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Initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a Monte Carlo method to estimate the conservation of gene order. The method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. The raw distances were then corrected for gene order convergence using an adaptation of the Jukes-Cantor model, as well as using the common distance correction D' = -ln(1-D). First, we compared the distances found via the order of six orthologs to distances found based on ortholog gene content and small subunit rRNA sequences. The Jukes-Cantor gene order distances are reasonably well correlated with the divergence of rRNA (R (2) = 0.24), especially at rRNA Jukes-Cantor distances of less than 0.2 (R (2) = 0.52). Gene content is only weakly correlated with rRNA divergence (R (2) = 0.04) over all distances, however, it is especially strongly correlated at rRNA Jukes-Cantor distances of less than 0.1 (R (2) = 0.67). This initial work suggests that gene order may be useful in conjunction with other methods to help understand the relatedness of genomes. Using the gene order distances in 143 genomes, the relations of prokaryotes were studied using neighbor joining and agreement subtrees. We then repeated our study of the relations of prokaryotes using gene order in 172 complete genomes better representing a wider-diversity of prokaryotes. Consistently, our trees show the Actinobacteria as a sister group to the bulk of the Firmicutes. In fact, the robustness of gene order support was found to be considerably greater for uniting these two phyla than for uniting any of the proteobacterial classes together. The results are supportive of the idea that Actinobacteria and Firmicutes are closely related, which in turn implies a single origin for the gram-positive cell.

Initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a Monte Carlo method to estimate the conservation of gene order. The method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. The raw distances were then corrected for gene order convergence using an adaptation of the Jukes-Cantor model, as well as using the common distance correction D' = -ln(1-D). First, we compared the distances found via the order of six orthologs to distances found based on ortholog gene content and small subunit rRNA sequences. The Jukes-Cantor gene order distances are reasonably well correlated with the divergence of rRNA (R (2) = 0.24), especially at rRNA Jukes-Cantor distances of less than 0.2 (R (2) = 0.52). Gene content is only weakly correlated with rRNA divergence (R (2) = 0.04) over all distances, however, it is especially strongly correlated at rRNA Jukes-Cantor distances of less than 0.1 (R (2) = 0.67). This initial work suggests that gene order may be useful in conjunction with other methods to help understand the relatedness of genomes. Using the gene order distances in 143 genomes, the relations of prokaryotes were studied using neighbor joining and agreement subtrees. We then repeated our study of the relations of prokaryotes using gene order in 172 complete genomes better representing a wider-diversity of prokaryotes. Consistently, our trees show the Actinobacteria as a sister group to the bulk of the Firmicutes. In fact, the robustness of gene order support was found to be considerably greater for uniting these two phyla than for uniting any of the proteobacterial classes together. The results are supportive of the idea that Actinobacteria and Firmicutes are closely related, which in turn implies a single origin for the gram-positive cell.

The great oxidation event (GOE), ~2.4 billion years ago, caused fundamental changes to the chemistry of Earth's surface environments. However, the effect of these changes on the biosphere is unknown, due to a worldwide lack of well‐preserved fossils from this time. Here, we investigate exceptionally preserved, large spherical aggregate (SA) microfossils permineralised in chert from the c. 2.4 Ga Turee Creek Group in Western Australia. Field and petrographic observations, Raman spectroscopic mapping, and in situ carbon isotopic analyses uncover insights into the morphology, habitat, reproduction and metabolism of this unusual form, whose distinctive, SA morphology has no known counterpart in the fossil record. Comparative analysis with microfossils from before the GOE reveals the large SA microfossils represent a step‐up in cellular organisation. Morphological comparison to extant micro‐organisms indicates the SAs have more in common with coenobial algae than coccoidal bacteria, emphasising the complexity of this microfossil form. The remarkable preservation here provides a unique window into the biosphere, revealing an increase in the complexity of life coinciding with the GOE. [ABSTRACT FROM AUTHOR]

Hydrothermal systems are areas in which heated fluids and organic molecules rush through basaltic material rich in metals and minerals. By studying malononitrile and acetonitrile, we examine the effects of metal and mineral nanoparticles on nitrile compounds in anoxic, hydrothermal conditions representing a prebiotic environment of early Earth. Polymerization, reduction, cyclization, and a phenomenon colloquially known as 'chemical gardening' (structure building via reprecipitation of metal compounds or complexing with organics) are all potential outcomes with the addition of metals and minerals. Reduction occurs with the addition of rhodium (Rh) or iron (II) sulfide (FeS), with positive identification of ethanol and ethylamine forming from acetonitrile reduction. We find that polymerization and insoluble product formation were associated with oxide minerals, metallic nickel (Ni), and metallic cobalt (Co) acting as catalysts. Oxide minerals strongly promoted polymerization into insoluble, tar-like products of nitriles. FeS, iron-nickel alloy (FeNi), and rhodium are unique cases that appear to act as reagents by actively participating in chemical gardening without returning to their initial state. Further, FeS tentatively had a phase change into the mineral parabutlerite. This research aims to identify metals and metal minerals that could best serve nitrile catalysis and reactions on early Earth. [ABSTRACT FROM AUTHOR]