What Is the Tree of Life?

Early Divergence and Gene Exchange Highways in the Evolutionary History of Mesoaciditogales

The placement of a nonhyperthermophilic order Mesoaciditogales as the earliest branching clade within the Thermotogota phylum challenges the prevailing hypothesis that the last common ancestor of Thermotogota was a hyperthermophile. Yet, given the long branch leading to the only two Mesoaciditogales described to date, the phylogenetic position of the order may be due to the long branch attraction artifact. By testing various models and applying data recoding in phylogenetic reconstructions, we observed that early branching of Mesoaciditogales within Thermotogota is strongly supported by the conserved marker genes assumed to be vertically inherited. However, based on the taxonomic content of 1,181 gene families and a phylogenetic analysis of 721 gene family trees, we also found that a substantial number of Mesoaciditogales genes are more closely related to species from the order Petrotogales. These genes contribute to coenzyme transport and metabolism, fatty acid biosynthesis, genes known to respond to heat and cold stressors, and include many genes of unknown functions. The Petrotogales comprise moderately thermophilic and mesophilic species with similar temperature tolerances to that of Mesoaciditogales. Our findings hint at extensive horizontal gene transfer (HGT) between, or parallel independent gene gains by, the two ecologically similar lineages and suggest that the exchanged genes may be important for adaptation to comparable temperature niches.

Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome

BACKGROUND

Cumulative sequencing efforts have yielded enough genomes to construct pangenomes for dozens of bacterial species and elucidate intraspecies gene conservation. Given the diversity of organisms for which this is achievable, similar analyses for ancestral species are feasible through the integration of pangenomics and phylogenetics, promising deeper insights into the nature of ancient life.

RESULTS

We construct pangenomes for 183 bacterial species from 54,085 genomes and identify their core genomes using a novel statistical model to estimate genome-specific error rates and underlying gene frequencies. The core genomes are then integrated into a phylogenetic tree to reconstruct the core genome of the last bacterial common ancestor (LBCA), yielding three main results: First, the gene content of modern and ancestral core genomes are diverse at the level of individual genes but are similarly distributed by functional category and share several poorly characterized genes. Second, the LBCA core genome is distinct from any individual modern core genome but has many fundamental biological systems intact, especially those involving translation machinery and biosynthetic pathways to all major nucleotides and amino acids. Third, despite this metabolic versatility, the LBCA core genome likely requires additional non-core genes for viability, based on comparisons with the minimal organism, JCVI-Syn3A.

CONCLUSIONS

These results suggest that many cellular systems commonly conserved in modern bacteria were not just present in ancient bacteria but were nearly immutable with respect to short-term intraspecies variation. Extending this analysis to other domains of life will likely provide similar insights into more distant ancestral species.

Very early evolution from the perspective of microbial ecology

The universal ancestor at the root of the species tree of life depicts a population of organisms with a surprising degree of complexity, posessing genomes and translation systems much like that of microbial life today. As the first life forms were most likely to have been simple replicators, considerable evolutionary change must have taken place prior to the last universal common ancestor. It is often assumed that the lack of earlier branches on the tree of life is due to a prevalence of random horizontal gene transfer that obscured the delineations between lineages and hindered their divergence. Therefore, principles of microbial evolution and ecology may give us some insight into these early stages in the history of life. Here, we synthesize the current understanding of organismal and genome evolution from the perspective of microbial ecology and apply these evolutionary principles to the earliest stages of life on Earth. We focus especially on broad evolutionary modes pertaining to horizontal gene transfer, pangenome structure, and microbial mat communities.

Old genes in new places: A taxon-rich analysis of interdomain lateral gene transfer events

