Phylogeny of Rhus gall aphids (Hemiptera: Aphididae) reveals an earlier origin than their primary host plant

Rhus gall aphids (Hemiptera: Aphididae: Eriosomatinae: Fordini) only use Rhus species (Anacardiaceae) as their primary host plants, and each aphid specifically lives on only one or two sister host plants with the same disjunct distribution pattern between Eastern Asia and Eastern North America. We assembled complete mitochondrial genomes and universal single-copy nuclear genes for Rhus gall aphids using a genome skimming method, and the phylogenetic relationships strongly supported the monophyly of the Rhus gall aphids and two genera, Floraphis and Melaphis. However, the relationships among genera are inconsistent across different datasets. The cpDNA analysis on the host plant Rhus species strongly supported the Rhus monophyly and relationship of the Rhus interspecies. Cophylogeny analysis indicated that the origin of Rhus gall aphids was earlier than that of their host plants. However, the divergence time and relatio..., We collected 45 samples representing 14 Rhus gall aphid species and three subspecies and some closely related aphids. We extracted genomic DNA using three to five individuals from each gall sample with the TIANamp Genomic DNA Kit (TIANGEN) following the manufacturer’s instructions. We sent the genomic DNAs of all the samples to the Genomic Sequencing and Analysis Co. (Shanghai, China) for library construction and sequencing using the shotgun genome skimming method on an Illumina HiSeq 4000 platform. Paired-end reads of 2×150 bp were generated with an insert size of 400 bp. After filtering out low-quality and adapter-contaminated reads with Trimmomatic v. 0.35 , high-quality clean reads were used to do de novo  assemblies using the program SPAdes v.3.10.1  with the kmers 21, 33, 55, 77, 99 and 127. We used the mapping method in the software Geneious 10.2.4 to obtain the complete mitochondrial genome from contigs (Kearse et al. 2012). We obtained the complete..., , # **Phylogeny of *Rhus* gall aphids (Hemiptera: Aphididae) reveals an earlier origin than their primary host plants**

[https://doi.org/10.5061/dryad.sxksn03c2](https://doi.org/10.5061/dryad.sxksn03c2)

## Description of the data and file structure

The dataset includes the original alignments, tree files, and divergence time estimation results based on the aphid mitochondrial genome, single-copy nuclear genes, and host plant chloroplast genome for phylogenetic analysis.

Here are the list of the files and respective details.

a) **Plant_BItree** in TRE format, the original tree file from Bayesian Inference (BI) analysis using MrBayes v3.2.7 for 69 chloroplast protein-coding genes of 17 species of *Rhus* and its closely related species.

b) **Plant_dating** in TRE format, the original file for divergence time estimation using the mcmctree program in PAML for 69 chloroplast protein-coding genes of 17 species of *Rhus* and its closely related species.

c) **Plant_MLtree** in TREEFILE form...,