Ancient phylogenetic relationships

Phylogenetic and structural analysis of centromeric DNA and kinetochore proteins

Analysis of centromeric DNA and kinetochore proteins suggests that critical structural features of kinetochores have been well conserved from yeast to man.

Background

Kinetochores are large multi-protein structures that assemble on centromeric DNA (CEN DNA) and mediate the binding of chromosomes to microtubules. Comprising 125 base-pairs of CEN DNA and 70 or more protein components, Saccharomyces cerevisiae kinetochores are among the best understood. In contrast, most fungal, plant and animal cells assemble kinetochores on CENs that are longer and more complex, raising the question of whether kinetochore architecture has been conserved through evolution, despite considerable divergence in CEN sequence.

Results

Using computational approaches, ranging from sequence similarity searches to hidden Markov model-based modeling, we show that organisms with CENs resembling those in S. cerevisiae (point CENs) are very closely related and that all contain a set of 11 kinetochore proteins not found in organisms with complex CENs. Conversely, organisms with complex CENs (regional CENs) contain proteins seemingly absent from point-CEN organisms. However, at least three quarters of known kinetochore proteins are present in all fungi regardless of CEN organization. At least six of these proteins have previously unidentified human orthologs. When fungi and metazoa are compared, almost all have kinetochores constructed around Spc105 and three conserved multi-protein linker complexes (MIND, COMA, and the NDC80 complex).

Conclusion

Our data suggest that critical structural features of kinetochores have been well conserved from yeast to man. Surprisingly, phylogenetic analysis reveals that human kinetochore proteins are as similar in sequence to their yeast counterparts as to presumptive Drosophila melanogaster or Caenorhabditis elegans orthologs. This finding is consistent with evidence that kinetochore proteins have evolved very rapidly relative to components of other complex cellular structures.

RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits

Background

Until today, analysis of 16S ribosomal RNA (rRNA) sequences has been the de-facto gold standard for the assessment of phylogenetic relationships among prokaryotes. However, the branching order of the individual phlya is not well-resolved in 16S rRNA-based trees. In search of an improvement, new phylogenetic methods have been developed alongside with the growing availability of complete genome sequences. Unfortunately, only a few genes in prokaryotic genomes qualify as universal phylogenetic markers and almost all of them have a lower information content than the 16S rRNA gene. Therefore, emphasis has been placed on methods that are based on multiple genes or even entire genomes. The concatenation of ribosomal protein sequences is one method which has been ascribed an improved resolution. Since there is neither a comprehensive database for ribosomal protein sequences nor a tool that assists in sequence retrieval and generation of respective input files for phylogenetic reconstruction programs, RibAlign has been developed to fill this gap.

Results

RibAlign serves two purposes: First, it provides a fast and scalable database that has been specifically adapted to eubacterial ribosomal protein sequences and second, it provides sophisticated import and export capabilities. This includes semi-automatic extraction of ribosomal protein sequences from whole-genome GenBank and FASTA files as well as exporting aligned, concatenated and filtered sequence files that can directly be used in conjunction with the PHYLIP and MrBayes phylogenetic reconstruction programs.

Conclusion

Up to now, phylogeny based on concatenated ribosomal protein sequences is hampered by the limited set of sequenced genomes and high computational requirements. However, hundreds of full and draft genome sequencing projects are on the way, and advances in cluster-computing and algorithms make phylogenetic reconstructions feasible even with large alignments of concatenated marker genes. RibAlign is a first step in this direction and may be particularly interesting to scientists involved in whole genome sequencing of representatives of new or sparsely studied eubacterial phyla. RibAlign is available at

Large-scale genome clustering across life based on a linguistic approach

With the availability of genome sequences, the possibility of new phylogenetic reconstructions arises in order to reveal genomic relationships among organisms. According to the compositional-spectra (CS) approach proposed in our previous studies, any genomic sequence can be characterized by a distribution of frequencies of imperfect matching of words (oligonucleotides). In the current application of CS-analysis, we attempted to analyze the cluster structure of genomes across life. It appeared that compositional spectra show a clear three-group clustering of the compared prokaryotic and eukaryotic genomes. Unexpectedly, this grouping seriously differs from the classical Universal Tree of Life structure represented by common kingdoms known as Eubacteria, Archaebacteria, and Eukarya. The revealed CS-clustering displays high stability, putatively reflecting its objective nature, and still enigmatic biological significance that may result from convergent evolution driven by ecological selection. We believe that our approach provides a new and wider (compared to traditional methods) perspective of extracting genomic information of high evolutionary relevance.

Origins of life and biochemistry under high-pressure conditions

Life on Earth can be traced back to as far as 3.8 billion years (Ga) ago. The catastrophic meteoritic bombardment ended between 4.2 and 3.9 Ga ago. Therefore, if life emerged, and we know it did, it must have emerged from nothingness in less than 400 million years. The most recent scenarios of Earth accretion predict some very unstable physico-chemical conditions at the surface of Earth, which, in such a short time period, would impede the emergence of life from a proto-biotic soup. A possible alternative would be that life originated in the depth of the proto-ocean of the Hadean Earth, under high hydrostatic pressure. The large body of water would filter harmful radiation and buffer physico-chemical variations, and therefore would provide a more stable radiation-free environment for pre-biotic chemistry. After a short introduction to Earth history, the current tutorial review presents biological and physico-chemical arguments in support of high-pressure origin for life on Earth.

Extreme life on Earth—past, present and possibly beyond

Life may have been present on Earth since about 3.8 billion years ago or earlier. Multidisciplinary research, especially on the paleobiology and evolution of early microorganisms on Earth and the microbiology of extremophiles in the Earth's environments and under space conditions, enables the defining of strategies for the detection of potential extraterrestrial life by determining biosignatures and the environmental envelope of life.