Vertical inheritance is foundational to Darwinian evolution, but fails to explain major innovations such as the rapid spread of antibiotic resistance among bacteria and the origin of photosynthesis in eukaryotes. While lateral gene transfer (LGT) is recognized as an evolutionary force in prokaryotes, the role of LGT in eukaryotic evolution is less clear. With the exception of the transfer of genes from organelles to the nucleus, a process termed endosymbiotic gene transfer (EGT), the extent of interdomain transfer from prokaryotes to eukaryotes is highly debated. A common critique of studies of interdomain LGT is the reliance on the topology of single-gene trees that attempt to estimate more than one billion years of evolution. We take a more conservative approach by identifying cases in which a single clade of eukaryotes is found in an otherwise prokaryotic gene tree (i.e. exclusive presence). Starting with a taxon-rich dataset of over 13,600 gene families and passing data through several rounds of curation, we identify and categorize the function of 306 interdomain LGT events into diverse eukaryotes, including 189 putative EGTs, 52 LGTs into Opisthokonta (i.e. animals, fungi and their microbial relatives), and 42 LGTs nearly exclusive to anaerobic eukaryotes. To assess differential gene loss as an explanation for exclusive presence, we compare branch lengths within each LGT tree to a set of vertically-inherited genes subsampled to mimic gene loss (i.e. with the same taxonomic sampling) and consistently find shorter relative distance between eukaryotes and prokaryotes in LGT trees, a pattern inconsistent with gene loss. Our methods provide a framework for future studies of interdomain LGT and move the field closer to an understanding of how best to model the evolutionary history of eukaryotes.

Reconstructing the Last Common Ancestor: Epistemological and Empirical Challenges

Reconstructing the genetic traits of the Last Common Ancestor (LCA) and the Tree of Life (TOL) are two examples of the reaches of contemporary molecular phylogenetics. Nevertheless, the whole enterprise has led to paradoxical results. The presence of Lateral Gene Transfer poses epistemic and empirical challenges to meet these goals; the discussion around this subject has been enriched by arguments from philosophers and historians of science. At the same time, a few but influential research groups have aimed to reconstruct the LCA with rich-in-detail hypotheses and high-resolution gene catalogs and metabolic traits. We argue that LGT poses insurmountable challenges for detailed and rich in details reconstructions and propose, instead, a middle-ground position with the reconstruction of a slim LCA based on traits under strong pressures of Negative Natural Selection, and for the need of consilience with evidence from organismal biology and geochemistry. We defend a cautionary perspective that goes beyond the statistical analysis of gene similarities and assumes the broader consequences of evolving empirical data and epistemic pluralism in the reconstruction of early life.

A thermodynamic atlas of proteomes reveals energetic innovation across the tree of life

Protein stability is a fundamental molecular property enabling organisms to adapt to their biological niches. How this is facilitated and whether there are kingdom specific or more general universal strategies is not known. A principal obstacle to addressing this issue is that the vast majority of proteins lack annotation, specifically thermodynamic annotation, beyond the amino acid and chromosome information derived from genome sequencing. To address this gap and facilitate future investigation into large-scale patterns of protein stability and dynamics within and between organisms, we applied a unique ensemble-based thermodynamic characterization of protein folds to a substantial portion of extant sequenced genomes. Using this approach, we compiled a database resource focused on the position-specific variation in protein stability. Interrogation of the database reveals; 1) domains of life exhibit distinguishing thermodynamic features, with eukaryotes particularly different from both archaea and bacteria, 2) the optimal growth temperature of an organism is proportional to the average apolar enthalpy of its proteome, 3) intrinsic disorder content is also proportional to the apolar enthalpy (but unexpectedly not the predicted stability at 25 °C), and 4) secondary structure and global stability information of individual proteins is extractable. We hypothesize that wider access to residue-specific thermodynamic information of proteomes will result in deeper understanding of mechanisms driving functional adaptation and protein evolution. Our database is free for download at https://afc-science.github.io/thermo-env-atlas/.

Multi-model approaches to phylogenetics: Implications for idealization

Phylogenetic models traditionally represent the history of life as having a strictly-branching tree structure. However, it is becoming increasingly clear that the history of life is often not strictly-branching; lateral gene transfer, endosymbiosis, and hybridization, for example, can all produce lateral branching events. There is thus motivation to allow phylogenetic models to have a reticulate structure. One proposal involves the reconciliation of genealogical discordance. Briefly, this method uses patterns of disagreement - discordance - between trees of different genes to add lateral branching events to phylogenetic trees of taxa, and to estimate the most likely cause of these events. I use this practice to argue for: (1) a need for expanded accounts of multiple-models idealization, (2) a distinction between automatic and manual de-idealization, and (3) recognition that idealization may serve the meso-level aims of science in a different way than hitherto acknowledged.

