Biology subjects

Sergei Maslov

Publications and source records attributed to Sergei Maslov.

3 recordsLinked to original sources

bioRxiv2016

Recombination-driven genome evolution and stability of bacterial species

While bacteria divide clonally, horizontal gene transfer followed by homologous recombination is now recognized as an important and sometimes even dominant contributor to their evolution. However, the details of how the competition between clonal inheritance and recombination shapes genome diversity, population structure, and species stability remains poorly understood. Using a computational model, we find two principal regimes in bacterial evolution and identify two composite parameters that dictate the evolutionary fate of bacterial species. In the divergent regime, characterized by either a low recombination frequency or strict barriers to recombination, cohesion due to recombination is not sufficient to overcome the mutational drift. As a consequence, the divergence between any pair of genomes in the population steadily increases in the course of their evolution. The species as a whole lacks genetic coherence with sexually isolated clonal sub-populations continuously formed and dissolved. In contrast, in the metastable regime, characterized by a high recombination frequency combined with low barriers to recombination, genomes continuously recombine with the rest of the population. The population remains genetically cohesive and stable over time. The transition between these two regimes can be affected by relatively small changes in evolutionary parameters. Using the Multi Locus Sequence Typing (MLST) data we classify a number of well-studied bacterial species to be either the divergent or the metastable type. Generalizations of our framework to include fitness and selection, ecologically structured populations, and horizontal gene transfer of non-homologous regions are discussed.

Evolutionary Biology↗

bioRxiv2016

Pan- and core- network analysis of co-expression genes in a model plant

Genome-wide gene expression experiments have been performed using the model plant Arabidopsis during the last decade. Some studies involved construction of coexpression networks, a popular technique used to identify groups of co-regulated genes, to infer unknown gene functions. One approach is to construct a single coexpression network by combining multiple expression datasets generated in different labs. We advocate a complementary approach in which we construct a large collection of 134 coexpression networks based on expression datasets reported in individual publications. To this end we reanalyzed public expression data. To describe this collection of networks we introduced concepts of pan-network and core-network representing union and intersection between a sizeable fractions of individual networks, respectively. We showed that these two types of networks are different both in terms of their topology and biological function of interacting genes. For example, the modules of the pan-network are enriched in regulatory and signaling functions, while the modules of the core-network tend to include components of large macromolecular complexes such as ribosomes and photosynthetic machinery. Our analysis is aimed to help the plant research community to better explore the information contained within the existing vast collection of gene expression data in Arabidopsis.\n\nResearch AreaSystems and Synthetic Biology\n\nSummaryBy analyzing 134 microarray datasets for Arabidopsis, we found that gene coexpression networks are highly context-dependent.\n\nFinancial sourceWork at Brookhaven was supported by grants PM-031 from the Office of Biological Research of the U.S. Department of Energy.

Bioinformatics↗

bioRxiv2015

Diversity waves in collapse-driven population dynamics

Populations of species in ecosystems are often constrained by availability of resources within their environment. In effect this means that a growth of one population, needs to be balanced by comparable reduction in populations of others. In neutral models of biodiversity all populations are assumed to change incrementally due to stochastic births and deaths of individuals. Here we propose and model another redistribution mechanism driven by abrupt and severe collapses of the entire population of a single species freeing up resources for the remaining ones. This mechanism may be relevant e.g. for communities of bacteria, with strain-specific collapses caused e.g. by invading bacteriophages, or for other ecosystems where infectious diseases play an important role.\n\nThe emergent dynamics of our system is cyclic \"diversity waves\" triggered by collapses of globally dominating populations. The population diversity peaks at the beginning of each wave and exponentially decreases afterwards. Species abundances are characterized by a bimodal time-aggregated distribution with the lower peak formed by populations of recently collapsed or newly introduced species, while the upper peak - species that has not yet collapsed in the current wave. In most waves both upper and lower peaks are composed of several smaller peaks. This self-organized hierarchical peak structure has a long-term memory transmitted across several waves. It gives rise to a scale-free tail of the time-aggregated population distribution with a universal exponent of 1.7. We show that diversity wave dynamics is robust with respect to variations in the rules of our model such as diffusion between multiple environments, species-specific growth and extinction rates, and bet-hedging strategies.

Ecology↗