A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective

Using an algorithm for ancestral state inference of gene content, given a large number of extant genome sequences and a phylogenetic tree, we aim to reconstruct the gene content of the last universal common ancestor (LUCA), a hypothetical life form that presumably was the progenitor of the three domains of life. The method allows for gene loss, previously found to be a major factor in shaping gene content, and thus the estimate of LUCA's gene content appears to be substantially higher than that proposed previously, with a typical number of over 1000 gene families, of which more than 90% are also functionally characterized. More precisely, when only prokaryotes are considered, the number varies between 1006 and 1189 gene families while when eukaryotes are also included, this number increases to between 1344 and 1529 families depending on the underlying phylogenetic tree. Therefore, the common belief that the hypothetical genome of LUCA should resemble those of the smallest extant genomes of obligate parasites is not supported by recent advances in computational genomics. Instead, a fairly complex genome similar to those of free-living prokaryotes, with a variety of functional capabilities including metabolic transformation, information processing, membrane/transport proteins and complex regulation, shared between the three domains of life, emerges as the most likely progenitor of life on Earth, with profound repercussions for planetary exploration and exobiology.

Characterization of chaperonin 10 (Cpn10) from the intestinal human pathogen Entamoeba histolytica

Entamoeba histolytica is the causative agent of amoebiasis, a poverty-related disease that kills an estimated 100 000 people each year. E. histolytica does not contain "standard mitochondria", but harbours mitochondrial remnant organelles called mitosomes. These organelles are characterized by the presence of mitochondrial chaperonin Cpn60, but little else is known about the functions and molecular composition of mitosomes. In this study, a gene encoding molecular chaperonin Cpn10--the functional partner of Cpn60--was cloned, and its structure and expression were characterized, as well as the cellular localization of its encoded protein. The 5' untranslated region of the gene contains all of the structural promoter elements required for transcription in this organism. The amoebic Cpn10, like Cpn60, is not significantly upregulated upon heat-shock treatment. Computer-assisted protein modelling, and specific antibodies against Cpn10 and Cpn60, suggest that both proteins interact with each other, and that they function in the same intracellular compartment. Thus, E. histolytica appears to have retained at least two of the key molecular components required for the refolding of imported mitosomal proteins.

Ancient gene duplications and the root(s) of the tree of life

Tracing organismal histories on the timescale of the tree of life remains one of the challenging tasks in evolutionary biology. The hotly debated questions include the evolutionary relationship between the three domains of life (e.g., which of the three domains are sister domains, are the domains para-, poly-, or monophyletic) and the location of the root within the universal tree of life. For the latter, many different points of view have been considered but so far no consensus has been reached. The only widely accepted rationale to root the universal tree of life is to use anciently duplicated paralogous genes that are present in all three domains of life. To date only few anciently duplicated gene families useful for phylogenetic reconstruction have been identified. Here we present results from a systematic search for ancient gene duplications using twelve representative, completely sequenced, archaeal and bacterial genomes. Phylogenetic analyses of identified cases show that the majority of datasets support a root between Archaea and Bacteria; however, some datasets support alternative hypotheses, and all of them suffer from a lack of strong phylogenetic signal. The results are discussed with respect to the impact of horizontal gene transfer on the ability to reconstruct organismal evolution. The exchange of genetic information between divergent organisms gives rise to mosaic genomes, where different genes in a genome have different histories. Simulations show that even low rates of horizontal gene transfer dramatically complicate the reconstruction of organismal evolution, and that the different most recent common molecular ancestors likely existed at different times and in different lineages.

Congruence of evidence for a Methanopyrus-proximal root of life based on transfer RNA and aminoacyl-tRNA synthetase genes

Among 60 organisms, the intraspecies genetic distances between tRNAs cognate for different amino acids, between the initiator and elongator tRNAs for Met, and between potentially paralogous pairs of aminoacyl-tRNA synthetases are found to be at a minimum within the Methanopyrus kandleri genome. These results indicate an exact congruence between the evidence from tRNA and aminoacyl-tRNA synthetase genes locating the root of life closest to this organism.

Role of selection in fixation of gene duplications

New genes commonly appear through complete or partial duplications of pre-existing genes. Duplications of long DNA segments are constantly produced by rare mutations, may become fixed in a population by selection or random drift, and are subject to divergent evolution of the paralogous sequences after fixation, although gene conversion can impede this process. New data shed some light on each of these processes. Mutations which involve duplications can occur through at least two different mechanisms, backward strand slippage during DNA replication and unequal crossing-over. The background rate of duplication of a complete gene in humans is 10(-9)-10(-10) per generation, although many genes located within hot-spots of large-scale mutation are duplicated much more often. Many gene duplications affect fitness strongly, and are responsible, through gene dosage effects, for a number of genetic diseases. However, high levels of intrapopulation polymorphism caused by presence or absence of long, gene-containing DNA segments imply that some duplications are not under strong selection. The polymorphism to fixation ratios appear to be approximately the same for gene duplications and for presumably selectively neutral nucleotide substitutions, which, according to the McDonald-Kreitman test, is consistent with selective neutrality of duplications. However, this pattern can also be due to negative selection against most of segregating duplications and positive selection for at least some duplications which become fixed. Patterns in post-fixation evolution of duplicated genes do not easily reveal the causes of fixations. Many gene duplications which became fixed recently in a variety of organisms were positively selected because the increased expression of the corresponding genes was beneficial. The effects of gene dosage provide a unified framework for studying all phases of the life history of a gene duplication. Application of well-known methods of evolutionary genetics to accumulating data on new, polymorphic, and fixed duplication will enhance our understanding of the role of natural selection in the evolution by gene duplication.

Biases in phylogenetic estimation can be caused by random sequence segments

We consider the effects of fully or partially random sequences on the estimation of four-taxon phylogenies. Fully or partially random sequences occur when whole subsets of sequences or some sites for subsets of sequences are independent of sequence data for the other taxa. Random sequences can be a consequence of misalignment or because sites evolve at very fast rates in some portions of a tree, a situation that occurs especially in analyses involving deep divergence times. One might reasonably speculate that random sites will only add noise to the estimation of a phylogeny. We show that in the case that a random sequence is added to a three-taxa alignment, it is more likely to be a neighbor of the sequence corresponding to the longest branch in the three-taxon tree. Surprisingly, when only about half of the sites show randomness, a long-branch-repels form of small sample bias occurs, and when a minority of sites show randomness this becomes a long-branch-attraction bias again. The most serious bias, one that does not vanish with increasing sequence length, occurs when more than one sequence is partially random. If there is a large amount of overlap in the random sites for two sequences, those two sequences will be attracted to each other; otherwise, they will repel each other. Random sequences or sites can, therefore, cause complicated biases in phylogenetic inference. We suggest performing analyses with and without potentially saturated sequences and/or misaligned sites, to check that these biases are not affecting the inferred branching pattern.

