What will happen to the hybrid zone between Hooded and Carrion Crow?

Mathematical modelling provides insights into the fate of this classic hybrid zone.

“Prediction is very difficult, especially about the future.” This quote – often attributed to the Danish physicist Niels Bohr – perfectly captures the challenge of forecasting complex phenomena. Yet, this challenge rarely deters scientists. A common strategy is to construct mathematical models and explore how systems might behave under different assumptions and conditions. Of course, as George Box famously reminded us, “all models are wrong, but some are useful.”

A recent study in the journal Evolution offers a nice example of this modelling approach. Dirk Metzler and his colleagues developed a mathematical model to explore the future of the classic hybrid zone between the Hooded Crow (Corvus [c.] cornix) and the Carrion Crow (Corvus [c.] corone).

Epistatic Interactions

The hybrid zone between the all-black Carrion Crow and the grey-coated Hooded Crow stretches across Central Europe. Previous studies have shown that their distinct plumage patterns are controlled by two interacting genes: a genomic region on chromosome 18 and the NDP gene on chromosome 1 (see this blog post for details). Building on this knowledge, the researchers developed a two-locus model to capture the underlying genetics. They represented the variants on chromosome 18 with capital letters (D = dark, L = light) and the variants of the NDP gene with lowercase letters (d = dark, l = light). The interaction between these variants (known as epistasis) produced seven distinct plumage phenotypes.

When the researchers compared the model predictions with real-world data, they found strong evidence for this epistatic genetic architecture. In contrast, a purely additive model – where each gene contributes independently and the total effect is simply the sum of individual effects – fitted the data poorly. In other words, the observed plumage patterns are not just a matter of adding up gene effects. They depend on how the genes interact. One gene can enhance, mask, or even alter the effect of another.

An overview of the seven plumage phenotypes and the underlying genetic variants. Capital letters refer to the locus on chromosome 18, whereas small letters correspond to the NDP gene. From: Metzler et al. (2021).

Assortative Mating

Next, the researchers examined how mate choice influences the dynamics of the hybrid zone. They modeled assortative mating, where individuals prefer partners that share their own appearance. In this scenario, hybrids are at a disadvantage because their rarer, intermediate phenotype makes it harder to find similar mates (a form of postzygotic isolation). This setup produced results that fit the empirical data much better than simpler models, which considered only three broad categories (black, hooded, and hybrid) or assumed no fitness costs for rare phenotypes.

Additional analyses showed that assortative mating could arise either through self-reference or imprinting on the appearance of a parent. Together, these findings highlight the complex interplay between prezygotic (assortative mating) and postzygotic (fitness cost for rare phenotypes) isolation mechanisms in hybrid zones (see also this blog post).

Comparison between the empirical data (Figure A) and the main mathematical model (Figure B). The lines represent the frequency of the two genetic loci across the hybrid zone. The matrix shows the preference scores between different genotypes. From: Metzler et al. (2021).

A Disappearing Hybrid Zone

Overall, the modeling exercise confirmed the epistatic interaction between two genetic loci and revealed “a moderate degree of assortative mating inducing pre- and postzygotic isolation via positive frequency-dependent selection”. With this foundation in place, the researchers projected their model into the future to see how the hybrid zone might develop. Interestingly, their results suggested that the hybrid zone will eventually disappear, either because one color morph completely takes over or because the differences between the two forms gradually fade away. Let’s explore one scenario.

Because of the epistatic genetic architecture, several different gene combinations can produce the all-black plumage of Carrion Crows. This means that early on, many hybrids will also appear dark, giving them a mating advantage. As a result, dark morphs become even more common, and the genetic variants responsible for dark plumage spread eastward, slowly shifting the hybrid zone in that direction (arrow C in the figure below).

However, the “light” alleles can move westward without being strongly selected against, slowly mixing into the dark population. Over time, this gradual introgression reduces the overall frequency of “dark” alleles near the hybrid zone (arrows D and E). As the number of dark birds declines, the advantage of being dark fades, and eventually, the movement of the hybrid zone stops. In the long run, the balance tips in the opposite direction: lighter morphs gain the upper hand, pushing the hybrid zone back westward (arrow G). After thousands of generations, the dark alleles are lost entirely, leaving only the lighter Hooded Crows across the region.

