Phylosystemics: Merging Phylogenomics, Systems Biology, and Ecology to Study Evolution.

We define phylosystemics, a multidisciplinary strategy uniting short timescale interaction studies from systems biologists and ecologists with the longer timescale studies familiar to evolutionary biologists, taking advantage of methods from network sciences. Phylosystemics superimposes evolutionary information on entities/edges forming interaction networks produced by systems biology and ecology. At the molecular level, phylosystemics could provide evidence to infer and to time the evolution of molecular processes within a single branch of a phylogeny, in particular between the first and last common ancestors of a group arising during a major evolutionary transition. At the ecosystemic level, phylosystemics could culminate with the development of multilayer temporal networks encompassing biotic and abiotic interactions, whose analyses could unravel ecological interactions with evolutionary consequences.

Evolution of genetic diversity using networks: the human gut microbiome as a case study.

In order to study complex microbial communities and their associated mobile genetic elements, such as the human gut microbiome, evolutionists could explore their genetic diversity with shared sequence networks. In particular, the detection of remarkable structures in gene networks of the gut microbiome could serve to identify important functions within the community, and would ease comparison of data sets from microbiomes of various sources (human, ape, mouse etc.) in a single analysis.

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.

Visualizing and assessing phylogenetic congruence of core gene sets: a case study of the gamma-proteobacteria.

Here, we address a much-debated topic: is there or is there not an organismal tree of gamma-proteobacteria that can be unambiguously inferred from a core of shared genes? We apply several recently developed analytical methods to this problem, for the first time. Our heat map analyses of P values and of bootstrap bipartitions show the presence of conflicting phylogenetic signals among these core genes. Our synthesis reconstruction suggests that at least 10% of these genes have been laterally transferred during the divergence of the gamma-proteobacteria, and that for most of the rest, there is too little phylogenetic signal to permit firm conclusions about the mode of inheritance. Although there is clearly a central tendency in this data set (it is far from random), lateral gene transfers cannot be ruled out. Instead of an organismal tree, we propose that these core genes could be used to define a more subtle and partially reticulated pattern of relationships.

The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea.

Saturated thalassic brines are among the most physically demanding habitats on Earth: few microbes survive in them. Salinibacter ruber is among these organisms and has been found repeatedly in significant numbers in climax saltern crystallizer communities. The phenotype of this bacterium is remarkably similar to that of the hyperhalophilic Archaea (Haloarchaea). The genome sequence suggests that this resemblance has arisen through convergence at the physiological level (different genes producing similar overall phenotype) and the molecular level (independent mutations yielding similar sequences or structures). Several genes and gene clusters also derive by lateral transfer from (or may have been laterally transferred to) haloarchaea. S. ruber encodes four rhodopsins. One resembles bacterial proteorhodopsins and three are of the haloarchaeal type, previously uncharacterized in a bacterial genome. The impact of these modular adaptive elements on the cell biology and ecology of S. ruber is substantial, affecting salt adaptation, bioenergetics, and photobiology.

Do orthologous gene phylogenies really support tree-thinking?

BACKGROUND: Since Darwin's Origin of Species, reconstructing the Tree of Life has been a goal of evolutionists, and tree-thinking has become a major concept of evolutionary biology. Practically, building the Tree of Life has proven to be tedious. Too few morphological characters are useful for conducting conclusive phylogenetic analyses at the highest taxonomic level. Consequently, molecular sequences (genes, proteins, and genomes) likely constitute the only useful characters for constructing a phylogeny of all life. For this reason, tree-makers expect a lot from gene comparisons. The simultaneous study of the largest number of molecular markers possible is sometimes considered to be one of the best solutions in reconstructing the genealogy of organisms. This conclusion is a direct consequence of tree-thinking: if gene inheritance conforms to a tree-like model of evolution, sampling more of these molecules will provide enough phylogenetic signal to build the Tree of Life. The selection of congruent markers is thus a fundamental step in simultaneous analysis of many genes. RESULTS: Heat map analyses were used to investigate the congruence of orthologues in four datasets (archaeal, bacterial, eukaryotic and alpha-proteobacterial). We conclude that we simply cannot determine if a large portion of the genes have a common history. In addition, none of these datasets can be considered free of lateral gene transfer. CONCLUSION: Our phylogenetic analyses do not support tree-thinking. These results have important conceptual and practical implications. We argue that representations other than a tree should be investigated in this case because a non-critical concatenation of markers could be highly misleading.

On the conceptual difficulties in rooting the tree of life.

Rooting the 'tree of life' represents a major challenge for evolutionists. Without such a root, many of the first steps in biological evolution cannot be reconstructed. However, the nature of the last common ancestor of all living beings remains elusive, proof of the difficulty in shedding light on such an ancient event. Here, we highlight the practical difficulties and conceptual reasons that hinder the placement of a universal root. We discuss how, when addressing the question of the root of the tree of life, scientists unconsciously risk using the reasoning pattern of ancient skeptics, unfortunately known only to lead to further uncertainty. Hence, we argue that the root of the tree of life will not be established unless radically new approaches are considered. We propose a hypothetical means to overcome several of the conceptual difficulties pointed out, and suggest that a so-called 'transition analysis' of the structural evolution of the cytoplasmic membrane might be helpful, especially if evolutionary steps involving the rooting issue are polarized accounting more for physicochemical knowledge rather than hypothetical and controversial selective advantages.