Protein import, replication, and inheritance of a vestigial mitochondrion

Mitochondrial remnant organelles (mitosomes) that exist in a range of "amitochondrial" eukaryotic organisms represent ideal models for the study of mitochondrial evolution and for the establishment of the minimal set of proteins required for the biogenesis of an endosymbiosis-derived organelle. Giardia intestinalis, often described as the earliest branching eukaryote, contains double membrane-bounded structures involved in iron-sulfur cluster biosynthesis, an essential function of mitochondria. Here we present evidence that Giardia mitosomes also harbor Cpn60, mtHsp70, and ferredoxin and that despite their advanced state of reductive evolution they have retained vestiges of presequence-dependent and -independent protein import pathways akin to those that operate in mammalian mitochondria. Although import of IscU and ferredoxin is still reliant on their amino-terminal presequences, targeting of Giardia Cpn60, IscS, or mtHsp70 into mitosomes no longer requires cleavable presequences, a derived feature from their mitochondrial homologues. In addition, we found that division and segregation of a single centrally positioned mitosome tightly associated with the microtubular cytoskeleton is coordinated with the cell cycle, whereas peripherally located mitosomes are inherited into daughter cells stochastically.

Higher-Order Phylogeny of Plasmodial Slime Molds (Myxogastria) Based on Elongation Factor 1-A and Small Subunit rRNA Gene Sequences

The Myxogastria are common soil microorganisms with a life cycle comprised of a plasmodial trophic stage and large fruiting bodies generally visible with the unaided eye. Until now, their classification has been based exclusively on a combination of morphological, ultrastructural, and developmental characters. Our study is the first attempt to examine phylogenetic relationships among these taxa using molecular data. Partial small-subunit ribosomal RNA and/or elongation factor 1-alpha gene sequences were obtained from eleven, mostly field-collected species representing the five orders of Myxogastria. Nineteen sequences were obtained and subjected to phylogenetic analysis together with 10 sequences available from GenBank. Separate and combined analyses of the two data sets support the division of Myxogastria into three distinct groups. The most basal clade consists of the Echinosteliales, an order considered to have affinities with Protostelia. The three species examined possess unpigmented or slightly pigmented spores. The second group consists of Liceales and Trichiales, taxa characterized by the presence of clear, but pigmented, spores. The third group consists of the two remaining orders, Physarales and Stemonitales, both possessing dark spores. This suggests that spore pigmentation is an evolutionarily conservative character in myxogastrians, and that the simple morphology of echinostelids is not a derived feature.

Predicted highly expressed genes in archaeal genomes

Based primarily on 16S rRNA sequence comparisons, life has been broadly divided into the three domains of Bacteria, Archaea, and Eukarya. Archaea is further classified into Crenarchaea and Euryarchaea. Archaea generally thrive in extreme environments as assessed by temperature, pH, and salinity. For many prokaryotic organisms, ribosomal proteins (RP), transcription/translation factors, and chaperone genes tend to be highly expressed. A gene is predicted highly expressed (PHX) if its codon usage is rather similar to the average codon usage of at least one of the RP, transcription/translation factors, and chaperone gene classes and deviates strongly from the average gene of the genome. The thermosome (Ths) chaperonin family represents the most salient PHX genes among Archaea. The chaperones Trigger factor and HSP70 have overlapping functions in the folding process, but both of these proteins are lacking in most archaea where they may be substituted by the chaperone prefoldin. Other distinctive PHX proteins of Archaea, absent from Bacteria, include the proliferating cell nuclear antigen PCNA, a replication auxiliary factor responsible for tethering the catalytic unit of DNA polymerase to DNA during high-speed replication, and the acidic RP P0, which helps to initiate mRNA translation at the ribosome. Other PHX genes feature Cell division control protein 48 (Cdc48), whereas the bacterial septation proteins FtsZ and minD are lacking in Crenarchaea. RadA is a major DNA repair and recombination protein of Archaea. Archaeal genomes feature a strong Shine-Dalgarno ribosome-binding motif more pronounced in Euryarchaea compared with Crenarchaea.

Phylogenomics and the reconstruction of the tree of life

As more complete genomes are sequenced, phylogenetic analysis is entering a new era - that of phylogenomics. One branch of this expanding field aims to reconstruct the evolutionary history of organisms on the basis of the analysis of their genomes. Recent studies have demonstrated the power of this approach, which has the potential to provide answers to several fundamental evolutionary questions. However, challenges for the future have also been revealed. The very nature of the evolutionary history of organisms and the limitations of current phylogenetic reconstruction methods mean that part of the tree of life might prove difficult, if not impossible, to resolve with confidence.

Application of a recN sequence similarity analysis to the identification of species within the bacterial genus Geobacillus

Full-length recN and 16S rRNA gene sequences were determined for a collection of 68 strains from the thermophilic Gram-positive genus Geobacillus, members of which have been isolated from geographically and ecologically diverse locations. Phylogenetic treeing methods clustered the isolates into nine sequence similarity groups, regardless of which gene was used for analysis. Several of these groups corresponded unambiguously to known Geobacillus species, whereas others contained two or more type strains from species with validly published names, highlighting a need for a re-assessment of the taxonomy for this genus. For taxonomic analysis of bacteria related at a genus, species or subspecies level, recN sequence comparisons had a resolving power nearly an order or magnitude greater than 16S rRNA gene comparisons. Mutational saturation rendered recN comparisons much less powerful than 16S rRNA gene comparisons for analysis of higher taxa, however. Analysis of recN sequences should prove a powerful tool for assigning strains to species within Geobacillus, and perhaps within other genera as well.

