An archaeal origin of eukaryotes supports only two primary domains of life

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

A congruent phylogenomic signal places eukaryotes within the Archaea

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

The archaebacterial origin of eukaryotes

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

Multiple phase transitions in a system of exclusion processes with limited reservoirs of particles and fuel carriers

The TASEP is a paradigmatic model from non-equilibrium statistical physics, which describes particles hopping along a lattice of discrete sites. The TASEP is applicable to a broad range of different transport systems, but does not consider the fact that in many such systems the availability of resources required for the transport is limited. In this paper we extend the TASEP to include the effect of a limited number of two different fundamental transport resources: the hopping particles, and the "fuel carriers", which provide the energy required to drive the system away from equilibrium. As as consequence, the system's dynamics are substantially affected: a "limited resources" regime emerges, where the current is limited by the rate of refuelling, and the usual coexistence line between low and high particle density opens into a broad region on the phase plane. Due to the combination of a limited amount of both resources, multiple phase transitions are possible when increasing the exit rate beta for a fixed entry rate alpha. This is a new feature that can only be obtained by the inclusion of both kinds of limited resources. We also show that the fluctuations in particle density in the LD and HD phases are unaffected by fluctuations in the number of loaded fuel carriers, except by the fact that when these fuel resources become limited, the particle hopping rate is severely reduced

Eruptive modes and hiatus of volcanism at West Mata seamount, NE Lau basin : 1996–2012

Author Posting. © American Geophysical Union, 2014. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry, Geophysics, Geosystems 15 (2014): 4093–4115, doi:10.1002/2014GC005387.We present multiple lines of evidence for years to decade-long changes in the location and character of volcanic activity at West Mata seamount in the NE Lau basin over a 16 year period, and a hiatus in summit eruptions from early 2011 to at least September 2012. Boninite lava and pyroclasts were observed erupting from its summit in 2009, and hydroacoustic data from a succession of hydrophones moored nearby show near-continuous eruptive activity from January 2009 to early 2011. Successive differencing of seven multibeam bathymetric surveys of the volcano made in the 1996–2012 period reveals a pattern of extended constructional volcanism on the summit and northwest flank punctuated by eruptions along the volcano's WSW rift zone (WSWRZ). Away from the summit, the volumetrically largest eruption during the observational period occurred between May 2010 and November 2011 at ∼2920 m depth near the base of the WSWRZ. The (nearly) equally long ENE rift zone did not experience any volcanic activity during the 1996–2012 period. The cessation of summit volcanism recorded on the moored hydrophone was accompanied or followed by the formation of a small summit crater and a landslide on the eastern flank. Water column sensors, analysis of gas samples in the overlying hydrothermal plume and dives with a remotely operated vehicle in September 2012 confirmed that the summit eruption had ceased. Based on the historical eruption rates calculated using the bathymetric differencing technique, the volcano could be as young as several thousand years.Support for R.W.E. during this study was by internal NOAA funding to the NOAA Vents Program (now Earth-Ocean Interactions Program). The NSF Ridge 2000 and MARGINS programs played a major role in the planning and justification for the 2009 rapid response proposal that funded the May 2009 expedition. MBARI provided support and outstanding postprocessing of the multibeam bathymetry from the D. Allan B. AUV multibeam sonar used in this study. NSF also provided major funding for the 2009 expedition (OCE930025 and OCE-0934660 to JAR) and for the 210Po-210Pb radiometric dating (OCE-0929881 and for the 210Po-210Pb radiometric dating (OCE-0929881 to KHR)). The NOAA Office of Exploration and Research provided major funding for the 2009 and 2012 field programs.2015-04-3

Informational Gene Phylogenies Do Not Support a Fourth Domain of Life for Nucleocytoplasmic Large DNA Viruses

Mimivirus is a nucleocytoplasmic large DNA virus (NCLDV) with a genome size (1.2 Mb) and coding capacity ( 1000 genes) comparable to that of some cellular organisms. Unlike other viruses, Mimivirus and its NCLDV relatives encode homologs of broadly conserved informational genes found in Bacteria, Archaea, and Eukaryotes, raising the possibility that they could be placed on the tree of life. A recent phylogenetic analysis of these genes showed the NCLDVs emerging as a monophyletic group branching between Eukaryotes and Archaea. These trees were interpreted as evidence for an independent “fourth domain” of life that may have contributed DNA processing genes to the ancestral eukaryote. However, the analysis of ancient evolutionary events is challenging, and tree reconstruction is susceptible to bias resulting from non-phylogenetic signals in the data. These include compositional heterogeneity and homoplasy, which can lead to the spurious grouping of compositionally-similar or fast-evolving sequences. Here, we show that these informational gene alignments contain both significant compositional heterogeneity and homoplasy, which were not adequately modelled in the original analysis. When we use more realistic evolutionary models that better fit the data, the resulting trees are unable to reject a simple null hypothesis in which these informational genes, like many other NCLDV genes, were acquired by horizontal transfer from eukaryotic hosts. Our results suggest that a fourth domain is not required to explain the available sequence data