It’s a fascinating prediction, but only time will tell whether this scenario will unfold in nature.

According to the main model, the hybrid zone first shifts eastward, then reverses its direction westward with carrion crows eventually going extinct. From: Metzler et al. (2021).

References

Metzler, D., Knief, U., Peñalba, J. V., & Wolf, J. B. (2021). Assortative mating and epistatic mating-trait architecture induce complex movement of the crow hybrid zone. Evolution, 75(12), 3154-3174.

Featured image: Hooded Crow in Berlin © Pelican | Wikimedia Commons

Hybridization between Yellow Cardinal and Diuca Finch aligns with Darwin’s Corollary to Haldane’s Rule

Although there are other explanations for the observed patterns.

Most evolutionary biologists are familiar with Haldane’s Rule, which states that “when in the F₁ offspring of two different animal races one sex is absent, rare, or sterile, that sex is always the heterogametic sex.” In this context, heterogametic refers to individuals with two different sex chromosomes, such as males in mammals (XY) and females in birds (ZW). Remarkably, this prediction has proven to be highly accurate. Numerous review papers – including one of my own – have found consistent empirical support for Haldane’s Rule.

Less well known, however, is an intriguing extension of this pattern known as Darwin’s Corollary to Haldane’s Rule. This principle describes the observation that reciprocal crosses between two species often produce hybrids with differing levels of viability or fertility. For instance, a cross between species A (female) and species B (male) may yield less fit offspring than the reciprocal cross between species B (female) and species A (male). Such asymmetries in hybrid fitness are thought to arise from factors such as mito-nuclear incompatibilities and other epistatic interactions among specific genes.

A recent study in the journal Ecology and Evolution presents a nice example of hybridization between two bird species illustrating both Haldane’s Rule and Darwin’s Corollary.

Three Hybrids

Marisol Domínguez and her colleagues examined the genetic make-up of putative hybrids between the Yellow Cardinal (Gubernatrix cristata) and the Diuca Finch (Diuca diuca). Using genomic data, they identified two first-generation hybrids and one backcross with the Yellow Cardinal. Interestingly, all three admixed individuals were males. Analyses of mitochondrial DNA (which is maternally inherited) showed that “the three hybrids clustered within the Yellow Cardinal lineage, indicating that hybridization events occurred between female Yellow Cardinals and male Diuca Finches or male F1 hybrids.”

Genomic analyses uncovered three admixed individuals (indicated in red) between Yellow Cardinal (yellow) and Diuca Finch (gray). From: Domínguez et al. (2025).

A Scarcity of Males

Although the sample size is small (with only three individuals), the observed patterns appear consistent with both Haldane’s Rule and Darwin’s Corollary to Haldane’s Rule. First, all admixed individuals were males. In birds, female hybrids are the heterogametic sex (ZW) and are therefore expected to exhibit reduced fitness compared to male hybrids. The absence of female hybrids thus aligns with the prediction of Haldane’s Rule. Second, all hybrids possessed mitochondrial DNA from the Yellow Cardinal, indicating that each cross involved a female Yellow Cardinal and a male Diuca Finch. The absence of the reciprocal cross suggests that such pairings may be unviable, consistent with the asymmetries predicted by Darwin’s Corollary.

However, there is an alternative explanation for the asymmetric crosses between female Yellow Cardinals and male Diuca Finches. The Yellow Cardinal is among the most sought-after species in the illegal bird trade. Extensive capture of these birds may result in a scarcity of males, thereby constraining the mating options available to females. As a consequence, female Yellow Cardinals may pair with Diuca Finches simply due to limited availability of conspecific mates. This interpretation aligns with the sexual selection hypothesis for unidirectional hybridization, which proposes that females of the rarer species may mate with heterospecific males from a more common species when males of their own species become scarce.

