Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome

Pangenomes exhibit remarkable variability in many prokaryotic species, much of which is maintained through the processes of horizontal gene transfer and gene loss. Repeated acquisitions of near-identical homologs can easily be observed across pangenomes, leading to the question of whether these parallel events potentiate similar evolutionary trajectories, or whether the remarkably different genetic backgrounds of the recipients mean that postacquisition evolutionary trajectories end up being quite different. In this study, we present a machine learning method that predicts the presence or absence of genes in the Escherichia coli pangenome based on complex patterns of the presence or absence of other accessory genes within a genome. Our analysis leverages the repeated transfer of genes through the E. coli pangenome to observe patterns of repeated evolution following similar events. We find that the presence or absence of a substantial set of genes is highly predictable from other genes alone, indicating that selection potentiates and maintains gene-gene co-occurrence and avoidance relationships deterministically over long-term bacterial evolution and is robust to differences in host evolutionary history. We propose that at least part of the pangenome can be understood as a set of genes with relationships that govern their likely cohabitants, analogous to an ecosystem's set of interacting organisms. Our findings indicate that intragenomic gene fitness effects may be key drivers of prokaryotic evolution, influencing the repeated emergence of complex gene-gene relationships across the pangenome.

Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types

The Escherichia coli species contains a diverse set of sequence types and there remain important questions regarding differences in genetic content within this population that need to be addressed. Pangenomes are useful vehicles for studying gene content within sequence types. Here, we analyse 21 E. coli sequence type pangenomes using comparative pangenomics to identify variance in both pangenome structure and content. We present functional breakdowns of sequence type core genomes and identify sequence types that are enriched in metabolism, transcription and cell membrane biogenesis genes. We also uncover metabolism genes that have variable core classification, depending on which allele is present. Our comparative pangenomics approach allows for detailed exploration of sequence type pangenomes within the context of the species. We show that ongoing gene gain and loss in the E. coli pangenome is sequence type-specific, which may be a consequence of distinct sequence type-specific evolutionary drivers.

Prokaryotic Pangenomes Act as Evolving Ecosystems

Understanding adaptation to the local environment is a central tenet and a major focus of evolutionary biology. But this is only part of the adaptionist story. In addition to the external environment, one of the main drivers of genome composition is genetic background. In this perspective, I argue that there is a growing body of evidence that intra-genomic selective pressures play a significant part in the composition of prokaryotic genomes and play a significant role in the origin, maintenance and structuring of prokaryotic pangenomes.

Prokaryote pangenomes are dynamic entities

Prokaryote pangenomes are influenced heavily by environmental factors and the opportunity for gene gain and loss events. As the field of pangenome analysis has expanded, so has the need to fully understand the complexity of how eco-evolutionary dynamics shape pangenomes. Here, we describe current models of pangenome evolution and discuss their suitability and accuracy. We suggest that pangenomes are dynamic entities under constant flux, highlighting the influence of two-way interactions between pangenome and environment. New classifications of core and accessory genes are also considered, underscoring the need for continuous evaluation of nomenclature in a fast-moving field. We conclude that future models of pangenome evolution should incorporate eco-evolutionary dynamics to fully encompass their dynamic, changeable nature.

Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility

The pangenome contains all genes encoded by a species, with the core genome present in all strains and the accessory genome in only a subset. Coincident gene relationships are expected within the accessory genome, where the presence or absence of one gene is influenced by the presence or absence of another. Here, we analysed the accessory genome of an Escherichia coli pangenome consisting of 400 genomes from 20 sequence types to identify genes that display significant co-occurrence or avoidance patterns with one another. We present a complex network of genes that are either found together or that avoid one another more often than would be expected by chance, and show that these relationships vary by lineage. We demonstrate that genes co-occur by function, and that several highly connected gene relationships are linked to mobile genetic elements. We find that genes are more likely to co-occur with, rather than avoid, another gene in the accessory genome. This work furthers our understanding of the dynamic nature of prokaryote pangenomes and implicates both function and mobility as drivers of gene relationships.

Evidence for Selection in the Abundant Accessory Gene Content of a Prokaryote Pangenome

A pangenome is the complete set of genes (core and accessory) present in a phylogenetic clade. We hypothesize that a pangenome's accessory gene content is structured and maintained by selection. To test this hypothesis, we interrogated the genomes of 40 Pseudomonas species for statistically significant coincident (i.e., co-occurring/avoiding) gene patterns. We found that 86.7% of common accessory genes are involved in ≥1 coincident relationship. Further, genes that co-occur and/or avoid each other-but are not vertically inherited-are more likely to share functional categories, are more likely to be simultaneously transcribed, and are more likely to produce interacting proteins, than would be expected by chance. These results are not due to coincident genes being adjacent to one another on the chromosome. Together, these findings suggest that the accessory genome is structured into sets of genes that function together within a given strain. Given the similarity of the Pseudomonas pangenome with open pangenomes of other prokaryotic species, we speculate that these results are generalizable.

