Related papers: The genomic impacts of drift and selection for hyb…
High-dimensional time series phenotypic data is becoming increasingly common within plant breeding programmes. However, analysing and integrating such data for genetic analysis and genomic prediction remains difficult. Here we show how…
Some species exhibit very high levels of DNA sequence variability; there is also evidence for the existence of heritable epigenetic variants that experience state changes at a much higher rate than sequence variants. In both cases, the…
Plant breeding underpins global food security through incremental, accumulating improvements in crop yield, quality and sustainability, achieved via repeated cycles of crop ranking, selection and crossing. Climate change disrupts this…
In this study, we propose an improvement to the direct mating method, a constraint handling approach for multi-objective evolutionary algorithms, by hybridizing it with local mating. Local mating selects another parent from the feasible…
In subdivided populations, migration acts together with selection and genetic drift and determines their evolution. Building up on a recently proposed method, which hinges on the emergence of a time scale separation between local and global…
Feature selection plays a pivotal role in the data preprocessing and model-building pipeline, significantly enhancing model performance, interpretability, and resource efficiency across diverse domains. In population-based optimization…
Divergence between populations for a given trait can be driven by natural or sexual selection, interacting with migration behaviour. Mating preference for different phenotypes can lead to the emergence and persistence of differentiated…
Many plants harbor complex mechanisms that promote outcrossing and efficient pollen transfer. These include floral adaptations as well as genetic mechanisms, such as molecular self-incompatibility (SI) systems. The maintenance of such…
Migrations have played an important role in shaping the genetic diversity of human populations. Understanding genomic data thus requires careful modeling of historical gene flow. Here we consider the effect of relatively recent population…
How self-incompatibility systems are maintained in plant populations is still a debated issue. Theoretical models predict that self-incompatibility systems break down according to the intensity of inbreeding depression and number of…
Sweepstakes reproduction may be generated by chance matching of reproduction with favorable environmental conditions. Gene genealogies generated by sweepstakes reproduction are in the domain of attraction of multiple-merger coalescents…
Population genetic studies have found evidence for dramatic population growth in recent human history. It is unclear how this recent population growth, combined with the effects of negative natural selection, has affected patterns of…
Intragenomic recombination (crossover) is a very important evolutionary mechanism. The crossover events are not evenly distributed along the natural chromosomes. Monte Carlo simulations revealed that frequency of recombinations decides…
The Moran process is a classic stochastic process that models the rise and takeover of novel traits in network-structured populations. In biological terms, a set of mutants, each with fitness $m\in(0,\infty)$ invade a population of…
Populations of widely distributed species often encounter and adapt to specific environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple…
Despite the advent of several novel, synthetic gene drive mechanisms and their potential to one-day control a number of devastating diseases, among other applications, practical use of these systems remains contentious and risky. In…
Inferring concerted changes among biological traits along an evolutionary history remains an important yet challenging problem. Besides adjusting for spurious correlation induced from the shared history, the task also requires sufficient…
We updated the agent based Monte Carlo code HERITAGE that simulates human evolution within restrictive environments such as interstellar, sub-light speed spacecraft in order to include the effects of population genetics. We incorporated a…
Horizontal transfer (HT) of heritable information or `traits' (carried by genetic elements, endosymbionts, or culture) is widespread among living organisms. Yet current ecological and evolutionary theory addressing HT is limited. We present…
The emerging field of high-throughput compartmentalized in vitro evolution is a promising new approach to protein engineering. In these experiments, libraries of mutant genotypes are randomly distributed and expressed in microscopic…