A dynamical theory for the evolution of genetic code is presented, which accounts its universality and optimality. The central concept that a variety collective, but non-Darwinian, mechanisms likely to be present in early communal life generically lead refinement selection innovation-sharing protocols, such as code. Our proposal illustrated using simplified computer model, placed within context sequence transitions may have made, prior emergence vertical descent.

Soil grains harbor an astonishing diversity of Streptomyces strains producing diverse secondary metabolites. However, it is not understood how this genotypic and chemical ecologically maintained. While metabolites are known to mediate signaling warfare among strains, no systematic measurement the resulting interaction networks has been available. We developed a high-throughput platform measure all pairwise interactions 64 isolated from several individual soil. acquired more than 10,000...

Multiplexing multiple samples during Illumina sequencing is a common practice and rapidly growing in importance as the throughput of platform increases. Misassignments de-multiplexing, where sequences are associated with wrong sample, an overlooked error mode on platform. This results low rate cross-talk among multiplexed can cause detrimental effects studies requiring detection rare variants or when multiplexing large number samples. We observed rates averaging 0.24 % 14 different unique i5...

Abstract It is largely unknown how the process of microbial community assembly affected by order species arrival, initial abundances and interactions between species. A minimal way capturing competitive abilities in a frequency-dependent manner with an invasibility network specifying whether at low abundance can increase frequency environment dominated another Here, using panel prolific small-molecule producers habitat feast-and-famine cycles, we show that most abundant strain often exclude...

How did chemicals first become organized into systems capable of self-propagation and adaptive evolution? One possibility is that the evolvers were chemical ecosystems localized on mineral surfaces composed sets molecular species could catalyze each other’s formation. We used a bottom-up experimental framework, ecosystem selection (CES), to evaluate this perspective search for surface-associated mutually catalytic based changes in chemistry they are expected induce. Here, we report results...

Genomes exhibit diverse patterns of species-specific GC content, and AT skews, codon bias, mutation bias. Despite intensive investigations the rapid accumulation sequence data, causes these a priori different genome biases have not been agreed on seem multifactorial idiosyncratic. We show that can arise generically from an instability coevolutionary dynamics between composition resource allocation for translation, transcription, replication. Thus, we offer unifying framework understanding...

Most experimental work on the origin of life has focused either characterizing chemical synthesis particular biochemicals and their precursors or designing simple systems that manifest life-like properties such as self-propagation adaptive evolution. Here we propose a new class experiments, analogous to artificial ecosystem selection, where select for spontaneously forming self-propagating assemblages in lab then seek evidence response selection key indicator have arisen. Since surfaces...

Variance in reproductive success is a major determinant of the degree genetic drift population. While many plants and animals exhibit high variance their number progeny, far less known about these distributions for microorganisms. Here, we used strain barcoding approach to quantify variability offspring among replicate bacterial populations developed Bayesian method infer distribution descendants from this variability. We applied our measure five strains bacteria genus Streptomyces after...

We model the competition between recombination and point mutation in microbial genomes, present evidence for two distinct phases, one uniform, other genetically diverse. Depending on specifics of homologous recombination, we find that global sequence divergence can be mediated by fronts propagating along genome, whose characteristic signature genome structure is elucidated, apparently observed closely-related {\it Bacillus} strains. Front propagation provides an emergent, generic mechanism...

Microbial communities can have dramatically different compositions even among similar environments. This might be due to the existence of multiple alternative stable states, yet there exists little experimental evidence supporting this possibility. Here, we gathered a large collection absolute population abundances capturing dynamics in one- four-strain soil bacteria with complex life cycle feast-or-famine environment. dataset led several observations: (i) some pairwise competitions resulted...

Soil grains harbor an astonishing diversity of Streptomyces strains producing diverse secondary metabolites.However, it is not understood how this genotypic and chemical ecologically maintained.While metabolites are known to mediate signaling warfare among strains, no systematic measurement the resulting interaction networks has been available.We developed a high-throughput platform measure all pairwise interactions 64 isolated from several individual soil.We acquired more than 10,000...

A case can be made for stochastic germination and interactions among germinating spores as beneficial strategies in uncertain environments. However, there is little data on how widespread, species-specific or diverse such phenomena are. Focusing Streptomycetes, a platform was developed quantification of early growth within communities spores. We found that the process at three levels: vary their times, mycelium networks grow different rates, fraction germlings stall shortly after...

Abstract Summary: For numerous experimental applications, PCR primers must be designed to efficiently amplify a set of homologous DNA sequences while giving rise amplicons with maximally diverse signatures. We developed DesignSignatures automate the process designing for high-resolution melting (HRM), fragment length polymorphism (FLP) and sequencing experiments. The program also finds best restriction enzyme further diversify HRM or FLP This enables efficient comparison across many designs...

We present a phase-field model of solidification which allows efficient computations in the regime when interface kinetic effects dominate over capillary effects. The asymptotic analysis required to relate parameters phase field with those original sharp-interface is straightforward, and resultant can be used for wide range material parameters.

Abstract Ecological and evolutionary dynamics of communities are inexorably intertwined. The ecological state determines the fate newly arising mutants, mutations that increase in frequency can reshape dynamics. Evolutionary game theory its extensions within adaptive (AD) have been mathematical frameworks for understanding this interplay, leading to notions such as Stable States (ESS) which no favored, branching points near population diversifies. A central assumption behind these...

ABSTRACT Variance in reproductive success is a major determinant of the degree genetic drift population. While many plants and animals exhibit high variance their number progeny, far less known about these distributions for microorganisms. Here, we used strain barcoding approach to quantify variability offspring among replicate bacterial populations developed Bayesian method infer distribution descendants from this variability. We applied our measure 5 strains bacteria genus Streptomyces...

Abstract A major puzzle in ecology is how antibiotic resistant, sensitive and producer species coexist close proximity. Recently, we showed that degrading dramatically alter community dynamics: replacing intrinsic resistance with through degradation generates stable communities resilient to spatial mixing, large abundance perturbations, changes interaction strengths, differences growth rates 1 . In addition ecological stability, it interesting consider evolutionary stability of these the...