Mechanisms That Shape Microbial Pangenomes

Analyses of multiple whole-genome sequences from the same species have revealed that differences in gene content can be substantial, particularly in prokaryotes. Such variation has led to the recognition of pangenomes, the complete set of genes present in a species - consisting of core genes, present in all individuals, and accessory genes whose presence is variable. Questions now arise about how pangenomes originate and evolve. We describe how gene content variation can arise as a result of the combination of several processes, including random drift, selection, gain/loss balance, and the influence of ecological and epistatic interactions. We believe that identifying the contributions of these processes to pangenomes will need novel theoretical approaches and empirical data.

Horizontal Gene Transfer as a Source of Conflict and Cooperation in Prokaryotes

Horizontal gene transfer (HGT) is one of the most important processes in prokaryote evolution. The sharing of DNA can spread neutral or beneficial genes, as well as genetic parasites across populations and communities, creating a large proportion of the variability acted on by natural selection. Here, we highlight the role of HGT in enhancing the opportunities for conflict and cooperation within and between prokaryote genomes. We discuss how horizontally acquired genes can cooperate or conflict both with each other and with a recipient genome, resulting in signature patterns of gene co-occurrence, avoidance, and dependence. We then describe how interactions involving horizontally transferred genes may influence cooperation and conflict at higher levels (populations, communities, and symbioses). Finally, we consider the benefits and drawbacks of HGT for prokaryotes and its fundamental role in understanding conflict and cooperation from the gene-gene to the microbiome level.

Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human

Gene fusion occurs when two or more individual genes with independent open reading frames becoming juxtaposed under the same open reading frame creating a new fused gene. A small number of gene fusions described in detail have been associated with novel functions, for example, the hominid-specific PIPSL gene, TNFSF12, and the TWE-PRIL gene family. We use Sequence Similarity Networks and species level comparisons of great ape genomes to identify 45 new genes that have emerged by transcriptional readthrough, that is, transcription-derived gene fusion. For 35 of these putative gene fusions, we have been able to assess available RNAseq data to determine whether there are reads that map to each breakpoint. A total of 29 of the putative gene fusions had annotated transcripts (9/29 of which are human-specific). We carried out RT-qPCR in a range of human tissues (placenta, lung, liver, brain, and testes) and found that 23 of the putative gene fusion events were expressed in at least one tissue. Examining the available ribosome foot-printing data, we find evidence for translation of three of the fused genes in human. Finally, we find enrichment for transcription-derived gene fusions in regions of known segmental duplication in human. Together, our results implicate chromosomal structural variation brought about by segmental duplication with the emergence of novel transcripts and translated protein products.

Eukaryote Genes Are More Likely than Prokaryote Genes to Be Composites

The formation of new genes by combining parts of existing genes is an important evolutionary process. Remodelled genes, which we call composites, have been investigated in many species, however, their distribution across all of life is still unknown. We set out to examine the extent to which genomes from cells and mobile genetic elements contain composite genes. We identify composite genes as those that show partial homology to at least two unrelated component genes. In order to identify composite and component genes, we constructed sequence similarity networks (SSNs) of more than one million genes from all three domains of life, as well as viruses and plasmids. We identified non-transitive triplets of nodes in this network and explored the homology relationships in these triplets to see if the middle nodes were indeed composite genes. In total, we identified 221,043 (18.57%) composites genes, which were distributed across all genomic and functional categories. In particular, the presence of composite genes is statistically more likely in eukaryotes than prokaryotes.

Bipartite Network Analysis of Gene Sharings in the Microbial World

Extensive microbial gene flows affect how we understand virology, microbiology, medical sciences, genetic modification, and evolutionary biology. Phylogenies only provide a narrow view of these gene flows: plasmids and viruses, lacking core genes, cannot be attached to cellular life on phylogenetic trees. Yet viruses and plasmids have a major impact on cellular evolution, affecting both the gene content and the dynamics of microbial communities. Using bipartite graphs that connect up to 149,000 clusters of homologous genes with 8,217 related and unrelated genomes, we can in particular show patterns of gene sharing that do not map neatly with the organismal phylogeny. Homologous genes are recycled by lateral gene transfer, and multiple copies of homologous genes are carried by otherwise completely unrelated (and possibly nested) genomes, that is, viruses, plasmids and prokaryotes. When a homologous gene is present on at least one plasmid or virus and at least one chromosome, a process of "gene externalization," affected by a postprocessed selected functional bias, takes place, especially in Bacteria. Bipartite graphs give us a view of vertical and horizontal gene flow beyond classic taxonomy on a single very large, analytically tractable, graph that goes beyond the cellular Web of Life.

