Fine-scale recombination landscape in the wood white butterfly Leptidea sinapis

Recombination is a genetic process of extreme importance in evolutionary biology. It creates novel haplotypes and breaks down existing ones, and can affect the levels of genetic diversity and the efficacy of selection. It also plays an important role in the evolution of sex chromosomes and the divergence process leading to speciation. Considering the particularities of the wood white (Leptidea sinapis) genome, with holocentric chromosomes, female achiasmy and a population-level cline in chromosome number, the study of its recombination landscape represents an opportunity to deepen the understanding of both this particular study system, and the underpinnings and consequences of recombination rate variation in general. After DNA extraction and sequencing of 96 wood whites sampled across Sweden, population structure analyses were carried out together with a demographic history inference, which was used together with linkage disequilibrium information to establish the recombination rate in short intervals along the different chromosomes. Population structure analyses showed that the sample set included 12 individuals of a cryptic species (cryptic wood white, L. juvernica) and, consistent with previous studies, a single population of L. sinapis in Sweden. Demographic inference analyses for independent scaffolds showed similar trend, with effective population size (Ne) decreasing considerably over the last 10,000 generations. The obtained recombination maps had a high resolution, and allowed for the identification of 553 putative recombination hotspots with a mean length of 3,770 bp. The genome-wide recombination rate was 9.98 cM/Mb, higher than in any vertebrate and butterfly species previously analysed, but lower than in the honey bee. A negative correlation between recombination rate and chromosome size was found, as well as a lower recombination rate on the Z chromosomes compared to the autosomes. The results are important for understanding the mechanisms underlying regional recombination rate variation in holocentric organisms and the potential for chromosome rearrangements to affect the recombination frequency, and consequently, rates and patterns of molecular evolution.