Networks: expanding evolutionary thinking

Bapteste, Éric; Iersel, Leo van; Janke, Axel; Kelchner, Scot A.; Kelk, Steven; McInerney, James O.; Morrison, David A.; Nakhleh, Luay; Steel, Mike; Stougie, Leen; Whitfield, James B.

doi:10.1016/j.tig.2013.05.007

Cited by 201 publications

(141 citation statements)

References 12 publications

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“…If such genomic endogenous retrovirus (ERV) sequences are also produced by QS-mediated evolution, then their involvement in the formation of new or edited networks regulating host functions might be understood as resulting from a consortial RNAbased process with inherent coherence. Indeed, understanding the origin of transposable RNA-based networks (and network security) has always been challenging as networks do not fit into tree-based analogies (Bapteste et al 2013;Daly et al 2011;Feschotte 2008). It also appears that various small non-coding RNAs participate in 'multi-task' networks and such RNAs tend to be transcribed from 'junk' retroposons (Mattick 2011;Mattick and Gagen 2001;Mattick and Makunin 2006;Pheasant and Mattick 2007).…”

Section: Retroviral Network Regulate Evolution and Developmentmentioning

confidence: 99%

When Competing Viruses Unify: Evolution, Conservation, and Plasticity of Genetic Identities

Villarreal

Witzany

2015

J Mol Evol

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In the early 1970s, Manfred Eigen and colleagues developed the quasispecies model (qs) for the population-based origin of RNAs representing the early genetic code. The Eigen idea is basically that a halo of mutants is generated by error-prone replication around the master fittest type which will behave similarly as a biological population. But almost from the start, very interesting and unexpected observations were made regarding competition versus co-operation which suggested more complex interactions. It thus became increasingly clear that although viruses functioned similar to biological species, their behavior was much more complex than the original theory could explain, especially adaptation without changing the consensus involving minority populations. With respect to the origin of natural codes, meaning, and code-use in interactions (communication), it also became clear that individual fittest type-based mechanisms were likewise unable to explain the origin of natural codes such as the genetic code with their context-and consortia-dependence (pragmatic nature). This, instead, required the participation of groups of agents competent in the code and able to edit code because natural codes do not code themselves. Three lines of inquiry, experimental virology, quasispecies theory, and the study of natural codes converged to indicate that consortia of cooperative RNA agents such as viruses must be involved in the fitness of RNA and its involvement in communication, i.e., code-competent interactions. We called this co-operative form quasispecies consortia (qs-c). They are the essential agents that constitute the possibility of evolution of biological group identity. Finally, the basic interactional motifs for the emergence of group identity, communication, and cooperation-together with its opposing functions-are explained by the ''Gangen'' hypothesis.

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Section: Retroviral Network Regulate Evolution and Developmentmentioning

confidence: 99%

When Competing Viruses Unify: Evolution, Conservation, and Plasticity of Genetic Identities

Villarreal

Witzany

2015

J Mol Evol

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“…A more general diagram is a phylogenetic network. These are found in two varieties-networks that display uncertainty and networks that display recombination [24]. Recombination networks also have a restrictive set of assumptions-the data are required to be homologous along its entirety, and reticulations on phylogenetic network graphs indicate places where recombination events between homologous regions have occurred.…”

Section: What Is the Problem With Trees In Prokaryotic Evolution?mentioning

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 histories are commonly represented by phylogenetic trees, and can be used, for example, to inform genomics studies, analyse virus epidemics and understand the origins of humans [23]. Even so, in case evolutionary processes such as recombination and hybridization are involved, it can be more appropriate to represent histories using phylogenetic networks instead of trees [2].…”

Section: Introductionmentioning

confidence: 99%

Reconstructing Phylogenetic Level-1 Networks from Nondense Binet and Trinet Sets

et al. 2015

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Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set T of binary binets or trinets over a taxon set X , and constructing such a network whenever it exists. We show that this is NP-hard for trinets but polynomial-time solvable for binets. Moreover, we show that the problem is still polynomial-time solvable for inputs consisting of binets and trinets as long as the cycles in the trinets have size three. Finally, we present an O(3 |X | poly(|X |)) time algorithm for general sets of binets and trinets. The latter two algorithms generalise to instances containing level-1 networks with arbitrarily many leaves, and thus provide some of the first supernetwork algorithms for computing networks from a set of rooted phylogenetic networks. B Leo van Iersel

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Networks: expanding evolutionary thinking

Cited by 201 publications

References 12 publications

When Competing Viruses Unify: Evolution, Conservation, and Plasticity of Genetic Identities

When Competing Viruses Unify: Evolution, Conservation, and Plasticity of Genetic Identities

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

Reconstructing Phylogenetic Level-1 Networks from Nondense Binet and Trinet Sets

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