Natural deletion is not unique in the coat protein (CP) of recombinant Plum pox virus (PPV) isolates in Hungary

Three Plum pox virus (PPV) isolates (Soskut1, Godollo2, Szigetcsep1), collected from apricot (Prunus armeniaca L.) trees in Hungary in 2008, were characterized in this study by sequence analysis of the RT-PCR amplified 3’ part of the viral genome spanning the 3’ part of the NIb gene the complete CP gene and the 3’UTR [3’NIb–CP–3’UTR] and also by restriction analysis of the PCR products derived from the 3’ part of the P3, the complete 6K1 and the 5’ end of the CI genes [3’P3–6K1–5’CI]. Phylogenetic analysis of the 3’NIb–5’CP region showed that one isolate (Godollo2) could be classified as a member of the PPV-Rec group, while the other two (Soskut1 and Szigetcsep1) belonged to PPV-D isolates. In the case of the recombinant Godollo2 isolate a 33-nucleotide (nt) in frame natural deletion was detected in the 5’ part of the CP gene during the sequence analysis of the cDNA fragment corresponding to the 3’NIb–CP–3’UTR region. Currently we have reported on another Hungarian PPV-Rec isolate (PPV-B1298) collected from plum that also had a shorter CP gene bearing a much larger 135-nt in frame natural deletion at a similar position to that of the Godollo2. The PPV-D type Soskut1 isolate showed an atypical restriction pattern in the 3’P3–6K1–5’CI region using EcoRI and DdeI endonucleases, respectively. Nucleotide sequence analysis of this region indicated that its unusual pattern is as a result of a point mutation affecting the EcoRI restriction site.Keywords: Plum pox virus, PPV, natural CP deletion mutant, EcoRI restriction sit

Group selection models in prebiotic evolution

The evolution of enzyme production is studied analytically using ideas of the group selection theory for the evolution of altruistic behavior. In particular, we argue that the mathematical formulation of Wilson's structured deme model ({\it The Evolution of Populations and Communities}, Benjamin/Cumings, Menlo Park, 1980) is a mean-field approach in which the actual environment that a particular individual experiences is replaced by an {\it average} environment. That formalism is further developed so as to avoid the mean-field approximation and then applied to the problem of enzyme production in the prebiotic context, where the enzyme producer molecules play the altruists role while the molecules that benefit from the catalyst without paying its production cost play the non-altruists role. The effects of synergism (i.e., division of labor) as well as of mutations are also considered and the results of the equilibrium analysis are summarized in phase diagrams showing the regions of the space of parameters where the altruistic, non-altruistic and the coexistence regimes are stable. In general, those regions are delimitated by discontinuous transition lines which end at critical points.Comment: 22 pages, 10 figure

Variation of some morphological and molecular characteristics of Hungarian Crivellia and Brachycladium isolates from opium poppy (Papaver somniferum L.)

A destructive seed-borne pathogen, formerly described as Pleospora papaveracea affects opium poppy (Papaver somniferum L.) plants, grown in Hungary, causing considerable qualitative and quantitative losses. The symptoms of the disease were frequently observed in the field between 1999 and 2006. Seventeen Hungarian isolates were obtained from poppy and cultures were established on malt extract agar from naturally infected seeds, diseased foliage, pods and stem. The pathogens proved to be Crivellia papaveracea and a distinct taxon, Brachycladium papaveris based on morphological characterization of conidia, conidiophores and cultures, moreover molecular investigation of the ITS region. Significant morphological differences were observed among the isolates originating from distinct plant parts, however, cultural characteristics were similar. Molecular studies revealed that morphological and cultural differences or similarities do not correspond with taxonomic position of the isolates. Morphological variation of the isolates mainly depended on their origin and might be explained with the differences of microclimatic conditions

The origin of life: chemical evolution of a metabolic system in a mineral honeycomb?

