scholarly journals Did viruses evolve as a distinct supergroup from common ancestors of cells?

2016 ◽  
Author(s):  
Ajith Harish ◽  
Aare Abroi ◽  
Julian Gough ◽  
Charles Kurland
Keyword(s):  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Marker Gene ◽  
Host Cells ◽  
Data Driven ◽  
Evolutionary Origins ◽  
Phylogenetic Methods ◽  
Universal Common Ancestor ◽  
Phylogenomic Analyses ◽  
Genome Scale

AbstractThe evolutionary origins of viruses according to marker gene phylogenies, as well as their relationships to the ancestors of host cells remains unclear. In a recent article Nasir and Caetano-Anollés reported that their genome-scale phylogenetic analyses identify an ancient origin of the “viral supergroup” (Nasir et al (2015) A phylogenomic data-driven exploration of viral origins and evolution. Science Advances, 1(8):e1500527). It suggests that viruses and host cells evolved independently from a universal common ancestor. Examination of their data and phylogenetic methods indicates that systematic errors likely affected the results. Reanalysis of the data with additional tests shows that small-genome attraction artifacts distort their phylogenomic analyses. These new results indicate that their suggestion of a distinct ancestry of the viral supergroup is not well supported by the evidence.

scholarly journals SepF is the FtsZ anchor in archaea, with features of an ancestral cell division system

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nika Pende ◽  
Adrià Sogues ◽  
Daniela Megrian ◽  
Anna Sartori-Rupp ◽  
Patrick England ◽  
...  
Keyword(s):  
Cell Division ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Super Resolution ◽  
Binding Mode ◽  
Last Universal Common Ancestor ◽  
Division Plane ◽  
Multiple Factors ◽  
Universal Common Ancestor ◽  
Super Resolution Microscopy

AbstractMost archaea divide by binary fission using an FtsZ-based system similar to that of bacteria, but they lack many of the divisome components described in model bacterial organisms. Notably, among the multiple factors that tether FtsZ to the membrane during bacterial cell constriction, archaea only possess SepF-like homologs. Here, we combine structural, cellular, and evolutionary analyses to demonstrate that SepF is the FtsZ anchor in the human-associated archaeon Methanobrevibacter smithii. 3D super-resolution microscopy and quantitative analysis of immunolabeled cells show that SepF transiently co-localizes with FtsZ at the septum and possibly primes the future division plane. M. smithii SepF binds to membranes and to FtsZ, inducing filament bundling. High-resolution crystal structures of archaeal SepF alone and in complex with the FtsZ C-terminal domain (FtsZCTD) reveal that SepF forms a dimer with a homodimerization interface driving a binding mode that is different from that previously reported in bacteria. Phylogenetic analyses of SepF and FtsZ from bacteria and archaea indicate that the two proteins may date back to the Last Universal Common Ancestor (LUCA), and we speculate that the archaeal mode of SepF/FtsZ interaction might reflect an ancestral feature. Our results provide insights into the mechanisms of archaeal cell division and pave the way for a better understanding of the processes underlying the divide between the two prokaryotic domains.

scholarly journals Origin of modern syphilis and emergence of a contemporary pandemic cluster

2016 ◽  
Author(s):  
Natasha Arora ◽  
Verena J. Schuenemann ◽  
Günter Jäger ◽  
Alexander Peltzer ◽  
Alexander Seitz ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Treponema Pallidum ◽  
Genome Data ◽  
Evolutionary Origins ◽  
15Th Century ◽  
Genetic Patterns ◽  
Clonal Nature ◽  
Dna Capture ◽  
Causative Bacterium

AbstractSyphilis swept across the world in the 16th century as one of most prominent documented pandemics and is re-emerging worldwide despite the availability of effective antibiotics. Little is known about the genetic patterns in current infections or the evolutionary origins of the disease due to the non-cultivable and clonal nature of the causative bacterium Treponema pallidum subsp. pallidum. In this study, we used DNA capture and next generation sequencing to obtain whole genome data from syphilis patient specimens and from treponemes propagated in laboratory settings. Phylogenetic analyses indicate that the syphilis strains examined here share a common ancestor after the 15th century. Moreover, most contemporary strains are azithromycin resistant and members of a globally dominant cluster named here as SS14-Ω. This cluster diversified from a common ancestor in the mid-20th century and has the population genetic and epidemiological features indicative of the emergence of a pandemic strain cluster.