While these findings are intriguing, it is important to note that the conclusions are based on a very limited sample size. With only three hybrid individuals detected, any interpretation should be made with caution. Nevertheless, even such small datasets can offer valuable insights into classic evolutionary principles (such as Haldane’s Rule and its corollary), highlighting the power of genomics to uncover hidden patterns in natural hybridization.

References

Domínguez, M., Arantes, L. S., Lavinia, P. D., Bergjürgen, N., Casale, A. I., Fracas, P. A., et al. (2025). Genomics reveal population structure and intergeneric hybridization in an endangered South American bird: Implications for management and conservation. Ecology and Evolution, 15(1), e70820.

Turelli, M., & Moyle, L. C. (2007). Asymmetric postmating isolation: Darwin’s corollary to Haldane’s rule. Genetics, 176(2), 1059-1088.

Wirtz, P. (1999). Mother species–father species: unidirectional hybridization in animals with female choice. Animal behaviour, 58(1), 1-12.

Featured image: Yellow Cardinal (Gubernatrix cristata) © Hector Bottai | Wikimedia Commons

Gene duplication might help Tree Sparrows adapt to industrial pollution

But how do these duplicated genes contribute to local adaptation?

One of the most fascinating engines of evolutionary innovation is gene duplication, the event where an organism ends up with extra copies of a particular gene. At first glance, this might seem redundant, but extra copies can be a huge advantage.

In some cases, the duplicated gene can take on a new function, as seen in the globin gene family, which diversified to fine-tune oxygen transport in different tissues and at different life stages. Two other notable examples concern the opsin genes that enable color vision in primates, which arose through duplications of light-sensitive receptor genes, and the antifreeze proteins in Antarctic fish, which evolved from duplicated digestive enzyme genes.

In other cases, simply having more copies of the same gene can be beneficial. For instance, plants often carry multiple copies of photosynthesis-related genes to boost productivity, and yeast cells with extra sugar-metabolizing genes can grow faster in rich environments. A similar situation might apply to a Tree Sparrow (Passer montanus) population in China where duplication of a particular gene appears to help these birds tolerate heavy metal pollution.

A Proliferation of PIMs

The Tree Sparrow is a common resident in the city of Baiyin which has been heavily contaminated with heavy metals from extensive mining and smelting activities. Such pollution is known to impair certain sperm traits, such as sperm count, viability, and motility. Interestingly, males from the Baiyin population have longer and faster sperm than those from a nearby unpolluted site (Liujiaxia), suggesting a possible adaptive response to environmental stress. However, the molecular mechanisms underlying these differences are still unknown.

In a recent Molecular Ecology study, Shengnan Wang and colleagues compared the genetic make-up of Tree Sparrows from polluted and unpolluted sites. Their analyses of genes under positive selection and genes showing different expression patterns between the two populations both converged on the same candidate: PIM1, a protein kinase gene that helps regulate cell growth and survival. Remarkably, further investigation revealed a massive expansion of this gene family in Tree Sparrows. The genome assembly contained 449 predicted PIM1 genes, including 142 complete copies with an intact kinase domain (suggesting that many of them are likely functional).

The distribution of duplicated PIM-genes (and several linked genes) across the Tree Sparrow genome. From: Wang et al. (2023).

Experimental Challenges

The duplicated PIM1 genes were often found next to genes from several other families, although it remains unclear whether these neighboring genes have any functional connection to PIM1. Because PIM1 showed strong overexpression in the testes (suggesting a potential role in sperm evolution), the researchers decided to focus on this gene in greater detail. They conducted an inhibition experiment, giving some birds a daily dose of a small-molecule compound designed to block PIM1 kinase activity. However, no clear differences emerged between the treated and control groups, which the authors attributed to methodological issues rather than the absence of a true biological effect.

In conclusion, the negative results of inhibition experiment could be dismissed as resulting from methodological limitation. We think some more advanced and effective technologies such as gene editing should be applied for further exploration of genetic function and regulation of PIM1.

Plenty of questions remain about the role of PIM1 (and its neighboring genes) in shaping sperm evolution under polluted conditions. Unraveling how these genetic changes contribute to adaptation will require much more work. If only we could duplicate the number of researchers studying these mysteries…

References

Wang, S., Zhang, Y., Yang, W., Shen, Y., Lin, Z., Zhang, S., & Song, G. (2023). Duplicate genes as sources for rapid adaptive evolution of sperm under environmental pollution in tree sparrow. Molecular Ecology, 32(7), 1673-1684.

