István Zachar

Centre for Ecological Research · Institute of Evolution

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 ar...

The origin of mitochondria was a major evolutionary transition leading to eukaryotes, and is a hotly debated issue. It is unknown whether mitochondria were acquired early or late, and whether it was captured via phagocytosis or syntrophic integration. We present dynamical models to directly simulate the emergence of mitochondria in an ecoevolutiona...

Endosymbiosis and organellogenesis are virtually unknown among prokaryotes. The single presumed example is the endosymbiogenetic origin of mitochondria, which is hidden behind the event horizon of the last eukaryotic common ancestor. While eukaryotes are monophyletic, it is unlikely that during billions of years, there were no other prokaryote–prok...

Background Signal reliability poses a central problem for explaining the evolution of communication. According to Zahavi’s Handicap Principle, signals are honest only if they are costly at the evolutionary equilibrium; otherwise, deception becomes common and communication breaks down. Theoretical signalling games have proved to be useful for unders...

Syntrophic cooperation among prokaryotes is ubiquitous and diverse. It relies on unilateral or mutual aid that may be both catalytic and metabolic in nature. Hypotheses of eukaryotic origins claim that mitochondrial endosymbiosis emerged from mutually beneficial syntrophy of archaeal and bacterial partners. However, there are no other examples of p...

Gabora and Steel (Gabora L, Steel M. 2021 An evolutionary process without variation and selection. J. R. Soc. Interface 18, 20210334. [doi:10.1098/rsif.2021.0334]) claim that cumulative adaptive evolution is possible without natural selection, that is, without variation and competition. To support this claim, the authors modelled a theoretical proc...

The emergence of multicellularity is one of the major transitions in evolution that happened multiple times independently. During aggregative multicellularity, genetically potentially unrelated lineages cooperate to form transient multicellular groups. Unlike clonal multicellularity, aggregative multicellular organisms do not rely on kin selection...

Background Quorum sensing (QS) is the ability of microorganisms to assess local clonal density by measuring the extracellular concentration of signal molecules that they produce and excrete. QS is also the only known way of bacterial communication that supports the coordination of within-clone cooperative actions requiring a certain threshold densi...

Explaining the evolution of honest versus dishonest signals under conflicts of interest has long posed a major challenge, but several recent developments should spur renewed interest in this problem. First, the Handicap Principle, which maintains that signals must be costly to be honest, has been refuted and the model that claimed to validate this...

Explaining the evolution of honest versus dishonest signals has long posed a major challenge, but several recent developments should spur renewed interest in this problem. First, the Handicap Principle, which maintains that signals must be costly to be honest, has been refuted since the model that claimed to validate this idea has been shown to hav...

Explaining the evolution of honest versus dishonest signals has long posed a major challenge, but several recent developments should spur renewed interest in this problem. First, the Handicap Principle, which maintains that signals must be costly to be honest, has been refuted since the model that claimed to validate this idea has been shown to hav...

Background: Quorum sensing (QS) is the ability of microorganisms to assess local clonal density by measuring the extracellular concentration of signal molecules that they produce and excrete. QS is also the only known way of bacterial communication that supports the coordination of within-clone cooperative actions requiring a certain threshold dens...

A modelling study suggests that the proposed energetic barrier between prokaryotes and eukaryotes may not be relevant to the complexity gap between the two domains. The energetic advantage of early mitochondria was probably small, and eukaryotes likely emerged without the help of an endosymbiont.

Explaining signal reliability poses a central problem in animal communication. According to Zahavi’s Handicap Principle (HP), signals are honest only when they are costly at the evolutionary equilibrium – hence the term ‘handicap’; otherwise, deception evolves, and communication breaks down. The HP has no theoretical or empirical support, despite c...

Metabolic cooperation is widespread, and it seems to be a ubiquitous and easily evolvable interaction in the microbial domain. Mutual metabolic cooperation, like syntrophy, is thought to have a crucial role in stabilizing interactions and communities, for example biofilms. Furthermore, cooperation is expected to feed back positively to the communit...

Complexity of life forms on the Earth has increased tremendously, primarily driven by subsequent evolutionary transitions in individuality, a mechanism in which units formerly being capable of independent replication combine to form higher-level evolutionary units. Although this process has been likened to the recursive combination of pre-adapted s...

A wide variety of human and non-human behavior is computationally well accounted for by probabilistic generative models, formalized consistently in a Bayesian framework. Recently, it has been suggested that another family of adaptive systems, namely, those governed by Darwinian evolutionary dynamics, are capable of implementing building blocks of B...

The “cost of begging” is a prominent prediction of costly signalling theory, suggesting that offspring begging has to be costly in order to be honest. Seminal signalling models predict that there is a unique equilibrium cost function for the offspring that results in honest signalling and this cost function must be proportional to parent’s fitness...

Video of interactive figure. (MP4)

Interactive figure as Mathematica notebook. (NB)

Sexual reproduction is widespread in nature despite the different kinds of cost that it entails. We do not know exactly when the first sexual process took place and especially why it was beneficial at first. It is clearer why sex is advantageous for the prokaryotes and eukaryotes but the benefit of sex for protocells with individually replicating r...

Complexity of life forms on Earth has increased tremendously, primarily driven by subsequent evolutionary transitions in individuality, a mechanism in which units formerly being capable of independent replication combine to form higher-level evolutionary units. Although this process has been likened to the recursive combination of pre-adapted sub-s...