Introns: mighty elements from the RNA world

The discovery of RNA-based enzymatic activity by Thomas Cech's and Sidney Altman's laboratories was a momentous event that led Walter Gilbert to the concept of an "RNA world"--a primitive ancient stage of life that existed before the appearance of DNA and protein molecules. A year later, Gilbert formulated "the exon theory of genes," which hypothesized that introns are very ancient genetic elements present at the earliest stages of life in the RNA world. This theory has been fiercely debated and still has vigorous supporters and opponents. In this communication, we explore peculiarities in the RNA-protein world and their effect on intron-exon structures. We demonstrate that these peculiarities, which exist in the absence of DNA, could shed light on introns' original functions as well as the important role they might have played in the origin of life. For ancient DNA-lacking cells, a crucial problem existed in distinguishing two distinct subsets of RNAs: those messenger molecules coding for proteins and those heritable genetic molecules complementary to messenger RNAs that propagate the genetic information through generations. We propose that ancient introns could act as markers of RNA subsets, directing them to different functions.

Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales?

An analysis of the position of Nanoarcheum equitans in the archaeal phylogeny using a large dataset of concatenated ribosomal proteins from 25 archaeal genomes suggests that N. equitans is likely to be the representative of a fast-evolving euryarchaeal lineage.

Background

Cultivable archaeal species are assigned to two phyla - the Crenarchaeota and the Euryarchaeota - by a number of important genetic differences, and this ancient split is strongly supported by phylogenetic analysis. The recently described hyperthermophile Nanoarchaeum equitans, harboring the smallest cellular genome ever sequenced (480 kb), has been suggested as the representative of a new phylum - the Nanoarchaeota - that would have diverged before the Crenarchaeota/Euryarchaeota split. Confirming the phylogenetic position of N. equitans is thus crucial for deciphering the history of the archaeal domain.

Results

We tested the placement of N. equitans in the archaeal phylogeny using a large dataset of concatenated ribosomal proteins from 25 archaeal genomes. We indicate that the placement of N. equitans in archaeal phylogenies on the basis of ribosomal protein concatenation may be strongly biased by the coupled effect of its above-average evolutionary rate and lateral gene transfers. Indeed, we show that different subsets of ribosomal proteins harbor a conflicting phylogenetic signal for the placement of N. equitans. A BLASTP-based survey of the phylogenetic pattern of all open reading frames (ORFs) in the genome of N. equitans revealed a surprisingly high fraction of close hits with Euryarchaeota, notably Thermococcales. Strikingly, a specific affinity of N. equitans and Thermococcales was strongly supported by phylogenies based on a subset of ribosomal proteins, and on a number of unrelated molecular markers.

Conclusion

We suggest that N. equitans may more probably be the representative of a fast-evolving euryarchaeal lineage (possibly related to Thermococcales) than the representative of a novel and early diverging archaeal phylum.

Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement

BACKGROUND

When organismal phylogenies based on sequences of single marker genes are poorly resolved, a logical approach is to add more markers, on the assumption that weak but congruent phylogenetic signal will be reinforced in such multigene trees. Such approaches are valid only when the several markers indeed have identical phylogenies, an issue which many multigene methods (such as the use of concatenated gene sequences or the assembly of supertrees) do not directly address. Indeed, even when the true history is a mixture of vertical descent for some genes and lateral gene transfer (LGT) for others, such methods produce unique topologies.

RESULTS

We have developed software that aims to extract evidence for vertical and lateral inheritance from a set of gene trees compared against an arbitrary reference tree. This evidence is then displayed as a synthesis showing support over the tree for vertical inheritance, overlaid with explicit lateral gene transfer (LGT) events inferred to have occurred over the history of the tree. Like splits-tree methods, one can thus identify nodes at which conflict occurs. Additionally one can make reasonable inferences about vertical and lateral signal, assigning putative donors and recipients.

CONCLUSION

A tool such as ours can serve to explore the reticulated dimensionality of molecular evolution, by dissecting vertical and lateral inheritance at high resolution. By this, we mean that individual nodes can be examined not only for congruence, but also for coherence in light of LGT. We assert that our tools will facilitate the comparison of phylogenetic trees, and the interpretation of conflicting data.

Phylogenetic relationships of methionine aminopeptidase 2 among Encephalitozoon species and genotypes of microsporidia

This report describes the characterization and phylogenetic analysis of the deduced amino acid sequences of methionine aminopeptidase 2 (MetAP-2) enzymes from microsporidian species and genotypes of the genus Encephalitozoon. Fragments of DNA encoding 318 to 335 amino acid residues of the MetAP-2 genes were isolated from genomic DNA prepared from cultured spores of Encephalitozoon hellem, Encephalitozoon intestinalis, and Encephalitozoon cuniculi genotypes I-III. Sequence comparisons of the deduced amino acid residues indicated that the microsporidian sequences are MetAP-2-like rather than MetAP-1-like. Alignments demonstrated that the new Encephalitozoon sequences included sequences and structures conserved in eukaryotic MetAP-2s, including the five conserved, active site residues, Asp, Asp, His, Glu, and His, considered to be critical for catalysis and for coordinating the cation (e.g., cobalt) co-factor, and included residues known to interact with the antibiotic, fumagillin. The primary structure of the Encephalitozoon MetAP-2s, however, showed some dissimilarity with human and yeast MetAP-2s, including the absence of the NH2-terminal polylysine tract. Phylogenetic comparison of these Encephalitozoon MetAP-2s with orthologues from related species and from other informative taxa confirmed that the MetAP-2s of these Encephalitozoon species and strains are closely related to each other and cluster with MetAP-2s.

Prokaryotic phylogenies inferred from protein structural domains

The determination of the phylogenetic relationships among microorganisms has long relied primarily on gene sequence information. Given that prokaryotic organisms often lack morphological characteristics amenable to phylogenetic analysis, prokaryotic phylogenies, in particular, are often based on sequence data. In this work, we explore a new source of phylogenetic information, the distribution of protein structural domains within fully sequenced prokaryotic genomes. The evolution of the structural domains we use has been studied extensively, allowing us to base our phylogenetic methods on testable theoretical models of structural evolution. We find that the methods that produce reasonable phylogenetic relationships are indeed the methods that are most consistent with theoretical evolutionary models. This work represents, to our knowledge, the first such theoretically motivated phylogeny, as well as the first application of structural information to phylogeny on this scale. Our results have strong implications for the phylogenetic relationships among prokaryotic organisms and for the understanding of protein evolution as a whole.

