Phylogenomics and the evolution of hemipteroid insects

Abstract

Hemipteroid insects (Paraneoptera), with over 10% of all known insect diversity, are a major component of terrestrial and aquatic ecosystems. Previous phylogenetic analyses have not consistently resolved the relationships among major hemipteroid lineages. We provide maximum likelihood-based phylogenomic analyses of a taxonomically comprehensive dataset comprising sequences of 2,395 single-copy, protein-coding genes for 193 samples of hemipteroid insects and outgroups. These analyses yield a well-supported phylogeny for hemipteroid insects. Monophyly of each of the three hemipteroid orders (Psocodea, Thysanoptera, and Hemiptera) is strongly supported, as are most relationships among suborders and families. Thysanoptera (thrips) is strongly supported as sister to Hemiptera. However, as in a recent large-scale analysis sampling all insect orders, trees from our data matrices support Psocodea (bark lice and parasitic lice) as the sister group to the holometabolous insects (those with complete metamorphosis). In contrast, four-cluster likelihood mapping of these data does not support this result. A molecular dating analysis using 23 fossil calibration points suggests hemipteroid insects began diversifying before the Carboniferous, over 365 million years ago. We also explore implications for understanding the timing of diversification, the evolution of morphological traits, and the evolution of mitochondrial genome organization. These results provide a phylogenetic framework for future studies of the group.

Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome

“…To investigate how aphid chromosome rearrangements compare to those of other hemipterans, we took advantage of two recently released chromosome-scale assemblies of the blood-feeding species Rhodnius prolixus (obtained from the DNA Zoo; Dudchenko et al 2017) and Triatoma rubrofasciata (Liu et al 2019). Both species belong to the hemipteran family Reduviidae and diverged from the aphid lineage approximately 386 million years ago (Figure 3a), representing a basal split in extant Hemiptera (Johnson et al 2018). Unlike aphids, most Reduviidae have an XY chromosomal sex determination system (male = XY, female = XX) which is thought to be the ancestral state of Hemiptera (Blackmon et al 2017) and reproduce exclusively through sexual reproduction.…”

“…We used OrthoFinder v2.2.3 Kelly 2015, 2019) with Diamond v0.9.14 (Buchfink et al 2014), MAFFT v7.305 (Katoh and Standley 2013) and FastTree v2.1.7 (Price et al 2009(Price et al , 2010 to cluster proteins into orthogroups, reconstruct gene trees and estimate the species tree. The OrthoFinder species tree was rooted according to Johnson et al (2018). To estimate approximate divergence times for our taxa of interest, we used penalised likelihood implemented in r8s with secondary calibration points derived from Johnson et al (2018) ( Supplementary Table 8).…”

How to make a haploid male

“…(B) Cladogram of all haplodiploid (arrhenotokous) clades and their diploid sistergroups. Tree topology based on Misof et al (), Blackmon et al (), Johnson et al () and the Tree of Life ( http://tolweb.org/tree/). Pie charts show the frequencies of different SD systems for each clade (see Table ), with X0 in pink, XY in red and haplodiploidy in blue.…”

Cave insects with sex‐reversed genitalia had their most recent common ancestor in West Gondwana (Psocodea: Prionoglarididae: Speleketorinae)

“…First, we estimated the substitution rate prior using 328 Ma for the deepest divergence date of Psocodea (Trogiomorpha and Troctomorpha + Psocomorpha) according to Johnson et al . () (Fig. , (A)).…”

“…For the dating analysis, we used a Bayesian method implemented in the software MCMCtree of the PAML 4.8 software package (Yang 2007). First, we estimated the substitution rate prior using 328 Ma for the deepest divergence date of Psocodea (Trogiomorpha and Troctomorpha + Psocomorpha) according to Johnson et al (2018) (Fig. 1, (A)).…”