Past, present and future of a huge inversion in the Common Quail

Where did this inversion come from and what will happen to it?

Talking about a massive discovery. In the journal Current Biology, Ines Sanchez-Donoso and her colleagues reported on a massive inversion in the Common Quail (Coturnix coturnix). An inversion is a genomic region that has been flipped around (see this blog post for more details). Think of a piece of text “THIS IS AN INVERSION” that is reversed to “NOISREVNI NA SI SIHT“. In the case of the Common Quail, this flipped text is about 115,000,000 DNA-letters long and contains roughly 7700 putative genes. Detailed analyses of individuals with and without the inversion revealed some interesting patterns:

Birds with the inversion are larger, have darker throat coloration and rounder wings, are inferred to have poorer flight efficiency, and are geographically restricted despite the high mobility of the species.

The exact mechanisms relating the inversion to these traits remain to be unraveled, but we can already contemplate the origin and future of the inverted region. But before we travel backward and forward into time, let’s start from the present-day: How did the researchers find this massive inversion?

Present: Is it really an inversion?

Our story starts with a standard population genomic analysis of 80 Common Quails from Italy, Spain, Portugal, Morocco, and the eastern Atlantic archipelagos of Canary Islands and Madeira. Genetic differentiation between these locations appeared to be concentrated in a large region on chromosome one. A closer look at this region uncovered two main clusters (A and B). Most quails belonged to one of these clusters, but 30 birds showed a 50-50 genetic ancestry. This pattern suggests that we are dealing with two genetic variants that can be arranged as homozygotes (AA or BB) and heterozygotes (AB).

To test whether these three genotypes (AA, BB and AB) can be explained by an inversion, the researchers turned to cytogenetics. They developed two probes that bind with certain sections of chromosome one. In the AA birds, these probes were further apart (23.80 μm) than in the BB birds (11.97 μm). The different locations of the probes are expected if there is a large chromosomal inversion. And indeed, whole genome sequencing of 16 individuals confirmed the presence of a huge inversion.

A differentiated region on chromosome one (top left) turned out to be an inversion. The researchers uncovered three genotypes (AA, BB and AB) using admixture analyses (bottom left). Cytogenetic probes (J-23 and K-19) showed patterns that were in line with an inverted region on chromosome one (right). From: Ines Sanchez-Donoso et al. (2022).

Past: Ancestral variation or introgression?

Now that we are confident that it is an inversion, let’s focus on the past. Using the genetic variants within the inversion, the researchers were able to estimate when this genomic region was flipped around. Based on a range of mutation rates, this inversion probably originated between 0.9 and 3.2 million years ago. An old origin.

However, the exact event that gave rise to the inversion is still uncertain. It could have occurred in an ancestral population and the resulting inversion was maintained until the present-day. Or the inversion could have occurred in another (now extinct) species and was consequently transferred to the Common Quail by introgressive hybridization. This “ghost introgression” scenario seems plausible because “several extinct species of quail have been described for the eastern Atlantic islands.” An exciting idea to explore.

The inversion (AB in blue and BB in red) mainly occurs in the southern part of the distribution range. Whether it originated in the Common Quail itself or was introgressed from an extinct species remains to be determined. From: Ines Sanchez-Donoso et al. (2022).

Future: Speciation or stability?

What will happen to this inversion in the future? It is impossible to know for sure, but the authors offer several possibilities. The inverted and non-inverted regions might continue to accumulate genetic differences, potentially culminating in the origin of two distinct quail species. At the moment, however, heterozygotes – carrying both an inverted and a non-inverted region – do not seem to suffer from any fitness reductions. Perhaps the inversion will be maintained in the quail population for several thousands of years. Indeed, frequency-dependent selection or temporally fluctuating selection can result in a stable polymorphism.

Speciation or stability? Only time will tell.


Sanchez-Donoso, I., Ravagni, S., Rodríguez-Teijeiro, J. D., Christmas, M. J., Huang, Y., Maldonado-Linares, A., … & Vilà, C. (2022). Massive genome inversion drives coexistence of divergent morphs in common quails. Current Biology32(2), 462-469.

Featured image: Common Quail (Coturnix coturnix) © Christoph Moning | Wikimedia Commons

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