Formation of chimeric genes with essential functions at the origin of eukaryotes

BACKGROUND

Eukaryotes evolved from the symbiotic association of at least two prokaryotic partners, and a good deal is known about the timings, mechanisms, and dynamics of these evolutionary steps. Recently, it was shown that a new class of nuclear genes, symbiogenetic genes (S-genes), was formed concomitant with endosymbiosis and the subsequent evolution of eukaryotic photosynthetic lineages. Understanding their origins and contributions to eukaryogenesis would provide insights into the ways in which cellular complexity has evolved.

RESULTS

Here, we show that chimeric nuclear genes (S-genes), built from prokaryotic domains, are critical for explaining the leap forward in cellular complexity achieved during eukaryogenesis. A total of 282 S-gene families contributed solutions to many of the challenges faced by early eukaryotes, including enhancing the informational machinery, processing spliceosomal introns, tackling genotoxicity within the cell, and ensuring functional protein interactions in a larger, more compartmentalized cell. For hundreds of S-genes, we confirmed the origins of their components (bacterial, archaeal, or generally prokaryotic) by maximum likelihood phylogenies. Remarkably, Bacteria contributed nine-fold more S-genes than Archaea, including a two-fold greater contribution to informational functions. Therefore, there is an additional, large bacterial contribution to the evolution of eukaryotes, implying that fundamental eukaryotic properties do not strictly follow the traditional informational/operational divide for archaeal/bacterial contributions to eukaryogenesis.

CONCLUSION

This study demonstrates the extent and process through which prokaryotic fragments from bacterial and archaeal genes inherited during eukaryogenesis underly the creation of novel chimeric genes with important functions.

The role of public goods in planetary evolution

Biological public goods are broadly shared within an ecosystem and readily available. They appear to be widespread and may have played important roles in the history of life on Earth. Of particular importance to events in the early history of life are the roles of public goods in the merging of genomes, protein domains and even cells. We suggest that public goods facilitated the origin of the eukaryotic cell, a classic major evolutionary transition. The recognition of genomic public goods challenges advocates of a direct graph view of phylogeny, and those who deny that any useful phylogenetic signal persists in modern genomes. Ecological spillovers generate public goods that provide new ecological opportunities.This article is part of the themed issue 'Reconceptualizing the origins of life'.

Function-related replacement of bacterial siderophore pathways

Bacterial genomes are rife with orphan biosynthetic gene clusters (BGCs) associated with secondary metabolism of unrealized natural product molecules. Often up to a tenth of the genome is predicted to code for the biosynthesis of diverse metabolites with mostly unknown structures and functions. This phenomenal diversity of BGCs coupled with their high rates of horizontal transfer raise questions about whether they are really active and beneficial, whether they are neutral and confer no advantage, or whether they are carried in genomes because they are parasitic or addictive. We previously reported that Salinispora bacteria broadly use the desferrioxamine family of siderophores for iron acquisition. Herein we describe a new and unrelated group of peptidic siderophores called salinichelins from a restricted number of Salinispora strains in which the desferrioxamine biosynthesis genes have been lost. We have reconstructed the evolutionary history of these two different siderophore families and show that the acquisition and retention of the new salinichelin siderophores co-occurs with the loss of the more ancient desferrioxamine pathway. This identical event occurred at least three times independently during the evolution of the genus. We surmise that certain BGCs may be extraneous because of their functional redundancy and demonstrate that the relative evolutionary pace of natural pathway replacement shows high selective pressure against retention of functionally superfluous gene clusters.

Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations

The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could provide unparalleled detail of the evolution of a bacterial population. Here we demonstrate this principle by applying it to a worldwide multi-host sample of the important pathogenic E. coli lineage ST131. Our approach reveals the existence of multiple circulating subtypes of the major drug–resistant clade of ST131 and provides the first ever population level evidence of core genome substitutions in gene regulatory regions associated with the acquisition and maintenance of different accessory genome elements.

We present an approach to evolutionary analysis of bacterial pathogens combining core genome, accessory genome, and gene regulatory region analyses. This enables unparalleled resolution of the evolution of a multi-drug resistant pandemic pathogen that would remain invisible to a core genome phylogenetic analysis alone. In particular, our combined analysis approach identifies population-level evidence for compensatory mutations offsetting the costs of resistance plasmid maintenance as a key event in the emergence of dominant MDR lineages of E. coli.

Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis

The origin of the eukaryotic cell is considered one of the major evolutionary transitions in the history of life. Current evidence strongly supports a scenario of eukaryotic origin in which two prokaryotes, an archaebacterial host and an α-proteobacterium (the free-living ancestor of the mitochondrion), entered a stable symbiotic relationship. The establishment of this relationship was associated with a process of chimerization, whereby a large number of genes from the α-proteobacterial symbiont were transferred to the host nucleus. A general framework allowing the conceptualization of eukaryogenesis from a genomic perspective has long been lacking. Recent studies suggest that the origins of several archaebacterial phyla were coincident with massive imports of eubacterial genes. Although this does not indicate that these phyla originated through the same process that led to the origin of Eukaryota, it suggests that Archaebacteria might have had a general propensity to integrate into their genomes large amounts of eubacterial DNA. We suggest that this propensity provides a framework in which eukaryogenesis can be understood and studied in the light of archaebacterial ecology. We applied a recently developed supertree method to a genomic dataset composed of 392 eubacterial and 51 archaebacterial genera to test whether large numbers of genes flowing from Eubacteria are indeed coincident with the origin of major archaebacterial clades. In addition, we identified two potential large-scale transfers of uncertain directionality at the base of the archaebacterial tree. Our results are consistent with previous findings and seem to indicate that eubacterial gene imports (particularly from δ-Proteobacteria, Clostridia and Actinobacteria) were an important factor in archaebacterial history. Archaebacteria seem to have long relied on Eubacteria as a source of genetic diversity, and while the precise mechanism that allowed these imports is unknown, we suggest that our results support the view that processes comparable to those through which eukaryotes emerged might have been common in archaebacterial history.

"Every Gene Is Everywhere but the Environment Selects": Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis

The spatial distribution of microbes on our planet is famously formulated in the Baas Becking hypothesis as “everything is everywhere but the environment selects.” While this hypothesis does not strictly rule out patterns caused by geographical effects on ecology and historical founder effects, it does propose that the remarkable dispersal potential of microbes leads to distributions generally shaped by environmental factors rather than geographical distance. By constructing sequence similarity networks from uncultured environmental samples, we show that microbial gene pool distributions are not influenced nearly as much by geography as ecology, thus extending the Bass Becking hypothesis from whole organisms to microbial genes. We find that gene pools are shaped by their broad ecological niche (such as sea water, fresh water, host, and airborne). We find that freshwater habitats act as a gene exchange bridge between otherwise disconnected habitats. Finally, certain antibiotic resistance genes deviate from the general trend of habitat specificity by exhibiting a high degree of cross-habitat mobility. The strong cross-habitat mobility of antibiotic resistance genes is a cause for concern and provides a paradigmatic example of the rate by which genes colonize new habitats when new selective forces emerge.

Endosymbiotic origin and differential loss of eukaryotic genes

Chloroplasts arose from cyanobacteria, mitochondria arose from proteobacteria. Both organelles have conserved their prokaryotic biochemistry, but their genomes are reduced, and most organelle proteins are encoded in the nucleus. Endosymbiotic theory posits that bacterial genes in eukaryotic genomes entered the eukaryotic lineage via organelle ancestors. It predicts episodic influx of prokaryotic genes into the eukaryotic lineage, with acquisition corresponding to endosymbiotic events. Eukaryotic genome sequences, however, increasingly implicate lateral gene transfer, both from prokaryotes to eukaryotes and among eukaryotes, as a source of gene content variation in eukaryotic genomes, which predicts continuous, lineage-specific acquisition of prokaryotic genes in divergent eukaryotic groups. Here we discriminate between these two alternatives by clustering and phylogenetic analysis of eukaryotic gene families having prokaryotic homologues. Our results indicate (1) that gene transfer from bacteria to eukaryotes is episodic, as revealed by gene distributions, and coincides with major evolutionary transitions at the origin of chloroplasts and mitochondria; (2) that gene inheritance in eukaryotes is vertical, as revealed by extensive topological comparison, sparse gene distributions stemming from differential loss; and (3) that continuous, lineage-specific lateral gene transfer, although it sometimes occurs, does not contribute to long-term gene content evolution in eukaryotic genomes.

Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears

Polar bears are uniquely adapted to life in the High Arctic and have undergone drastic physiological changes in response to Arctic climates and a hyper-lipid diet of primarily marine mammal prey. We analyzed 89 complete genomes of polar bear and brown bear using population genomic modeling and show that the species diverged only 479-343 thousand years BP. We find that genes on the polar bear lineage have been under stronger positive selection than in brown bears; nine of the top 16 genes under strong positive selection are associated with cardiomyopathy and vascular disease, implying important reorganization of the cardiovascular system. One of the genes showing the strongest evidence of selection, APOB, encodes the primary lipoprotein component of low-density lipoprotein (LDL); functional mutations in APOB may explain how polar bears are able to cope with life-long elevated LDL levels that are associated with high risk of heart disease in humans.

