Related papers: Towards angiosperms genome evolution in time
We consider the accumulation of beneficial and deleterious mutations in large asexual populations. The rate of adaptation is affected by the total mutation rate, proportion of beneficial mutations and population size $N$. We show that…
Body size drives the energetic demands of organisms, constraining trophic interactions between species and playing a significant role in shaping the feasibility of species' populations in a community. On macroevolutionary timescales, these…
We perform an exhaustive analysis of genome statistics for organisms, particularly extremophiles, growing in a wide range of physicochemical conditions. Specifically, we demonstrate how the correlation between the frequency of amino acids…
The long-term growth rate of populations in varying environments quantifies the evolutionary value of processing the information that biological individuals inherit from their ancestors and acquire from their environment. Previous models…
Organisms have evolved immune systems that can counter pathogenic threats. The adaptive immune system in vertebrates consists of a diverse repertoire of immune receptors that can dynamically reorganize to specifically target the…
We introduce a new model of evolution on a fitness landscape possessing a tunable degree of neutrality. The model allows us to study the general properties of molecular species undergoing neutral evolution. We find that a number of…
Understanding how a diversity of plants in agroecosystems affects the adaptation of pathogens in a key issue in agroecology. We analyze PDE systems describing the dynamics of adaptation of two phenotypically structured populations, under…
Understanding the co-evolution of complex life with Earth's geology is an enduring challenge. The rock record evidences remarkable correlations between changes in biology and the wider Earth system, yet cause and effect remain unclear.…
We investigated the growth-temperature relationship in plants using a quantitative perspective of a recently derived growth functional. We showed that auxin-induced growth is achieved by the diffusion rate, which is almost constant or…
We consider an asexual population under strong selection-weak mutation conditions evolving on rugged fitness landscapes with many local fitness peaks. Unlike the previous studies in which the initial fitness of the population is assumed to…
Phylogenetic trees are widely used to understand the evolutionary history of organisms. Tree shapes provide information about macroevolutionary processes. However, macroevolutionary models are unreliable for inferring the true processes…
Biomolecular communication demands that interactions between parts of a molecular system act as scaffolds for message transmission. It also requires an evolving and organized system of signs - a communicative agency - for creating and…
We study the Tangled Nature model of macro evolution and demonstrate that the co-evolutionary dynamics produces an increasingly correlated core of well occupied types. At the same time the entire configuration of types becomes increasing…
Sex chromosomes have independently evolved in species with separate sexes in most lineages across the tree of life. However, the well-accepted canonical model of sex chromosome evolution is not universally supported. There is no single…
Life systems are complex and hierarchical, with diverse components at different scales, yet they sustain themselves, grow, and evolve over time. How can a theory of such complex biological states be developed? Here we note that for a…
Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
We calculate the evolution of the early universe through the epochs of weak decoupling, weak freeze-out and big bang nucleosynthesis (BBN) by simultaneously coupling a full strong, electromagnetic, and weak nuclear reaction network with a…
The generation of anisotropic shapes occurs during morphogenesis of almost all organisms. With the recent renewal of the interest in mechanical aspects of morphogenesis, it has become clear that mechanics contributes to anisotropic forms in…
Developmental trajectories are known to be canalized, or robust to both environmental and genetic perturbations. However, even when these trajectories are decanalized by an environmental perturbation outside of the range of conditions to…