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Here, we provide the first complete mitochondrial genomes for two higher taxa of Peracarida, Lophogastrida and Stygiomysida. We examined Lophogaster typicus as a representative of Lophogastrida and Spelaeomysis bottazzii as a representative of Stygiomysida. Both mitogenomes have all typical metazoan genes (13 protein‐coding genes, two ribosomal RNA genes and 22 transfer RNAs). The mitogenomes have a length of 15,076 bp in L. typicus and 14,806 bp in S. bottazzii. Gene order differs markedly from the hypothetical pancrustacean/malacostracan ground pattern in both species, and in L. typicus, all genes were encoded on the heavy strand. This is the first time this is described for a crustacean. We also reconstruct eumalacostracan phylogenies using a data set consisting of 98 species based on alignments comprising all protein‐encoding genes as well as the protein‐encoding genes and the two ribosomal RNAs. We find support for the monophyly of Mysidacea based on species from all three higher taxa (Mysida, Lophogastrida, Stygiomysida). Moreover, our analyses also support a monophyletic Peracarida with Amphipoda or Amphipoda + Mysidacea as the sister group to the remaining Peracarida.

Morphological matrices, including the conceptualization of characters and character states and scoring thereof, still are a valuable and necessary tool for phylogenetic analyses. Although they are often seen only as numerically simplified summaries of observations for the purpose of cladistic analyses, they also hold value as collections of ideas, concepts and the current state of knowledge, conveying various hypotheses on character state identity, homology and evolutionary transformations. A common and persistent issue in scoring and analysing morphological matrices is the phenomenon of inapplicable characters (“inapplicables”). Inapplicables result from the ontological dependency (based on hierarchical relationships) between characters. Traditionally handled the same as “missing data”, inapplicables were shown to be problematic in holding the potential to result in unreasonable algorithmic preference for certain cladograms over others. Recently, though, this problem has been solved by approaching parsimony as a maximization of homology rather than a minimization of transformational steps. We herein aim to further improve our theoretical understanding of the underlying hierarchical nature of morphological characters, which causes the phenomenon of ontological dependencies and, thereby, inapplicables. As a result, we present a discussion of various character‐dependency scenarios and a new concept of hierarchical character relationships as being composed of four complementary sub‐aspects. Building on this, a new syntax for the designation of character dependencies as part of the character statement is proposed, to help identify and apply scoring constraints for manual and automated scoring of morphological character matrices and their cladistic analysis.

Within Malacostraca, legs are diversified variously throughout the groups. Most conspicuous is the transformation of anterior thoracopods, especially the first, into maxillipeds involved in feeding. However, the concept of a maxilliped is not precise, because it relates to a vague combination of morphological and functional deviation from a locomotory limb. Although general homology of the first thoracopod (maxilliped or not) is beyond doubt, special homology (synapomorphy) of the anteriormost maxillipeds remains uncertain. For better insights, we studied the musculature and exoskeletal structures of the first thoracopods in Anaspidacea, Euphausiacea, Lophogastrida, Mysida and Stygiomysida, using three-dimesional reconstruction of laser scanning microscopy and micro-computed tomography data. Our analysis shows high muscular and skeletal complexity of the first thoracopods. We herein reject the term ‘maxilliped’ for Anaspidacea and Euphausiacea, because their first thoracopods differ little from the posterior limbs, although specific correspondences between these taxa might represent synapomorphies. The ‘mysidacean maxilliped’ is morphologically well derived from the posterior thoracopods and appears synapomorphic for the mysidacean subtaxa. A comparison with other Peracarida additionally shows correspondences indicating a homologous ‘peracaridan maxilliped’. In contrast, we consider the peracaridan maxilliped not to be homologous to the decapodan maxilliped. As a distinction, we propose the term ‘unguiped’ for the peracaridan first thoracopod.