Phylogenomics resolves the higher-level phylogeny of herbivorous eriophyoid mites (Acariformes: Eriophyoidea)

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 E..., See our manuscript titled \"Phylogenomics resolves the higher-level phylogeny of herbivorous eriophyoid mites (Acariformes: Eriophyoidea)\", , # 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 Prot...

瘿螨总科（Eriophyoidea）的螨类是蜱螨亚纲（Acari）中最大的类群之一，然而由于可获取的形态学特征数量有限，且部分特征被认为存在趋同演化（homoplasy），其高级阶元系统发育关系至今仍未阐明。不过，迄今已测序的瘿螨类群其线粒体（mt）基因排列顺序呈现高度变异，这一特性或可用于阐明其高级阶元的系统发育关系。本研究对153种瘿螨的完整线粒体基因组进行了测序与比较分析，结果显示相较于节肢动物假想祖先的线粒体基因排列，这些螨类共存在54种线粒体基因重排模式。共有衍生的线粒体基因簇支持了瘿螨总科整体为单系群，以及瘿螨总科内6个演化支的单系性。这些单系类群及其亲缘关系，在基于线粒体基因组序列构建的系统发育树中也得到了广泛支持。本研究的分子定年结果显示……详见题为《系统基因组学解析植食性瘿螨的高级阶元系统发育（蜱螨形目：瘿螨总科）》的稿件，# 《系统基因组学解析植食性瘿螨的高级阶元系统发育（蜱螨形目：瘿螨总科）》

本数据包随附上述研究论文，该稿件已提交至《BMC Biology》期刊。

## 数据与文件结构说明
本数据集包含三个部分：
1. 比对文件文件夹：该文件夹包含3个FASTA格式的比对文件，分别为：(1) 氨基酸序列比对文件（共2268个氨基酸残基）；(2) 剔除蛋白编码基因（PCGs）第三密码子位点的核苷酸序列比对文件（共7153个核苷酸位点）；(3) 完整核苷酸序列比对文件（共10071个核苷酸位点）。另有1个ZIP格式文件，为未移除大片段空位的原始比对文件。本数据包同时提供了核苷酸序列与氨基酸序列的原始比对文件（共28个FASTA文件），这些文件以基因名称命名。
2. 系统树文件文件夹：包含22个用于补充分析的系统发育树文件。
3. 补充材料文件夹：包含6张补充表格与22幅补充插图。

### 缩写说明
Mt：线粒体（Mitochondrial）
PCGs：蛋白编码基因（Protein-coding genes）