title: Quasispecies in population of compositional assemblies.
abstract: BACKGROUND
  The quasispecies model refers to information carriers that undergo self-replication with errors. A quasispecies is a steady-state population of biopolymer sequence variants generated by mutations from a master sequence. A quasispecies error threshold is a minimal replication accuracy below which the population structure breaks down. Theory and experimentation of this model often refer to biopolymers, e.g. RNA molecules or viral genomes, while its prebiotic context is often associated with an RNA world scenario. Here, we study the possibility that compositional entities which code for compositional information, intrinsically different from biopolymers coding for sequential information, could show quasispecies dynamics.
  
  
  RESULTS
  We employed a chemistry-based model, graded autocatalysis replication domain (GARD), which simulates the network dynamics within compositional molecular assemblies. In GARD, a compotype represents a population of similar assemblies that constitute a quasi-stationary state in compositional space. A compotype's center-of-mass is found to be analogous to a master sequence for a sequential quasispecies. Using single-cycle GARD dynamics, we measured the quasispecies transition matrix (Q) for the probabilities of transition from one center-of-mass Euclidean distance to another. Similarly, the quasispecies' growth rate vector (A) was obtained. This allowed computing a steady state distribution of distances to the center of mass, as derived from the quasispecies equation. In parallel, a steady state distribution was obtained via the GARD equation kinetics. Rewardingly, a significant correlation was observed between the distributions obtained by these two methods. This was only seen for distances to the compotype center-of-mass, and not to randomly selected compositions. A similar correspondence was found when comparing the quasispecies time dependent dynamics towards steady state. Further, changing the error rate by modifying basal assembly joining rate of GARD kinetics was found to display an error catastrophe, similar to the standard quasispecies model. Additional augmentation of compositional mutations leads to the complete disappearance of the master-like composition.
  
  
  CONCLUSIONS
  Our results show that compositional assemblies, as simulated by the GARD formalism, portray significant attributes of quasispecies dynamics. This expands the applicability of the quasispecies model beyond sequence-based entities, and potentially enhances validity of GARD as a model for prebiotic evolution.
authors.affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel. renan.gross@weizmann.ac.il.
authors.forename: Renan
authors.initials: R
authors.lastname: Gross
authors.affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel. itzhak.fouxon@weizmann.ac.il.
authors.forename: Itzhak
authors.initials: I
authors.lastname: Fouxon
authors.affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel. doron.lancet@weizmann.ac.il.
authors.forename: Doron
authors.initials: D
authors.lastname: Lancet
authors.affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel. omermar@gmail.com.|Interdisciplinary Computing and Complex Bio-Systems research group, School of Computing Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK. omermar@gmail.com.
authors.forename: Omer
authors.initials: O
authors.lastname: Markovitch
mesh_terms: D002477:Cells / Q000737:chemistry*; D003198:Computer Simulation; D008956:Models, Chemical; D009154:Mutation; D012313:RNA / Q000737:chemistry / Q000235:genetics
chemical_list: D012313:RNA