DOI: 10.5061/dryad.w6m905qxj
title: Genomic analyses of the southern and eastern yellowjacket wasps (Hymenoptera: Vespidae) reveal evolutionary signatures of social life

description: The evolution of sociality in insects represented a remarkable development
 in biological history. Social wasps are particularly noteworthy because
 they display gradations in social behaviors. Here, we sequence the genomes
 of two highly diverged Vespula wasps to gain greater insight into the
 evolution of sociality. Both V. squamosa and V. maculifrons Buysson
 (Hymenoptera: Vespidae) are highly social wasps and live in large colonies
 characterized by distinct caste systems. However, V. squamosa is a
 facultative social parasite, and V. maculifrons is its frequent host. We
 found that the genomes of both species were ~200 Mbp in size, similar to
 the sizes of congeneric species. Analyses of gene expression from members
 of different castes and developmental stages revealed similarities in
 expression patterns among immature life stages. Next, we found evidence of
 DNA methylation within the genome of both species directly from PacBio
 HiFi DNA sequence reads. Patterns of gene expression were correlated with
 DNA methylation levels within genes; genes that were highly and uniformly
 expressed were also relatively highly methylated. Finally, we uncovered
 evidence of differences in patterns of molecular evolution in the two
 taxa, consistent with V. squamosa showing changes in selective constraint
 associated with its facultatively parasitic or polygyne life history.
 Moreover, rates of gene evolution were correlated with variation in gene
 expression between castes and developmental stages, as expected if more
 highly expressed genes were subject to stronger levels of selection.
 Overall, this study expands our understanding of genomic consequences of
 social evolution in insects. Keywords: Social Insects, Genetics, Behavior,
 Population Genetics, Vespidae Entomological Society of America Editorial
 Office: 170 Jennifer Road, Suite 230, Annapolis, MD 21401, USA. Editorial
 Office Phone: 1-301-731-4535.   --
description: <em>Vespula </em><em>squamosa</em> and
 <em>Vespula maculifrons</em> transposable elements and
 methylation coverage files. Transposable element annotation generated from
 EDTA v2.1.0 and methylation analysis conducted in SeqMonk
 v1.48.1.
description: # Genomic analyses of the southern and eastern yellowjacket wasps
 (Hymenoptera: Vespidae) reveal evolutionary signatures of social life
 [https://doi.org/10.5061/dryad.w6m905qxj](https://doi.org/10.5061/dryad.w6m905qxj) ## Description: This repository contains the pipeline used for the study of two *Vespula* species. The pipeline includes scripts and tools for quality control, alignment, assembly, quantification, methylation, and differential expression analysis. Additionally, it provides scripts for genomic feature extraction and various visualizations. The transposable element (TE) files from EDTA (https://github.com/oushujun/EDTA) contain annotations of all TEs (TEanno.gff3.gz), intact TEs only (intact.gff3.gz), a library of reconstructed TEs (TElib.fa.gz), and a summary statistic of the TEs (TEanno.sum.gz). The collinearity files come from running OrthoVenn3 (https://orthovenn3.bioinfotoolkits.net) and contain orthodox comparisons between multiple species. The genome alignment files come from running D-Genies (https://dgenies.toulouse.inra.fr) and contain full genome alignments files and visualizations. The methylation files are the coverage files that can be used to count the pileup of methylated reads in the standard bed file format. Some of the file formats in this dataset include: fasta (https://www.ncbi.nlm.nih.gov/genbank/fastaformat/), newick (https://phylipweb.github.io/phylip/newicktree.html), gff (https://www.ensembl.org/info/website/upload/gff.html?redirect=no), and bed (https://grch37.ensembl.org/info/website/upload/bed.html) file formats. Files may be tar gzipped in some cases. ## Repository Structures: Please see "All_paths_and_files_list.txt" for a complete list of files. A quick summary of the files can be found below. ./Data ├── TE_files │ ├── V.maculifrons.fasta.mod.EDTA.TEanno.gff3.gz │ ├── V.maculifrons.fasta.mod.EDTA.TEanno.sum.gz │ ├── V.maculifrons.fasta.mod.EDTA.TElib.fa.gz │ ├── V.maculifrons.fasta.mod.EDTA.intact.gff3.gz │ ├── V.squamosa.fasta.mod.EDTA.TEanno.gff3.gz │ ├── V.squamosa.fasta.mod.EDTA.TEanno.sum.gz │ ├── V.squamosa.fasta.mod.EDTA.TElib.fa.gz │ ├── V.squamosa.fasta.mod.EDTA.intact.gff3.gz │ └── ... ├── collinearity │ ├── Alignments_collinearity.txt │ ├── Multiple_sequence_alignment.fasta.gz │ ├── Orthogroups.txt.gz │ ├── Result_all_species_collinearity.txt │ ├── Species_divergence_time_tree.nwk.gz │ ├── Species_phylogenetic_tree.nwk.gz │ ├── cafe5.tar.gz │ ├── collinear.png │ ├── gene_families.txt.gz │ ├── orthologous.html │ ├── single_copy.tar.gz │ └── ... ├── genome_alignment_files │ ├── 46818775_map_V.germanica_to_V.maculifrons.paf │ ├── 46818778_map_V.vulgaris_to_V.maculifrons.paf │ ├── ... │ └── V.vulgaris_V.maculifrons_wpR0Z_20221122233916.html ├── methylation_files │ ├── Vespula_maculifrons_methylation_coverage.bed.gz │ └── Vespula_squamosa_methylation_coverage.bed.gz ./Software ├── 1_globus │ ├── 1_globus_maculifrons_download.slurm │ └── 1_globus_squamosa_download.slurm ├── 1_illumina │ └── 1_illumina_download.slurm ├── 2_SMRT │ ├── 2_pbmarkdup_v.maculifrons.slurm │ └── 2_pbmarkdup_v.squamosa.slurm ├── ... ├── 45_InterProScan │ ├── 45_InterProScan.slurm │ └── 45_InterProScan_2.slurm ├── 46_counts │ ├── 46_counts.slurm │ ├── TE_fa_list.txt │ └── prot_fa_list.txt └── 49_seqtk │ └── 49_seqtk.slurm