Do plants experience less introgression than animals?

A recent study suggests faster evolution of reproductive barriers in plants than in animals.

Which taxonomic group is more prone to hybridization: plants or animals? A 2005 review by James Mallet offered one of the earliest comparisons. He estimated that at least 25% of vascular plant species and 10% of animal species engage in hybridization and potential introgression. But he added an important nuance: animals show phylogenetic hotspots of hybridization that far exceed the average 25% rate seen across vascular plants. For example, three-quarters of British duck species and all four British game birds hybridize with at least one other species. Likewise, passion-flower butterflies (26%), birds-of-paradise (42%), American warblers (24%), and tits (29%) all show hybridization probabilities that are comparable to those of the average for vascular plants. Overall, plants still appear to hybridize more frequently than animals (on a species level).

A contrasting perspective came from a 2006 Nature paper by Loren Rieseberg, Troy Wood, and Eric Baack. Analyzing morphological and crossing relationships across more than 400 genera of plants and animals, they found that plant taxa were more likely than animal taxa to represent reproductively independent lineages (i.e. less prone to hybridize). However, their results also revealed substantial variation within both kingdoms. Ferns and their allies showed the highest levels of reproductive independence, whereas birds exhibited the lowest, highlighting the heterogeneity of hybridization patterns across taxonomic groups.

Taken together, the evidence suggests that hybridization rates vary widely across taxonomic groups, making a simple plant–animal comparison somewhat misleading. Nonetheless, a recent study in Science took a genomic approach to quantify patterns of introgression within these two kingdoms.

The ABC of gene flow

François Monnet and colleagues analyzed genomic data from 61 animal species pairs and 280 plant species pairs. Using an approximate Bayesian computation (ABC) framework, they inferred whether each pair showed signs of recent gene flow or not. This approach allowed them to classify species pairs as either “isolated” or “still exchanging genes” across a gradient of genetic divergence. The statistical analyses showed that genetic exchange stops at lower levels of genetic divergence in plants than in animals. In plants, the probability that two lineages remain connected by gene flow drops below 50% at roughly 0.3% net divergence. In animals, however, this inflection point occurs much later, at around 1.5% divergence. The results also suggest that plants shift more rapidly from having no barriers to gene flow to having semipermeable ones.

Logistic regressions show that animals (orange) stop to exchange genes at high levels of genetic divergence compared to plants (green). From: Monnet et al. (2025).

Apples and Oranges

Does this finding finally settle the debate over whether plants or animals hybridize more? I am not convinced. Although the analytical framework is solid, the underlying dataset raises some concerns. The animal dataset, in particular, mixes various invertebrates, mammals, reptiles, and birds into a single category. Given the enormous biological differences among these groups, treating them as one coherent unit (even when correcting for phylogenetic relatedness) feels problematic. Comparing this assortment of animals with a similarly broad assemblage of plants is not just comparing apples and oranges. It amounts to comparing two mixed bags of fruits and vegetables.

What I would like to see is the same analysis performed within taxonomic groups, followed by a statistical comparison of their respective inflection points. If every major animal group consistently exceeds the inflection point observed for plants, that would represent strong evidence for the pattern in this study. More likely, however, I would expect to find substantial variation among lineages. Mammals will probably lose the ability to hybridize at relatively low genetic divergences, whereas birds and amphibians appear capable of exchanging genes over much longer evolutionary timescales. This expectation comes from the classic work by Prager and Wilson (1975), who found that hybridizing bird and frog species pairs diverged, on average, about 21-22 million years ago, while hybridizing placental mammals typically diverged only 2–3 million years ago.

Finally, a closer look at the birds included in the new dataset (my own “pet” taxonomic group) reinforces my concerns. The avian sample consists of population pairs from species such as the Eurasian teal (Anas crecca), Red-backed Fairywren (Malurus melanocephalus), Eurasian Blue Tit (Cyanistes caeruleus), and a few penguin species (including rockhopper penguins in the genus Eudyptes and the king penguin Aptenodytes patagonicus). This selection is hardly a representative sample of avian diversity, especially considering the extensive literature documenting hybridization across many other bird lineages.

References

Mallet, J. (2005). Hybridization as an invasion of the genome. Trends in Ecology & Evolution, 20(5), 229-237.

