Prokaryotic evolution and the tree of life are two different things

Bapteste, Éric; O’Malley, Maureen A.; Beiko, Robert G.; Ereshefsky, Marc; Gogarten, J. Peter; Franklin-Hall, Laura; Lapointe, François‐Joseph; Dupré, John; Dagan, Tal; Boucher, Yan; Martin, William

doi:10.1186/1745-6150-4-34

Cited by 206 publications

(178 citation statements)

References 137 publications

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“…An entry in the literature of this debate is in [11]. In recent years the opposition between the two approaches has been overstepped by more unitary experimental and theoretical frames, taking into account energetic, evolutionary, proto-metabolic and ur-environmental aspects [12][13][14][15][16][17][18][19][20][21][22]. The productive interaction between vesicles and RNA replication was reported [23].…”

Section: The Need For a Unitary Physical-chemical Framementioning

confidence: 99%

Formamide and the origin of life

Saladino

Crestini

Pino

et al. 2012

Physics of Life Reviews

261

234

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The complexity of life boils down to the definition: "self-sustained chemical system capable of undergoing Darwinian evolution" (Joyce, 1994) [1]. The term "self-sustained" implies a set of chemical reactions capable of harnessing energy from the environment, using it to carry out programmed anabolic and catabolic functions. We briefly present our opinion on the general validity of this definition.Running anabolic and catabolic functions entails complex chemical information whose stability, reproducibility and evolution constitute the core of what is dubbed genetics.Life as-we-know-it is made of the intimate interaction of metabolism and genetics, both built around the chemistry of the most common elements of the Universe (hydrogen, oxygen, nitrogen, carbon). Other elements like phosphorus and sulphur play important but ancillary and potentially replaceable roles.The reproducible interaction of metabolic and genetic cycles results in the hypercycles of organization and de-organization of chemical information that we consider living entities. In order to approach the problem of the origin of life it is therefore reasonable to start from the assumption that both metabolism and genetics had a common origin, shared a common chemical frame, were embedded in physical-chemical conditions favourable for the onset of both.The most abundant three-atoms organic compound in interstellar environment is hydrogen cyanide HCN, the most abundant three-atoms inorganic compound is water H 2 O. The combination of the two results in the formation of formamide H 2 NCOH. We have explored the chemistry of formamide in conditions compatible with the synthesis and the stability of compounds of potential pre-genetic and pre-metabolic interest. We discuss evidence showing (i) that all the compounds necessary for the build-up of nucleic acids are easily obtained abiotically, (ii) that essentially all the steps leading to the spontaneous generation of RNA are abiotically possible, (iii) that the key compounds of extant metabolic cycles are obtained in the same chemical frame, often in the same test tube.How close are these observations to a plausible scenario for the origin of life?

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Section: The Need For a Unitary Physical-chemical Framementioning

confidence: 99%

Formamide and the origin of life

Saladino

Crestini

Pino

et al. 2012

Physics of Life Reviews

261

234

View full text Add to dashboard Cite

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“…Horizontal flows can be facilitated by plasmids [4], phage [5], viruses [6], transposons [7], gene transfer agents [8], intercellular nanotubes [9], or simply the hybridization of sexual species, followed by re-integration of the hybrid into one of the ancestral species [10,11]. Contemporary genomes are, and extinct genomes were, complex mixtures of genetic mergers [12,13], with the horizontal gene flows being as normal as vertical gene flows. This presents us with a problem if we are restricted to using tree-like processes that only depict vertical gene flows to model the data, as we would not be able to model and understand the impact of horizontal gene flows in evolution.…”

Section: Introductionmentioning

confidence: 99%

The ring of life hypothesis for eukaryote origins is supported by multiple kinds of data

McInerney

Pisani

O’Connell

2015

Phil. Trans. R. Soc. B

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One contribution of 17 to a theme issue 'Eukaryotic origins: progress and challenges'. The literature is replete with manuscripts describing the origin of eukaryotic cells. Most of the models for eukaryogenesis are either autogenous (sometimes called slow-drip), or symbiogenic (sometimes called big-bang). In this article, we use large and diverse suites of 'Omics' and other data to make the inference that autogeneous hypotheses are a very poor fit to the data and the origin of eukaryotic cells occurred in a single symbiosis.

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“…These methods include: SSNs, anchored sequence alignments and N-rooted graphs. Although conventional phylogenetic trees might be appropriate for visualising the evolution of many genes, they are not suitable for all evolutionary events [38][39][40][41] and are specifically unable to display evolutionary histories when these histories are entangled because of merging. In other words, when two evolving entities merge to form a single sequence, the histories of all the sequences cannot be represented by traditional phylogenetic trees.…”

Section: Discussionmentioning

confidence: 99%

Evolution by Pervasive Gene Fusion in Antibiotic Resistance and Antibiotic Synthesizing Genes

et al. 2015

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Phylogenetic (tree-based) approaches to understanding evolutionary history are unable to incorporate convergent evolutionary events where two genes merge into one. In this study, as exemplars of what can be achieved when a tree is not assumed a priori, we have analysed the evolutionary histories of polyketide synthase genes and antibiotic resistance genes and have shown that their history is replete with convergent events as well as divergent events. We demonstrate that the overall histories of these genes more closely resembles the remodelling that might be seen with the children's toy Lego, than the standard model of the phylogenetic tree. This work demonstrates further that genes can act as public goods, available for re-use and incorporation into other genetic goods.

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Prokaryotic evolution and the tree of life are two different things

Cited by 206 publications

References 137 publications

Formamide and the origin of life

Formamide and the origin of life

The ring of life hypothesis for eukaryote origins is supported by multiple kinds of data

Evolution by Pervasive Gene Fusion in Antibiotic Resistance and Antibiotic Synthesizing Genes

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