For the RNA-world hypothesis to be ecologically feasible, selection mechanisms acting on replicator communities need to be invoked and the corresponding scenarios of molecular evolution specified. Complementing our previous models of chemical evolution on mineral surfaces, in which selection was the consequence of the limited mobility of macromolecules attached to the surface, here we offer an alternative realization of prebiotic group-level selection: the physical encapsulation of local replicator communities into the pores of the mineral substrate. Based on cellular automaton simulations we argue that the effect of group selection in a mineral honeycomb could have been efficient enough to keep prebiotic ribozymes of different specificities and replication rates coexistent, and their metabolic cooperation protected from extensive molecular parasitism. We suggest that mutants of the mild parasites persistent in the metabolic system can acquire useful functions such as replicase activity or the production of membrane components, thus opening the way for the evolution of the first autonomous protocells on Earth

Cultural Lenses and Biological Filters On What Makes a Hungarian in the Present and in the Distant Past

The definition of a memoir is “an account of the personal experiences of an author.” This paper provides the reflections of a physical (biological) anthropologist specializing in the genetics of the Indigenous peoples of North America who was born in Hungary, raised in Canada, and served twelve years as president and vice chancellor of the University of Manitoba. This professional background may question the relevance of these reflections to Hungarian studies. However, issues raised by János Kenyeres, the keynote speaker of the 2019 American Hungarian Educators Association conference, in his examination of Hungarian identity manifest in Hungarian literature—specifically, regarding “essentialist thinking”—are related to fundamental issues about the nature of human diversity with which physical (biological) anthropologists have been grappling since the eighteenth century. In an era in which commercial genetic genealogical services promise to identify ancestors and ethnicity, and genetic studies of living peoples as well as archaeogenomic studies of skeletal remains seek to identify relationships, current perspectives on what does—or does not—constitute “the essence of an individual and the groups to which one belongs” are worth considering. Facts, wherever they occur, are subject to interpretation. It is the cultural interpretation that we give to genetic identity that imbues that concept with meaning. [email protected]

What can ecosystems learn? Expanding evolutionary ecology with learning theory.

BACKGROUND: The structure and organisation of ecological interactions within an ecosystem is modified by the evolution and coevolution of the individual species it contains. Understanding how historical conditions have shaped this architecture is vital for understanding system responses to change at scales from the microbial upwards. However, in the absence of a group selection process, the collective behaviours and ecosystem functions exhibited by the whole community cannot be organised or adapted in a Darwinian sense. A long-standing open question thus persists: Are there alternative organising principles that enable us to understand and predict how the coevolution of the component species creates and maintains complex collective behaviours exhibited by the ecosystem as a whole? RESULTS: Here we answer this question by incorporating principles from connectionist learning, a previously unrelated discipline already using well-developed theories on how emergent behaviours arise in simple networks. Specifically, we show conditions where natural selection on ecological interactions is functionally equivalent to a simple type of connectionist learning, 'unsupervised learning', well-known in neural-network models of cognitive systems to produce many non-trivial collective behaviours. Accordingly, we find that a community can self-organise in a well-defined and non-trivial sense without selection at the community level; its organisation can be conditioned by past experience in the same sense as connectionist learning models habituate to stimuli. This conditioning drives the community to form a distributed ecological memory of multiple past states, causing the community to: a) converge to these states from any random initial composition; b) accurately restore historical compositions from small fragments; c) recover a state composition following disturbance; and d) to correctly classify ambiguous initial compositions according to their similarity to learned compositions. We examine how the formation of alternative stable states alters the community's response to changing environmental forcing, and we identify conditions under which the ecosystem exhibits hysteresis with potential for catastrophic regime shifts. CONCLUSIONS: This work highlights the potential of connectionist theory to expand our understanding of evo-eco dynamics and collective ecological behaviours. Within this framework we find that, despite not being a Darwinian unit, ecological communities can behave like connectionist learning systems, creating internal conditions that habituate to past environmental conditions and actively recalling those conditions. REVIEWERS: This article was reviewed by Prof. Ricard V Solé, Universitat Pompeu Fabra, Barcelona and Prof. Rob Knight, University of Colorado, Boulder

Erratum to: What can ecosystems learn? Expanding evolutionary ecology with learning theory.