A New Analysis of Archaea-Bacteria Domain Separation: Variable Phylogenetic Distance and the Tempo of Early Evolution

Comparative genomics and molecular phylogenetics are foundational for understanding biological evolution. Although many studies have been made with the aim of understanding the genomic contents of early life, uncertainty remains. A study by Weiss et al. (Weiss MC, Sousa FL, Mrnjavac N, Neukirchen S, Roettger M, Nelson-Sathi S, Martin WF. 2016. The physiology and habitat of the last universal common ancestor. Nat Microbiol. 1(9):16116.) identified a number of protein families in the last universal common ancestor of archaea and bacteria (LUCA) which were not found in previous works. Here, we report new research that suggests the clustering approaches used in this previous study undersampled protein families, resulting in incomplete phylogenetic trees which do not reflect protein family evolution. Phylogenetic analysis of protein families which include more sequence homologs rejects a simple LUCA hypothesis based on phylogenetic separation of the bacterial and archaeal domains for a majority of the previously identified LUCA proteins (∼82%). To supplement limitations of phylogenetic inference derived from incompletely populated orthologous groups and to test the hypothesis of a period of rapid evolution preceding the separation of the domains, we compared phylogenetic distances both within and between domains, for thousands of orthologous groups. We find a substantial diversity of interdomain versus intradomain branch lengths, even among protein families which exhibit a single domain separating branch and are thought to be associated with the LUCA. Additionally, phylogenetic trees with long interdomain branches relative to intradomain branches are enriched in information categories of protein families in comparison to those associated with metabolic functions. These results provide a new view of protein family evolution and temper claims about the phenotype and habitat of the LUCA.

The past, present and future of the tree of life

The advent of comparative genomics in the late 1990s led to the discovery of extensive lateral gene transfer in prokaryotes. The resulting debate over whether life as a whole is best represented as a tree or a network has since given way to a general consensus in which trees and networks co-exist rather than stand in opposition. Embracing this consensus allows us to move beyond the question of which is true or false. The future of the tree of life debate lies in asking what trees and networks can, and should, do for science.

A Place for Viruses on the Tree of Life

Viruses are ubiquitous. They infect almost every species and are probably the most abundant biological entities on the planet, yet they are excluded from the Tree of Life (ToL). However, there can be no doubt that viruses play a significant role in evolution, the force that facilitates all life on Earth. Conceptually, viruses are regarded by many as non-living entities that hijack living cells in order to propagate. A strict separation between living and non-living entities places viruses far from the ToL, but this may be theoretically unsound. Advances in sequencing technology and comparative genomics have expanded our understanding of the evolutionary relationships between viruses and cellular organisms. Genomic and metagenomic data have revealed that co-evolution between viral and cellular genomes involves frequent horizontal gene transfer and the occasional co-option of novel functions over evolutionary time. From the giant, ameba-infecting marine viruses to the tiny Porcine circovirus harboring only two genes, viruses and their cellular hosts are ecologically and evolutionarily intertwined. When deciding how, if, and where viruses should be placed on the ToL, we should remember that the Tree functions best as a model of biological evolution on Earth, and it is important that models themselves evolve with our increasing understanding of biological systems.

Should Networks Supplant Tree Building?

Recent studies suggested that network methods should supplant tree building as the basis of genealogical analysis. This proposition is based upon two arguments. First is the observation that bacterial and archaeal lineages experience processes oppositional to bifurcation and hence the representation of the evolutionary process in a tree like structure is illogical. Second is the argument tree building approaches are circular-you ask for a tree and you get one, which pins a verificationist label on tree building that, if correct, should be the end of phylogenetic analysis as we currently know it. In this review, we examine these questions and suggest that rumors of the death of the bacterial tree of life are exaggerated at best.

The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions

The role and extent of horizontal gene transfer (HGT) in eukaryotes are hotly disputed topics that impact our understanding of the origin of metabolic processes and the role of organelles in cellular evolution. We addressed this issue by analyzing 10 novel Cyanidiales genomes and determined that 1% of their gene inventory is HGT-derived. Numerous HGT candidates share a close phylogenetic relationship with prokaryotes that live in similar habitats as the Cyanidiales and encode functions related to polyextremophily. HGT candidates differ from native genes in GC-content, number of splice sites, and gene expression. HGT candidates are more prone to loss, which may explain the absence of a eukaryotic pan-genome. Therefore, the lack of a pan-genome and cumulative effects fail to provide substantive arguments against our hypothesis of recurring HGT followed by differential loss in eukaryotes. The maintenance of 1% HGTs, even under selection for genome reduction, underlines the importance of non-endosymbiosis related foreign gene acquisition.

