On the Indonesian island of Flores, less than a mile from the cave where archaeologists discovered the fossil remains of the tiny hominids Homo floresiensis, there is a village called Rampasasa which is home to a small population of pygmies. “Pygmy” is the scientific term for a group of people where adult males are less than about four feet tall, but whose bodies are of average human proportions. Most people living in Rampasasa fit that description.
It would be easy to assume that they are related to the other small inhabitants of Flores, and in fact some Rampasasans themselves have made that claim in the past. But a new genetic study says that’s not the case. These people show no signs of H. floresiensis in their ancestors, but their genomes do show evidence of a relatively recent adaptation to shorter length. That means short stature humans evolved twice on the same island, tens of thousands of years apart.
The hobbits are gone
Evolutionary biologist Serena Tucci of Princeton University and her colleagues obtained DNA samples from 32 people in Rampasasa. They sequenced the entire genomes of 10 of those people and looked for signs of an ancient encounter with… H. floresiensis or other unknown humanoid relative.
We don’t have an example of H. floresiensis DNA, but Tucci and her colleagues used a statistical method that helps identify all segments of a chromosome with a large number of changes that are not visible in the rest of the population. Segments that stand out in this analysis could mean that a person’s ancestors once met and mixed together members of another species, such as Neanderthals or Denisovans, or even a genetically isolated group of other humans. Tucci and her colleagues were looking for unusual segments that did not match Neanderthals or Denisovans, because those segments may be traces of H. floresiensis or H. erectus ancestry.
In humans from Rampasasa, several sequences corresponded to Neanderthal or Denisovan genomes. That’s not too surprising, given that most human populations outside of Africa have some Neanderthal ancestry, and people in the island of Southeast Asia have the highest prevalence of Denisovan ancestry of all modern humans.
But the analysis found no sequences that appeared to come from older or more distantly related hominins, such as H. floresiensis. Tucci and her colleagues say they can’t rule out small-scale gene flow at some point in the distant past, but the now-extinct Pleistocene hobbits of Flores are not direct ancestors of today’s inhabitants, despite the similarities in elevation and geographic coincidence. So the people of Rampasasa must have developed their short stature separately.
Rampasasans’ short stature is recent
Height is what is called a polygenic trait, meaning that the combined effects of many genes affect your height (environment, lifestyle, and diet also play an important role). The genome of the same individual may contain some gene variants or alleles associated with increasing length and others associated with decreasing. Tucci and her colleagues compared the Rampasasan genomes to a list of alleles linked to height in European populations, and they found that those associated with shorter stature are more common in the Flores islanders than in Europeans, which is not a surprising result.
And those height-related alleles appear at different frequencies in Rampasasans than in neighboring groups of people — a greater difference than just random genetic drift could explain.
Tucci and her colleagues say the height of the Rampasasans may be an example of insular dwarfism (also called island dwarfism), an evolutionary process in which animals living on an island, or in other confined, isolated environments, gradually develop smaller body sizes than their ancestors. Some biologists have suggested that insular dwarfism is an adaptation to limited food sources or smaller prey species. If that’s the case for humans on Flores today, they’re part of a long evolutionary history of dwarfism on Flores. In addition H. floresiensisthe island was once home to stegodon, a now-extinct pygmy relative of modern elephants.
However, keep in mind that diet and environment also play an important role in determining one’s height, and Rampasasa is a relatively impoverished village. In 2010, a resident, Viktor Jehabut, then 80 years old, told an Associated Press reporter that his family struggled to find enough food when he was young, and he believed the malnutrition had stunted his growth.
A brief genetic history
The DNA of the Rampasasans also points to dietary changes in their collective past. The frequencies of alleles in certain regions of their genomes look like what you would expect if these regions had been the focus of a relatively recent process called a “selective sweep.” This happens when a single allele provides a significant advantage to members of a species and appears to “sweep” through a population, making it very common.
On Flores, this appears to have happened with two genes on chromosome 11, FADS1 and FADS2, which code for enzymes involved in the processing of fatty acids from plants. Tucci and her colleagues call these genes “an evolutionary ‘toggle switch’ in response to a changing diet,” and they appear to have been the focus of selective sweeps several times throughout human history. An allele that leads to a less efficient conversion of medium-chain fatty acids to long-chain fatty acids has a frequency of about 95 percent in the Flores population, which is comparable to the frequency in other Southeast Asian groups. That suggests that the selective search began in a population that contained shared ancestors of both modern groups.
The genomes of the Rampasasans shed new light on that lineage. While most of their ancestry comes from East Asian populations, especially Oceanic groups, nearly a quarter are from New Guinea. Tucci and her colleagues say the genetic history of the Rampasasans suggests that they shared ancestry with the current Oceanic population and that those populations mixed with East Asian groups sometime in more recent history.
Science2018. DOI: 10.1126/science.aar8486 (About DOIs).