A pluralistic account of homology: adapting the models to the data

Defining homologous genes is important in many evolutionary studies but raises obvious issues. Some of these issues are conceptual and stem from our assumptions of how a gene evolves, others are practical, and depend on the algorithmic decisions implemented in existing software. Therefore, to make progress in the study of homology, both ontological and epistemological questions must be considered. In particular, defining homologous genes cannot be solely addressed under the classic assumptions of strong tree thinking, according to which genes evolve in a strictly tree-like fashion of vertical descent and divergence and the problems of homology detection are primarily methodological. Gene homology could also be considered under a different perspective where genes evolve as “public goods,” subjected to various introgressive processes. In this latter case, defining homologous genes becomes a matter of designing models suited to the actual complexity of the data and how such complexity arises, rather than trying to fit genetic data to some a priori tree-like evolutionary model, a practice that inevitably results in the loss of much information. Here we show how important aspects of the problems raised by homology detection methods can be overcome when even more fundamental roots of these problems are addressed by analyzing public goods thinking evolutionary processes through which genes have frequently originated. This kind of thinking acknowledges distinct types of homologs, characterized by distinct patterns, in phylogenetic and nonphylogenetic unrooted or multirooted networks. In addition, we define “family resemblances” to include genes that are related through intermediate relatives, thereby placing notions of homology in the broader context of evolutionary relationships. We conclude by presenting some payoffs of adopting such a pluralistic account of homology and family relationship, which expands the scope of evolutionary analyses beyond the traditional, yet relatively narrow focus allowed by a strong tree-thinking view on gene evolution.

Integration of two ancestral chaperone systems into one: the evolution of eukaryotic molecular chaperones in light of eukaryogenesis

Eukaryotic genomes are mosaics of genes acquired from their prokaryotic ancestors, the eubacterial endosymbiont that gave rise to the mitochondrion and its archaebacterial host. Genomic footprints of the prokaryotic merger at the origin of eukaryotes are still discernable in eukaryotic genomes, where gene expression and function correlate with their prokaryotic ancestry. Molecular chaperones are essential in all domains of life as they assist the functional folding of their substrate proteins and protect the cell against the cytotoxic effects of protein misfolding. Eubacteria and archaebacteria code for slightly different chaperones, comprising distinct protein folding pathways. Here we study the evolution of the eukaryotic protein folding pathways following the endosymbiosis event. A phylogenetic analysis of all 64 chaperones encoded in the Saccharomyces cerevisiae genome revealed 25 chaperones of eubacterial ancestry, 11 of archaebacterial ancestry, 10 of ambiguous prokaryotic ancestry, and 18 that may represent eukaryotic innovations. Several chaperone families (e.g., Hsp90 and Prefoldin) trace their ancestry to only one prokaryote group, while others, such as Hsp40 and Hsp70, are of mixed ancestry, with members contributed from both prokaryotic ancestors. Analysis of the yeast chaperone–substrate interaction network revealed no preference for interaction between chaperones and substrates of the same origin. Our results suggest that the archaebacterial and eubacterial protein folding pathways have been reorganized and integrated into the present eukaryotic pathway. The highly integrated chaperone system of yeast is a manifestation of the central role of chaperone-mediated folding in maintaining cellular fitness. Most likely, both archaebacterial and eubacterial chaperone systems were essential at the very early stages of eukaryogenesis, and the retention of both may have offered new opportunities for expanding the scope of chaperone-mediated folding.

More than tree dimensions: inter-lineage evolution's ecological importance

Horizontal transfer of genes has sometimes been viewed as a nuisance for the work of understanding the evolutionary history of lineages. Recent work has shown that clever analysis of inter-lineage gene transfer is productive and has tremendous explanatory power, in particular, for niche adaptation. These studies alter our perception of what are the fundamental units of evolution and selection.

Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates

Synonymous codon usage patterns are shaped by a balance between mutation, drift, and natural selection. To date, detection of translational selection in vertebrates has proven to be a challenging task, obscured by small long-term effective population sizes in larger animals and the existence of isochores in some species. The consensus is that, in such species, natural selection is either completely ineffective at overcoming mutational pressures and genetic drift or perhaps is effective but so weak that it is not detectable. The aim of this research is to understand the interplay between mutation, selection, and genetic drift in vertebrates. We observe that although variation in mutational bias is undoubtedly the dominant force influencing codon usage, translational selection acts as a weak additional factor influencing synonymous codon usage. These observations indicate that translational selection is a widespread phenomenon in vertebrates and is not limited to a few species.

