Bottlenecks and Genetic Diversity

A population bottleneck is a sharp reduction in population size over a period of time. This could be caused by environmental factors such as droughts, viral diseases, or human-induced events like habitat destruction. During a bottleneck, only a fraction of the original population survives, which can have significant effects on genetic diversity.

In this practice, we will analyze how a population evolves over time due to a bottleneck.

You will be able to modify:

  • The population size before, during and after the bottleneck.

  • The duration of the bottleneck.

  • The time elapsed after the bottleneck.

Here, we will simulate the mutations and recombinations that occur in a genomic segment. At the end of the simulation, the genomic segment will contain variable loci that have arisen through mutation and have been reshuffled through recombination. You could have the option of modifying other parameters like:

  • The recombination rate.

  • The mutation rate.

  • The sequence length.

  • The sample size, the number of individuals taken from the population to calculate the different paramenters.

After running the simulation, you will have access to several genetic diversity metrics:

  • Expected heterozygosity (a measure of genetic variation).

  • Number of variant loci.

  • Number and proportion of polymorphic variants.

  • Allele Frequency Spectrum (AFS) (distribution of allele frequencies).

Bottleneck simulation application

Bottlenecks and diversity

Imagine a population goes through a bottleneck. How do you think this event will affect its genetic diversity?

Before running the simulation, consider what do you expect will happen to:

  • The expected heterozygosity?

  • The number of genetic variants?

  • The number and proportion of polymorphic variants?

  • After the bottleneck is over, do you think the population will recover its initial genetic diversity? Why or why not?

Run the simulation and examine the results before, during, and after the bottleneck. Compare your expectations with the observed changes in:

  • Expected heterozygosity.

  • The number of genetic variants.

  • The number and proportion of polymorphic variants (95% threshold).

Remember that you can get the values of these parameters before, during and after the bottleneck in the different plots and tables.

How does the bottleneck affect the Allele Frequency Spectrum? (Compare the oldest sample of the population and the most recent one (0))

Could you explain the effect of the bottleneck in the ratio of polymorphic (95%) variants?

After a bottleneck, a population can recover in size, but does this also restore its genetic diversity? Does the expected heterozygosity, number of variants and number of polymorphic (95%) variants recover its initial value after the bottleneck is over? Why?

Effect of the population size and time after the bottleneck

Scenario 1: Increasing Population Size After the Bottleneck

  • Increase the population size after the bottleneck and observe the effect.

  • Does a larger post-bottleneck population help restore genetic diversity? Why or why not?

  • What evolutionary force would drive this recovery over time?

Scenario 2: Time Elapsed Since the Bottleneck

  • Run simulations with different numbers of generations after the bottleneck.

  • Does increasing the time since the bottleneck help recover lost diversity?

  • Which genetic parameters recover, and which remain altered?

Effect of the bottleneck strength

Not all bottlenecks have the same severity. Let’s explore how different bottleneck conditions impact genetic diversity.

Vary the number of individuals that survive the bottleneck. How does the severity of the bottleneck (number of individuals surviving) affect:

  • Expected heterozygosity?

  • Number of variants?

  • Proportion of polymorphic loci?

  • Is there a minimum number of individuals that makes the bottleneck effect negligible?

Vary the duration of the bottleneck.

  • How does increasing the duration of the bottleneck influence diversity loss?

  • Would an extreme bottleneck, even a short one, still be problematic?

Real-World consequences: Conservation and Breeding

Bottlenecks are not just theoretical; they have real-world implications for population management.

Endangered Species Recovery

Imagine an endangered species that has gone through a severe bottleneck but later recovers in population size.

  • Will its genetic diversity fully recover over time?

  • What risks does low genetic diversity pose for long-term survival (e.g., inbreeding, disease susceptibility)?

Breeding Populations

Some domesticated populations, like for instance the cultivated tomato or the “piel de sapo” melon variety, originate from a handful of individuals. How could this impact their genetic diversity and long-term adaptability?

How can we restore genetic diversity?

Imagine that you are trying to improve the diversity of a population that has gone through a bottleneck. It could be, for instance, a population of a wild species that has suffered a drought or a particular variety of a cultivated plant that has lost most of its genetic diversity.

Could you propose an intervention to recover the lost genetic diversity?

  • Could controlled breeding programs help?

  • Would introducing individuals from other populations be beneficial?

  • What role does mutation play in restoring diversity?

Conclusions

Summarize your findings:

  • How does a bottleneck impact genetic diversity?

  • Can diversity recover after a bottleneck, and under what conditions?

Discuss key evolutionary forces at play:

  • What role does genetic drift play during and after a bottleneck?

  • How do mutation and natural selection contribute to long-term recovery?

Apply your knowledge to real-world cases:

  • What lessons can we learn for conservation biology and breeding programs?

  • How can we mitigate the negative effects of bottlenecks in endangered or managed or breeding populations?