Museum Genomes Explain the Plight of the Grauer’s Gorilla

When a population rapidly plummets, the chance sampling of genetic drift and inevitable inbreeding can accelerate the pace of extinction. A new report in Current Biology reveals the genetic evidence behind the dire situation for Grauer’s gorilla.

Ancestral gorillas split into eastern and western species about 150,000 years ago. The western animals then split to yield the western lowland gorilla and the cross river gorilla subspecies. The eastern contingent diverged to give rise to the mountain gorilla and Grauer’s gorilla (aka eastern lowland) subspecies. This last primate lives in the Democratic Republic of Congo and is critically endangered.

From 5 to 10 million years ago, eastern gorillas were doing just fine. Then about 100,000 years ago, their populations began to decline. About 10,000 years ago they split into the mountain and Grauer’s subspecies. Then from 5,000 to 10,000 years ago, the Grauer’s population took off, expanding so quickly that some dangerous mutations occurred and accrued. Mountain gorilla populations remained fairly small, the numbers not allowing many mutations to accumulate.

Then about twenty years ago, the Grauer’s group hit a population bottleneck, and the numbers crashed down to about 4,000 animals, thanks to habitat destruction and poaching.

Meanwhile, the populations of mountain gorillas, the superstars of the documentaries, have plugged along with small populations for a long time. Sometimes things got dicey. The largest population hovered just below 1,000 animals beginning in the 1950s, getting down to about 250 until conservation efforts let to an increase in population size to 450 or so animals in 2013. In the long run, the new study shows, the different growth patterns make a difference in population genetic diversity and in predicting the future.

Sampling from Museums

In the new work, Tom van der Valk, a PhD student in the lab of Katerina Guschanski at Uppsala University in Sweden and their colleagues there and in Spain, sequenced the genomes of gorillas from 59 museum specimens. They selected 7 Grauer’s and 4 mountain gorillas with the best coverage (number of times the genome is sequenced to minimize gaps). The samples had been collected between 1910 and 1962, encompassing 4 or 5 generations. The team also sequenced the genomes of modern gorillas: 8 Grauer’s, 7 mountain, and 17 western lowland.

They then compared the old to the new to reveal the hallmarks of crashing genetic diversity. “We found that the genetic diversity in Grauer’s gorilla has declined significantly in just a few generations,” says van der Valk.

Genetic uniformity of the Grauer’s gorilla showed up in 3 ways:

1. Heterozygosity: Modern Gauer’s gorillas were genetically similar even if they came from the edges of their turf. (A 20% decrease in the number of genome sites that are different on the two chromosomes of a pair.) The older, museum Gauer’s genomes, in contrast, had considerably more genetic diversity.

2. Runs of homozygosity: The museum Gauer’s gorillas have fewer and smaller regions where the DNA sequence is the same on both chromosomes of a pair, compared to their contemporary relatives. An “ROH” is a telltale sign of inbreeding, and the modern contingent showed an increase in 24 percent of the affected part of the genome. That is, modern Gauer’s gorilla genomes harbor the marks of inbreeding. The genomes of mountain gorillas, used as controls, do not.

3. Genetic glitches. The genomes of modern Gauer’s gorillas were littered with mutations. Compared to their ancestors from just a century ago, the newer genomes had lots of missense mutations (replacing one encoded amino acid with another) as well as “loss-of-function” mutations that delete or obliterate a gene and its encoded protein. The technical term for a genome going rogue like this is “genetic load” – and the modern apes have it worse than their predecessors. Furthermore, the new mutations in Gauer’s gorillas affect immunity and methylation of genes, setting the stage for eventual lapse in protection against pathogens. The subspecies is weakening.

The genomes of the modern mountain gorillas, however, showed no such changes. The researchers think that’s because their declining numbers happened gradually. A sudden plunge in genetic diversity introduces genetic drift, which is a sampling error that can amplify the effects of mutant genes.

An interesting aside is that both modern Grauer’s gorillas and mountain gorillas have an increase in syndactyly – fused digits. Apparently the trait doesn’t impair their ability to find food or each other.

Sequencing the genomes of bits of tissue nondestructively removed from museum specimens can provide compelling views of the past. Concludes Dr. Guschanski, “Our study highlights that historical museum specimens constitute a unique resource for monitoring recent changes in the genetic status of endangered species.”

The message: endangerment and extinction are often blamed on sweeping effects like poaching, geographic upheaval, and climate change. But the small genetic changes, the chance sampling and inbreeding illustrating evolution at work, are what eventually doom a species.