Chromosome Size as a Robust Predictor of Recombination Rate: Insights from Holocentric and Monocentric Systems

Abstract

Recombination is a fundamental evolutionary process essential for generating genetic diversity, facilitating adaptation, and driving speciation. However, direct measurement of recombination rate remains challenging, as standard methods--such as chiasma counts or genetic linkage maps--are labor-intensive and often infeasible for non-model species. In this study, we identify chromosome number and mean chromosome size as practical proxies for genome-wide recombination rate by analyzing genetic map data from 73 insect species and supplementary analyses of 157 monocentric flowering plants. We confirm the long-standing hypothesis that monocentric species have nearly twice as many crossovers per chromosome as holocentric species, reflecting structural constraints imposed by diffuse centromeres. Using both ordinary and phylogenetically informed Bayesian regression models, we show that recombination rate increases with chromosome number and decreases with mean chromosome size. Crucially, mean chromosome size is a significantly better predictor, particularly in holocentric species. This insight enables recombination rate estimation in thousands of species with known genome and chromosome sizes, thereby allowing hypothesis testing at scales previously unattainable. Building on these results, we present predictive models applicable to poorly studied holocentric plants. Overall, our study highlights the pivotal role of chromosome architecture in recombination evolution and provides an accessible framework for evolutionary genomic research across diverse lineages. Article summaryWhy do some species have more genetic shuffling than others? We investigated 73 insect species with detailed genetic maps and found that mean chromosome size is the best predictor of genome-wide recombination rate, not the number of chromosomes. This means we can now estimate recombination rates even in species where genetic maps are unavailable, using only genome size and chromosome number. We also show that chromosome structure matters--species with a single centromere per chromosome (monocentric) have nearly double the recombination compared to those with diffuse centromeres (holocentric). These insights open new doors for studying evolution across many organisms.