Weighted genome trees: refinements and applications

There are many ways to group completed genome sequences in hierarchical patterns (trees) reflecting relationships between their genes. Such groupings help us organize biological information and bear crucially on underlying processes of genome and organismal evolution. Genome trees make use of all comparable genes but can variously weight the contributions of these genes according to similarity, congruent patterns of similarity, or prevalence among genomes. Here we explore such possible weighting strategies, in an analysis of 142 prokaryotic and 5 eukaryotic genomes. We demonstrate that alternate weighting strategies have different advantages, and we propose that each may have its specific uses in systematic or evolutionary biology. Comparisons of results obtained with different methods can provide further clues to major events and processes in genome evolution.

Mitochondrial genomes of two demosponges provide insights into an early stage of animal evolution

Mitochondrial DNA (mtDNA) of multicellular animals (Metazoa) is typically a small ( approximately 16 kbp), circular-mapping molecule that encodes 37 tightly packed genes. The structures of mtDNA-encoded transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs) are usually highly unorthodox, and proteins are translated with multiple deviations from the standard genetic code. In contrast, mtDNA of the choanoflagellate Monosiga brevicollis, the closest unicellular relative of animals, is four times larger, contains 1.5 times as many genes, and lacks mentioned peculiarities of animal mtDNA. To investigate the evolutionary transition that led to the specific organization of metazoan mtDNA, we determined complete mitochondrial sequences from the demosponges Geodia neptuni and Tethya actinia, two representatives of the most basal animal phylum, the Porifera. We found that poriferan mtDNAs resemble those of other animals in their compact organization, lack of introns, and a well-conserved animal-like gene order. Yet, they contain several extra genes, encode bacterial-like rRNAs and tRNAs, and use a minimally derived genetic code. Our findings suggest that the evolution of the typical metazoan mtDNA has been a multistep process in which the compact genome organization and the reduced gene content were established prior to the reduction of tRNA and rRNA structures and the introduction of multiple changes of the translation code.

Measuring genome conservation across taxa: divided strains and united kingdoms

Species evolutionary relationships have traditionally been defined by sequence similarities of phylogenetic marker molecules, recently followed by whole-genome phylogenies based on gene order, average ortholog similarity or gene content. Here, we introduce genome conservation--a novel metric of evolutionary distances between species that simultaneously takes into account, both gene content and sequence similarity at the whole-genome level. Genome conservation represents a robust distance measure, as demonstrated by accurate phylogenetic reconstructions. The genome conservation matrix for all presently sequenced organisms exhibits a remarkable ability to define evolutionary relationships across all taxonomic ranges. An assessment of taxonomic ranks with genome conservation shows that certain ranks are inadequately described and raises the possibility for a more precise and quantitative taxonomy in the future. All phylogenetic reconstructions are available at the genome phylogeny server: <http://maine.ebi.ac.uk:8000/cgi-bin/gps/GPS.pl>.

Mitochondrion‐Derived Organelles in Protists and Fungi

The mitochondrion is generally considered to be a defining feature of eukaryotic cells, yet most anaerobic eukaryotes lack this organelle. Many of these were previously thought to derive from eukaryotes that diverged prior to acquisition of the organelle through endosymbiosis. It is now known that all extant eukaryotes are descended from an ancestor that had a mitochondrion and that in anaerobic eukaryotes the organelle has been modified into either hydrogenosomes, which continue to generate energy for the host cell, or mitosomes, which do not. These organelles have each arisen independently several times. Recent evidence suggests a shared derived characteristic that may be responsible for the retention of the organelles in the absence of the better-known mitochondrial functions--iron-sulfur cluster assembly. This review explores the events leading to this new understanding of mitochondrion-derived organelles in amitochondriate eukaryotes, the current state of our knowledge, and future areas for investigation.

On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes

A global phylogeny of major eukaryotic lineages is a significant and ongoing challenge to molecular phylogenetics. Currently, there are five hypothesized major lineages or ‘supergroups' of eukaryotes. One of these, the chromalveolates, represents a large fraction of protist and algal diversity. The chromalveolate hypothesis was originally based on similarities between the photosynthetic organelles (plastids) found in many of its members and has been supported by analyses of plastid-related genes. However, since plastids can move between eukaryotic lineages, it is important to provide additional support from data generated from the nuclear-cytosolic host lineage. Genes coding for six different cytosolic proteins from a variety of chromalveolates (yielding 68 new gene sequences) have been characterized so that multiple gene analyses, including all six major lineages of chromalveolates, could be compared and concatenated with data representing all five hypothesized supergroups. Overall support for much of the phylogenies is decreased over previous analyses that concatenated fewer genes for fewer taxa. Nevertheless, four of the six chromalveolate lineages (apicomplexans, ciliates, dinoflagellates and heterokonts) consistently form a monophyletic assemblage, whereas the remaining two (cryptomonads and haptophytes) form a weakly supported group. Whereas these results are consistent with the monophyly of chromalveolates inferred from plastid data, testing this hypothesis is going to require a substantial increase in data from a wide variety of organisms.

The transcriptional regulator pool of the marine bacteriumRhodopirellula balticaSH 1Tas revealed by whole genome comparisons

Rhodopirellula baltica (strain SH 1T) is a free-living marine representative of the phylogenetically independent and environmentally relevant phylum Planctomycetes. Little is known about the regulatory strategies of free-living bacteria with large (7.15 Mb) genomes. Therefore, a consistent, quantitative and qualitative description was produced by comparing R. baltica's transcriptional regulator pool with that of 123 publicly available bacterial genomes. The overall results are congruous with earlier observations that in Bacteria, the proportion of genes encoding transcriptional regulators generally increases with genome size. However, R. baltica distinctly stands out from this trend with only 2.4% (174) of all genes predicted to encode transcriptional regulators. The qualitative investigation of R. baltica's transcriptional regulators revealed a clear shift towards high numbers of two-component systems (66) as well as high numbers of sigma factors (49), with more than 76% (37) belonging to the extra-cytoplasmic function subfamily of sigma-70. Only one predicted sigma factor showed a relatively close phylogenetic relationship to that of another bacterium, the sigma factor SigZ of Bacillus subtilis. In summary, analysis of the R. baltica genome revealed disparate regulatory mechanisms and a clear bias towards direct environmental sensing. This strategy might provide a selective advantage for organisms living in habitats with frequently changing environmental conditions.

