Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny

It has recently been proposed that a well-resolved Tree of Life can be achieved through concatenation of shared genes. There are, however, several difficulties with such an approach, especially in the prokaryotic part of this tree. We tackled some of them using a new combination of maximum likelihood-based methods, developed in order to practice as safe and careful concatenations as possible. First, we used the application concaterpillar on carefully aligned core genes. This application uses a hierarchical likelihood-ratio test framework to assess both the topological congruence between gene phylogenies (i.e., whether different genes share the same evolutionary history) and branch-length congruence (i.e., whether genes that share the same history share the same pattern of relative evolutionary rates). We thus tested if these core genes can be concatenated or should be instead categorized into different incongruent sets. Second, we developed a heat map approach studying the evolution of the phylogenetic support for different bipartitions, when the number of sites of different phylogenetic quality in the concatenation increases. These heatmaps allow us to follow which phylogenetic signals increase or decrease as the concatenation progresses and to detect emerging artifactual groupings, that is, groups that are more and more supported when more and more homoplasic sites are thrown in the analysis. We showed that, as far as 7 major prokaryotic lineages are concerned, only 22 core genes can be said to be congruent and can be safely concatenated. This number is even smaller than the number of genes retained to reconstruct a "Tree of One Per Cent." Furthermore, the concatenation of these 22 markers leads to an unresolved tree as the only groupings in the concatenation tree seem to reflect emerging artifacts. Using concatenated core genes as a valid framework to classify uncharacterized environmental sequences can thus be misleading.     

Hidden diversity of Acoelomorpha revealed through metabarcoding

Animals with bilateral symmetry comprise the majority of the described species within Metazoa. However, the nature of the first bilaterian animal remains unknown. As most recent molecular phylogenies point to Xenacoelomorpha as the sister group to the rest of Bilateria, understanding their biology, ecology and diversity is key to reconstructing the nature of the last common bilaterian ancestor (Urbilateria). To date, sampling efforts have focused mainly on coastal areas, leaving potential gaps in our understanding of the full diversity of xenacoelomorphs. We therefore analysed 18S rDNA metabarcoding data from three marine projects covering benthic and pelagic habitats worldwide. Our results show that acoels have a greater richness in planktonic environments than previously described. Interestingly, we also identified a putative novel clade of acoels in the deep benthos that branches as sister group to the rest of Acoela, thus representing the earliest-branching acoel clade. Our data highlight deep-sea environments as an ideal habitat to sample acoels with key phylogenetic positions, which might be useful for reconstructing the early evolution of Bilateria.     

Regulation of sedimentation rate shapes the evolution of multicellularity in a close unicellular relative of animals

Significant increases in sedimentation rate accompany the evolution of multicellularity. These increases should lead to rapid changes in ecological distribution, thereby affecting the costs and benefits of multicellularity and its likelihood to evolve. However, how genetic and cellular traits control this process, their likelihood of emergence over evolutionary timescales, and the variation in these traits as multicellularity evolves are still poorly understood. Here, using isolates of the ichthyosporean genus Sphaeroforma-close unicellular relatives of animals with brief transient multicellular life stages-we demonstrate that sedimentation rate is a highly variable and evolvable trait affected by at least 2 distinct physical mechanisms. First, we find extensive (>300×) variation in sedimentation rates for different Sphaeroforma species, mainly driven by size and density during the unicellular-to-multicellular life cycle transition. Second, using experimental evolution with sedimentation rate as a focal trait, we readily obtained, for the first time, fast settling and multicellular Sphaeroforma arctica isolates. Quantitative microscopy showed that increased sedimentation rates most often arose by incomplete cellular separation after cell division, leading to clonal “clumping” multicellular variants with increased size and density. Strikingly, density increases also arose by an acceleration of the nuclear doubling time relative to cell size. Similar size- and density-affecting phenotypes were observed in 4 additional species from the Sphaeroforma genus, suggesting that variation in these traits might be widespread in the marine habitat. By resequencing evolved isolates to high genomic coverage, we identified mutations in regulators of cytokinesis, plasma membrane remodeling, and chromatin condensation that may contribute to both clump formation and the increase in the nuclear number-to-volume ratio. Taken together, this study illustrates how extensive cellular control of density and size drive sedimentation rate variation, likely shaping the onset and further evolution of multicellularity.

The transition to multicellularity is associated with the emergence of new features, including an increase in sedimentation rate, but how does such a key transition first occur? An experimental evolution study of ichthyosporeans, close unicellular relatives of animals, shows how cellular control of density and size drive sedimentation rate variation, likely shaping the evolution of multicellularity.