Microaerobic steroid biosynthesis and the molecular fossil record of Archean life

Waldbauer, Jacob R.; Newman, Dianne K.; Summons, Roger E.

doi:10.1073/pnas.1104160108

Cited by 93 publications

(62 citation statements)

References 54 publications

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“…Cyanobacteria are distinguished among prokaryotes by a relative abundance of microfossil and biomarker records (29). However, even this relative abundance reduces to a handful calibration points for the timing of cyanobacterial evolution: (i) the presence of free oxygen in late Archean oceans (30) and the rapid rise in atmospheric oxygen 2.45-2.32 billion years ago (Ga) (31) is attributed to cyanobacteria (32), but many details of these associations continue to be investigated (33,34); (ii) unambiguous microfossil evidence dates to ∼2.0 Ga, by which time diversification was advanced with fossils of filamentous forms dating from 1.9 Ga (35) and akinete forming Cyanobacteria from 2.1 Ga (29); and (iii) by 1.4 Ga diversification of major extant morphologically distinguishable lineages was complete (22,36).…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

Szöllősi

Boussau

Abby

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

157

187

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The timing of the evolution of microbial life has largely remained elusive due to the scarcity of prokaryotic fossil record and the confounding effects of the exchange of genes among possibly distant species. The history of gene transfer events, however, is not a series of individual oddities; it records which lineages were concurrent and thus provides information on the timing of species diversification. Here, we use a probabilistic model of genome evolution that accounts for differences between gene phylogenies and the species tree as series of duplication, transfer, and loss events to reconstruct chronologically ordered species phylogenies. Using simulations we show that we can robustly recover accurate chronologically ordered species phylogenies in the presence of gene tree reconstruction errors and realistic rates of duplication, transfer, and loss. Using genomic data we demonstrate that we can infer rooted species phylogenies using homologous gene families from complete genomes of 10 bacterial and archaeal groups. Focusing on cyanobacteria, distinguished among prokaryotes by a relative abundance of fossils, we infer the maximum likelihood chronologically ordered species phylogeny based on 36 genomes with 8,332 homologous gene families. We find the order of speciation events to be in full agreement with the fossil record and the inferred phylogeny of cyanobacteria to be consistent with the phylogeny recovered from established phylogenomics methods. Our results demonstrate that lateral gene transfers, detected by probabilistic models of genome evolution, can be used as a source of information on the timing of evolution, providing a valuable complement to the limited prokaryotic fossil record. molecular dating | gene tree reconciliation | birth-death model A central aspect of Earth's history is the pattern and timing of diversification of the species that inhabit it. In macroorganisms such as animals or plants, an abundant fossil record, the accumulation of genomic data, and the development of models of molecular evolution accommodating for varying rates of evolutionary changes among lineages are progressively yielding an intelligible picture (1-4). In contrast, the dating of the evolution of microbial life remains largely elusive (5, 6). This situation results from the convergence of two main factors: first, fossils, especially bacterial and archaeal ones, are scarce or cannot be traced to a specific lineage. Therefore, any inference of the timing of microbial evolution must rely almost exclusively on molecular data constrained only by a handful of dates during the course of more than three billion years of evolution. Second, molecular data can be difficult to interpret in terms of patterns of species diversification. Lateral gene transfers (LGTs), the exchange of genes among possibly distant species, have tangled gene phylogenies to the extent that they provide a deeply blurred view of the relationships between lineages. Different approaches [e.g., concatenation, supertrees (7, 8)] have been proposed to ove...

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Section: Discussionmentioning

confidence: 99%

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

Szöllősi

Boussau

Abby

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

157

187

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“…It is nearly impossible to prove that cyanobacteria were not present, so most of the debate rests on what is sufficient evidence to prove that they were. I prefer not to delve into this debate here, but the interested reader can consult a number of recent papers for updates (Buick, 2008;Kirschvink and Kopp, 2008;Rasmussen et al, 2008;Waldbauer et al, 2011). Rather, we will take our cues from the geologic record of Fe and sulphur geochemistry.…”

Section: The Archean Eonmentioning

confidence: 99%

The Iron Biogeochemical Cycle Past and Present

Raiswell¹,

Canfield²

2012

GeochemPersp

581

445

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“…Sterols figure into issues both on eukaryote age and on the relationship of eukaryotes to oxygen. This is because oxygen is required as a cofactor in known eukaryotic sterol biosynthesis pathways: a squalene epoxidation step, three demethylation reactions, and other modifications consume about 12 molecules of O 2 per sterol backbone (547). Accordingly, sterols are widely used as geochemical proxies for the presence of oxygen in the ancient Earth environment, but the crucial question is, How much oxygen does biological sterol synthesis indicate?…”

Section: Ecological Implications Over Geological Timementioning

confidence: 99%

Biochemistry and Evolution of Anaerobic Energy Metabolism in Eukaryotes

Müller

Mentel

Hellemond

et al. 2012

Microbiol Mol Biol Rev

695

904

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SUMMARY Major insights into the phylogenetic distribution, biochemistry, and evolutionary significance of organelles involved in ATP synthesis (energy metabolism) in eukaryotes that thrive in anaerobic environments for all or part of their life cycles have accrued in recent years. All known eukaryotic groups possess an organelle of mitochondrial origin, mapping the origin of mitochondria to the eukaryotic common ancestor, and genome sequence data are rapidly accumulating for eukaryotes that possess anaerobic mitochondria, hydrogenosomes, or mitosomes. Here we review the available biochemical data on the enzymes and pathways that eukaryotes use in anaerobic energy metabolism and summarize the metabolic end products that they generate in their anaerobic habitats, focusing on the biochemical roles that their mitochondria play in anaerobic ATP synthesis. We present metabolic maps of compartmentalized energy metabolism for 16 well-studied species. There are currently no enzymes of core anaerobic energy metabolism that are specific to any of the six eukaryotic supergroup lineages; genes present in one supergroup are also found in at least one other supergroup. The gene distribution across lineages thus reflects the presence of anaerobic energy metabolism in the eukaryote common ancestor and differential loss during the specialization of some lineages to oxic niches, just as oxphos capabilities have been differentially lost in specialization to anoxic niches and the parasitic life-style. Some facultative anaerobes have retained both aerobic and anaerobic pathways. Diversified eukaryotic lineages have retained the same enzymes of anaerobic ATP synthesis, in line with geochemical data indicating low environmental oxygen levels while eukaryotes arose and diversified.

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Microaerobic steroid biosynthesis and the molecular fossil record of Archean life

Cited by 93 publications

References 54 publications

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

The Iron Biogeochemical Cycle Past and Present

Biochemistry and Evolution of Anaerobic Energy Metabolism in Eukaryotes

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