The unresolved phylogenomic tree of butterflies and moths (Lepidoptera): Assessing the potential causes and consequences

Abstract

The field of molecular phylogenetics is being revolutionized with next‐generation sequencing technologies making it possible to sequence large numbers of genomes for non‐model organisms ushering us into the era of phylogenomics. The current challenge is no longer how to get enough data, but rather how to analyse the data and how to assess the support for the inferred phylogeny. Here, we focus on one of the largest animal groups on the planet – butterflies and moths (order Lepidoptera), whose phylogeny remains unresolved despite several recent phylogenomic studies. In this study, we assess the potential causes and consequences of the conflicting phylogenetic hypotheses. With a dataset consisting of 331 protein‐coding genes and the alignment length over 290,000 base pairs, including 200 taxa representing 83% of lepidopteran superfamilies, we compare phylogenetic hypotheses inferred from amino acid and nucleotide alignments. The resulting two phylogenies are discordant, especially with respect to the placement of the superfamily Gelechioidea, which is likely due to compositional bias and possible other model violations. Furthermore, we employed a series of analyses to dissect our dataset and demonstrate that there is sufficient phylogenetic signal to resolve much – but not all – of the lepidopteran tree of life. The relationships among superfamilies within Ditrysia, the most species rich lepidopteran clade containing 98% of the extant species, remain poorly resolved. We conclude that taxon sampling remains an issue even in phylogenomic analyses and recommend that poorly sampled highly diverse groups, such as Gelechioidea in Lepidoptera, should receive extra attention in the future.

Insights into the species evolution of Calanus copepods in the northern seas revealed by de novo transcriptome sequencing

“…Gene concordance factor (gCF) is defined as the percentage of decisive gene trees supporting a branch, while sCF is the percentage of decisive alignment sites supporting a branch in a reference tree (Minh et al, 2020). These concepts are important for phylogenomics datasets because genes that are from different chromosomes or from distant regions of the genome tend to show different levels of resolution or phylogenetic signals (see Minh et al, 2020;Rota et al, 2021). The results of our con- between lineages are common and have also been observed in several studies using gene orthologs derived from transcriptomes (i.e., in frogs, Chan et al, 2020;in spiders, Kallal et al, 2020;in butterflies Rota et al, 2021;in ants van Elst et al, 2021).…”

Hiding in Plain Sight: Phylogenomics Reveals a New Branch on the Noctuoidea Tree of Life

“…This conundrum then requires different optimization of this trait since our data would suggest that the "notodontid orientation" could have evolved first in either the MRCA of Noctuoidea (if Scranciidae are sister to the remainder of the superfamily), or in the MRCA of Scranciidae + other clades (if Oenosandridae are sister to other noctuoids). Further highlighting the plasticity of this trait (and that of trifid venation), we note that Doidae were removed from Noctuoidea to the distantly related Drepanoidea, despite sharing the ventral-facing tympanal position of Scranciidae and Notodontidae, as well as trifid wing venation (Miller 1991;Rota et al 2022). We include Doidae in our phylogenetic analyses (as an outgroup) as well as in Table S2 to stress the apparently homoplastic nature of these characters that have long been considered stable in Noctuoidea classification (e.g., Kitching and Rawlins 1998).…”

“…The purpose of these analyses was to identify whether the statistical support for topology A was higher than for any competing constrained topology. Datasets 60_percent_recovery_NA Our analyses with DiscoVista served three purposes: (1) to visualize discordance across analyses, (2) to further evaluate quantitative evidence for locus-level discordance, and (3) to illustrate the distribution of GC content across taxa since high GC content has shown to lead to topological discordance in Lepidoptera phylogenetics (Rota et al 2022). For the first point, in ML and parsimony analyses, high bootstrap values are obtained for the monophyly of Oenosandridae, quadrifids, Scranciidae, and Notodontidae, although bootstrap support for Notodontidae is weaker when datasets are reduced (90_percent_recovery_AA and Oeno_limited_AA), at which point support also breaks down considerably with respect to the various possible placements of Scranciidae and Oenosandridae across Noctuoidea.…”

Phylogenomics of the family Lachesillidae (Insecta: Psocodea: Psocomorpha)

“…However, conflict among nucleotides or amino acids topologies is relatively common in phylogenomics, affecting Lepidoptera, Hymenoptera, Coleoptera, Hemiptera, amount others groups (see Rota et al, 2022, for a summary of insect phylogenomics with topologies conflict).…”

“…Here, the topological conflict observed between nucleotide vs amino acid analysis could be caused by a model misspecification, which has been proposed as source of inaccurate phylogeny estimation and potentially resulting in conflicting topologies hypothesis under nucleotide vs amino acid (Gillung et al, 2018). However, conflict among nucleotides or amino acids topologies is relatively common in phylogenomics, affecting Lepidoptera, Hymenoptera, Coleoptera, Hemiptera, amount others groups (see Rota et al, 2022, for a summary of insect phylogenomics with topologies conflict).…”