Abstract
Predictions about the consequences of a small population size on genetic and deleterious variation are fundamental to population genetics. As small populations are more affected by genetic drift, purifying selection acting against deleterious alleles is predicted to be less efficient, therefore increasing the risk of inbreeding depression. However, the extent to which small populations are subjected to genetic drift depends on the nature and time frame in which the bottleneck occurs. Domesticated species are an excellent model to investigate the consequences of population bottlenecks on genetic and deleterious variation in small populations. This is because their history is dominated by known bottlenecks associated with domestication, breed formation and intense selective breeding. Here, we use whole‐genome sequencing data from 97 chickens representing 39 traditional fancy breeds to directly examine the consequences of two types of bottlenecks for deleterious variation: the severe domestication bottleneck and the recent population decline accompanying breed formation. We find that recently bottlenecked populations have a higher proportion of deleterious variants relative to populations that have been kept at small population sizes since domestication. We also observe that long tracts of homozygous genotypes (runs of homozygosity) are proportionally more enriched in deleterious variants than the rest of the genome. This enrichment is particularly evident in recently bottlenecked populations, suggesting that homozygosity of these variants is likely to occur due to genetic drift and recent inbreeding. Our results indicate that the timing and nature of population bottlenecks can substantially shape the deleterious variation landscape in small populations.
Highlights
Deleterious mutations are expected to be held at low frequency by an equilibrium between the rate at which they arise by mutation and the efficacy of purifying selection at removing them from the population (Lynch, 2010; Ohta, 1992)
We find that recently bottlenecked populations have a higher proportion of deleterious variants relative to populations that have been kept at small population sizes since domestication
We find that the recent population bottleneck associated with the creation of neo‐bantams has resulted in a higher proportion of deleterious variants relative to large fowl and bantam counterparts, as genetic drift has reduced the efficacy of purifying selection to eliminate harmful mutations
Summary
Deleterious mutations are expected to be held at low frequency by an equilibrium between the rate at which they arise by mutation and the efficacy of purifying selection at removing them from the population (mutation–selection balance) (Lynch, 2010; Ohta, 1992). | 331 of chicken were used as a model species to investigate the conse‐ quences of two types of bottlenecks on deleterious variation: the severe domestication bottleneck occurred some thousands of years ago and the recent population decline accompanying breed forma‐ tion in the last decades Since their development in the 16th and 18th century (Dana et al, 2011), traditional fancy breeds have persisted at small population sizes and comprised normal‐sized (large fowl) and miniature (bantam) breeds. We find that the recent population bottleneck associated with the creation of neo‐bantams has resulted in a higher proportion of deleterious variants relative to large fowl and bantam counterparts, as genetic drift has reduced the efficacy of purifying selection to eliminate harmful mutations. Our results indicate that the time frame and nature of the bottleneck can substantially shape the deleterious variation landscape in small populations
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