genetic diversity in small populations


Maintaining diversity and fitness in small animal populations

Published on
June 16, 2015

High genetic diversity in a population is not always better. Using information from genetic markers is the best way to maintain high genetic diversity, but this can have consequences for fitness and selected traits.

Small animal populations like in zoos, often face the threat of inbreeding. When individuals that are related to each other produce offspring, the same genetic material is inherited through both parents. This way, rare recessive mutations can become homozygous and may have strong deleterious effects for the individual carrying these variants. In the July issue of the influential journal Genome Research, we demonstrate that maximizing the genetic diversity of a population has not always the desired effect of increasing fitness.

The reason for this effect is that the frequency of rare deleterious variants is increased as well, and  these can contribute to lower overall fitness. By using genotype and resequencing data from two pig populations, we examined the best way to optimize diversity and fitness levels in small captive populations. Looking at optimal contributions (OC) of parents that should leave offspring to the next generation, we simulated ten generations of management on a zoo population of the endangered pig species Sus cebifrons and a population of the commercial pig breed Pietrain. We demonstrate that when mating is based on information about relatedness of individuals, the genetic diversity in the population is much higher after 10 generations than with random mating.  Moreover, genetic markers outperforms pedigree information when it comes to maintaining diversity.

The genomes of Sus cebifrons displayed signs of past as well as recent inbreeding with a relatively high genetic load. OC based on avoiding long stretches of homozygous sequence in the genome of offspring turned out to be most effective in maintaining high levels of diversity and fitness. However, we also caution for the effect such strategies can have on selection. We demonstrate that signatures of selection can be counteracted in the commercial Pietrain breed when diversity levels are increased. These findings show the importance of genomic and next-generation sequencing information in the optimal design of breeding or conservation programs.