Heterogeneous models place the root of the placental mammal phylogeny

Heterogeneity among life traits in mammals has resulted in considerable phylogenetic conflict, particularly concerning the position of the placental root. Layered upon this are gene- and lineage-specific variation in amino acid substitution rates and compositional biases. Life trait variations that may impact upon mutational rates are longevity, metabolic rate, body size, and germ line generation time. Over the past 12 years, three main conflicting hypotheses have emerged for the placement of the placental root. These hypotheses place the Atlantogenata (common ancestor of Xenarthra plus Afrotheria), the Afrotheria, or the Xenarthra as the sister group to all other placental mammals. Model adequacy is critical for accurate tree reconstruction and by failing to account for these compositional and character exchange heterogeneities across the tree and data set, previous studies have not provided a strongly supported hypothesis for the placental root. For the first time, models that accommodate both tree and data set heterogeneity have been applied to mammal data. Here, we show the impact of accurate model assignment and the importance of data sets in accommodating model parameters while maintaining the power to reject competing hypotheses. Through these sophisticated methods, we demonstrate the importance of model adequacy, data set power and provide strong support for the Atlantogenata over other competing hypotheses for the position of the placental root.

New approaches for unravelling reassortment pathways

BACKGROUND

Every year the human population encounters epidemic outbreaks of influenza, and history reveals recurring pandemics that have had devastating consequences. The current work focuses on the development of a robust algorithm for detecting influenza strains that have a composite genomic architecture. These influenza subtypes can be generated through a reassortment process, whereby a virus can inherit gene segments from two different types of influenza particles during replication. Reassortant strains are often not immediately recognised by the adaptive immune system of the hosts and hence may be the source of pandemic outbreaks. Owing to their importance in public health and their infectious ability, it is essential to identify reassortant influenza strains in order to understand the evolution of this virus and describe reassortment pathways that may be biased towards particular viral segments. Phylogenetic methods have been used traditionally to identify reassortant viruses. In many studies up to now, the assumption has been that if two phylogenetic trees differ, it is because reassortment has caused them to be different. While phylogenetic incongruence may be caused by real differences in evolutionary history, it can also be the result of phylogenetic error. Therefore, we wish to develop a method for distinguishing between topological inconsistency that is due to confounding effects and topological inconsistency that is due to reassortment.

RESULTS

The current work describes the implementation of two approaches for robustly identifying reassortment events. The algorithms rest on the idea of significance of difference between phylogenetic trees or phylogenetic tree sets, and subtree pruning and regrafting operations, which mimic the effect of reassortment on tree topologies. The first method is based on a maximum likelihood (ML) framework (MLreassort) and the second implements a Bayesian approach (Breassort) for reassortment detection. We focus on reassortment events that are found by both methods. We test both methods on a simulated dataset and on a small collection of real viral data isolated in Hong Kong in 1999.

CONCLUSIONS

The nature of segmented viral genomes present many challenges with respect to disease. The algorithms developed here can effectively identify reassortment events in small viral datasets and can be applied not only to influenza but also to other segmented viruses. Owing to computational demands of comparing tree topologies, further development in this area is necessary to allow their application to larger datasets.

Increased genome sampling reveals a dynamic relationship between gene duplicability and the structure of the primate protein-protein interaction network

Although gene duplications occur at a higher rate, only a small fraction of these are retained. The position of a gene's encoded product in the protein-protein interaction network has recently emerged as a determining factor of gene duplicability. However, the direction of the relationship between network centrality and duplicability is not universal: In Escherichia coli, yeast, fly, and worm, duplicated genes more often act at the periphery of the network, whereas in humans, such genes tend to occupy the most central positions. Herein, we have inferred duplication events that took place in the different branches of the primate phylogeny. In agreement with previous observations, we found that duplications generally affected the most central network genes, which is presumably the process that has most influenced the trend in humans. However, the opposite trend--that is, duplication being more common in genes whose encoded products are peripheral in the network--is observed for three recent branches, including, quite counterintuitively, the external branch leading to humans. This indicates a shift in the relationship between centrality and duplicability during primate evolution. Furthermore, we found that genes encoding interacting proteins exhibit phylogenetic tree topologies that are more similar than expected for random pairs and that genes duplicated in a given branch of the phylogeny tend to interact with those that duplicated in the same lineage. These results indicate that duplication of a gene increases the likelihood of duplication of its interacting partners. Our observations indicate that the structure of the primate protein-protein interaction network affects gene duplicability in previously unrecognized ways.

