Genetic bottleneck

Genetic bottlenecks are events that reduce the genetic diversity of a group through a temporary reduction in the number of individuals in a population. Genetic bottlenecks occur frequently among populations, and have had major effects on the diversity of many species of interest.

Modern humans, for example, underwent a bottleneck at the time of our emergence in Africa (see OUT OF AFRICA HYPOTHESIS) between 100,000 and 200,000 years ago, and again when a fraction of the African population migrated to Eurasia roughly 50,000 to 60,000 years ago (Ramachandran et al. 2005). These events are partially responsible for the low levels of genetic diversity observed in modern humans, both inside and outside of Africa, relative to other primate species.

When populations shrink in size, genetic diversity is lost primarily through two mechanisms. First, many alleles (see GENE (ALLELE)) are lost during the period of population decline because the individuals carrying them do not reproduce, and thus those alleles are unavailable to subsequent generations. This is the case when primate populations decline rapidly due to disease, hunting, or a rapid reduction of resources.

The effect of this reduction is felt for many generations, as periods of small population size have major impacts on long-term diversity (see below). Orangutans are one primate population with declining numbers whose genetic diversity will be significantly reduced for many generations even if conservation efforts dramatically increase the number of individuals.

Second, the reduced population size increases the impact of genetic drift, which is the stochastic fluctuation of allele frequencies between generations due to sampling error (Wright 1921; 1931). The effect of genetic drift is to reduce heterozygosity (see HETEROZYGOSITY) and increase homozygosity in a population over time, and thus reduce genetic diversity.

In large populations, sampling error is relatively low and the effect of drift is negligible. However, in small populations, such as those during a bottleneck, the effect of drift is much greater. In small populations, alleles may be lost to drift quite rapidly, especially those present at low frequency. Very small populations might experience increased levels of inbreeding due to scarcity of available mates, which also decreases heterozygosity. For these reasons, genetic bottlenecks nearly always result in decreases in heterozygosity, with the magnitude determined by the severity and duration of the reduced population size.

Population bottlenecks, even brief ones lasting few generations, have a disproportionate impact on long-term diversity. Though populations may shrink and then grow rapidly to attain their initial size (or larger), the diversity of the population does not rebound as quickly. A brief reduction in the census population size (the number of individuals in a population) may have little effect on the arithmetic mean population size over time, and thus seem trivial. However, the effective population size (the number of individuals in an idealized population with random mating that has the same genetic diversity or experiences the same effect of genetic drift; Wright 1931) over time is measured as the harmonic mean of effective population sizes (see EFFECTIVE POPULATION SIZE) (Wright 1938).

Thus, periods of reduced population size have disproportionate effects on overall effective population size and diversity for many subsequent generations. Even brief periods of effective population size therefore may impact a population’s ability to respond to future selective constraints by greatly reducing diversity.

Other mechanisms may reduce diversity, such as natural selection. In sexually reproducing organisms that experience regular recombination, the effect of selection is typically localized to parts of the genome (see GENOMES) that directly affect the phenotypic trait (see PHENOTYPE (GENETICS)) under selection. For example, in the case of a selective sweep (see SELECTIVE SWEEP), only genomic elements in linkage with the locus under selection will have significantly reduced diversity (Maynard-Smith and Haigh 1974). In contrast to localized reductions of diversity, genetic bottlenecks are demographic events (changes in population dynamics such as size or connectedness) that affect the entire genome equally.

This is because all genomic elements are equally affected by changes in population size. Another effect of a bottleneck is to increase the overall level of linkage disequilibrium across the genome (reviewed in Slatkin 2008). Therefore, genetic bottlenecks can be distinguished from reductions in diversity due to selection by the fact that bottlenecks reduce heterozygosity and increase linkage across the entire genome, whereas selection results in reductions in diversity or increases in linkage that are localized to specific regions.

One particular type of genetic bottleneck, the founder effect (Mayr 1942), has profoundly patterned the diversity of human populations globally (Ramachandran et al. 2005). Founder effects occur when small groups separate themselves from larger populations and found new descendant populations. The bottleneck occurs at the moment of separation, and the descendant population(s) experiences the same reduction in diversity and effective population size as if the founder group were the only survivors of the original, larger population.