Milan Malinsky

The paper quantifies recombination landscape divergence across percomorph fish species using PRDI and finds divergence increases with genetic differentiation and divergence time, with variation among species pairs.

This study shows rapid genome-wide adaptive introgression in threespine stickleback following immigration, with beneficial alleles driving evolutionary change.

This study shows that temporal niche partitioning, through distinct activity patterns, contributed to the adaptive radiation of cichlid fishes in Lake Tanganyika.

Hi-reComb estimates recombination maps from bulk gamete Hi-C data, showing accurate results in fish sperm and enabling structural variant analysis.

The paper analyzes 1,375 Malawi cichlid genomes to show that sex-linked chromosomal inversions drive adaptive speciation through introgression and selection on neuro-sensory, physiological, and reproductive genes.

The paper shows that recombination landscapes diverge between two cichlid fish ecotypes despite similar allele frequency and diversity, suggesting recombination suppression in heterozygotes.

This study examines hemoglobin gene evolution in teleost and cichlid fishes, showing gene duplications and rearrangements drive diversity in oxygen transport systems.

The paper investigates epigenetic divergence in two ecomorphs of Astatotilapia calliptera, finding methylome differences linked to ecological adaptation and showing that these differences can be inherited across generations.

The paper examines methylome and transcriptome divergence in Lake Malawi cichlid fishes, finding links between epigenetic changes and ecological adaptation.

The paper summarizes methods and lessons from assembling 16 vertebrate genomes, highlights the importance of long-read sequencing, and introduces the Vertebrate Genomes Project to generate complete reference genomes for all vertebrate species.

Dsuite, a C++ tool, computes D and f4-ratio statistics across all trios of tens to hundreds of taxa directly from VCF, plus windowed fd/fdM and f-branch.

trio-sga improves de novo genome assembly for highly heterozygous organisms using parent-child trio data, reducing heterozygous sites and enabling cost-effective assembly.