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Abstract Evolutionary mechanisms that underlie the origins of coloniality among organisms are diverse. Some animal colonies may be comprised strictly of clonal individuals formed from asexual budding or comprised of a chimera of clonal and sexually produced individuals that fuse secondarily. This investigation focuses on select members of the lophophorates and entoprocts whose evolutionary relationships remain enigmatic even in the age of genomics. Using transcriptomic data sets, two coloniality‐based hypotheses are tested in a phylogenetic context to find candidate genes showing evidence of positive selection and potentially convergent molecular signatures among solitary species and taxa‐forming colonies from aggregate groups or clonal budding. Approximately 22% of the 387 orthogroups tested showed evidence of positive selection in at least one of the three branch‐site tests (CODEML, BUSTED, and aBSREL). Only 12 genes could be reliably associated with a developmental function related to traits linked with coloniality, neuroanatomy, or ciliary fields. Genes testing for both positive selection and convergent molecular characters include orthologues of Radial spoke head,Elongation translation initiation factors,SEC13,andImmediate early response gene5. Maximum likelihood analyses included here resulted in tree topologies typical of other phylogenetic investigations based on wider genomic information. Further genomic and experimental evidence will be needed to resolve whether a solitary ancestor with multiciliated cells that formed aggregate groups gave rise to colonial forms in bryozoans (and perhaps the entoprocts) or that the morphological differences exhibited by phoronids and brachiopods represent trait modifications from a colonial ancestor. 

Abstract Evolution in the chronic cold of the Southern Ocean has had a profound influence on the physiology of cryonotothenioid fishes. However, the suite of genetic changes underlying the physiological gains and losses in these fishes is still poorly surveyed. By identifying the genomic signatures of selection, this study aims to identify the functional classes of genes that have been changed following two major physiological transitions: the onset of freezing temperatures, and the loss of hemoproteins. Looking at the changes that followed the onset of freezing temperatures, positive selective pressure was found among a set of broadly acting gene regulatory factors, suggesting a route through which cryonotothenioid gene expression has been retooled for life in the cold. Further, genes related to the cell cycle and cellular adhesion were found under positive selection suggesting that both present key challenges to life in freezing waters. By contrast, genes showing signatures of the relaxation of selective pressure showed a narrower biological impact, acting on genes related to mitochondrial function. Finally, while chronic cold-water temperatures appear correlated with substantial genetic change, the loss of hemoproteins resulted in little observable change in protein-coding genes relative to their red-blooded relatives. Combined, the influence of positive and relaxed selection shows that long-term exposure to cold has led to profound changes in cryonotothenioid genomes that may make it challenging for them to adapt to a rapidly changing climate. 

Abstract Freshwater sponges (Spongillida) are a unique lineage of demosponges that secondarily colonized lakes and rivers and are now found ubiquitously in these ecosystems. They developed specific adaptations to freshwater systems, including the ability to survive extreme thermal ranges, long-lasting dessication, anoxia, and resistance to a variety of pollutants. Although spongillids have colonized all freshwater systems, the family Lubomirskiidae is endemic to Lake Baikal and plays a range of key roles in this ecosystem. Our work compares the genomic content and microbiome of individuals of three species of the Lubomirskiidae, providing hypotheses for how molecular evolution has allowed them to adapt to their unique environments. We have sequenced deep (>92% of the metazoan “Benchmarking Universal Single-Copy Orthologs” [BUSCO] set) transcriptomes from three species of Lubomirskiidae and a draft genome resource for Lubomirskia baikalensis. We note Baikal sponges contain unicellular algal and bacterial symbionts, as well as the dinoflagellate Gyrodinium. We investigated molecular evolution, gene duplication, and novelty in freshwater sponges compared with marine lineages. Sixty one orthogroups have consilient evidence of positive selection. Transporters (e.g., zinc transporter-2), transcription factors (aristaless-related homeobox), and structural proteins (e.g. actin-3), alongside other genes, are under strong evolutionary pressure in freshwater, with duplication driving novelty across the Spongillida, but especially in the Lubomirskiidae. This addition to knowledge of freshwater sponge genetics provides a range of tools for understanding the molecular biology and, in the future, the ecology (e.g., colonization and migration patterns) of these key species.