Recombination is a fundamental genetic process. It contributes to generating the genetic diversity upon which natural selection acts and mechanistically it ensures proper formation of sperm and egg cells. Studies of fine-scale distribution of recombination along chromosomes, and how this is regulated, have so far been possible only in a limited number of species. This is now changing.
In this project, I am constructing fine-scale recombination maps for over 30 species to (i) explore links between recombination landscapes and genetic differentiation between pairs of populations or closely related species; and (ii) to follow up on preliminary results suggesting the mechanisms for specifying recombination hot-spots in a large group of fishes (Percomorpha) may be distinct from other vertebrates.
For more background see:
Coop, G. & Przeworski, M. (2007) An evolutionary view of human recombination. Nat. Rev. Genet. 8, 23–34. doi: https://doi.org/10.1038/nrg1947.
Baker, Z. et al. (2017) Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates. eLife 6, 403. doi: https://doi.org/10.7554/eLife.24133.001.
Evolutionary Radiations of Cichlid Fishes
Evolutionary radiations are responsible for much of the variation in biodiversity among animal groups. Cichlid fishes are well known for spectacular evolutionary radiations, as they have repeatedly evolved into large and phenotypically diverse arrays of species. Cichlid genomes carry signatures of these past events and, at the same time, are the substrate for ongoing evolution. For an up-to-date summary of cichlid genomics see our review (Svardal et al., 2021).
Over the years I have focused on several aspects of cichlid evolution:
Early stages of speciation in the tiny crater lake Masoko in southern Tanzania (Malinsky et al., 2015)
In depth genomic investigation of the adaptive radiation in Lake Malawi (Malinsky et al., 2018)
Signatures of gene flow among species in the Lake Tanganyika radiation (in Ronco et al., 2021)
Genetic basis of phenotypic convergence between species in Malawi and Tanganyika (ongoing)
In my new project on recombination, I am starting to work with Ole Seehausen on Lake Victoria cichlids to integrate findings from all three East African Great Lakes.
Methods and Software
Some of my software is used by the broader Evolutionary Genomics community. This includes:
Dsuite - for calculating admixture/introgression statistics including Patterson's D and related measures from VCF files (Malinsky et al., 2021).
fineRADstructure - for population structure inference from RAD-seq data, with high resolution based on nearest-neighbour haplotype comparisons (Malinsky et al., 2018)
I have an interest in de novo genome assembly, having contributed to the PacBio assembly pipeline used by the Vertebrate Genomes Project and generated the PacBio A. calliptera cichlid genome assembly (Rhie et al. 2021). In the realm of de novo assembly I also developed trio-sga - a set of three algorithms designed to take advantage of mother-father-offspring trio Illumina sequencing to facilitate better quality genome assembly in organisms with moderate to high levels of heterozygosity (Malinsky et al., 2016).