynonymous substitutions per nonsynonymous site Ks Number of
 synonymous substitutions per synonymous site Bp Breakpoints K/Pg The
 Cretaceous–Paleogene extinction event