Phylogenetic analysis of AAA proteins

AAA ATPases form a large protein family with manifold cellular roles. They belong to the AAA+ superfamily of ringshaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. Phylogenetic analyses have suggested the existence of five major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, and the MSP1/katanin/spastin group), as well as a number of deeply branching minor clades. These analyses however have been characterized by a lack of consistency in defining the boundaries of the AAA family. We have used cluster analysis to delineate unambiguously the group of AAA sequences within the AAA+ superfamily. Phylogenetic and cluster analysis of this sequence set revealed the existence of a sixth major AAA clade, comprising the mitochondrial, membrane-bound protein BCS1 and its homologues. In addition, we identified several deep branches consisting mainly of hypothetical proteins resulting from genomic projects. Analysis of the AAA N-domains provided direct support for the obtained phylogeny for most branches, but revealed some deep splits that had not been apparent from phylogenetic analysis and some unexpected similarities between distant clades. It also revealed highly degenerate D1 domains in plant MSP1 sequences and in at least one deeply branching group of hypothetical proteins (YC46), showing that AAA proteins with two ATPase domains arose at least three times independently.

When molecules and morphology clash: reconciling conflicting phylogenies of the Metazoa by considering secondary character loss

Molecular and morphological data sets have yielded conflicting phylogenies for the Metazoa. So far, no general explanation for the existence of this conflict has been suggested. However, I believe that a neglected aspect of metazoan cladistics has introduced a systematic and substantial bias into morphological phylogenetic analyses. Most characters used for metazoan cladistics are coded as binary absence/presence characters. For most of these characters, the absence states are assumed to be uninformative default plesiomorphies, if they are defined at all. This character coding strategy could seriously underestimate the number of informative apomorphic absences or secondary character losses. Because nodes in morphological metazoan phylogenies are typically supported by relatively small numbers of characters each with a potentially strong impact on tree topology, failure to distinguish between primary absence and secondary loss of characters before a cladistic analysis may mislead morphological cladistics. This may falsely suggest conflict with molecular phylogenies, which are not sensitive to this bias. To test the existence of this bias, I compare the phylogenetic placement of a variety of metazoan taxa in molecular and morphological trees. In all instances investigated here, phylogenetic conflict can be resolved by allowing for secondary loss of morphological characters, which were assumed to be primitively absent in cladistic analyses. These findings suggest that we should be cautious in interpreting the results of morphological metazoan cladistic analyses and additionally illustrate the value of a more functional approach to comparative morphology in certain circumstances.

The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise

Phylogenetic trees based on gene repertoires are remarkably similar to the current consensus of life history. Yet it has been argued that shared gene content is unreliable for phylogenetic reconstruction because of convergence in gene content due to horizontal gene transfer and parallel gene loss. Here we test this argument, by filtering out as noise those orthologous groups that have an inconsistent phylogenetic distribution, using two independent methods. The resulting phylogenies do indeed contain small but significant improvements. More importantly, we find that the majority of orthologous groups contain some phylogenetic signal and that the resulting phylogeny is the only detectable signal present in the gene distribution across genomes. Horizontal gene transfer or parallel gene loss does not cause systematic biases in the gene content tree.

Codon bias signatures, organization of microorganisms in codon space, and lifestyle

New and simple numerical criteria based on a codon adaptation index are applied to the complete genomic sequences of 80 Eubacteria and 16 Archaea, to infer weak and strong genome tendencies toward content bias, translational bias, and strand bias. These criteria can be applied to all microbial genomes, even those for which little biological information is known, and a codon bias signature, that is the collection of strong biases displayed by a genome, can be automatically derived. A codon bias space, where genomes are identified by their preferred codons, is proposed as a novel formal framework to interpret genomic relationships. Principal component analysis confirms that although GC content has a dominant effect on codon bias space, thermophilic and mesophilic species can be identified and separated by codon preferences. Two more examples concerning lifestyle are studied with linear discriminant analysis: suitable separating functions characterized by sets of preferred codons are provided to discriminate: translationally biased (hyper)thermophiles from mesophiles, and organisms with different respiratory characteristics, aerobic, anaerobic, facultative aerobic and facultative anaerobic. These results suggest that codon bias space might reflect the geometry of a prokaryotic "physiology space." Evolutionary perspectives are noted, numerical criteria and distances among organisms are validated on known cases, and various results and predictions are discussed both on methodological and biological grounds.

What Does the Microsporidian E. cuniculi Tell Us About the Origin of the Eukaryotic Cell?

The relationship among the three cellular domains Archaea, Bacteria, and Eukarya has become a central problem in unraveling the tree of life. This relationship can now be studied as the completely sequenced genomes of representatives of these cellular domains become available. We performed a bioinformatic investigation of the Encephalitozoon cuniculi proteome. E. cuniculi has the smallest sequenced eukaryotic genome, 2.9 megabases coding for 1997 proteins. The proteins of E. cuniculi were compared with a previously characterized set of eukaryotic signature proteins (ESPs). ESPs are found in a eukaryotic cell, whether from an animal, a plant, a fungus, or a protozoan, but are not found in the Archaea and the Bacteria. We demonstrated that 85% of the ESPs have significant sequence similarity to proteins in E. cuniculi. Hence, E. cuniculi, a minimal eukaryotic cell that has removed all inessential proteins, still preserves most of the ESPs that make it a member of the Eukarya. The locations and functions of these ESPs point to the earliest history of eukaryotes.