scholarly journals Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads

2013 ◽  
Vol 280 (1769) ◽  
pp. 20131755 ◽  
Author(s):  
Matthew W. Brown ◽  
Susan C. Sharpe ◽  
Jeffrey D. Silberman ◽  
Aaron A. Heiss ◽  
B. Franz Lang ◽  
...  
Keyword(s):  
Protein Complex ◽  
Phylogenetic Analyses ◽  
Estuarine Sediment ◽  
The Other ◽  
Rrna Gene ◽  
Rna Seq ◽  
Phylogenetic Methods ◽  
Eukaryote Evolution ◽  
Phylogenomic Analyses

Most eukaryotic lineages belong to one of a few major groups. However, several protistan lineages have not yet been robustly placed in any of these groups. Both the breviates and apusomonads are two such lineages that appear to be related to the Amoebozoa and Opisthokonta (i.e. the ‘unikonts’ or Amorphea); however, their precise phylogenetic positions remain unclear. Here, we describe a novel microaerophilic breviate, Pygsuia biforma gen. nov. sp. nov . , isolated from a hypoxic estuarine sediment. Ultrastructurally, this species resembles the breviate genera Breviata and Subulatomonas but has two cell morphologies, adherent and swimming. Phylogenetic analyses of the small sub-unit rRNA gene show that Pygsuia is the sister to the other breviates. We constructed a 159-protein supermatrix, including orthologues identified in RNA-seq data from Pygsuia . Phylogenomic analyses of this dataset show that breviates, apusomonads and Opisthokonta form a strongly supported major eukaryotic grouping we name the Obazoa. Although some phylogenetic methods disagree, the balance of evidence suggests that the breviate lineage forms the deepest branch within Obazoa. We also found transcripts encoding a nearly complete integrin adhesome from Pygsuia , indicating that this protein complex involved in metazoan multicellularity may have evolved earlier in eukaryote evolution than previously thought.

scholarly journals The sunlit microoxic niche of the archaeal eukaryotic ancestor comes to light

2018 ◽  
Author(s):  
Paul-Adrian Bulzu ◽  
Adrian-Ştefan Andrei ◽  
Michaela M. Salcher ◽  
Maliheh Mehrshad ◽  
Keiichi Inoue ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Phylogenetic Analyses ◽  
Kynurenine Pathway ◽  
Compelling Evidence ◽  
Genomic Information ◽  
Genomic Dataset ◽  
Specific Proteins ◽  
Phylogenomic Analyses ◽  
Genome Scale ◽  
Shed Light

SummaryRecent advances in phylogenomic analyses and increased genomic sampling of uncultured prokaryotic lineages brought compelling evidence in support of the emergence of eukaryotes from within the Archaea domain of life. The discovery of Asgardaeota archaea and their recognition as the closest extant relative of eukaryotes fuelled the revival of a decades-old debate regarding the topology of the tree of life. While it is apparent that Asgardaeota encode a plethora of eukaryotic-specific proteins (the highest number identified to date in prokaryotes), the lack of genomic information and metabolic characterization has precluded inferences about their lifestyles and the metabolic landscape that may have favoured the emergence of the hallmark eukaryotic subcellular architecture. Here, we use advanced phylogenetic analyses to infer the deep ancestry of eukaryotes and genome-scale metabolic reconstructions to shed light on the metabolic milieu of the closest archaeal eukaryotic ancestors discovered till date. In doing so, we: i) generate the largest Asgardaeota genomic dataset available so far, ii) describe a new clade of rhodopsins encoded within the recovered genomes, iii) provide unprecedented evidence for mixotrophy within Asgardaeota, iv) present first-ever proofs that the closest extant archaeal relatives to all eukaryotes (Heimdallarchaeia) have microoxic lifestyles with aerobic metabolic pathways unique among Archaea (i.e. kynurenine pathway) and v) generate the first images of Asgardaeota.

scholarly journals Birth of Archaeal Cells: Molecular Phylogenetic Analyses of G1P Dehydrogenase, G3P Dehydrogenases, and Glycerol Kinase Suggest Derived Features of Archaeal Membranes Having G1P Polar Lipids