BACKGROUND: The structure and organisation of ecological interactions within an ecosystem is modified by the evolution and coevolution of the individual species it contains. Understanding how historical conditions have shaped this architecture is vital for understanding system responses to change at scales from the microbial upwards. However, in the absence of a group selection process, the collective behaviours and ecosystem functions exhibited by the whole community cannot be organised or adapted in a Darwinian sense. A long-standing open question thus persists: Are there alternative organising principles that enable us to understand and predict how the coevolution of the component species creates and maintains complex collective behaviours exhibited by the ecosystem as a whole? RESULTS: Here we answer this question by incorporating principles from connectionist learning, a previously unrelated discipline already using well-developed theories on how emergent behaviours arise in simple networks. Specifically, we show conditions where natural selection on ecological interactions is functionally equivalent to a simple type of connectionist learning, 'unsupervised learning', well-known in neural-network models of cognitive systems to produce many non-trivial collective behaviours. Accordingly, we find that a community can self-organise in a well-defined and non-trivial sense without selection at the community level; its organisation can be conditioned by past experience in the same sense as connectionist learning models habituate to stimuli. This conditioning drives the community to form a distributed ecological memory of multiple past states, causing the community to: a) converge to these states from any random initial composition; b) accurately restore historical compositions from small fragments; c) recover a state composition following disturbance; and d) to correctly classify ambiguous initial compositions according to their similarity to learned compositions. We examine how the formation of alternative stable states alters the community's response to changing environmental forcing, and we identify conditions under which the ecosystem exhibits hysteresis with potential for catastrophic regime shifts. CONCLUSIONS: This work highlights the potential of connectionist theory to expand our understanding of evo-eco dynamics and collective ecological behaviours. Within this framework we find that, despite not being a Darwinian unit, ecological communities can behave like connectionist learning systems, creating internal conditions that habituate to past environmental conditions and actively recalling those conditions. REVIEWERS: This article was reviewed by Prof. Ricard V Solé, Universitat Pompeu Fabra, Barcelona and Prof. Rob Knight, University of Colorado, Boulder

A New Replicator: A theoretical framework for analysing replication

<p>Abstract</p> <p>Background</p> <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 entity, in a detailed and formal way.</p> <p>Results</p> <p>Replication is basically an autocatalytic process which enables us to rest on the notions of formal chemistry. This statement has major implications. Simple autocatalytic cycle intermediates are considered as non-informational replicators. A consequence of which is that any autocatalytically multiplying entity is a replicator, be it simple or overly complex (even nests). A stricter definition refers to entities which can inherit acquired changes (informational replicators). Simple autocatalytic molecules (and nests) are excluded from this group. However, in turn, any entity possessing copiable information is to be named a replicator, even multicellular organisms. In order to deal with the situation, an abstract, formal framework is presented, which allows the proper identification of various types of replicators. This sheds light on the old problem of the units and levels of selection and evolution. A hierarchical classification for the partition of the replicator-continuum is provided where specific replicators are nested within more general ones. The classification should be able to be successfully applied to known replicators and also to future candidates.</p> <p>Conclusion</p> <p>This paper redefines the concept of the replicator from a bottom-up theoretical approach. The formal definition and the abstract models presented can distinguish between among all possible replicator types, based on their quantity of variable and heritable information. This allows for the exact identification of various replicator types and their underlying dynamics. The most important claim is that replication, in general, is basically autocatalysis, with a specific defined environment and selective force. A replicator is not valid unless its working environment, and the selective force to which it is subject, is specified.</p

Random replicators with high-order interactions

We use tools of the equilibrium statistical mechanics of disordered systems to study analytically the statistical properties of an ecosystem composed of N species interacting via random, Gaussian interactions of order p >= 2, and deterministic self-interactions u <= 0. We show that for nonzero u the effect of increasing the order of the interactions is to make the system more cooperative, in the sense that the fraction of extinct species is greatly reduced. Furthermore, we find that for p > 2 there is a threshold value which gives a lower bound to the concentration of the surviving species, preventing then the existence of rare species and, consequently, increasing the robustness of the ecosystem to external perturbations.Comment: 7 pages, 4 Postscript figure

Multi-level selectional stalemate in a simple artificial chemistry

We describe a simple artificial chemistry which abstracts a small number of key features from the origin of life "replicator world" hypotheses. We report how this can already give rise to moderately complex and counter-intuitive evolutionary phenomena, including macro- evolutionary deterioration in replication fidelity (which corresponds to intrinsic replicator fitness in this model). We briefly describe the extension of this model to incorporate a higher, protocell, level of selection. We show that the interaction between the two levels of selection then serves to control parasitic exploitation at the molecular level, while still significantly constraining accessible evolutionary trajectories at the protocell level. We conclude with a brief discussion of the implications for further work