We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the approximately 160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion, in conjunction with the shaping of metabolic pathways that likely transpired through lateral gene transfer from bacteria, and amplification of specific gene families implicated in pathogenesis and phagocytosis of host proteins may exemplify adaptations of the parasite during its transition to a urogenital environment. The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria.

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Compositional heterogeneity among lineages can compromise phylogenetic analyses, because models in common use assume compositionally homogeneous data. Models that can accommodate compositional heterogeneity with few extra parameters are described here, and used in two examples where the true tree is known with confidence. It is shown using likelihood ratio tests that adequate modeling of compositional heterogeneity can be achieved with few composition parameters, that the data may not need to be modelled with separate composition parameters for each branch in the tree. Tree searching and placement of composition vectors on the tree are done in a Bayesian framework using Markov chain Monte Carlo (MCMC) methods. Assessment of fit of the model to the data is made in both maximum likelihood (ML) and Bayesian frameworks. In an ML framework, overall model fit is assessed using the Goldman-Cox test, and the fit of the composition implied by a (possibly heterogeneous) model to the composition of the data is assessed using a novel tree-and model-based composition fit test. In a Bayesian framework, overall model fit and composition fit are assessed using posterior predictive simulation. It is shown that when composition is not accommodated, then the model does not fit, and incorrect trees are found; but when composition is accommodated, the model then fits, and the known correct phylogenies are obtained.

The discovery of the Archaea and the proposal of the three-domains 'universal' tree, based on ribosomal RNA and core genes mainly involved in protein translation, catalysed new ideas for cellular evolution and eukaryotic origins. However, accumulating evidence suggests that the three-domains tree may be incorrect: evolutionary trees made using newer methods place eukaryotic core genes within the Archaea, supporting hypotheses in which an archaeon participated in eukaryotic origins by founding the host lineage for the mitochondrial endosymbiont. These results provide support for only two primary domains of life-Archaea and Bacteria-because eukaryotes arose through partnership between them.S ince their discovery by Carl Woese and his co-workers in 1977, the Archaea have figured prominently in hypotheses for eukaryotic origins 1,2 . Although similar to Bacteria in terms of cell structure, molecular phylogenies for ribosomal RNA and a small core of genes, that mainly have essential roles in protein translation 3 , suggested that the Archaea were more closely related to the eukaryotic nuclear lineage; that is, to the host cell that acquired the mitochondrion 4 . The idea that Archaea and eukaryotes are more closely related to each other than either is to Bacteria depends on analyses suggesting that the root of the tree should be placed on the bacterial stem, or within the Bacteria 5-12 , implying that the prokaryotes-cells that lack a nucleus-are a paraphyletic group 13 . The main question now debated is whether core components of the eukaryotic nuclear lineage descend from a common ancestor shared with Archaea, as in the three-domains tree 14 (Fig. 1), which is also often called the 'universal tree' or 'tree of life' 15-17 , or from within the Archaea, as proposed by archaeal-host hypotheses for eukaryotic origins 2 . The archaeal-host scenario with the greatest phylogenetic support is the eocyte hypothesis 18 , which proposes a sister-group relationship between eukaryotes and the eocytes (or Crenarchaeota 14 ), one of the major archaeal divisions (Fig. 1). However, the three-domains-eocyte debate remains controversial because different phylogenetic methods have delivered different results, often from the same data 19 . This disagreement is due, at least in part, to the difficulties associated with resolving ancient divergences in phylogenetic trees. Challenges of reconstructing ancient relationshipsA major issue in reconstructing ancient relationships is the strength and quality of historical signal remaining after the millions of years since the divergence of Archaea and eukaryotes. The earliest fossils identified as eukaryotic appeared by about 1.8 billion years ago 20 ; over this enormous span of time, the accumulation of multiple substitutions in DNA and protein sequences might have erased any signal that would allow the relationship between archaeal and eukaryotic core genes to be established 21 . However, more recent simulations and empirical studies suggest that there are reasons to be cautiously optimistic ...

