A genomic continuum from feral to wild Red Junglefowl in Singapore

The admixed nature of the population raises several conservation issues.

Hybridization and the consequent exchange of genetic material (i.e. introgression) is not limited to wild populations. Domesticated animals or plants regularly interbreed with their wild relatives and genes flow both ways. These hybridization events can be accidental. After the disaster at the Fukushima Nuclear Power Plant in 2011, for example, several domestic pigs (Sus scrofa) escaped into the Japanese nature and hybridized with local wild boars. In other cases, captive animals are intentionally released into the wild, such as the restocking of European partridge populations with the non-native Chukar Partridge (Alectoris chukar) for hunting purposes. Unsurprisingly, the introduced partridges interbred with the local birds. Another example of hybridization between domestic and wild birds concerns chickens (Gallus gallus) in Singapore and was recently described in the journal Evolutionary Applications. Time for a trip to Asia!

 

Museum Samples

Wild chickens – the Red Junglefowl – were thought to be extinct in Singapore until they were rediscovered on the island Ubin in 1970. These birds probably crossed the 800 meter wide sea channel from the neighboring island Johor (part of Malaysia). Years later, Red Junglefowl also roamed the main island of Singapore. This recolonization was accompanied by an increase in domestic chickens (whether intentionally released or escaped remains uncertain) that occasionally hybridized with their wild relatives. This situation leads to an interesting discussion: are the Red Junglefowl populations on Singapore really wild? Or are they a mixture of wild and domesticated birds? Meng Yue Wu and her colleagues turned to genomic data to solve this mystery.

Studying introgression in chickens is challenging because there has been gene flow between several species and breeds (as explained in this blog post). To obtain a genomic reference for the wild Red Junglefowl, the researchers used two museum samples that were collected about 150 years ago on Malaysia. Next, they sequenced the DNA of 70 free-roaming birds from Singapore. The genomic analyses revealed a continuum from domestic to wild chickens with varying levels of introgression. There were no clear spatial patterns, suggesting that the wild and domestic chickens are freely mixing in Singapore (although most wild-type birds seem to cluster around Singapore’s largest national park).

Genomic analyses revealed a continuum from domestic (orange) to wild (blue) birds in Singapore. Each column represents an individual and the colors indicate the percentage of wild and domestic ancestry in the genome. The museum samples are indicated with stars in figure a. The three graphs represent different analyses: (a) all genomic samples, (b) all genomic samples without museum specimens, and (c) all genomic samples + additional RADseq samples. From: Wu et al. (2020) Evolutionary Applications.

 

Conservation

These findings result in a conservation conundrum. On the one hand, managers might warn that the wild Red Junglefowl on Singapore have been “genetically contaminated” by domestic genes. On the other hand, the exchange of genetic material might lead to higher genetic diversity and could potentially speed up adaptation.

Morphological analyses of the Singaporean chickens indicated that a handful of traits (tarsus and primary feather coloration for females and tail feather, primary feather, and lappet coloration for males) can be used to confidently discriminate between wild and domestic chickens. It is thus feasible to detect and remove “introgressed” individuals from the population. Should we intervene or not? I will not try to answer this question here, but feel free to share your thoughts in the comments below.

The researchers studied several traits to see whether it is possible to tell the difference between wild, domestic and mixed individuals. From: Wu et al. (2020) Evolutionary Applications.

 

References

Wu, M. Y., Low, G. W., Forcina, G., van Grouw, H., Lee, B. P. Y. H., Oh, R. R. Y., & Rheindt, F. E. (2020). Historic and modern genomes unveil a domestic introgression gradient in a wild red junglefowl population. Evolutionary Applications13(9), 2300-2315.

Featured Image: © Seng Alvin | Singapore Bird Group

 

This paper has been added to the Galliformes page.

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