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Runs of homozygosity under different demographic histories and selection scenarios in red deer

Abstract:

The relative effect of demographic history and selection on the number and length of runs of homozygosity (ROH) has been poorly studied in wild populations. A recent study that combined evolutionary simulations with empirical data for red deer (Cervus elaphus) found that population history has a stronger effect than selection on the distribution of ROH. Here, we investigate the relative influence of demographic history and selection on the number and length of ROH using wild red deer populations with varying demographic histories and selection scenarios related to male-male competition for mates. We genotyped 167 individuals with > 38,000 genome-wide autosomal SNPs and compared ROH features between red deer under different combinations of demographic histories and selection scenarios. We found that red deer with lower historic effective population size (N<inf>e</inf>) had higher number and length of ROH than the red deer with higher historic N<inf>e</inf>. In contrast, red deer under strong selection pressure (high male mating competition) did not exhibit different ROH features compared to those under weaker selection pressure (low male mating competition). Additionally, we did not find clear evidence that genome regions with ROH were affected by selection. Therefore, our results support the conclusion that, under the study conditions in our red deer populations, demographic history plays a more significant role than selection in shaping ROH patterns.