The origin of the eukaryotic genetic apparatus is thought to be central to understanding the evolution of the eukaryotic cell. Disagreement about the source of the relevant genes has spawned competing hypotheses for the origins of the eukaryote nuclear lineage. The iconic rooted 3-domains tree of life shows eukaryotes and archaebacteria as separate groups that share a common ancestor to the exclusion of eubacteria. By contrast, the eocyte hypothesis has eukaryotes originating within the archaebacteria and sharing a common ancestor with a particular group called the Crenarchaeota or eocytes. Here, we have investigated the relative support for each hypothesis from analysis of 53 genes spanning the 3 domains, including essential components of the eukaryotic nucleic acid replication, transcription, and translation apparatus. As an important component of our analysis, we investigated the fit between model and data with respect to composition. Compositional heterogeneity is a pervasive problem for reconstruction of ancient relationships, which, if ignored, can produce an incorrect tree with strong support. To mitigate its effects, we used phylogenetic models that allow for changing nucleotide or amino acid compositions over the tree and data. Our analyses favor a topology that supports the eocyte hypothesis rather than archaebacterial monophyly and the 3-domains tree of life.archaebacteria ͉ evolution ͉ eocyte ͉ nucleus ͉ phylogenetics T he rooted universal 3-domains tree of Life (Fig. 1A) based on small subunit (SSU) ribosomal (r)RNA sequences, shows eukaryotes and archaebacteria as monophyletic groups that share a common ancestor to the exclusion of eubacteria (1). The 3-domains tree has also been recovered by analyses of other core components of the eukaryotic transcription and translation machinery, suggesting that the tree provides an insight into the origin of the eukaryotic nuclear lineage itself (2-4). By contrast, some analyses of the paralogous protein translation elongation factors, used to root the 3-domains tree, do not actually recover the 3 domains (5, 6). Instead, they show a tree where the eukaryotic proteins branch as the sister group of a specific group of archaebacteria called the Crenarchaeota or the eocytes. The ''eocyte hypothesis,'' whereby the eukaryotic nuclear lineage is posited to have arisen from within a paraphyletic archaebacteria (Fig. 1B), was first proposed based on structural features of eukaryotic and archaebacterial ribosomes (7). It received further support from some early analyses of SSU rRNA sequences (8-10) and from the identification of an 11-aa insertion in the GTPase domain of the elongation factor 1␣ (EF-1␣, also called EF-Tu) genes of eocytes and eukaryotes (5, 6, 11). Subsequently, the eocyte hypothesis has been neglected in the literature in favor of the 3-domains tree, although published phylogenetic analyses are actually more equivocal (12). Thus, there are many examples where one analysis of a eukaryotic gene or protein has recovered the 3-domains tree, but a differen...

Hydrogenosomes are double-membraned ATP-producing and hydrogen-producing organelles of diverse anaerobic eukaryotes. In some versions of endosymbiotic theory they are suggested to be homologues of mitochondria, but alternative views suggest they arose from an anaerobic bacterium that was distinct from the mitochondrial endosymbiont. Here we show that the 51-kDa and 24-kDa subunits of the NADH dehydrogenase module in complex I, the first step in the mitochondrial respiratory chain, are active in hydrogenosomes of Trichomonas vaginalis. Like mitochondrial NADH dehydrogenase, the purified Trichomonas enzyme can reduce a variety of electron carriers including ubiquinone, but unlike the mitochondrial enzyme it can also reduce ferredoxin, the electron carrier used for hydrogen production. The presence of NADH dehydrogenase solves the long-standing conundrum of how hydrogenosomes regenerate NAD+ after malate oxidation. Phylogenetic analyses show that the Trichomonas 51-kDa homologue shares common ancestry with the mitochondrial enzyme. Recruitment of complex I subunits into a H2-producing pathway provides evidence that mitochondria and hydrogenosomes are aerobic and anaerobic homologues of the same endosymbiotically derived organelle.

A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. This model uses evidence from gene duplications, horizontal transfers, and gene losses contained in 31,236 archaeal gene families to identify the most likely root for the tree. Our analyses support the monophyly of DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea), a recently discovered cosmopolitan and genetically diverse lineage, and, in contrast to previous work, place the tree root between DPANN and all other Archaea. The sister group to DPANN comprises the Euryarchaeota and the TACK Archaea, including Lokiarchaeum, which our analyses suggest are monophyletic sister lineages. Metabolic reconstructions on the rooted tree suggest that early Archaea were anaerobes that may have had the ability to reduce CO 2 to acetate via the Wood-Ljungdahl pathway. In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses infer a relatively small-genomed archaeal ancestor that subsequently increased in complexity via gene duplication and horizontal gene transfer.evolution | phylogenetics | Archaea

Hypotheses about the origin of eukaryotic cells are classically framed within the context of a universal "tree of life" based upon conserved core genes. Vigorous ongoing debate about eukaryote origins is based upon assertions that the topology of the tree of life depends on the taxa included and the choice and quality of genomic data analysed. Here we have reanalysed the evidence underpinning those claims and bring more data to bear on the question by using supertree and coalescent methods to interrogate >3000 gene families in Archaea and eukaryotes. We find that eukaryotes consistently originate from within the Archaea in a two-domains tree when due consideration is given to the fit between model and data. Our analyses support a close relationship between eukaryotes and Asgard Archaea and identify the Heimdallarchaeota as the current best candidate for the closest archaeal relatives of the eukaryotic nuclear lineage.Current hypotheses about eukaryotic origins generally propose at least two partners in that process: a bacterial endosymbiont that became the mitochondrion and a host cell for that Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: