The phylogeny of insects in the data‐driven era

Abstract

Maturation of omics and DNA barcode programs along with advances in sequence analysis tools and phyloinformatics protocols are enabling the realization of comprehensive and robust phylogenies of even the most diverse lineages. Several lineages in insects have undergone hyper‐radiations, and thus a unified picture of their evolution is ultimately required for understanding the process of diversification. In this study I further develop informatics protocols for de novo phylogenetic construction, and present the most species‐comprehensive insect phylogeny to date, constructed hierarchically using c. 440 transcriptomes, 1490 mitogenomes, DNA barcodes for 69 000 species, and several additional species‐rich markers. Even with this expanded transcriptome backbone, support is still insufficient for some historically problematic nodes, particularly in Polyneoptera and Paraneoptera. Low support (measured by internode certainty) was observed for the node separating Dictyoptera from its sister polyneopeterans; configuration of the Paraneoptera was not resolved; the recently proposed Hymenoptera grouping Eusymphyta received high support, while Parasitoida did not; and Orthorrhapha (Diptera) was not recovered. Sampling is uneven across the insects, and while highly sequenced lineages (e.g. Lepidoptera) boast greater information content, this accompanies computational burdens. The protocol and resulting tree represent an advance in the analytic and phylogenetic framework, for an objectively and consistently determined species‐comprehensive phylogeny.

Molecular Phylogeny and Infraordinal Classification of Zoraptera (Insecta)

“…The systematic placement of this group has always been controversial (see "the Zoraptera problem" introduced by Beutel and Weide [6]), and different insect lineages, such as Psocoptera, Isoptera, and Embioptera, have been proposed as the closest relatives of Zoraptera (see Mashimo et al [1] for a review). Recent phylogenomic analyses suggest that Zoraptera is a sister group of Dermaptera [3,[7][8][9], which had previously been proposed by Terry and Whiting [10].…”

Functional and phylogenetic relationships link predators to plant diversity via trophic and non-trophic pathways

“…For spider species identification, we combined morphological identification and molecular species delimitation. We further constructed a phylogenetic tree of spiders sampled following the method described by Chesters [34]. We used a set of functional traits related to spider survival and physical activity.…”

Phylogenetic relatedness, functional traits, and spatial scale determine herbivore co‐occurrence in a subtropical forest

“…To select the most internally consistent method for further analysis, we used the clues package (Wang et al 2007) in R to calculate the Hubert and Arabie-adjusted Rand index, a measure of clustering congruence (Hubert & Arabie 1985). We constructed a phylogeny of the Lepidoptera barcodes following Wang et al (2020) and Chesters (2020), in which we used two approaches to improve phylogenetic structure and provide more accurate diversity indicators (Macı ´as-Hernández et al 2020); the incorporation of a reference framework and a high-quality backbone topology. Reference DNA barcodes were mined and processed as described in Wang et al (2020).…”

“…The phylogeny was then constructed in two steps, with constrained phylogenetic inference followed by phylogenetic placement of the MOTU plot. Constraints were inferred through analysis of taxonomic overlap of the reference barcodes with three previously published backbone trees, using the method described in Chesters (2020). The backbone trees selected were of the ditrysian group (Heikkilä et al 2015), Lepidoptera (Kawahara et al 2019) and Noctuoidea (Regier et al 2017).…”