Meland, K. | bioRxiv Science

bioRxiv2025

Phylogenomics supports monophyly of marsupial crustaceans: a journey to direct development

Peracarida (marsupial crustaceans) represent one of the most diverse and ecologically important crustacean groups, yet their evolutionary relationships have long been debated. Here, we present the most comprehensive phylogenomic analysis of Peracarida to date, incorporating the relict taxa Thermosbaenacea, Mictacea, Ingolfiellida, and Spelaeogriphacea for the first time in a phylogenomic framework. Our results robustly confirm peracarid monophyly and recover a well-supported clade uniting Mancoida (Isopoda, Tanaidaca, Cumacea), Mictacea, and Spelaeogriphacea. We propose the new taxon Panmancoida to encompass this expanded lineage defined by shared developmental and morphological traits. The inferred phylogeny further suggests that peracarid evolution involved a transition from an intermediate "pseudodirect" developmental mode to the direct development seen in most lineages. We further show that the shift to extensive brood care within the marsupium, accompanied by the loss of a free-swimming larval stage, may have accelerated rates of molecular evolution across lineages. Together, these findings provide a robust evolutionary framework for this major malacostracan lineage and highlight how key reproductive innovations reshaped the genomic and life-history trajectories of the marsupial crustaceans.

evolutionary biology↗

bioRxiv2022

Major revisions in pancrustacean phylogeny with recommendations for resolving challenging nodes

The clade Pancrustacea, comprising crustaceans and hexapods, is the most diverse group of animals on earth, containing over 80% of animal species. It has been the subject of several recent phylogenomic analyses, but despite analyzing hundreds of genes, relationships within Pancrustacea show a notable lack of stability. Here, the phylogeny is estimated with expanded taxon sampling, particularly of malacostracans, using a precise tree-based approach to infer orthology. Our results show that small changes in taxon sampling have a large impact on phylogenetic estimation. By analyzing only shared orthologs between two slightly different taxon sets, we show that the differences in the resulting topologies are due to the effects of taxon sampling on the phylogenetic reconstruction method, not on ortholog identification. We compare trees resulting from our phylogenomic analyses with those from the literature to explore the large tree space of pancrustacean phylogenetic hypotheses and find that statistical topology tests reject the previously published trees in favor of the ML trees produced here. Our results reject several clades including Caridoida, Eucarida, Multicrustacea, Vericrustacea, and Syncarida. We recover a novel relationship between decapods, euphausiids, and syncarids that we refer to as the Syneucarida. With denser taxon sampling, we find Stomatopoda sister to this clade, which we name Stomatocaridea, dividing Malacostraca into three clades: Leptostraca, Peracarida, and Stomatocaridea. A new Bayesian divergence time estimation is conducted using 13 vetted fossils. We review our results in the context of other pancrustacean phylogenetic hypotheses and highlight the key taxa to sample in future studies.

evolutionary biology↗