Phylogenomics resolves the higher-level phylogeny of herbivorous eriophyoid mites (Acariformes: Eriophyoidea)
Cite this dataset
Zhang, Qi et al. (2024). Phylogenomics resolves the higher-level phylogeny of herbivorous eriophyoid mites (Acariformes: Eriophyoidea) [Dataset]. Dryad. https://doi.org/10.5061/dryad.612jm647k
Abstract
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.
README: Phylogenomics resolves the higher-level phylogeny of herbivorous eriophyoid mites (Acariformes: Eriophyoidea)
https://doi.org/10.5061/dryad.612jm647k
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
Methods
See our manuscript titled "Phylogenomics resolves the higher-level phylogeny of herbivorous eriophyoid mites (Acariformes: Eriophyoidea)"
Funding
National Natural Science Foundation of China, Award: 31970437
National Natural Science Foundation of China, Award: 32161143014
National Natural Science Foundation of China, Award: 31672337