Archaea ◽  
2016 ◽  
Vol 2016 ◽  
pp. 1-16 ◽  
Author(s):  
Shin-ichi Yokobori ◽  
Yoshiki Nakajima ◽  
Satoshi Akanuma ◽  
Akihiko Yamagishi
Keyword(s):  
Lipid Membranes ◽  
Phylogenetic Trees ◽  
Common Ancestor ◽  
Lipid Membrane ◽  
Phylogenetic Analyses ◽  
Glycerol Kinase ◽  
Universal Common Ancestor ◽  
Archaeal Lineage ◽  
Terrestrial Life ◽  
Molecular Phylogenetic

Bacteria and Eukarya have cell membranes withsn-glycerol-3-phosphate (G3P), whereas archaeal membranes containsn-glycerol-1-phosphate (G1P). Determining the time at which cells with either G3P-lipid membranes or G1P-lipid membranes appeared is important for understanding the early evolution of terrestrial life. To clarify this issue, we reconstructed molecular phylogenetic trees of G1PDH (G1P dehydrogenase; EgsA/AraM) which is responsible for G1P synthesis and G3PDHs (G3P dehydrogenase; GpsA and GlpA/GlpD) and glycerol kinase (GlpK) which is responsible for G3P synthesis. Together with the distribution of these protein-encoding genes among archaeal and bacterial groups, our phylogenetic analyses suggested that GlpA/GlpD in the Commonote (the last universal common ancestor of all extant life with a cellular form,Commonote commonote) acquired EgsA (G1PDH) from the archaeal common ancestor (Commonote archaea) and acquired GpsA and GlpK from a bacterial common ancestor (Commonote bacteria). In our scenario based on this study, the Commonote probably possessed a G3P-lipid membrane synthesized enzymatically, after which the archaeal lineage acquired G1PDH followed by the replacement of a G3P-lipid membrane with a G1P-lipid membrane.

scholarly journals Universal markers support a long inter-domain branch between Archaea and Bacteria

2021 ◽  
Author(s):  
Edmund R. R. Moody ◽  
Tara A. Mahendrarajah ◽  
Nina Dombrowski ◽  
James W. Clark ◽  
Celine Petitjean ◽  
...  
Keyword(s):  
Gene Evolution ◽  
Phylogenetic Analyses ◽  
Marker Gene ◽  
Branch Length ◽  
Ribosomal Gene ◽  
Marker Genes ◽  
Cellular Processes ◽  
Accelerated Evolution ◽  
Universal Common Ancestor ◽  
Domains Of Life

AbstractThe tree of life is generally estimated from a core set of 16-56 genes coding for proteins predominantly involved in translation and other conserved informational and cellular processes. These markers represent only a fraction of the genes that were likely present in the last universal common ancestor (LUCA), but are useful for deep phylogenetic reconstructions because their mode of inheritance appears to be mainly vertical, which satisfies the assumptions of gene concatenation and supertree methods. Previous phylogenetic analyses of these genes recovered a long branch between Archaea and Bacteria. By contrast, a recent study made use of a greatly expanded set of 381 marker genes and recovered a much shorter branch length between Archaea and Bacteria, comparable to some divergences within the domains. These analyses suggest that the apparent deep split between Archaea and Bacteria may be the result of accelerated evolution of ribosomal genes. Here we re-evaluate the evolutionary history of the expanded marker gene set and show that substitutional saturation, inter-domain gene transfer, hidden paralogy, and poor model fit contribute to the inference of an artificially shortened inter-domain branch. Our results do not exclude a moderately faster rate of ribosomal gene evolution during the divergence of Archaea and Bacteria, but indicate that vertically-evolving marker genes across all functional categories support a major genetic divergence between the two primary domains of life.

scholarly journals A congruent phylogenomic signal places eukaryotes within the Archaea

2012 ◽  
Vol 279 (1749) ◽  
pp. 4870-4879 ◽  
Author(s):  
Tom A. Williams ◽  
Peter G. Foster ◽  
Tom M. W. Nye ◽  
Cymon J. Cox ◽  
T. Martin Embley
Keyword(s):  
Ribosomal Rna ◽  
Biological Diversity ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Small Subunit ◽  
Evolutionary Models ◽  
Protein Coding ◽  
Cellular Life ◽  
Phylogenetic Methods

