DOI: 10.5061/dryad.sxksn03c2
title: Phylogeny of Rhus gall aphids (Hemiptera: Aphididae) reveals an earlier origin than their primary host plant

description: 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
 relationships among some Rhus gall aphid species, particularly
 those with later divergence times, were consistent
 with the origin of their corresponding primary host
 plants. This may suggest that the Rhus gall aphids established
 the initial association with the ancestors between
 Rhus and the related groups, or acquired current
 Rhus hosts through host switching. The divergence time
 estimations imply that the separation of North America and
 Eurasia in the Laurasia supercontinent and the disappearance of the Bering
 Land Bridge, respectively, have played an important role in the divergence
 of the eastern North American Melaphis and an East Asian
 lineage. Our current results provide new insights into the
 coevolution of insects and host plants.
description: We collected 45 samples representing 14 <em>Rhus</em>
 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 <em>de novo</em>  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 mitogenome sequence by aligning, comparing and
 manually checking to the available consensus sequences. We captured
 single-copy nuclear genes directly from contigs, which was assembled by
 SPAdes v.3.10.1, and using OrthoDB database of Hemiptera with default
 parameters. Then we used MAFFT for alignment and obtained the alignment
 results.
description: # **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 format, the original tree file from Maximum Likelihood (ML) analysis using RAxML 8.2.12 for 69 chloroplast protein-coding genes of 17 species of *Rhus* and its closely related species. d) **SCN_genetree_dating** in TRE format, the original file for divergence time estimation using the mcmctree program in PAML after constructing a tree with SCN_alignment using RAxML 8.2.12. e) **SCN_MLtree** in CONTREE format, the original tree file constructed using SCN_alignment with RAxML 8.2.12. f) **Plant_alignment** in NEX format, containing a concatenated alignment of 69 chloroplast protein-coding genes for 17 species of *Rhus* and its closely related species, with detailed parameters from the MrBayes v3.2.7 run at the end of the file. g) **SCN_speciestree** in TRE format, the original file for the species tree constructed from amino acids of single-copy nuclear genes for 44 aphids using ASTRAL-III software. h) **SCN_speciestree_dating** in TRE format, the original file for divergence time estimation using the SCN_speciestree.TRE file with the mcmctree program in PAML. i) **SCN_alignment** in NEX format, containing a concatenated alignment of amino acids for single-copy nuclear genes from 44 aphids. j) **mtDNA_alignment** in NEX format, containing a concatenated alignment of mitochondrial 13 protein-coding genes + 2 rRNA genes for 44 species of *Rhus* gall aphids and outgroups, with detailed parameters from the MrBayes v3.2.7 run at the end of the file. k) **mtDNA_BItree** in TRE format, the original tree file from BI using MrBayes v3.2.7 for mitochondrial 13 protein-coding genes + 2 rRNA genes of 44 species of *Rhus* gall aphids and outgroup species. l) **mtDNA_MLtree** in TRE format, the original tree file from ML analysis using RAxML 8.2.12 for mitochondrial 13 protein-coding genes + 2 rRNA genes of 44 species of *Rhus* gall aphids and outgroup species.