The Public Goods Hypothesis for the evolution of life on Earth

It is becoming increasingly difficult to reconcile the observed extent of horizontal gene transfers with the central metaphor of a great tree uniting all evolving entities on the planet. In this manuscript we describe the Public Goods Hypothesis and show that it is appropriate in order to describe biological evolution on the planet. According to this hypothesis, nucleotide sequences (genes, promoters, exons, etc.) are simply seen as goods, passed from organism to organism through both vertical and horizontal transfer. Public goods sequences are defined by having the properties of being largely non-excludable (no organism can be effectively prevented from accessing these sequences) and non-rival (while such a sequence is being used by one organism it is also available for use by another organism). The universal nature of genetic systems ensures that such non-excludable sequences exist and non-excludability explains why we see a myriad of genes in different combinations in sequenced genomes. There are three features of the public goods hypothesis. Firstly, segments of DNA are seen as public goods, available for all organisms to integrate into their genomes. Secondly, we expect the evolution of mechanisms for DNA sharing and of defense mechanisms against DNA intrusion in genomes. Thirdly, we expect that we do not see a global tree-like pattern. Instead, we expect local tree-like patterns to emerge from the combination of a commonage of genes and vertical inheritance of genomes by cell division. Indeed, while genes are theoretically public goods, in reality, some genes are excludable, particularly, though not only, when they have variant genetic codes or behave as coalition or club goods, available for all organisms of a coalition to integrate into their genomes, and non-rival within the club. We view the Tree of Life hypothesis as a regionalized instance of the Public Goods hypothesis, just like classical mechanics and euclidean geometry are seen as regionalized instances of quantum mechanics and Riemannian geometry respectively. We argue for this change using an axiomatic approach that shows that the Public Goods hypothesis is a better accommodation of the observed data than the Tree of Life hypothesis.

Planctomycetes and eukaryotes: a case of analogy not homology

Planctomycetes, Verrucomicrobia and Chlamydia are prokaryotic phyla, sometimes grouped together as the PVC superphylum of eubacteria. Some PVC species possess interesting attributes, in particular, internal membranes that superficially resemble eukaryotic endomembranes. Some biologists now claim that PVC bacteria are nucleus-bearing prokaryotes and are considered evolutionary intermediates in the transition from prokaryote to eukaryote. PVC prokaryotes do not possess a nucleus and are not intermediates in the prokaryote-to-eukaryote transition. Here we summarise the evidence that shows why all of the PVC traits that are currently cited as evidence for aspiring eukaryoticity are either analogous (the result of convergent evolution), not homologous, to eukaryotic traits; or else they are the result of horizontal gene transfers.

The human genome retains relics of its prokaryotic ancestry: human genes of archaebacterial and eubacterial origin exhibit remarkable differences

Eukaryotes are generally thought to stem from a fusion event involving an archaebacterium and a eubacterium. As a result of this event, contemporaneous eukaryotic genomes are chimeras of genes inherited from both endosymbiotic partners. These two coexisting gene repertoires have been shown to differ in a number of ways in yeast. Here we combine genomic and functional data in order to determine if and how human genes that have been inherited from both prokaryotic ancestors remain distinguishable. We show that, despite being fewer in number, human genes of archaebacterial origin are more highly and broadly expressed across tissues, are more likely to have lethal mouse orthologs, tend to be involved in informational processes, are more selectively constrained, and encode shorter and more central proteins in the protein–protein interaction network than eubacterium-like genes. Furthermore, consistent with endosymbiotic theory, we show that proteins tend to interact with those encoded by genes of the same ancestry. Most interestingly from a human health perspective, archaebacterial genes are less likely to be involved in heritable human disease. Taken together, these results show that more than 2 billion years after eukaryogenesis, the human genome retains at least two somewhat distinct communities of genes.

Gene and genome trees conflict at many levels

Horizontal gene transfer (HGT) plays a significant role in microbial evolution. It can accelerate the adaptation of an organism, it can generate new metabolic pathways and it can completely remodel an organism's genome. We examine 27 closely related genomes from the YESS group of gamma proteobacteria and a variety of four-taxon datasets from a diverse range of prokaryotes in order to explore the kinds of effects HGT has had on these organisms.

Molecular phylogeny of the Drosophila tripunctata and closely related species groups (Diptera: Drosophilidae)

We suggest a new phylogenetic hypothesis for the tripunctata radiation based on sequences of mitochondrial genes. Phylogenetic trees were reconstructed by parsimony, maximum likelihood and Bayesian methods. We performed tests for hypotheses of monophyly for taxonomic groups and other specific hypotheses. Results reject the monophyly for the tripunctata group whereas monophyly is not rejected for the tripunctata radiation and other specific groups within the radiation. Although most of the basal nodes were unresolved we were able to identify four clusters within the tripunctata radiation. These results suggest the collection of additional data before a proper taxonomic revision could be proposed.

Recurring cluster and operon assembly for Phenylacetate degradation genes

Background

A large number of theories have been advanced to explain why genes involved in the same biochemical processes are often co-located in genomes. Most of these theories have been dismissed because empirical data do not match the expectations of the models. In this work we test the hypothesis that cluster formation is most likely due to a selective pressure to gradually co-localise protein products and that operon formation is not an inevitable conclusion of the process.

