February 2016 By guest author Christopher A. Emerling, PhD, NSF Postdoctoral Fellow, UC Berkeley Museum of Vertebrate Zoology

Where's the evolution?

Cheetahs (Acinonyx jubatus) are extremely inbred. You might even call them the royalty of the cat family because of how inbred they are. You may know that genetic differences among humans mean that when we have an organ transplant, we have to take intense immune system-suppressing drugs to keep our bodies from rejecting the organ, even if it’s from a parent or sibling. Cheetahs, on the other hand, wouldn’t have to because they are so genetically similar to one another. If a cheetah needed a kidney transplant, it could probably get one from any other individual. Siblings, third cousins twice removed and even complete strangers on the other side of Africa could all probably donate a kidney to a fellow cheetah.

A recent study by Stephen J. O’Brien and his colleagues set out to precisely quantify the genetic similarity of cheetahs by sequencing the genomes of seven individuals: four from Namibia and three from Tanzania. They used several different measures of genetic variation, including: the number of genome-wide differences in single nucleotides, the length of stretches of DNA that were homozygous, the proportion of sites that are heterozygous, and the number of single nucleotide variants in major histocompatibility complex genes, a group of genes that help the immune system recognize friendly vs. foreign tissue. Cheetahs were dead last in almost every measurement of genetic variation among the species that the authors examined, emphasizing the depletion of variation in their genomes.

Though being able to receive an organ donation from any individual in your species might sound appealing, being so excessively inbred can lead to an increase in the expression of deleterious recessive alleles. This can lead to a decrease in fitness in the entire population, a phenomenon known as inbreeding depression. A potential example of this inbreeding depression is that cheetahs have little success with reproducing, likely due to the fact that cheetahs have a high proportion of malformed sperm. The scientists responsible for the new research suggested that this is related to the accumulation of excessive deleterious mutations in genes tied to reproduction. Being inbred also means that the lineage is less likely to evolve in response to new environmental conditions or pathogens. For natural selection to work, it requires genetic variation to act on. So if variation is absent, the species simply cannot adapt. It may only take a novel virus or a changed climate to wipe out the cheetah for good.

So what caused cheetahs to reach such a dismally low level of genetic variability? The prevailing hypothesis is that cheetahs experienced what is known as a genetic bottleneck. Just as a bottle narrows from its base to its neck, a genetic bottleneck occurs when a gene pool is narrowed to a fraction of its former diversity. This can happen via a natural disaster, such as a volcano wiping out all but a small portion of a population. Alternatively, it can happen through dispersal to a new habitat, a phenomenon known as the founder effect. If a population disperses to a new location, and is isolated from the source population, perhaps because of a difficult-to-cross river, gene flow will cease. As a result, this small founder population may contain only a miniscule fraction of the original gene pool. In other words, a species can evolve and become a less adaptable population via genetic bottlenecks. Survival of the fittest is not the only way evolution can happen.

Using sophisticated modeling of evolution, the authors estimated that a founder event for modern cheetahs took place over 100,000 years ago, leading to an initial reduction in genetic variation. Then, approximately 12,000 years ago, the population crashed again, taking many gene variants with it, leading to today’s inbred cheetahs. What may have led to these genetic bottlenecks?

Despite Cheetahs appearing similar to the spotted jaguar and leopards, they are actually a type of small cat (Felinae), being more closely related to your homegrown tabby cat than to these large, roaring cats (Pantherinae). In fact, molecular phylogenetics suggest that the cheetah’s closest living relatives are the American puma (Puma concolor) and a smaller cat known as the jaguarundi (Puma yagouaroundi), which ranges from South America to Mexico. Modern cheetahs currently live in Africa, with a small population surviving in Iran, though they formerly ranged across much of Asia and Europe. So which lineage dispersed where? The authors point to fossils of “American cheetahs” (Miracinonyx), which were anatomically very similar to modern day cheetahs, and suggest that today’s cheetahs originated in North America and crossed over to Asia via a land bridge before dispersing again to Africa. They posit that the Asian dispersal may have caused the first genetic bottleneck, with the African dispersal being associated with the second bottleneck. This narrative has been picked up by many news outlets, perhaps because it’s fascinating to think of such an iconic African mammal as being American in origin.

However, the authors also note that an ancient DNA analysis suggests that “American cheetahs” were actually more closely related to the puma and jaguarundi than true cheetahs. In addition, fossils of an extinct puma species (Puma pardoides) have been discovered in Europe or Asia, suggesting instead that pumas, jaguarundis and “American cheetahs” may have instead descended from one or more lineages that dispersed from Asia to North America. It’s worth noting that the estimated timing of the second bottleneck 12,000 years ago coincides with the Late Pleistocene extinctions, during which many large-bodied mammals, including “American cheetahs” went extinct around the world. Researchers hypothesize that these extinctions were caused by climate change, overpredation by humans, or both. Notably, African mammals were largely spared, but perhaps the cheetah just barely survived this extinction event and the result was a genetic bottleneck.

However it happened, the bottlenecks that cheetahs experienced led to the species having a drastically reduced gene pool (gene puddle?). As a result, this magnificent species is perpetually at risk of extinction, whether due to human interactions or otherwise. Despite what evolution has wrought upon this species it still ekes out a living by hunting antelope and other prey on the African savannahs. Though it may seem like a losing battle, as long as it continues to impress people with its beauty and speed, there’s a good chance that conservation efforts will buffer cheetahs from anything that threatens to wipe them out.