Related papers: Optimality of mutation and selection in germinal c…
One of the key phenomena in the adaptive immune response to infection and immunization is affinity maturation, during which antibody genes are mutated and selected, typically resulting in a substantial increase in binding affinity to the…
Adaptation often involves the acquisition of a large number of genomic changes which arise as mutations in single individuals. In asexual populations, combinations of mutations can fix only when they arise in the same lineage, but for…
B cells develop high affinity receptors during the course of affinity maturation, a cyclic process of mutation and selection. At the end of affinity maturation, a number of cells sharing the same ancestor (i.e. in the same "clonal family")…
In order to grow in any given environment, bacteria need to collect information about the medium composition and implement suitable growth strategies by adjusting their regulatory and metabolic degrees of freedom. In the standard sense,…
Modern biological techniques enable very dense genetic sampling of unfolding evolutionary histories, and thus frequently sample some genotypes multiple times. This motivates strategies to incorporate genotype abundance information in…
We study the equilibrium behaviour of a deterministic four-state mutation-selection model as a model for the evolution of a population of nucleotide sequences in sequence space. The mutation model is the Kimura 3ST mutation scheme, and the…
Many biological populations exhibit diversity in their strategy for survival and reproduction in a given environment, and microbes are an example. We explore the fate of different strategies under sustained environmental change by…
Populations can evolve in order to adapt to external changes. The capacity to evolve and adapt makes successful treatment of infectious diseases and cancer difficult. Indeed, therapy resistance has quickly become a key challenge for global…
The evolution of the adaptive immune system is characterized by changes in the relative abundances of the B- and T-cell clones that make up its repertoires. To fully capture this evolution, we need to describe the complex dynamics of the…
Evolutionary algorithms are sensitive to the mutation rate (MR); no single value of this parameter works well across domains. Self-adaptive MR approaches have been proposed but they tend to be brittle: Sometimes they decay the MR to zero,…
Population-based evolutionary algorithms (EAs) have been widely applied to solve various optimization problems. The question of how the performance of a population-based EA depends on the population size arises naturally. The performance of…
Germinal centres are anatomically defined lymphoid organ structures that mediate B cell affinity maturation and affect the quality of humoral immune responses. Mathematical models based on differential equations or agent-based simulations…
In unicellular organisms such as bacteria and in most viruses, mutations mainly occur during reproduction. Thus, genotypes with a high birth rate should have a higher mutation rate. However, standard models of asexual adaptation such as the…
Establishing a quantitative connection between the population growth rate and the generation times of single cells is a prerequisite for understanding evolutionary dynamics of microbes. However, existing theories fail to account for the…
In large asexual populations, beneficial mutations have to compete with each other for fixation. Here, I derive explicit analytic expressions for the rate of substitution and the mean beneficial effect of fixed mutations, under the…
Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to…
We compare and contrast the long-time dynamical properties of two individual-based models of biological coevolution. Selection occurs via multispecies, stochastic population dynamics with reproduction probabilities that depend nonlinearly…
The adaptive immune system provides a diverse set of molecules that can mount specific responses against a multitude of pathogens. Memory is a key feature of adaptive immunity, which allows organisms to respond more readily upon…
Somatic hypermutations of immunoglobulin (Ig) genes occuring during affinity maturation drive B-cell receptors' ability to evolve strong binding to their antigenic targets. The landscape of these mutations is highly heterogeneous, with…
The persistence of life requires populations to adapt at a rate commensurate with the dynamics of their environment. Successful populations that inhabit highly variable environments have evolved mechanisms to increase the likelihood of…