Root of the Eukaryota Tree as Inferred from Combined Maximum Likelihood Analyses of Multiple Molecular Sequence Data

Extensive studies aiming to establish the structure and root of the Eukaryota tree by phylogenetic analyses of molecular sequences have thus far not resulted in a generally accepted tree. To re-examine the eukaryotic phylogeny using alternative genes, and to obtain a more robust inference for the root of the tree as well as the relationship among major eukaryotic groups, we sequenced the genes encoding isoleucyl-tRNA and valyl-tRNA synthetases, cytosolic-type heat shock protein 90, and the largest subunit of RNA polymerase II from several protists. Combined maximum likelihood analyses of 22 protein-coding genes including the above four genes clearly demonstrated that Diplomonadida and Parabasala shared a common ancestor in the rooted tree of Eukaryota, but only when the fast-evolving sites were excluded from the original data sets. The combined analyses, together with recent findings on the distribution of a fused dihydrofolate reductase-thymidylate synthetase gene, narrowed the possible position of the root of the Eukaryota tree on the branch leading to Opisthokonta or to the common ancestor of Diplomonadida/Parabasala. However, the analyses did not agree with the position of the root located on the common ancestor of Opisthokonta and Amoebozoa, which was argued by Stechmann and Cavalier-Smith [Curr. Biol. 13:R665-666, 2003] based on the presence or absence of a three-gene fusion of the pyrimidine biosynthetic pathway: carbamoyl-phosphate synthetase II, dihydroorotase, and aspartate carbamoyltransferase. The presence of the three-gene fusion recently found in the Cyanidioschyzon merolae (Rhodophyta) genome sequence data supported our analyses against the Stechmann and Cavalier-Smith-rooting in 2003.

Only six kingdoms of life

There are many more phyla of microbes than of macro-organisms, but microbial biodiversity is poorly understood because most microbes are uncultured. Phylogenetic analysis of rDNA sequences cloned after PCR amplification of DNA extracted directly from environmental samples is a powerful way of exploring our degree of ignorance of major groups. As there are only five eukaryotic kingdoms, two claims using such methods for numerous novel 'kingdom-level' lineages among anaerobic eukaryotes would be remarkable, if true. By reanalysing those data with 167 known species (not merely 8-37), I identified relatives for all 8-10 'mysterious' lineages. All probably belong to one of five already recognized phyla (Amoebozoa, Cercozoa, Apusozoa, Myzozoa, Loukozoa) within the basal kingdom Protozoa, mostly in known classes, sometimes even in known orders, families or genera. This strengthens the idea that the ancestral eukaryote was a mitochondrial aerobe. Analogous claims of novel bacterial divisions or kingdoms may reflect the weak resolution and grossly non-clock-like evolution of ribosomal rRNA, not genuine phylum-level biological disparity. Critical interpretation of environmental DNA sequences suggests that our overall picture of microbial biodiversity at phylum or division level is already rather good and comprehensive and that there are no uncharacterized kingdoms of life. However, immense lower-level diversity remains to be mapped, as does the root of the tree of life.

Evaluation of the phylogenetic position of the planctomycete 'Rhodopirellula baltica' SH 1 by means of concatenated ribosomal protein sequences, DNA-directed RNA polymerase subunit sequences and whole genome trees

In recent years, the planctomycetes have been recognized as a phylum of environmentally important bacteria with habitats ranging from soil and freshwater to marine ecosystems. The planctomycetes form an independent phylum within the bacterial domain, whose exact phylogenetic position remains controversial. With the completion of sequencing of the genome of 'Rhodopirellula baltica' SH 1, it is now possible to re-evaluate the phylogeny of the planctomycetes based on multiple genes and genome trees in addition to single genes like the 16S rRNA or the elongation factor Tu. Here, evidence is presented based on the concatenated amino acid sequences of ribosomal proteins and DNA-directed RNA polymerase subunits from 'Rhodopirellula baltica' SH 1 and more than 90 other publicly available genomes that support a relationship of the Planctomycetes and the Chlamydiae. Affiliation of 'Rhodopirellula baltica' SH 1 and the Chlamydiae was reasonably stable regarding site selection since, during stepwise filtering of less-conserved sites from the alignments, it was only broken when rigorous filtering was applied. In a few cases, 'Rhodopirellula baltica' SH 1 shifted to a deep branching position adjacent to the Thermotoga/Aquifex clade. These findings are in agreement with recent publications, but the deep branching position was dependent on site selection and treeing algorithm and thus not stable. A genome tree calculated from normalized BLASTP scores did not confirm a close relationship of 'Rhodopirellula baltica' SH 1 and the Chlamydiae, but also indicated that the Planctomycetes do not emerge at the very root of the Bacteria. Therefore, these analyses rather contradict a deep branching position of the Planctomycetes within the bacterial domain and reaffirm their earlier proposed relatedness to the Chlamydiae.

Proteomic signatures: amino acid and oligopeptide compositions differentiate among phyla

Availability of complete genome sequences allows in-depth comparison of single-residue and oligopeptide compositions of the corresponding proteomes. We have used principal component analysis (PCA) to study the landscape of compositional motifs across more than 70 genera from all three superkingdoms. Unexpectedly, the first two principal components clearly differentiate archaea, eubacteria, and eukaryota from each other. In particular, we contrast compositional patterns typical of the three superkingdoms and characterize differences between species and phyla, as well as among patterns shared by all compositional proteomic signatures. These species-specific patterns may even extend to subsets of the entire proteome, such as proteins pertaining to individual yeast chromosomes. We identify factors that affect compositional signatures, such as living habitat, and detect strong eukaryotic preference for homopeptides and palindromic tripeptides. We further detect oligopeptides that are either universally over- or underabundant across the whole proteomic landscape, as well as oligopeptides whose over- or underabundance is phylum- or species-specific. Finally, we report that species composition signatures preserve evolutionary memory, providing a new method to compare phylogenetic relationships among species that avoids problems of sequence alignment and ortholog detection.

Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox

This article presents a phylogenetic analysis of the Archea based on sets of transcription and translation proteins. The phylogenies shed light on the evolutionary position of Methanopyrus kandleri.

