The unreal voyages and trials of Madagascar’s Malagasy people
Of rice and men
Note: this is the second of two related pieces; you can read the first one here.
One of the consistent patterns that emerge in Madagascar’s human genetics is that highland populations display more Asian ancestry and lowland populations less. This tendency is evident in facial features. Highlanders like the Merina, the island’s most numerous group, have more Asian-like hair and facial features than lowland populations like the Betsimisaraka, the second-most numerous group.
A simple explanation for this trend is that gene flow from Africa literally disembarked first in the coastal regions, where Muslim traders were more active than in the more remote highlands. It’s easy to imagine African ancestry only percolated up into the more isolated highlands later after the lowland tribes had already become mixed. But another factor that impacts the evolution of any population is natural selection, and in Madagascar, you have an environment where human populations expanded lightning fast into a very novel ecology. Might adaptive selection pressures have reshaped the genomes of the Malagasy, altering the proportion of African and Asian ancestry and leaving a signature in their very DNA?
A research group tested this hypothesis by sampling the genomes of 700 Malagasy from 257 villages across the island. What they immediately remarked on was a sharp drop in Asian ancestry across much of chromosome 1:
The target of selection on chromosome 1 in this case is the Duffy locus; and specifically, the null allele that fails to produce the Duffy antigen is under selection. This gene is well known in population genetics because of a marked contrast in variants between African and non-African populations; most Africans are Duffy-negative while most non-Africans are Duffy-positive. Duffy-negative individuals lack the receptor used by the Plasmodium vivax malarial parasite to invade red blood cells, a deficit that confers malaria resistance on its bearer. In Malagasy populations today, the region of Chromosome 1 around Duffy spikes to over 90% African in local ancestry whereas across the rest of the genome, the African ancestry proportion hovers around only 60%. Researchers calculate that this change was driven by a selection coefficient on the order of 0.20. We can translate this into plain English as an individual carrying the Duffy-negative allele has 20% more surviving offspring than one who does not. This is a staggeringly powerful selection coefficient; very few genes have been subject to such drive in humans; indeed a coefficient of 0.01 or above is by convention usually considered strong selection. The authors conclude that adaptation to malaria reduced Asian ancestry by as much as 10% in the Malagasy in a space of less than 600 years.
Biogeographically distinct from mainland Africa though Madagascar might have been, it was still much more ecologically similar to humanity’s original home than it was to Southeast Asia. This is made clear with the presence of P. vivax, which originated in Africa (African apes are endemically infected with related parasites). The Austronesian ancestors of the Malagasy arrived with neither biological nor cultural adaptations to African environments. When they began clearing forests and turning the land into cultivated fields, they created vast pools of standing water perfect for incubating swarms of mosquitoes harboring malaria parasites. To this day, malaria is one of Madagascar’s top five causes of death. Given enough time, the Austronesians would have developed their own genetic adaptations, but they didn’t have the luxury of time. Luckily for them, they soon became a hybrid population whose counterparts came equipped with such protection. So the Malagasy simply adapted via admixture, as the beneficial variants common in Africans swept through their genomes. Without the arrival of the Africans, the local Malagasy would surely have struggled to maintain their small population numbers in the face of the ravages of disease. It would have been a race against the clock to evolve and spread a de novo protection against malaria.