The danger of few genetic markers: Revisiting introgression between Chukar and Red-legged Partridge

In contrast to previous studies, genomic analyses point to little gene flow between these species.

For decades, people have been releasing the non-native Chukar Partridge (Alectoris chukar) and farm-reared hybrids into the range of the native Red-legged Partridge (A. rufa). Conservationists feared that these practices would impact the genetic integrity of European Red-legged Partridge populations. And indeed, several genetic studies reported extensive introgression from the Chukar into the Red-legged Partridge (see the Galliformes page for an overview). However, the introgression patterns were based on a limited set of genetic markers, such as microsatellites. These markers only capture a fraction of the genetic variation. Genomic data will tell a more complete story that might be very different. The possible discrepancy between microsatellites and genomic data was nicely illustrated by Mallards (Anas platyrhynchos) and American Black Ducks (A. rubripes). Analyses of microsatellites suggested that hybridization between these duck species might lead to the genetic extinction of the latter species. However, genomic studies of this system revealed little gene flow between the species, indicating that hybridization is not threatening the genetic integrity of the American Black Duck. A recent study in the Proceedings of the Royal Society B investigated whether a similar scenario applies to the Chukar and Red-legged Partridge situation.

Limited Introgression

Giovanni Forcina and his colleagues sequenced the genomes of 81 birds (75 Red-legged Partridges and 6 Chukar Partridges) and obtained almost 170,000 molecular markers. Analyses of this large dataset indicated that introgression from the non-native Chukar into the native Red-legged Partridge was quite limited. Specifically, the authors reported the following patterns for several subspecies (rufa, intercedens and hispanica) of the Red-legged Partridge:

While most populations within the ranges of A. r. rufa and A. r. intercedens showed a low yet detectable level of A. chukar introgression, those of A. r. rufa from Corsica and A. r. hispanica turned out to be probably unaffected.

All in all, the genetic impact of restocking practices appears to be relatively minor. Although there are clear signs of introgression from the Chukar Partridge, the genetic integrity of the Red-legged Partridge is not in serious jeopardy. It is possible that lower fitness of hybrids prevents most of them from mating and contributing to the next generation.

A principal component analysis clearly separated the Chukar Partridges (white squares) from the Red-legged Partridges (colored dots). More detailed analyses pointed to limited introgression between these species. From: Forcina et al. (2021).

Genomic Landscape

The observation of limited introgression between these partridges is certainly good news, but why did previous genetic studies point to high levels of gene flow? In a recent review, I warned about the use of a few markers (such as microsatellites) in conservation because of the so-called genomic landscape of differentiation. When comparing the genomes of closely related species, we generally observe that genetic differences are heterogeneously distributed across the genome. Some genomic regions will be drastically different, while others are largely undifferentiated. The random selection of a few genetic markers might result in a marker set that only captures the undifferentiated section of the genome, giving the impression that the studied species are genetically similar. When the species interbreed, researchers can be quick to conclude that this similarity is due to introgressive hybridization. However, a genomic perspective might lead to very different conclusions, as we have seen with the partridges. Do not underestimate the power of genomic data.

References

Forcina, G., Tang, Q., Cros, E., Guerrini, M., Rheindt, F. E., & Barbanera, F. (2021). Genome-wide markers redeem the lost identity of a heavily managed gamebird. Proceedings of the Royal Society B288(1947), 20210285.

Featured image: Red-legged Partridge (Alectoris rufa) © Juan Lacruz | Wikimedia Commons

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