Featured image: Tree Sparrow (Passer montanus) © Peter P. Othagoer | Wikimedia Commons

Habitat type shapes genetic population structure in Amazonian birds

Species in dynamic environments show higher levels of gene flow.

Clear communication is essential in science. Yet, scientific terms can sometimes mean different things depending on the context, potentially causing confusion. Take the concept of dispersal. In different studies, it has been used to describe both the movement of individuals and the movement of alleles. But these two processes are not always the same. The movement of individuals doesn’t necessarily lead to the movement of alleles, because not every individual that reaches a new location will reproduce and pass on its genes to the local population.

Although the dispersal of individuals doesn’t always lead to gene flow, dispersal ability can still shape a species’ genetic structure over evolutionary timescales. In fact, many studies have found an inverse relationship between dispersal ability and population genetic structure. Species with high dispersal ability tend toward panmixia (where individuals interbreed freely across populations), while species with limited dispersal ability generally show greater genetic subdivision.

Of course, the potential for gene flow isn’t solely determined by dispersal ability. The surrounding environment plays an important role in creating or restricting opportunities for movement. This aspect was beautifully illustrated in a recent Molecular Ecology study that compared the genetic population structure of Amazonian birds living in three distinct habitat types.

Environmental Stability

Oscar Johnson and his colleagues investigated the genetic population structure of 66 bird species across three habitats that differ in their environmental stability: (1) riverine islands, (2) seasonally flooded forests, and (3) upland forests. Riverine islands are highly dynamic as they form, erode, and shift over time as rivers change course. This constant reshaping creates opportunities for frequent dispersal, because birds must move between islands to track suitable habitat. Seasonally flooded forests, by contrast, experience regular but predictable cycles of flooding and drying, providing a moderate level of environmental change. Upland forests, the most stable of the three, are rarely disturbed by flooding and offer a relatively permanent habitat.

The researchers uncovered a clear pattern: birds of upland forests showed greater population structure than those of flooded forests, and birds of flooded forests showed greater structure than those of riverine islands (see figure below). In other words, the more dynamic the habitat, the weaker the genetic differentiation among populations. This pattern was further supported by measures of gene flow. Species inhabiting the ever-changing riverine islands exhibited higher levels of gene flow, consistent with greater dispersal in these environments.

Population genetic structure is shaped by the environmental stability. Dynamic habitats, such as riverine islands, show less population subdivision compared to stable habitats, such as upland forests. From: Johnson et al. (2023).

Morphological Traits

Interestingly, the researchers found no clear relationship between genetic structure and morphological proxies of dispersal ability, such as wing shape. This result brings us back to the key distinction between the movement of individuals and the movement of alleles. Morphological traits might help predict how far or how often individuals move over short timescales (see for example Sheard et al. 2020). But over evolutionary timescales, other factors – such as the availability and stability of suitable habitats – play a much larger role in determining how both individuals and genes spread across landscapes. Moreover, genetic data can capture the echoes of rare dispersal events, which may occur too infrequently to be reflected in morphological traits or directly observed in the field. In the end, the genetic structure of Amazonian birds mirrors both their capacity for movement and the ever-changing environments they inhabit.

References

Johnson, O., Ribas, C. C., Aleixo, A., Naka, L. N., Harvey, M. G., & Brumfield, R. T. (2023). Amazonian birds in more dynamic habitats have less population genetic structure and higher gene flow. Molecular Ecology, 32(9), 2186-2205.

Sheard, C., Neate-Clegg, M. H., Alioravainen, N., Jones, S. E., Vincent, C., MacGregor, H. E., Bregman, T. P., Claramunt, S. & Tobias, J. A. (2020). Ecological drivers of global gradients in avian dispersal inferred from wing morphology. Nature Communications, 11(1), 2463.

Featured image: Spot-backed Antbird (Hylophylax naevius) © Hector Bottai | Wikimedia Commons