Geological and Geochemical Constraints on the Origin and Evolution of Life

The traditional tree of life from molecular biology with last universal common ancestor (LUCA) branching into bacteria and archaea (though fuzzy) is likely formally valid enough to be a basis for discussion of geological processes on the early Earth. Biologists infer likely properties of nodal organisms within the tree and, hence, the environment they inhabited. Geologists both vet tenuous trees and putative origin of life scenarios for geological and ecological reasonability and conversely infer geological information from trees. The latter approach is valuable as geologists have only weakly constrained the time when the Earth became habitable and the later time when life actually existed to the long interval between ∼4.5 and ∼3.85 Ga where no intact surface rocks are known. With regard to vetting, origin and early evolution hypotheses from molecular biology have recently centered on serpentinite settings in marine and alternatively land settings that are exposed to ultraviolet sunlight. The existence of these niches on the Hadean Earth is virtually certain. With regard to inferring geological environment from genomics, nodes on the tree of life can arise from true bottlenecks implied by the marine serpentinite origin scenario and by asteroid impact. Innovation of a very useful trait through a threshold allows the successful organism to quickly become very abundant and later root a large clade. The origin of life itself, that is, the initial Darwinian ancestor, the bacterial and archaeal roots as free-living cellular organisms that independently escaped hydrothermal chimneys above marine serpentinite or alternatively from shallow pore-water environments on land, the Selabacteria root with anoxygenic photosynthesis, and the Terrabacteria root colonizing land are attractive examples that predate the geological record. Conversely, geological reasoning presents likely events for appraisal by biologists. Asteroid impacts may have produced bottlenecks by decimating life. Thermophile roots of bacteria and archaea as well as a thermophile LUCA are attractive.

Reconstruction of real and simulated phylogenies based on quartet plurality inference

BACKGROUND

Deciphering the history of life on Earth has long been regarded as one of the most central tasks in biology. In past years, widespread discordance between the evolutionary histories of different groups of orthologous genes of prokaryotes have been revealed, primarily due to horizontal gene transfers (HGTs). Nonetheless, evidence that support a strong tree-like signal of evolution have been uncovered, despite the presence of HGT events. Therefore, a challenging task is to distill this tree-like signal from the noise induced by all sources of non-tree-like events.

RESULTS

In this work we tackle this question, using real and simulated data. We first tighten a recent related theoretical result in this field. In a simulation study, we infer individual quartet topologies, and then use the inferred quartets to reconstruct simulated species trees. We demonstrate that accurate tree reconstruction is feasible despite surprisingly high rates of HGT. In a real data study, we construct phylogenies of two sets of prokaryotes, and show that our tree reconstruction scheme is comparable with (and complementary better than) other commonly used methods.

CONCLUSIONS

Using a blend of theoretical and empirical investigations, our study proves the feasibility of accurate quartet-based phylogenetic reconstruction, the vast impact of HGT events notwithstanding.

No wisdom in the crowd: genome annotation in the era of big data - current status and future prospects

Science and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery-driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential in biological research and reflects the nature of biology itself. Annotation systems, rather than being repositories of facts, should be tools that support multiple modes of inference. By combining deduction, induction and abduction, investigators can generate hypotheses when accurate knowledge is extracted from model databases. A key stance is to depart from 'the sequence tells the structure tells the function' fallacy, placing function first. We illustrate our approach with examples of critical or unexpected pathways, using MicroScope to demonstrate how tools can be implemented following the principles we advocate. We end with a challenge to the reader.

Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes

Background

Genomes rearrangements carry valuable information for phylogenetic inference or the elucidation of molecular mechanisms of adaptation. However, the detection of genome rearrangements is often hampered by current deficiencies in data and methods: Genomes obtained from short sequence reads have generally very fragmented assemblies, and comparing multiple gene orders generally leads to computationally intractable algorithmic questions.

Results

We present a computational method, ADseq, which, by combining ancestral gene order reconstruction, comparative scaffolding and de novo scaffolding methods, overcomes these two caveats. ADseq provides simultaneously improved assemblies and ancestral genomes, with statistical supports on all local features. Compared to previous comparative methods, it runs in polynomial time, it samples solutions in a probabilistic space, and it can handle a significantly larger gene complement from the considered extant genomes, with complex histories including gene duplications and losses. We use ADseq to provide improved assemblies and a genome history made of duplications, losses, gene translocations, rearrangements, of 18 complete Anopheles genomes, including several important malaria vectors. We also provide additional support for a differentiated mode of evolution of the sex chromosome and of the autosomes in these mosquito genomes.