Determining the relationships among the major groups of cellular life is important for understanding the evolution of biological diversity, but is difficult given the enormous time spans involved. In the textbook ‘three domains’ tree based on informational genes, eukaryotes and Archaea share a common ancestor to the exclusion of Bacteria. However, some phylogenetic analyses of the same data have placed eukaryotes within the Archaea, as the nearest relatives of different archaeal lineages. We compared the support for these competing hypotheses using sophisticated phylogenetic methods and an improved sampling of archaeal biodiversity. We also employed both new and existing tests of phylogenetic congruence to explore the level of uncertainty and conflict in the data. Our analyses suggested that much of the observed incongruence is weakly supported or associated with poorly fitting evolutionary models. All of our phylogenetic analyses, whether on small subunit and large subunit ribosomal RNA or concatenated protein-coding genes, recovered a monophyletic group containing eukaryotes and the TACK archaeal superphylum comprising the Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota. Hence, while our results provide no support for the iconic three-domain tree of life, they are consistent with an extended eocyte hypothesis whereby vital components of the eukaryotic nuclear lineage originated from within the archaeal radiation.

scholarly journals SARS-CoV-2 convergent evolution cannot be reliably inferred from phylogenetic analyses

2021 ◽  
Author(s):  
Yoon-Seo Jo ◽  
Asif U. Tamuri ◽  
Greg J. Towers ◽  
Richard A Goldstein
Keyword(s):  
Convergent Evolution ◽  
Phylogenetic Trees ◽  
Common Ancestor ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Fitness Advantage ◽  
Phylogenetic Methods ◽  
Recurrent Mutations ◽  
Limited Support ◽  
Statistical Support

A homoplasy is a trait shared between individuals that did not arise in a common ancestor, but rather is the result of convergent evolution. SARS-CoV-2 homoplasic mutations are important to characterise, because the evidence for a mutation conferring a fitness advantage is strengthened if this mutation has evolved independently and repeatedly in separate viral lineages. Yet detecting homoplasy is difficult due to insufficient variation between sequences to construct reliable phylogenetic trees. Here, we develop a method to more robustly identify confident homoplasies. We derive a maximum likelihood (ML) tree, with taxa bearing seemingly recurrent mutations dispersed across the tree, and then, for each potentially homoplasic mutation, we derive an alternative tree where the same taxa are constrained to one clade such that the mutation is no longer homoplasic. We then compare how well the two trees fit the sequence data. Applying this method to SARS-CoV-2 yields only a few instances where the constrained trees have significantly less statistical support than unconstrained tree, suggesting phylogenetics can provide limited support for homoplasy in SARS-CoV-2 and that caution is needed when inferring evidence of convergent evolution from phylogenetic methods in the absence of evidence from other sources.

Evolution of vacuolar H+-ATPases: immunological relationships of the nucleotide-binding subunits

1989 ◽  
Vol 67 (6) ◽  
pp. 306-310 ◽  
Author(s):  
Morris F. Manolson ◽  
Judith M. Percy ◽  
David K. Apps ◽  
Xiao-Song Xie ◽  
Dennis K. Stone ◽  
...  
Keyword(s):  
Anaerobic Bacterium ◽  
Common Ancestor ◽  
Sequence Data ◽  
Structural Features ◽  
Eukaryotic Cells ◽  
Clostridium Pasteurianum ◽  
Chromaffin Granules ◽  
Α Subunit ◽  
Evolutionary Origins ◽  
Vacuolar Membranes

The evolution of the endomembrane systems of eukaryotic cells can be examined by exploring the evolutionary origins of the endomembrane H+-ATPases. Recent studies suggest that certain polypeptides are common to all H+ pumps of this type. Tonoplast H+ -ATPase from Beta vulgaris L. was purified and antibodies raised to two of its subunits. Each of these antisera reacted with a polypeptide of the corresponding size in bovine chromaffin granules, bovine clathrincoated vesicles, and yeast vacuolar membranes, suggesting common structural features and a common ancestor for endomembrane H+-ATPases of different organelles and different kingdoms. The antiserum raised against the 57-kDa polypeptide of plant tonoplast H+ -ATPase also reacted with subunit "a" of the H+-ATPase from the obligately anaerobic bacterium Clostridium pasteurianum and to the α subunit of the H+ -ATPase from Escherichia coli. There was no reactivity with chloroplast or mitochondrial ATPases. These results are discussed in relation to recent sequence data which suggest that endomembrane H+-ATPases may be evolutionarily related to the F0F1 ATPases.Key words: H+ -ATPase, evolution, immunology, vacuole, endomembrane.

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