The “cost of begging” is a prominent prediction of costly signalling theory, suggesting that offspring begging has to be costly in order to be honest. More specifically, it predicts that there is a single cost function for the offspring (depending on e.g. offspring quality) that maintains honesty and it must be proportional to parent’s fitness loss...

As of today, the most credible scientific paradigm pertaining to the origin of life on Earth is undoubtedly the RNA World scenario. It is built on the assumption that catalytically active replicators (most probably RNA-like macromolecules) may have been responsible for booting up life almost four billion years ago. The many different incarnations o...

Background : The fact that surplus connections and neurons are pruned during development is well established. We complement this selectionist picture by a proof-of-principle model of evolutionary search in the brain, that accounts for new variations in theory space. We present a model for Darwinian evolutionary search for candidate solutions in the...

In this paper, we show that a neurally implemented a cognitive architecture with evolutionary dynamics can solve the four-tree problem. Our model, called Darwinian Neurodynamics, assumes that the unconscious mechanism of problem solving during insight tasks is a Darwinian process. It is based on the evolution of patterns that represent candidate so...

Background: The fact that surplus connections and neurons are pruned during development is well established. We complement this selectionist picture by a proof-of-principle model of evolutionary search in the brain, that accounts for new variations in theory space. We present a model for Darwinian evolutionary search for candidate solutions in the...

The human brain can generate new ideas, hypotheses and candidate solutions to difficult tasks with surprising ease. We argue that this process has evolutionary dynamics, with multiplication, inheritance and variability all implemented in neural matter. This inspires our model, whose main component is a population of recurrent attractor networks wit...

The RNA world hypothesis of the origin of life, in which RNA emerged as both enzyme and information carrier, is receiving solid experimental support. The prebiotic synthesis of biomolecules, the catalytic aid offered by mineral surfaces, and the vast enzymatic repertoire of ribozymes are only pieces of the origin of life puzzle; the full picture ca...

Correlation plot of the fitness landscape as a function of Hamming distances for sequence pairs of length . (TIF)

Examples of coexistence for . (XLS)

Coexistence plots of pairs of double-stranded sequences of length (upper panel) and (lower panel) using two monomers (, ) in case of uniform degradation and identical elongation rate constants and non-complementary pairing. The green indicates stable coexistence, grey indicates structurally unstable coexistence, i.e. compositional identity (no coex...

Examples of coexistence for . (XLS)

Supporting text with sections on 1) Parameters for methods M1, M2, M3 and M4; 2) Analysis of non-complementary pairing with antiparallel polarity; 3) Analysis and analytical results of non-complementary pairing and uniform degradation rates; 4) Proofs; 5) Discussion of the fitness landscape; 6) Examples of coexistence of longer sequences. (PDF)

Split plot of the coexistence of two non-complementary sequence pairs with antiparallel strand polarity (4 sequences per pair) of length . Lower left half: coexistence is marked by green, extinction of the first sequence pair by red and extinction of the second sequence pair by blue. Upper right half: stability of coexistence according to the leadi...

Analysis of coexistence of non-complementary pairs of sequences of length according to method M1. Second column shows the number of scanned sequences (and the amount as a fraction of the whole combined sequence space). The third column shows the fraction of coexisting sequences in the scanned domain, i.e. the probability of coexistence of random se...

Examples of coexistence for . (XLS)

Analysis of coexistence of non-complementary pairs of length according to method M2. Second column shows the number of scanned sequences (and the amount as a fraction of the combined sequence space). The third column shows the fraction of coexisting sequences averaged over the scanned sequence groups and over 1000 random degradation rate sets for i...

Models of competitive template replication, although basic for replicator dynamics and primordial evolution, have not yet taken different sequences explicitly into account, neither have they analyzed the effect of resource partitioning (feeding on different resources) on coexistence. Here we show by analytical and numerical calculations that Gause'...

Here we review chemical and biological replicators that were either engineered (artificially) or evolved (either naturally or artificially). They are automata even though they need not be electro-mechanical machines or computer programs. Gánti has described the class of fluid automata (Gánti, 2003a) into which almost (but perhaps not) all biologica...

Replicators are the most important objects of evolutionary biology. Their cumulative evolution lead to the emergence of complex, adaptive systems, like life. All major transitions of evolution are outcomes of the evolution of replicators. However, replication (and evolution) are universal concepts, independent of the level of biological organizatio...

The simulation of complex biochemical systems, consisting of intertwined subsystems, is a challenging task in computational biology. The complex biochemical organization of the cell is effectively modeled by the minimal cell model called chemoton, proposed by Gánti. Since the chemoton is a system consisting of a large but fixed number of interactin...

An important question in language evolution is whether segmentation as a linguistic process is able to yield compositionality. Segmentation is hypothesized to be a process to bridge the gap between holistic and compositional lexicons. However, to date no thorough analytical method has been provided to test the feasibility of segmentation. In this p...

Replicators are the crucial entities in evolution. The notion of a replicator, however, is far less exact than the weight of its importance. Without identifying and classifying multiplying entities exactly, their dynamics cannot be determined appropriately. Therefore, it is importance to decide the nature and characteristics of any multiplying enti...

It is justified to assume that part of our genetic endowment contributes to our language skills, yet it is impossible to tell at this moment exactly how genes affect the language faculty. We complement experimental biological studies by an in silico approach in that we simulate the evolution of neuronal networks under selection for language-related...