Integrative modeling of gene and genome evolution roots the archaeal tree of life.

A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. This model uses evidence from gene duplications, horizontal transfers, and gene losses contained in 31,236 archaeal gene families to identify the most likely root for the tree. Our analyses support the monophyly of DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea), a recently discovered cosmopolitan and genetically diverse lineage, and, in contrast to previous work, place the tree root between DPANN and all other Archaea. The sister group to DPANN comprises the Euryarchaeota and the TACK Archaea, including Lokiarchaeum, which our analyses suggest are monophyletic sister lineages. Metabolic reconstructions on the rooted tree suggest that early Archaea were anaerobes that may have had the ability to reduce CO2 to acetate via the Wood-Ljungdahl pathway. In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses infer a relatively small-genomed archaeal ancestor that subsequently increased in complexity via gene duplication and horizontal gene transfer.

The Effect of Nonreversibility on Inferring Rooted Phylogenies.

Most phylogenetic models assume that the evolutionary process is stationary and reversible. In addition to being biologically improbable, these assumptions also impair inference by generating models under which the likelihood does not depend on the position of the root. Consequently, the root of the tree cannot be inferred as part of the analysis. Yet identifying the root position is a key component of phylogenetic inference because it provides a point of reference for polarizing ancestor-descendant relationships and therefore interpreting the tree. In this paper, we investigate the effect of relaxing the unrealistic reversibility assumption and allowing the position of the root to be another unknown. We propose two hierarchical models that are centered on a reversible model but perturbed to allow nonreversibility. The models differ in the degree of structure imposed on the perturbations. The analysis is performed in the Bayesian framework using Markov chain Monte Carlo methods for which software is provided. We illustrate the performance of the two nonreversible models in analyses of simulated data using two types of topological priors. We then apply the models to a real biological data set, the radiation of polyploid yeasts, for which there is robust biological opinion about the root position. Finally, we apply the models to a second biological alignment for which the rooted tree is controversial: the ribosomal tree of life. We compare the two nonreversible models and conclude that both are useful in inferring the position of the root from real biological data.

Bayesian modelling of compositional heterogeneity in molecular phylogenetics.

In molecular phylogenetics, standard models of sequence evolution generally assume that sequence composition remains constant over evolutionary time. However, this assumption is violated in many datasets which show substantial heterogeneity in sequence composition across taxa. We propose a model which allows compositional heterogeneity across branches, and formulate the model in a Bayesian framework. Specifically, the root and each branch of the tree is associated with its own composition vector whilst a global matrix of exchangeability parameters applies everywhere on the tree. We encourage borrowing of strength between branches by developing two possible priors for the composition vectors: one in which information can be exchanged equally amongst all branches of the tree and another in which more information is exchanged between neighbouring branches than between distant branches. We also propose a Markov chain Monte Carlo (MCMC) algorithm for posterior inference which uses data augmentation of substitutional histories to yield a simple complete data likelihood function that factorises over branches and allows Gibbs updates for most parameters. Standard phylogenetic models are not informative about the root position. Therefore a significant advantage of the proposed model is that it allows inference about rooted trees. The position of the root is fundamental to the biological interpretation of trees, both for polarising trait evolution and for establishing the order of divergence among lineages. Furthermore, unlike some other related models from the literature, inference in the model we propose can be carried out through a simple MCMC scheme which does not require problematic dimension-changing moves. We investigate the performance of the model and priors in analyses of two alignments for which there is strong biological opinion about the tree topology and root position.

Encapsulated Nanodroplet Crystallization of Organic-Soluble Small Molecules.

Single-crystal X-ray diffraction analysis (SCXRD) constitutes a universal approach for the elucidation of molecular structure and the study of crystalline forms. However, the discovery of viable crystallization conditions remains both experimentally challenging and resource intensive in both time and the quantity of analyte(s). We report a robot-assisted, high-throughput method for the crystallization of organic-soluble small molecules in which we employ only micrograms of analyte per experiment. This allows hundreds of crystallization conditions to be screened in parallel with minimal overall sample requirements. Crystals suitable for SCXRD are grown from nanoliter droplets of a solution of analyte in organic solvent(s), each of which is encapsulated within an inert oil to control the rate of solvent loss. This encapsulated nanodroplet crystallization methodology can also be used to search for new crystal forms, as exemplified through both our discovery of a new (13th) polymorph of the olanzapine precursor ROY and SCXRD analysis of the "uncrystallizable" agrochemical dithianon.

New substitution models for rooting phylogenetic trees.

The root of a phylogenetic tree is fundamental to its biological interpretation, but standard substitution models do not provide any information on its position. Here, we describe two recently developed models that relax the usual assumptions of stationarity and reversibility, thereby facilitating root inference without the need for an outgroup. We compare the performance of these models on a classic test case for phylogenetic methods, before considering two highly topical questions in evolutionary biology: the deep structure of the tree of life and the root of the archaeal radiation. We show that all three alignments contain meaningful rooting information that can be harnessed by these new models, thus complementing and extending previous work based on outgroup rooting. In particular, our analyses exclude the root of the tree of life from the eukaryotes or Archaea, placing it on the bacterial stem or within the Bacteria. They also exclude the root of the archaeal radiation from several major clades, consistent with analyses using other rooting methods. Overall, our results demonstrate the utility of non-reversible and non-stationary models for rooting phylogenetic trees, and identify areas where further progress can be made.

Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics.

Microsporidia are an abundant group of obligate intracellular parasites of other eukaryotes, including immunocompromised humans, but the molecular basis of their intracellular lifestyle and pathobiology are poorly understood. New genomes from a taxonomically broad range of microsporidians, complemented by published expression data, provide an opportunity for comparative analyses to identify conserved and lineage-specific patterns of microsporidian genome evolution that have underpinned this success. In this study, we infer that a dramatic bottleneck in the last common microsporidian ancestor (LCMA) left a small conserved core of genes that was subsequently embellished by gene family expansion driven by gene acquisition in different lineages. Novel expressed protein families represent a substantial fraction of sequenced microsporidian genomes and are significantly enriched for signals consistent with secretion or membrane location. Further evidence of selection is inferred from the gain and reciprocal loss of functional domains between paralogous genes, for example, affecting transport proteins. Gene expansions among transporter families preferentially affect those that are located on the plasma membrane of model organisms, consistent with recruitment to plug conserved gaps in microsporidian biosynthesis and metabolism. Core microsporidian genes shared with other eukaryotes are enriched in orthologs that, in yeast, are highly expressed, highly connected, and often essential, consistent with strong negative selection against further reduction of the conserved gene set since the LCMA. Our study reveals that microsporidian genome evolution is a highly dynamic process that has balanced constraint, reductive evolution, and genome expansion during adaptation to an extraordinarily successful obligate intracellular lifestyle.