Conclusions

We demonstrate the method’s ability to improve extant assemblies accurately through a procedure simulating realistic assembly fragmentation. We study a debated issue regarding the phylogeny of the Gambiae complex group of Anopheles genomes in the light of the evolution of chromosomal rearrangements, suggesting that the phylogenetic signal they carry can differ from the phylogenetic signal carried by gene sequences, more prone to introgression.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4466-7) contains supplementary material, which is available to authorized users.

How and Why to Build a Unified Tree of Life

Phylogenetic trees are a crucial backbone for a wide breadth of biological research spanning systematics, organismal biology, ecology, and medicine. In 2015, the Open Tree of Life project published a first draft of a comprehensive tree of life, summarizing digitally available taxonomic and phylogenetic knowledge. This paper reviews, investigates, and addresses the following questions as a follow-up to that paper, from the perspective of researchers involved in building this summary of the tree of life: Is there a tree of life and should we reconstruct it? Is available data sufficient to reconstruct the tree of life? Do we have access to phylogenetic inferences in usable form? Can we combine different phylogenetic estimates across the tree of life? And finally, what is the future of understanding the tree of life?

A program to compute the soft Robinson-Foulds distance between phylogenetic networks

Background

Over the past two decades, phylogenetic networks have been studied to model reticulate evolutionary events. The relationships among phylogenetic networks, phylogenetic trees and clusters serve as the basis for reconstruction and comparison of phylogenetic networks. To understand these relationships, two problems are raised: the tree containment problem, which asks whether a phylogenetic tree is displayed in a phylogenetic network, and the cluster containment problem, which asks whether a cluster is represented at a node in a phylogenetic network. Both the problems are NP-complete.

Results

A fast exponential-time algorithm for the cluster containment problem on arbitrary networks is developed and implemented in C. The resulting program is further extended into a computer program for fast computation of the Soft Robinson–Foulds distance between phylogenetic networks.

Conclusions

Two computer programs are developed for facilitating reconstruction and validation of phylogenetic network models in evolutionary and comparative genomics. Our simulation tests indicated that they are fast enough for use in practice. Additionally, the distribution of the Soft Robinson–Foulds distance between phylogenetic networks is demonstrated to be unlikely normal by our simulation data.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3500-5) contains supplementary material, which is available to authorized users.

Unknown unknowns: essential genes in quest for function

The experimental design of a minimal synthetic genome revealed the presence of a large number of genes without ascribed function, in part because the abstract laws of life must be implemented within ad hoc material contraptions. Creating a function needs recruitment of some pre‐existing structure and this reveals kludges in their set‐up and history. Here, we show that looking for functions as an engineer would help in discovery of a significant number of those, proposed together with conceptual handles allowing investigators to pursue this endeavour in other contexts.

Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification

Analyses of genome sequences, by some approaches, suggest that the widespread occurrence of horizontal gene transfers (HGTs) in prokaryotes disguises their evolutionary relationships and have led to questioning of the Darwinian model of evolution for prokaryotes. These inferences are critically examined in the light of comparative genome analysis, characteristic synapomorphies, phylogenetic trees and Darwin's views on examining evolutionary relationships. Genome sequences are enabling discovery of numerous molecular markers (synapomorphies) such as conserved signature indels (CSIs) and conserved signature proteins (CSPs), which are distinctive characteristics of different prokaryotic taxa. Based on these molecular markers, exhibiting high degree of specificity and predictive ability, numerous prokaryotic taxa of different ranks, currently identified based on the 16S rRNA gene trees, can now be reliably demarcated in molecular terms. Within all studied groups, multiple CSIs and CSPs have been identified for successive nested clades providing reliable information regarding their hierarchical relationships and these inferences are not affected by HGTs. These results strongly support Darwin's views on evolution and classification and supplement the current phylogenetic framework based on 16S rRNA in important respects. The identified molecular markers provide important means for developing novel diagnostics, therapeutics and for functional studies providing important insights regarding prokaryotic taxa.