Results

We have selected an exemplar well-characterised biochemical pathway, the phenylacetate degradation pathway, and we show that its complex history is only compatible with a model where a selective advantage accrues from moving genes closer together. This selective pressure is likely to be reasonably weak and only twice in our dataset of 102 genomes do we see independent formation of a complete cluster containing all the catabolic genes in the pathway. Additionally, de novo clustering of genes clearly occurs repeatedly, even though recombination should result in the random dispersal of such genes in their respective genomes. Interspecies gene transfer has frequently replaced in situ copies of genes resulting in clusters that have similar content but very different evolutionary histories.

Conclusion

Our model for cluster formation in prokaryotes, therefore, consists of a two-stage selection process. The first stage is selection to move genes closer together, either because of macromolecular crowding, chromatin relaxation or transcriptional regulation pressure. This proximity opportunity sets up a separate selection for co-transcription.

Trees from trees: construction of phylogenetic supertrees using clann

Supertree methods combine multiple phylogenetic trees to produce the overall best "supertree." They can be used to combine phylogenetic information from datasets only partially overlapping and from disparate sources (like molecular and morphological data), or to break down problems thought to be computationally intractable. Some of the longest standing phylogenetic conundrums are now being brought to light using supertree approaches. We describe the most widely used supertree methods implemented in the software program "clann" and provide a step by step tutorial for investigating phylogenetic information and reconstructing the best supertree. Clann is freely available for Windows, Mac and Unix/Linux operating systems under the GNU public licence at (http://bioinf.nuim.ie/software/clann).

The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods

BACKGROUND

In the past decade or more, the emphasis for reconstructing species phylogenies has moved from the analysis of a single gene to the analysis of multiple genes and even completed genomes. The simplest method of scaling up is to use familiar analysis methods on a larger scale and this is the most popular approach. However, duplications and losses of genes along with horizontal gene transfer (HGT) can lead to a situation where there is only an indirect relationship between gene and genome phylogenies. In this study we examine five widely-used approaches and their variants to see if indeed they are more-or-less saying the same thing. In particular, we focus on Conditioned Reconstruction as it is a method that is designed to work well even if HGT is present.

RESULTS

We confirm a previous suggestion that this method has a systematic bias. We show that no two methods produce the same results and most current methods of inferring genome phylogenies produce results that are significantly different to other methods.

CONCLUSION

We conclude that genome phylogenies need to be interpreted differently, depending on the method used to construct them.

MultiPhyl: a high-throughput phylogenomics webserver using distributed computing

With the number of fully sequenced genomes increasing steadily, there is greater interest in performing large-scale phylogenomic analyses from large numbers of individual gene families. Maximum likelihood (ML) has been shown repeatedly to be one of the most accurate methods for phylogenetic construction. Recently, there have been a number of algorithmic improvements in maximum-likelihood-based tree search methods. However, it can still take a long time to analyse the evolutionary history of many gene families using a single computer. Distributed computing refers to a method of combining the computing power of multiple computers in order to perform some larger overall calculation. In this article, we present the first high-throughput implementation of a distributed phylogenetics platform, MultiPhyl, capable of using the idle computational resources of many heterogeneous non-dedicated machines to form a phylogenetics supercomputer. MultiPhyl allows a user to upload hundreds or thousands of amino acid or nucleotide alignments simultaneously and perform computationally intensive tasks such as model selection, tree searching and bootstrapping of each of the alignments using many desktop machines. The program implements a set of 88 amino acid models and 56 nucleotide maximum likelihood models and a variety of statistical methods for choosing between alternative models. A MultiPhyl webserver is available for public use at: http://www.cs.nuim.ie/distributed/multiphyl.php.

Supertrees Disentangle the Chimerical Origin of Eukaryotic Genomes

Eukaryotes are traditionally considered to be one of the three natural divisions of the tree of life and the sister group of the Archaebacteria. However, eukaryotic genomes are replete with genes of eubacterial ancestry, and more than 20 mutually incompatible hypotheses have been proposed to account for eukaryote origins. Here we test the predictions of these hypotheses using a novel supertree-based phylogenetic signal-stripping method, and recover supertrees of life based on phylogenies for up to 5,741 single gene families distributed across 185 genomes. Using our signal-stripping method, we show that there are three distinct phylogenetic signals in eukaryotic genomes. In order of strength, these link eukaryotes with the Cyanobacteria, the Proteobacteria, and the Thermoplasmatales, an archaebacterial (euryarchaeotes) group. These signals correspond to distinct symbiotic partners involved in eukaryote evolution: plastids, mitochondria, and the elusive host lineage. According to our whole-genome data, eukaryotes are hardly the sister group of the Archaebacteria, because up to 83% of eukaryotic genes with a prokaryotic homolog have eubacterial, not archaebacterial, origins. The results reject all but two of the current hypotheses for the origin of eukaryotes: those assuming a sulfur-dependent or hydrogen-dependent syntrophy for the origin of mitochondria.