Insects, the most diverse group of organisms, are nested within crustaceans, arguably the most abundant group of marine animals. However, to date, no consensus has been reached as to which crustacean taxon is the closest relative of hexapods. A majority of studies have proposed that Branchiopoda (e.g., fairy shrimps) is the sister group of Hexapoda [1-7]. However, these investigations largely excluded two equally important taxa, Remipedia and Cephalocarida. Other studies suggested Remipedia [8-11] or Remipedia + Cephalocarida [12, 13] as potential sister groups of hexapods, but they either did not include Cephalocarida or used only Sanger sequence data and morphology [9, 12]. Here we present the first phylogenomic study specifically addressing the origins of hexapods, including transcriptomes for two species each of Cephalocarida and Remipedia. Phylogenetic analyses of selected matrices, ranging from 81 to 1,675 orthogroups and up to 510,982 amino acid positions, clearly reject a sister-group relationship between Hexapoda and Branchiopoda [1-7]. Nonetheless, support for a hexapod sister-group relationship to Remipedia or to Cephalocarida-Remipedia was highly dependent on the employed analytical methodology. Further analyses assessing the effects of gene evolutionary rate and targeted taxon exclusion support Remipedia as the sole sister taxon of Hexapoda and suggest that the prior grouping of Remipedia + Cephalocarida is an artifact, possibly due to long branch attraction and compositional heterogeneity. We further conclude that terrestrialization of Hexapoda probably occurred in the late Cambrian to early Ordovician, an estimate that is independent of their proposed sister group [4, 8, 12, 14].

Understanding the evolution of Tetraconata or Pancrustacea-the clade that includes crustaceans and insects-requires a well-resolved hypothesis regarding the relationships within and among its constituent taxa. Here, we assembled a taxon-rich phylogenomic dataset focusing on crustacean lineages based solely on genomes and new-generation Illumina-generated transcriptomes, including 89 representatives of Tetraconata. This constitutes, to our knowledge, the first phylogenomic study specifically addressing internal relationships of Malacostraca (with 26 species included) and Branchiopoda (36 species). Seven matrices comprising 81-684 orthogroups and 17 690-242 530 amino acid positions were assembled and analysed under five different analytical approaches. To maximize gene occupancy and to improve resolution, taxon-specific matrices were designed for Malacostraca and Branchiopoda. Key tetraconatan taxa (i.e. Oligostraca, Multicrustacea, Branchiopoda, Malacostraca, Thecostraca, Copepoda and Hexapoda) were monophyletic and well supported. Within Branchiopoda, Phyllopoda, Diplostraca, Cladoceromorpha and Cladocera were monophyletic. Within Malacostraca, the clades Eumalacostraca, Decapoda and Reptantia were well supported. Recovery of Caridoida or Peracarida was highly dependent on the analysis for the complete matrix, but it was consistently monophyletic in the malacostracan-specific matrices. From such examples, we demonstrate that taxon-specific matrices and particular evolutionary models and analytical methods, namely CAT-GTR and Dayhoff recoding, outperform other approaches in resolving certain recalcitrant nodes in phylogenomic analyses.

Colonization of body epithelial surfaces with a highly specific microbial community is a fundamental feature of all animals, yet the underlying mechanisms by which these communities are selected and maintained are not well understood. Here, we show that sensory and ganglion neurons in the ectodermal epithelium of the model organism hydra (a member of the animal phylum Cnidaria) secrete neuropeptides with antibacterial activity that may shape the microbiome on the body surface. In particular, a specific neuropeptide, which we call NDA-1, contributes to the reduction of Gram-positive bacteria during early development and thus to a spatial distribution of the main colonizer, the Gram-negative Curvibacter sp., along the body axis. Our findings warrant further research to test whether neuropeptides secreted by nerve cells contribute to the spatial structure of microbial communities in other organisms.

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