Toward major evolutionary transitions theory 2.0

The impressive body of work on the major evolutionary transitions in the last 20 y calls for a reconstruction of the theory although a 2D account (evolution of informational systems and transitions in individuality) remains. Significant advances include the concept of fraternal and egalitarian transitions (lower-level units like and unlike, respectively). Multilevel selection, first without, then with, the collectives in focus is an important explanatory mechanism. Transitions are decomposed into phases of origin, maintenance, and transformation (i.e., further evolution) of the higher level units, which helps reduce the number of transitions in the revised list by two so that it is less top-heavy. After the transition, units show strong cooperation and very limited realized conflict. The origins of cells, the emergence of the genetic code and translation, the evolution of the eukaryotic cell, multicellularity, and the origin of human groups with language are reconsidered in some detail in the light of new data and considerations. Arguments are given why sex is not in the revised list as a separate transition. Some of the transitions can be recursive (e.g., plastids, multicellularity) or limited (transitions that share the usual features of major transitions without a massive phylogenetic impact, such as the micro- and macronuclei in ciliates). During transitions, new units of reproduction emerge, and establishment of such units requires high fidelity of reproduction (as opposed to mere replication)

Breath-giving cooperation: critical review of origin of mitochondria hypotheses Major unanswered questions point to the importance of early ecology

The origin of mitochondria is a unique and hard evolutionary problem, embedded within the origin of eukaryotes. The puzzle is challenging due to the egalitarian nature of the transition where lower-level units took over energy metabolism. Contending theories widely disagree on ancestral partners, initial conditions and unfolding of events. There are many open questions but there is no comparative examination of hypotheses. We have specified twelve questions about the observable facts and hidden processes leading to the establishment of the endosymbiont that a valid hypothesis must address. We have objectively compared contending hypotheses under these questions to find the most plausible course of events and to draw insight on missing pieces of the puzzle. Since endosymbiosis borders evolution and ecology, and since a realistic theory has to comply with both domains' constraints, the conclusion is that the most important aspect to clarify is the initial ecological relationship of partners. Metabolic benefits are largely irrelevant at this initial phase, where ecological costs could be more disruptive. There is no single theory capable of answering all questions indicating a severe lack of ecological considerations. A new theory, compliant with recent phylogenomic results, should adhere to these criteria

Genetic hitchhiking can promote the initial spread of strong altruism

Background: The evolutionary origin of strong altruism (where the altruist pays an absolute cost in terms of fitness) towards non-kin has never been satisfactorily explained since no mechanism (except genetic drift) seems to be able to overcome the fitness disadvantage of the individual who practiced altruism in the first place. Results: Here we consider a multilocus, single-generation random group model and demonstrate that with low, but realistic levels of recombination and social heterosis (selecting for allelic diversity within groups) altruism can evolve without invoking kin selection, because sampling effects in the formation of temporary groups and selection for complementary haplotypes generate nonrandom associations between alleles at polymorphic loci. Conclusion: By letting altruism get off the ground, selection on other genes favourably interferes with the eventual fate of the altruistic trait due to genetic hitchhiking

Founder of systems chemistry and foundational theoretical biologist: Tibor Ganti (1933-2009)

With his chemoton theory theoretical biologist and chemical engineer Tibor Ganti was one of the most outstanding intellects behind systems chemistry and the at the foundations of theoretical biology. A brief review of his oeuvre is presented. This essay introduces a special issue dedicated to his memory. (C) 2015 Published by Elsevier Ltd

The Evolution of cooperation

L'aproximació a l'evolució centrada en el gen o del gen egoista aparentment entra en conflicte amb l'observació que la cooperació és freqüent en les interaccions socials humanes i també es pot reconèixer en animals no humans. Sense cooperació no haurien pogut sorgir les unitats evolutives de nivells superiors. Aquí resumim el pensament evolutiu actual sobre com poden evolucionar la cooperació i l'altruisme. A més, discutim els resultats dels experiments de la teoria de jocs per estudiar les interaccions socials que indiquen que els humans no s'ajusten a les prediccions de l'equilibri de Nash «racional». Aquests resultats són de gran interès per als biòlegs i científics socials, especialment si es desitja tenir un marc de referència comú per entendre com sorgeix la sociabilitat.The gene-centred or selfish-gene approach to evolution apparently conflicts with the observation that cooperation is commonplace in human social interactions, and can also be recognized in non-human animals. Without cooperation, higher-level units of evolution could not have emerged. Here we summarize current evolutionary thinking on how cooperation and altruism can evolve. We also discuss the results reached by game theoretic experiments for studying social interactions, which indicate that humans do not conform to Nash equilibrium (“rational”) predictions. These results are of wide interest to biologists and social scientists, particularly if we want to have a common framework to understand how sociality arises

"Synergistic selection": A Darwinian frame for the evolution of complexity

Non-Darwinian theories about the emergence and evolution of complexity date back at least to Lamarck, and include those of Herbert Spencer and the "emergent evolution" theorists of the later nineteenth and early twentieth centuries. In recent decades, this approach has mostly been espoused by various practitioners in biophysics and complexity theory. However, there is a Darwinian alternative - in essence, an economic theory of complexity - proposing that synergistic effects of various kinds have played an important causal role in the evolution of complexity, especially in the "major transitions". This theory is called the "synergism hypothesis". We posit that otherwise unattainable functional advantages arising from various cooperative phenomena have been favored over time in a dynamic that the late John Maynard Smith characterized and modeled as "synergistic selection". The term highlights the fact that synergistic "wholes" may become interdependent "units" of selection. We provide some historical perspective on this issue, as well as a brief explication of the underlying theory and the concept of synergistic selection, and we describe two relevant models. (C) 2015 Elsevier Ltd. All rights reserved

Lack of evolvability in self-sustaining autocatalytic networks constraints metabolism-first scenarios for the origin of life

A basic property of life is its capacity to experience Darwinian evolution. The replicator concept is at the core of genetics-first theories of the origin of life, which suggest that self-replicating oligonucleotides or their similar ancestors may have been the first “living” systems and may have led to the evolution of an RNA world. But problems with the nonenzymatic synthesis of biopolymers and the origin of template replication have spurred the alternative metabolism-first scenario, where self-reproducing and evolving proto-metabolic networks are assumed to have predated self-replicating genes. Recent theoretical work shows that “compositional genomes” (i.e., the counts of different molecular species in an assembly) are able to propagate compositional information and can provide a setup on which natural selection acts. Accordingly, if we stick to the notion of replicator as an entity that passes on its structure largely intact in successive replications, those macromolecular aggregates could be dubbed “ensemble replicators” (composomes) and quite different from the more familiar genes and memes. In sharp contrast with template-dependent replication dynamics, we demonstrate here that replication of compositional information is so inaccurate that fitter compositional genomes cannot be maintained by selection and, therefore, the system lacks evolvability (i.e., it cannot substantially depart from the asymptotic steady-state solution already built-in in the dynamical equations). We conclude that this fundamental limitation of ensemble replicators cautions against metabolism-first theories of the origin of life, although ancient metabolic systems could have provided a stable habitat within which polymer replicators later evolved

Local Neutral Networks Help Maintain Inaccurately Replicating Ribozymes

The error threshold of replication limits the selectively maintainable genome size against recurrent deleterious mutations for most fitness landscapes. In the context of RNA replication a distinction between the genotypic and the phenotypic error threshold has been made; where the latter concerns the maintenance of secondary structure rather than sequence. RNA secondary structure is treated as a proxy for function. The phenotypic error threshold allows higher per digit mutation rates than its genotypic counterpart, and is known to increase with the frequency of neutral mutations in sequence space. Here we show that the degree of neutrality, i.e. the frequency of nearest-neighbour (one-step) neutral mutants is a remarkably accurate proxy for the overall frequency of such mutants in an experimentally verifiable formula for the phenotypic error threshold; this we achieve by the full numerical solution for the concentration of all sequences in mutation-selection balance up to length 16. We reinforce our previous result that currently known ribozymes could be selectively maintained by the accuracy known from the best available polymerase ribozymes. Furthermore, we show that in silico stabilizing selection can increase the mutational robustness of ribozymes due to the fact that they were produced by artificial directional selection in the first place. Our finding offers a better understanding of the error threshold and provides further insight into the plausibility of an ancient RNA world