Comparative Mitochondrial Genomics of 104 Darwin Wasps (Hymenoptera: Ichneumonidae) and Its Implication for Phylogeny

Abstract

Ichneumonidae is one of the largest families of insects with a mega-diversity of specialized morphological and biological characteristics. We newly sequenced 92 mitochondrial genomes of ichneumonid wasps and found that they have a conserved base composition and a lower evolutionary rate than that of other families of parasitic Hymenoptera. There are 38 types of gene order in the ichneumonid mitochondrial genome, with 30 novel types identified in 104 ichneumonids. We also found that the rearrangement events occur more frequently in Ophioniformes than in Ichneumoniformes and Pimpliformes. Furthermore, the higher Ophioniformes and their relative lineages shared the transposition of trnL2 to trnI-trnQ-trnM tRNA cluster. We confirmed five higher-level groupings of Ichneumonidae: Brachycyrtiformes, Ichneumoniformes, Ophioniformes, Pimpliformes and Xoridiformes. Two formerly unplaced subfamilies, Eucerotinae and Microleptinae, were placed in Brachycyrtiformes and Ichneumoniformes, respectively. The results will improve our understanding of the diversity and evolution of Ichneumonidae.

Keywords: divergence; gene rearrangement; ichneumonid wasps; mitochondrial genome; phylogeny.

Figure 1

Base composition of the majority strand and the protein-coding genes (PCGs) of mitochondrial genomes (A–D) and the codon and amino acid usage bias in PCGs (E–G) for Ichneumonidae, Braconidae and other parasitoid Hymenoptera. (A) A + T content of the majority strand. (B) GC skew against AT skew of the majority strand. (C) GC skew against AT skew of PCGs. (D) GC12 against GC3s values of PCGs and the regression lines and equations with R values. (E) The ENc value against GC3s values and the standard curve representing the functional relation between ENc and GC3s under mutation pressure without selection. (C) The RUSC variation on the two principal correspondence analysis axes. The total inertia is 0.073018. The explanation of the variation of Axis1 is 46.69% and Axis2 is 11.01%, and others are lower than 5%. The abnormal species are demonstrated by their position on Axis1. (D) The amino acid usage variation on the two principal correspondence analysis axes. The total inertia is 0.008047. The explanation of the variation of Axis1 is 41.46% and Axis2 is 16.36%, and others are lower than 13%.

Figure 2

The evolution per site for 13 protein-coding genes (PCGs). (A) The base substitutional saturation plots. The transitions (ts, blue) and transversions (tv, orange) against p- distance for both of them. The sites included were three codon positions of PCGs. (B) The average dN-dS is the plot per site of 4225 PCGs.

Figure 3

All types of gene rearrangement in the Ichneumonidae mapping of the consensus tree mainly based on AA matrices. The tRNA genes were colored out and the lines in the bottom of gene blocks indicate the gene coding on the minority strand. The ancestral type of tRNA gene clusters for insect is in the box at the lower right corner. The triangles represent the stable monophyletic groups, of which the triangles filled in gray indicate that the group has more than one type of gene rearrangement. The numbers of species are in the brackets. The genes rearrangement types are near to the corresponding branch, and the branches with R1 (rearrangement type 1) are colored in red. The complete gene orders for each species are in Figure S5 (types: R1–R38).

Figure 4

Phylogenetic relationships of Ichneumonid wasps. The topology is inferred from amino acid sequences of 13 protein-coding genes in mitochondrial genomes (AA matrices) using BI. The numbers close to the nodes separated by “/” represent the ultrafast bootstrap values and Bayesian posterior probabilities in different analysis, respectively. Additionally, “*” represents the full support and “-” represents nonsupport of the corresponding node by that analysis. The order of value for the corresponding analysis is AA by BI/AA by ML/NU by BI/NU by BI. The large “*” alone stands with full supports of all analyses. The triangles on the left confirm some conflicts nodes on the tree through likelihood mapping analysis. The relationship on the top of each triangle is supported by the colored area.

Figure 5

Results from likelihood mapping based on both AA and NU matrices. For analysis of conflict nodes, the conflict nodes in tests are at the top corners of rectangles. The relationship on the top of each triangle is supported by the colored area. (A) Test for the placement of Xoridi-formes, which indicates that Xoridiformes is close to Brachycytiformes by both AA and NU ma-trices. (B) Test for the placement of group (Lycorininae + Cremastinae), which indicates that group (Lycorininae + Cremastinae) is close to group (Anomaloninae + Nesomesochorinae + Campopleginae + Ophioninae) by both AA and NU matrices. (C) Test for the placement of group (Colpotrochia sp. + Triclistus sp.), which indicates that group (Colpotrochia sp. + Triclistus sp.) is close to group (Anomaloninae + Nesomesochorinae + Campopleginae + Ophioninae) by both AA and NU matrices. (D) Test for the placement of Diplazontinae, which indicates that Diplazonti-nae is close to the Pimpliformes excepting for Acaenitinae by both AA and NU matrices.