Summary of Insect Phylogenomics and Evolution

## Introduction Insect phylogeny reconstructs the evolutionary relationships among extant groups (orders) and their ancient ancestors, allowing us to estimate when key characteristics emerged, such as flight, specialized mouthparts, and metamorphosis. This material summarizes recent phylogenomic findings based on analyses of thousands of genes and multiple fossils, and explains how divergence times are determined and their evolutionary implications. ## Key Concepts Broken Down ### Phylogeny and Phylogenomics > Phylogeny is the reconstruction of evolutionary relationships among organisms; phylogenomics uses massive genomic/transcriptomic datasets to infer these relationships. - Data sources: single-copy genes, transcriptomes, and genomes. - Common challenges: missing data, paralogy, incorrect alignments, and violations of evolutionary models. - Solutions: selection of reliable loci, filtering of conflicting data, and partitioning by domains/proteins. ### Divergence Timing > Divergence time estimates combine phylogenetic trees with fossil calibrations to calculate the age of nodes (lineage origins). - Utilizing multiple validated fossils (e.g., 37 calibrations) and tree sampling to obtain confidence intervals. - Example age notation: origin of Hexapoda ~479 Ma with a confidence interval of $509$ to $452$ Ma. ### Essential Terminology > Hexapoda: The clade that includes insects and ancestral groups such as Collembola, Protura, and Diplura. > Pterygota: Winged insects (extant or ancestral). > Neoptera and Palaeoptera: Major groupings of winged insects; Palaeoptera includes Ephemeroptera and Odonata. ## Key Phylogenetic Findings ### Origin and Early Diversification - The origin of insects (Hexapoda) is estimated to be in the Early Ordovician, approximately $479\,$Ma (CI $509$ to $452\,$Ma). - Ectognathous insects underwent radiation in the Early Silurian: ~ $441\,$Ma (CI $465$ to $421\,$Ma). - Implication: Insect terrestrial colonization occurred almost simultaneously with the expansion of land plants. ### Notable Internal Relationships - Insect monophyly is confirmed, with **Collembola** and **Protura** as close relatives within Hexapoda. - **Diplura** appears as a close relative to groups such as bristletails (Archaeognatha), silverfish (Zygentoma), and Pterygota. - **Remipedia** (cave-dwelling crustaceans) is the closest extant relative to insects. ### Silverfish and Tricholepidion - Silverfish (Zygentoma) are found to be monophyletic in recent analyses. - Tricholepidion diverged from other silverfish in the Late Triassic (~214 Ma) in some analyses; this implies parallel morphological losses among lineages. ### Origin of Flight and Palaeoptera - Fossils with wings are present from the Late Mississippian (~324 Ma), suggesting a pre-Carboniferous origin of flight. - Findings such as †Rhyniognatha (~412 Ma) might indicate an even older origin for the winged lineage. - The relationship between Ephemeroptera and Odonata (Palaeoptera) shows moderate support; key nodes require additional sampling. ### Polyneoptera and Other Clades - Strong monophyly of **Polyneoptera** (a group that includes Orthoptera, Blattodea, Mantodea, etc.). - The estimated origin of polyneopterans is ~ $302\,$Ma (Pennsylvanian; CI $377$ to $231\,$Ma). ### Hemiptera, Thysanoptera, and Acercaria - Hemiptera and Thysanoptera (with piercing-sucking mouthparts) originated ~ $373\,$Ma (CI $401$ to $346\,$Ma), which allows for consideration of a possible hemipteroid explanation for Late Devonian fossil stylet marks. - Acercaria (a traditional grouping that includes Psocoptera, Phthiraptera, and Hemiptera) has debated phylogenetic support; recent phylogenomic results place **Psocodea** (bark lice and true lice) as potential closest relatives of Holometabola in some analyses, but this is not conclusive. ### Radiations of Holometabola - Holometabolous clades (beetles, flies, wasps/bees/ants, butterflies/moths, etc.) show the origin of archaic lineages in the