Hexapoda — insects together with the primitively wingless Collembola (springtails), Protura, and Diplura — is nested within Pancrustacea, the clade that unites hexapods with crustaceans. Which crustacean lineage is the closest living relative of hexapods nevertheless remains unresolved after more than a decade of phylogenomic analysis. Candidate answers include Remipedia (cave-dwelling blind crustaceans), Branchiopoda (fairy shrimps, water fleas, and tadpole shrimps), Remipedia + Cephalocarida (the "Xenocarida" pairing), and configurations involving Copepoda, all within the contentious clade Allotriocarida. Recent large-scale studies disagree sharply: the results flip among these hypotheses under small changes in taxon sampling, substitution model, or statistical summary method, and the field's most recent analyses explicitly describe deep pancrustacean relationships, including the hexapod sister group, as recalcitrant. The open problem is to determine, with robustness to taxon sampling, analytical model, and data type, the sister group of Hexapoda within Pancrustacea — and thereby to establish from which crustacean lineage insects descended.

Background

Hexapoda comprises insects and three primitively wingless hexapod groups (Collembola or springtails, Protura, and Diplura); all share a six-legged thorax. Since the 1990s, molecular evidence has shown that Hexapoda is not an independent phylum but is nested within Crustacea, the two together forming Pancrustacea (also called Tetraconata) — a result summarized in the aphorism that "hexapods are terrestrial crustaceans" (Regier, Shultz and Kambic, 2005). This nesting immediately raises the question of which crustacean lineage is the sister group of Hexapoda, i.e., which group is the insect ancestors' nearest living kin.

Several small, morphologically enigmatic crustacean lineages are the principal candidates. Remipedia are blind, many-segmented, cave-anchialine-pool crustaceans first described in 1981. Cephalocarida are tiny, elongate marine interstitial crustaceans. Branchiopoda are mostly freshwater crustaceans (fairy shrimps, clam shrimps, water fleas, tadpole shrimps). Copepoda are abundant aquatic crustaceans (e.g., planktonic copepods). Combinations of these taxa define named hypotheses: "Xenocarida" (Remipedia + Cephalocarida) as sister to Hexapoda (Regier et al., 2010); Remipedia alone as sister (von Reumont et al., 2012; Oakley et al., 2013); and "Allotriocarida", the clade comprising Hexapoda, Remipedia, Cephalocarida, Branchiopoda — in some analyses also Copepoda — whose internal branching is the current locus of disagreement (Schwentner et al., 2017; Lozano-Fernandez et al., 2019; Bernot et al., 2023). Within Allotriocarida, a Remipedia + Hexapoda clade has been named Labiocarida.

The problem has proven hard for reasons characteristic of deep phylogenetics. First, the relevant divergences occurred during rapid ancient (Cambrian-to-Ordovician, roughly 450–550 million years ago) radiations, leaving short internal branches with weak signal and substantial incomplete lineage sorting (ILS) — the persistence of ancestral polymorphisms across successive speciation events, which makes individual gene trees disagree with the species tree. Second, long-branch attraction (LBA) — the artifactual grouping of independently fast-evolving lineages — and compositional heterogeneity in sequence data bias standard analyses; diagnostic remedies include site-heterogeneous substitution models (such as CAT-GTR, which lets amino-acid preferences vary across alignment sites), Dayhoff6 recoding (collapsing amino acids into six physicochemical groups to dampen saturation and composition bias), and removal of fast-evolving taxa. Third, results depend on how data are assembled and summarized: orthology assignment, matrix reduction, taxon sampling, and the choice between concatenation (all genes analyzed as one supermatrix) and coalescent species-tree methods (which model gene-tree discordance, e.g., ASTRAL) have all been shown to change the answer (von Reumont et al., 2012; Bernot et al., 2023). Older mitochondrial-genome analyses added a further axis of conflict, at one point even suggesting that Hexapoda as classically defined is paraphyletic (Nardi et al., 2003). Nearly half of all crustacean orders still lack genomic-scale sampling, and the rare, cave-restricted, or tiny-bodied key taxa (remipedes, cephalocarids, and certain copepods) are difficult to collect and sequence (Bernot et al., 2023).

Problem Statement

Determine the sister group of Hexapoda within Pancrustacea: establish, with robustness to taxon sampling, analytical model, and data type, which crustacean lineage — Remipedia, Branchiopoda, Remipedia + Cephalocarida (Xenocarida), or a configuration including Copepoda — shares the most recent common ancestor with hexapods. The required deliverable is the identity of this hexapod sister group; resolving the remaining interrelationships of Allotriocarida, and the crustacean ancestry from which insects descended, is the wider context this result bears on rather than a separate required deliverable. A resolution must demonstrate that the recovered placement is stable under the perturbations that currently flip the result between these hypotheses (at least the addition/removal of small numbers of taxa, changes of substitution model such as site-homogeneous versus site-heterogeneous CAT-GTR treatments, Dayhoff6 recoding, and concatenation versus coalescent species-tree summaries; this list is illustrative rather than exhaustive), with the systematic biases implicated by prior work addressed as follows: long-branch attraction and compositional heterogeneity diagnosed and controlled, and incomplete lineage sorting — a property of the data rather than a controllable bias — tested for and its presence or absence reported. If no placement proves robustly stable under these perturbations, establishing and characterizing that instability — identifying which perturbation axes drive the conflict between the candidate hypotheses — is itself a valid resolution.

References

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