Background

Phylogenetic analysis of the Archaea has been mainly established by 16S rRNA sequence comparison. With the accumulation of completely sequenced genomes, it is now possible to test alternative approaches by using large sequence datasets. We analyzed archaeal phylogeny using two concatenated datasets consisting of 14 proteins involved in transcription and 53 ribosomal proteins (3,275 and 6,377 positions, respectively).

Results

Important relationships were confirmed, notably the dichotomy of the archaeal domain as represented by the Crenarchaeota and Euryarchaeota, the sister grouping of Sulfolobales and Aeropyrum pernix, and the monophyly of a large group comprising Thermoplasmatales, Archaeoglobus fulgidus, Methanosarcinales and Halobacteriales, with the latter two orders forming a robust cluster. The main difference concerned the position of Methanopyrus kandleri, which grouped with Methanococcales and Methanobacteriales in the translation tree, whereas it emerged at the base of the euryarchaeotes in the transcription tree. The incongruent placement of M. kandleri is likely to be the result of a reconstruction artifact due to the high evolutionary rates displayed by the components of its transcription apparatus.

Conclusions

We show that two informational systems, transcription and translation, provide a largely congruent signal for archaeal phylogeny. In particular, our analyses support the appearance of methanogenesis after the divergence of the Thermococcales and a late emergence of aerobic respiration from within methanogenic ancestors. We discuss the possible link between the evolutionary acceleration of the transcription machinery in M. kandleri and several unique features of this archaeon, in particular the absence of the elongation transcription factor TFS.

An improved probability mapping approach to assess genome mosaicism

BACKGROUND

Maximum likelihood and posterior probability mapping are useful visualization techniques that are used to ascertain the mosaic nature of prokaryotic genomes. However, posterior probabilities, especially when calculated for four-taxon cases, tend to overestimate the support for tree topologies. Furthermore, because of poor taxon sampling four-taxon analyses suffer from sensitivity to the long branch attraction artifact. Here we extend the probability mapping approach by improving taxon sampling of the analyzed datasets, and by using bootstrap support values, a more conservative tool to assess reliability.

RESULTS

Quartets of orthologous proteins were complemented with homologs from selected reference genomes. The mapping of bootstrap support values from these extended datasets gives results similar to the original maximum likelihood and posterior probability mapping. The more conservative nature of the plotted support values allows to focus further analyses on those protein families that strongly disagree with the majority or plurality of genes present in the analyzed genomes.

CONCLUSION

Posterior probability is a non-conservative measure for support, and posterior probability mapping only provides a quick estimation of phylogenetic information content of four genomes. This approach can be utilized as a pre-screen to select genes that might have been horizontally transferred. Better taxon sampling combined with subtree analyses prevents the inconsistencies associated with four-taxon analyses, but retains the power of visual representation. Nevertheless, a case-by-case inspection of individual multi-taxon phylogenies remains necessary to differentiate unrecognized paralogy and shared phylogenetic reconstruction artifacts from horizontal gene transfer events.

Preserving the tree of life

Phylogenies provide new ways to measure biodiversity, to assess conservation priorities, and to quantify the evolutionary history in any set of species. Methodological problems and a lack of knowledge about most species have so far hampered their use. In the future, as techniques improve and more data become accessible, we will have an expanded set of conservation options, including ways to prioritize outcomes from evolutionary and ecological processes.

The deep roots of eukaryotes

Most cultivated and characterized eukaryotes can be confidently assigned to one of eight major groups. After a few false starts, we are beginning to resolve relationships among these major groups as well. However, recent developments are radically revising this picture again, particularly (i) the discovery of the likely antiquity and taxonomic diversity of ultrasmall eukaryotes, and (ii) a fundamental rethinking of the position of the root. Together these data suggest major gaps in our understanding simply of what eukaryotes are or, when it comes to the tree, even which end is up.

Genome comparisons and analysis

As we enter the post-genomic era, with the accelerating availability of complete genome sequences, new theoretical approaches and new experimental techniques, our ability to dissect cellular processes at the molecular level continues to expand. Recent advances include the application of RNA interference methods to characterize loss-of-function phenotype genes in higher eukaryotes, comparative analysis of the human and mouse genome sequences, and methods for reconciling contradictory phylogenetic reconstructions. New developments feed into the increasingly rich content of databases such as the COG database. The next phase of research will be increasingly dominated by efforts to integrate the deluge of data into our understanding of biological systems.

Phylogeny for the faint of heart: a tutorial

Phylogenetic trees seem to be finding ever broader applications, and researchers from very different backgrounds are becoming interested in what they might have to say. This tutorial aims to introduce the basics of building and interpreting phylogenetic trees. It is intended for those wanting to understand better what they are looking at when they look at someone else's trees or to begin learning how to build their own. Topics covered include: how to read a tree, assembling a dataset, multiple sequence alignment (how it works and when it does not), phylogenetic methods, bootstrap analysis and long-branch artefacts, and software and resources.

Phylogenomics of type II DNA topoisomerases

Type II DNA topoisomerases (Topo II) are essential enzymes implicated in key nuclear processes. The recent discovery of a novel kind of Topo II (DNA topoisomerase VI) in Archaea led to a division of these enzymes into two non-homologous families, (Topo IIA and Topo IIB) and to the identification of the eukaryotic protein that initiates meiotic recombination, Spo11. In the present report, we have updated the distribution of all Topo II in the three domains of life by a phylogenomic approach. Both families exhibit an atypical distribution by comparison with other informational proteins, with predominance of Topo IIA in Bacteria, Eukarya and viruses, and Topo IIB in Archaea. However, plants and some Archaea contain Topo II from both families. We confront this atypical distribution with current hypotheses on the evolution of the three domains of life and origin of DNA genomes.

The future of bacteriophage biology

After an illustrious history as one of the primary tools that established the foundations of molecular biology, bacteriophage research is now undergoing a renaissance in which the primary focus is on the phages themselves rather than the molecular mechanisms that they explain. Studies of the evolution of phages and their role in natural ecosystems are flourishing. Practical questions, such as how to use phages to combat human diseases that are caused by bacteria, how to eradicate phage pests in the food industry and what role they have in the causation of human diseases, are receiving increased attention. Phages are also useful in the deeper exploration of basic molecular and biophysical questions.