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Sequencing Historical, Modern Gorilla Genomes Uncovers Genetic Ramifications of Population Decline

NEW YORK (GenomeWeb) – As their numbers dwindled in recent years, so has the genetic diversity found among Grauer's gorillas, according to a new analysis.

The Grauer's gorilla (Gorilla beringei graueri) population declined by about 80 percent in the last 20 years, largely due to poaching and habitat destruction. This, a Swedish-led team of researchers said, has led to concerns about the genetic health of this critically endangered species.

The researchers sequenced both modern and historical museum samples collected from Grauer's gorillas and the closely related mountain gorilla (Gorilla beringei beringei), which has also undergone population decline. As they reported in Current Biology this week, the researchers found that Grauer's gorillas have experienced a decline in genetic diversity, more so than mountain gorillas, a difference they attributed to the populations' different demographic histories.

"We found that the genetic diversity in Grauer's gorilla has declined significantly in just a few generations," first author Tom van der Valk, a graduate student at Uppsala University, said in a statement.

The researchers sequenced seven Grauer's gorilla and four mountain gorilla samples collected between 1910 and 1962 to between 3.1X and 10.8X coverage and aligned them to the gorilla reference genome. They then compared these historical gorilla sequences to published modern genomes from eight Grauer's gorillas, seven mountain gorillas, and 17 western lowland gorillas (Gorilla gorilla gorilla).

Using autosomal heterozygosity as a gauge, Grauer's gorillas experienced a decline in genetic diversity, the researchers found. The modern Grauer's gorillas had, on average, 20 percent fewer heterozygous sites than historical ones. Likewise, when the researchers estimated diversity at the population level based on the number of variable sites in the population, they also noted a reduction in diversity among modern Grauer's gorillas.

Their genomes also contained more runs of homozygosity than their historical counterparts, the researchers reported. This increase, they added, was fueled by a 24 percent increase in portion of very long runs — stretching between 2.5 megabases and 10 megabases in length — which they said also signals a likely increase in interbreeding.

Grauer's gorillas also accumulated deleterious mutations within their genomes. By examining the effects of their variants on protein-coding genes and the proteins themselves, the researchers found them to have increased numbers of missense and loss-of-function variants and damaging amino acid substitutions.

These loss-of-function mutations often affected genes involved in immunity and methylation, the researchers noted, adding that this suggested that Grauer's gorillas might have decreased pathogen resistance.

Population decline affected the mountain gorillas differently, the researchers noted. While they, too, experienced a decline in autosomal heterozygosity, it was smaller at three percent than what Grauer's gorillas experienced, as was their increase in runs of homozygosity. They also had a stable number of loss-of-function variants damaging amino acid substitutions.

The researchers said the two gorilla populations' demographic history might account for this disparity in genetic health. Grauer's gorillas and mountain gorillas split about 10,000 years ago, after which Grauer's gorillas underwent a period of population growth and range expansion. While this may have led to increased historical genetic diversity as compared to mountain gorillas, it may have also introduced a high number of low-frequency deleterious mutations. These deleterious mutations may have become more common as the number of Grauer's gorillas dropped in recent decades, they said.

In contrast, mountain gorillas have had a small population size for the past 10,000 years, which may have purged their genetic load, they added.

"This recent increase in harmful mutations really emphasizes the need to reverse the ongoing population decline in Grauer's gorillas," senior author Love Dalén from the Swedish Museum of Natural History said in a statement.