East or West Africa: Where was the Helmeted Guineafowl domesticated?

Genomic analyses help to solve this mystery.

We have a pretty good idea when and where the Chicken (Gallus gallus) was domesticated, although this history has been muddled by hybridization with several wild species. For other domesticated bird species, things are not so clear. Take the Helmeted Guineafowl (Numida meleagris) for example. Charles Darwin proposed that this species was domesticated in East Africa, whereas some archeological finds suggests West Africa. Luckily, we can turn to genomic data to resolve this issue. By reconstructing the evolutionary history of the Helmeted Guineafowl and characterizing the genetic make-up of different domestic populations, we can hone in on its most likely origin of domestication. A recent study in the journal Genome Biology and Evolution used a high quality reference genome to tackle this challenge.

Gene Flow

Based on 89 domestic and 34 wild Helmeted Guineafowl genomes, Quan-Kuan Shen and colleagues determined the phylogenetic relationships between different populations across the world. It turned out that the domestic clades were most closely related to birds from Nigeria. However, this result could be influenced by recent gene flow. Perhaps the Helmeted Guineafowl were domesticated in the east (Sudan and Kenya) and later interbred with western birds in Nigeria. To account for the possible effects of gene flow, the researchers tested several demographic scenarios. The most likely model indicated a single domestication event in West Africa about 5500 years ago. Apparently, Darwin was wrong about the Helmeted Guineafowl.

A phylogenetic analysis of more than 100 genomes revealed that domestic birds are most closely related to wild birds from Nigeria in western Africa. From: Shen et al. (2021) Genome Biology and Evolution.

Italian Breeds

Estimates of genetic diversity revealed that all domestic populations lost a significant amount of genetic variation. A common consequence of domestication with strong human-induced selection pressures. The lowest levels of genetic diversity were observed in the Italian populations which comprise two breeds: Camosciata and Selvatica. The first breed is known for its peculiar white plumage. The researchers screened the genome of this breed for signatures of selection to pinpoint promising candidate genes underlying this particular phenotype. Their analyses uncovered several genes, including TYR which is known to account for white plumage in chickens. A more detailed look at this gene revealed a mutation at position 218 (a tryptophan became a glycine) that was fixed in the Camosciata breed. This gene is linked to several other genes under selection (e.g., PGR and MMP13) and might thus influence multiple traits in these Italian birds.

An overview of genes under selection in the Italian breeds Selvatica and Camosciata. The white plumage in the Camosciata breed can be traced back to a mutation in the TYR-gene (indicated with a star in the alignment). From: Shen et al. (2021) Genome Biology and Evolution.

References

Shen, Q. K., Peng, M. S., Adeola, A. C., Kui, L., Duan, S., Miao, Y. W., … & Zhang, Y. P. (2021). Genomic Analyses of Unveil Helmeted Guinea Fowl (Numida meleagris) Domestication in West Africa. Genome Biology and Evolution, 13(6), evab090.

Featured image: Helemeted Guineafowl (Numida meleagris) © H. Zell | Wikimedia Commons