Modern pygmies living in a village near the Liang Bua cave on the Indonesian island of Flores, where fossils of the dwarfed human species Homo floresiensis were discovered in 2004, appears to have evolved short stature independently, according to new research.
Reconstruction of Homo floresiensis. Image credit: Elisabeth Daynes.
Flores Island has long been inhabited by small-bodied humans, including the extinct Homo floresiensis, which has an unknown relationship to modern humans. Additionally, the island is currently home to a population of pygmies.
To better understand the short-statured evolutionary history of the humans on the island, Princeton University researcher Serena Tucci and co-authors turned to the genetics of the Flores pygmy humans.
“In your genome — and in mine — there are genes that we inherited from Neanderthals,” Dr. Tucci said.
“Some modern humans inherited genes from another extinct species of humans, Denisovans, which we can check for because we have genetic information from Denisovans.”
“But if you want to look for another species, like Homo floresiensis, we have nothing to compare, so we had to develop another method. We ‘paint’ chunks of the genome based on the source. We scan the genome and look for chunks that come from different species — Neanderthal, Denisovans, or something unknown.”
The team collected and analyzed the DNA of 32 contemporary pygmy humans, which included 10 whole-genome sequences, and studied their genetic variation.
The analysis reveals a complex genetic history showing that the modern Flores pygmies have both Neanderthal and Denisovan ancestry. However, the researchers found no evidence of gene flow with other archaic hominins.
“They definitely have a lot of Neanderthal. They have a little bit of Denisovan. We expected that, because we knew there was some migration that went from Oceania to Flores, so there was some shared ancestry of these populations,” Dr. Tucci said.
“But there were no chromosomal ‘chunks’ of unknown origins.”
Dr. Tucci and colleagues also found evolutionary changes associated with diet and short stature.
Height is very heritable, and geneticists have identified many genes with variants linked to taller or shorter stature. The study authors analyzed the Flores pygmy genomes with respect to height-associated genes identified in Europeans, and they found a high frequency of genetic variants associated with short stature.
“It sounds like a boring result, but it’s actually quite meaningful,” said co-lead author Dr. Richard ‘Ed’ Green, from the University of California-Santa Cruz.
“It means that these gene variants were present in a common ancestor of Europeans and the Flores pygmies. They became short by selection acting on this standing variation already present in the population, so there’s little need for genes from an archaic hominin to explain their small stature.”
The Flores pygmy genome also showed evidence of selection in genes for enzymes involved in fatty acid metabolism, called fatty acid desaturase (FADS) enzymes.
These genes have been associated with dietary adaptations in other fish-eating populations, including the Inuit in Greenland.
Fossil evidence indicates Homo floresiensis was significantly smaller than the modern Flores pygmies, standing about 3.5 feet tall (106 cm), while modern pygmies average about 15 inches taller (145 cm).
“Homo floresiensis also differed from Homo sapiens and Homo erectus in their wrists and feet, probably due to the need to climb trees to evade Komodo dragons,” Dr. Tucci said.
Dramatic size changes in animals isolated on islands is a common phenomenon, often attributed to limited food resources and freedom from predators. In general, large species tend to get smaller and small species tend to get larger on islands.
At the time of Homo floresiensis, Flores was home to dwarf elephants, giant Komodo dragons, giant birds and giant rats, all of which left bones in the Liang Bua cave.
“Islands are very special places for evolution. This process, insular dwarfism, resulted in smaller mammals, like hippopotamus and elephants, and smaller humans,” Dr. Tucci said.
“Our results show that insular dwarfism arose independently at least twice on Flores Island, first in Homo floresiensis and again in the modern pygmies.”
“This is really intriguing, because it means that evolutionarily, we are not that special. Humans are like other mammals; we are subject to the same processes.”
The research is published in the journal Science.
_____
Serena Tucci et al. 2018. Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science 361 (6401): 511-516; doi: 10.1126/science.aar8486
