Purging of highly deleterious mutations through severe bottlenecks in Alpine Ibex

Grossen, C., Guillaume, F., Keller, L.F. et al. Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex. Nat Commun 11, 1001 (2020). https://doi.org/10.1038/s41467-020-14803-1

Summary by: Charlie Clarke

Introduction

With bottleneck events becoming more and more common among wild populations due to deforestation, climate change, and over hunting, we can examine “recovered” populations to learn about the after effects of these events. The health and ultimately the survival of a species is controlled by the number of harmful mutations in a population. In dogs it has been observed that in some populations with low genetic diversity, the number of highly deleterious mutations in the gene pool was reduced. This is due to the expression of recessive traits that makes the dog unfit for breeding and otherwise would have been hidden in a heterozygous dog. The genetic load of a population refers to the ratio of harmful mutations within a population to healthy alleles. Inbreeding can decrease the genetic load of severely harmful mutations in a population, but as this paper points out it leads to an accumulation of mildly and moderately harmful mutations.  This means that the total genetic load is actually increasing while the seriously impactful mutations are decreasing. 

In this paper, the researchers investigated 60 complete genomes of 6 ibex species and the domestic goat. Their goal is to show that the historic bottlenecks experienced by these wild goats predict genome variation rather than their current conservation status. A bottleneck event refers to a dramatic reduction in population size that causes a loss in genetic diversity. The researchers are utilizing measures of genetic drift to better probe the difference between an “endangered” species versus a recovered population that has low genetic diversity. Genetic drift is the change in frequency of a gene variant within the population over time due to chance. A bottleneck event is hypothesized to increase the speed of genetic drift and inbreeding; this then leads to a vast reduction in genetic diversity. When a population is inbred, purging will occur at the same time. Purging is the natural selection process that works on individuals with highly deleterious mutations. Those genetic variants are typically removed from the population by either predation or early death before the individuals are capable of reproducing. This paper asks whether the negative impacts of genetic drift towards mildly and moderately harmful traits outweigh the benefits of the highly deleterious variants being removed through inbreeding. 

In the early 19th century, the Alpine Ibex population was reduced to 100 individuals. In less than a century the population has recovered to 50,000 individuals. The recolonization efforts focused on growing up a small local population and then reseeding those offspring into other areas of the Alps. Some of the successful populations were then used to initiate secondary and even tertiary populations. Due to the difficulty of the landscape, the populations don’t regularly intermingle. This means that every establishment of a new location can be interpreted as a genetic bottleneck. Some of these new populations have encountered up to 4 bottleneck events. This species as a result has extremely low levels of genome wide variation. 

Results 

Within the 7 species of goats tested (Siberian Ibex, Alpine Ibex, Iberian Ibex, Bezoar, Markhor, Nubian Ibex, and the domestic goat) 3 species have undergone severe bottleneck events. As a result, these species, the Alpine Ibex, Iberian Ibex, and Markhor, have exceptionally low levels of genomic variation. The Iberian Ibex population was reduced to 1000 individuals, while the Alpine Ibex was reduced to 100. In contrast, the Siberian Ibex had the greatest genetic diversity, likely due to the relative connectedness of their populations and lack of human influence on their habitat. In the Alpine Ibex and Markhor, individuals were found to have 20% homozygosity. Homozygosity is a measure of how related in the population are, the higher the homozygosity, the more interrelated the individuals are. 100% homozygosity indicates genetic clones while greater than 28% indicates that the parents of the offspring are first degree relatives such as mother to son or father to daughter. At 20% homozygosity, these populations are likely as related as siblings. 

The researchers identified 370,853 single nucleotide mutations (SNPs) across the entire goat genome. These mutations were then categorized as highly deleterious (0.17%), moderate impact (19.1%), low impact (33.1%), and no impact (47.6%). The species that underwent the most severe reduction in population size showed the largest accumulation of total mutations. 

When comparing the Iberian Ibex to the Alpine Ibex, both populations showed a decreased rate of highly deleterious mutations. This indicates that purifying selection is culling those genes from the more homozygous populations. The Alpine Ibex had much lower rates of highly deleterious mutations than the Iberian Ibex, indicating that the purging occurred more heavily in the population that went through a greater bottleneck. However, low to moderate impact alleles showed overrepresentation in both populations. The proportion of deleterious mutations was much higher in the Alpine Ibex in comparison to the Iberian Ibex, even though the Alpine Ibex had fewer total highly deleterious mutations. This data taken together indicates that the selection pressure of a bottleneck dramatically increases the impact of moderate to low impact mutations.

The Alpine Ibex population post bottleneck was located in the Gran Paradiso region of northern Italy, labeled gp in the figure below. Once the population was steadily increasing due to restoration efforts, individuals were taken from the Gran Paradiso population and transplanted in multiple other regions across the Alps, labeled as br, pl, and al in the figure below. The first reestablished population showed a large reduction in nucleotide diversity from the parent population that remained in the Gran Paradiso region. Then the initial 3 reintroduced populations were used to establish additional populations, labeled bo, wh, and ob in the figure below. These reintroduction events are in essence bottleneck events, bringing the total bottleneck events to between 2 and 4 depending on the population. The more bottlenecks a population went through, the more nucleotide diversity was lost, and the greater the impact of genetic drift. 

The Alpi Marittime population, labeled am in the figure below, was a secondary reestablished population that originated from 25 individuals. Of that initial population, only 6 were able to reproduce. As expected from such an extreme bottleneck, this group showed a strong differentiation from all of the other populations of Alpine Ibex. They also ended up having the lowest rate of highly deleterious mutations and the highest rate of moderate impact mutations. In contrast, the Gran Paradiso population showed the lowest proportion of low and moderate impact gene variants, while the reintroduced populations were most heavily affected. 

Looking at the figure below, the box and whisker plots are separated into gene groups. Modifier refers to neutral gene variants (variants that aren’t believed to affect health), while low, moderate, and high refers to the impact of the gene on the health of the individual. The navy blue column referring to the Gran Paradiso population shows that in comparison to the other populations, there are a lot of neutral mutations, and that the number of low and moderate impact mutations was less than average while the number of high impact mutations was slightly more than average (compared to the other bottlenecked populations). The tertiary populations bo, wh, and ob showed a dramatic increase in moderate mutations; ob specifically showed a reduction in high impact alleles. Finally, am, in pink, representing the population which underwent the most extreme selection, shows very high levels of low and moderate impact alleles and extremely low frequency of the highly deleterious mutations. 

Discussion

The results of this study indicate that bottleneck events dramatically increase the homozygosity of a given population. The species that underwent the largest reductions in population size accumulated the greatest number of deleterious mutations. The strong bottlenecks that affected the Alpine and Iberian Ibex caused both populations to purge the highly deleterious mutations and accumulate the moderate and low impact mutations. Fundamentally, these species are worse off after bottleneck events, due to the dramatic increase in total mutation load. This paper demonstrated that even bottlenecks down to 1000 individuals can cause this pattern of accumulating maladaptive mutations. It also indicates that the smaller the bottleneck, the worse the prognosis for the species. Eventually genetic drift and inbreeding will cause a population depression as mutation load mounts.