Evolution and Genetic Dynamics

Comparison of the Distribution of Fitness Effects Across Primates

Across 38 catarrhine subspecies, the population-scaled distribution of fitness effects (DFE) tracks effective population size while the unscaled deleterious DFE appears conserved, with no detectable epistasis.

Replaying germinal center evolution on a quantified affinity landscape

Across 119 monoclonal germinal centers, B cell affinity rises reliably despite divergent phylogenies. Selection is noisy but persistent; mutability limits exploration. A DMS-based landscape shows saturating fitness and survivorship biases.

Inference and visualization of complex genotype-phenotype maps with gpmap-tools

gpmap-tools uses Gaussian processes to infer and visualize genotype-phenotype maps with higher-order epistasis; across 262,144 Shine-Dalgarno variants it reveals register-specific peaks linked by three-nucleotide-offset ridges.

The simplicity of protein sequence-function relationships

Reference-free analysis with a sigmoid link shows additive plus pairwise effects explain a median 96% of phenotypic variance across 20 combinatorial protein mutagenesis datasets.

Versatile detection of diverse selective sweeps with Flex-sweep

Flex-sweep, a convolutional neural network over 11 summary statistics (five new), detects weak, soft, incomplete and old selective sweeps up to 0.125 * 4Ne generations using one sequenced population.