Genetic architecture of inbreeding depression may explain its persistence in a population of wild red deer

Anna M. Hewett*, Susan E. Johnston, Alison Morris, Sean Morris, Josephine M. Pemberton

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Abstract Inbreeding depression is of major concern in declining populations, but relatively little is known about its genetic architecture in wild populations, such as the degree to which it is composed of large or small effect loci and their distribution throughout the genome. Here, we combine fitness and genomic data from a wild population of red deer to investigate the genomic distribution of inbreeding effects. Based on the runs of homozygosity (ROH)-based inbreeding coefficient, FROH, we use chromosome-specific inbreeding coefficients (FROHChr) to explore whether the effect of inbreeding varies between chromosomes. Under the assumption that within an individual the probability of being identical-by-descent is equal across all chromosomes, we used a multi-membership model to estimate the deviation of FROHChr from the average inbreeding effect. This novel approach ensures effect sizes are not overestimated whilst maximising the power of our available dataset of >3000 individuals genotyped on >35,000 autosomal SNPs. We find that most chromosomes confer a minor reduction in fitness-related traits, which when these effects are summed, results in the observed inbreeding depression in birth weight, survival and lifetime breeding success. However, no chromosomes had a significant detrimental effect compared to the overall effect of inbreeding, indicating no major effect loci. We conclude that in this population, inbreeding depression is likely the result of multiple mildly or moderately deleterious mutations spread across all chromosomes, which are difficult to detect with statistical confidence. Such mutations will be inefficiently purged, which may explain the persistence of inbreeding depression in this population.
Original languageEnglish
Article numbere17335
Number of pages11
JournalMolecular Ecology
Issue number9
Early online date28 Mar 2024
Publication statusPublished - 22 Apr 2024

Keywords / Materials (for Non-textual outputs)

  • inbreeding
  • inbreeding depression
  • quantitative genetics
  • runs of homozygosity


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