Monnet, F., Postel, Z., Touzet, P., Fraïsse, C., Van de Peer, Y., Vekemans, X., & Roux, C. (2025). Rapid establishment of species barriers in plants compared with that in animals. Science, 389(6765), 1147-1150.

Prager, E. M., & Wilson, A. C. (1975). Slow evolutionary loss of the potential for interspecific hybridization in birds: a manifestation of slow regulatory evolution. Proceedings of the National Academy of Sciences, 72(1), 200-204.

Rieseberg, L. H., Wood, T. E., & Baack, E. J. (2006). The nature of plant species. Nature, 440(7083), 524-527.

Featured image: Asian Slim Damselfly (Aciagrion occidentale) © Jee & Rani Nature Photography | Wikimedia Commons

Human-induced hybridization between Green Jay and Blue Jay

Recent range expansions probably culminated in a hybridization event.

Numerous friends and colleagues have sent me news articles about the so-called “grue jay”, a recently documented hybrid between the Blue Jay (Cyanocitta cristata) and the Green Jay (Cyanocorax yncas) in Texas. Most media outlets covered this unusual case well, although a few reporters made basic mistakes (no, it is not a hybrid species).

Beyond the media attention, this avian hybrid provides a nice example of how anthropogenic land-use change and climate change can shift species distributions in ways that facilitate hybridization. Indeed, in my review on hybridization in the Anthropocene, I already suggested that such events are likely to increase: “As human-mediated habitat modifications continue to change the environmental and sensory conditions for numerous taxa, more hybridization events are expected to arise in the near future.”

Range Expansion

In 1965, the Zoological Park in Fort Worth (Texas) reported a captive hybrid between these two species. The authors remarked that “The possibility of the Green Jay and the Blue Jay occurring naturally together during the breeding season is remote, so that hybrids are not expected in the wild.” At the time of writing, these species were indeed separated by about 200 km.

Since then, however, much has changed. In their recent paper, Brian Stokes and Timothy Keitt used Ecological Niche Models to evaluate both current and future ranges, revealing a clear region of overlap. Supporting this pattern, co-observations on eBird have steadily increased from 2000 to 2023. Both species are also frequently seen at artificial feeding stations, adding yet another anthropogenic element to the equation (similar to hummingbirds).

Ecological Niche Modelling of the Green Jay (green) and Blue Jay (blue) ranges revealed an area of overlap (orange). From: Stokes & Keitt (2025).

Supporting Evidence

The hybrid individual described in this study was first reported in the Facebook group TEXBIRDS. Its vocalizations and morphological traits already hinted at a hybrid identity, but genomic analyses ultimately confirmed it.

The hybrid produced vocalizations similar to common Blue Jay calls, usually in response to Blue Jay vocalizations and activity. The hybrid also produced bill-clicks and two-tone low rattling vocalizations typical of Green Jays in Texas. Overall, the hybrid’s plumage morphology was codominant intermediate, displaying distinct traits from both Blue Jay and Green Jay, rather than a blended phenotype.

The mitochondrial DNA matched with Green Jays from Texas, while the nuclear DNA showed a clear mixture of Cyanocitta and Cyanocorax lineages. Together, these lines of evidence strongly indicate that the bird is an F1 cross produced by a female Green Jay and a male Blue Jay. The first of many?

References

Ottenburghs, J. (2021). The genic view of hybridization in the Anthropocene. Evolutionary Applications, 14(10), 2342-2360.

Pulich, W. M., & Dellinger, R. M. (1981). An example of a hybrid Green jay× Blue jay. The Wilson Bulletin, 538-540.

Stokes, B. R., & Keitt, T. H. (2025). An Intergeneric Hybrid Between Historically Isolated Temperate and Tropical Jays Following Recent Range Expansion. Ecology and Evolution, 15(9), e72148.

Featured image: The hybrid jay (middle) with both parental species © Travis Maher (Cornell Lab of Ornithology/Macaulay Library)/Brian Stokes (University of Texas)/Dan O’Brien (Cornell Lab of Ornithology/Macaulay Library)

Why did Darwin compare pigeons and horses in the Origin of Species?

A clever argument to support common descent.

Although I have studied evolutionary biology for nearly fifteen years – as both a student and a professional scientist – I had never read On the Origin of Species from cover to cover. During the Christmas holidays, I finally decided to explore this groundbreaking work in detail. Despite its Victorian prose, the book remains remarkably accessible and rich with intriguing ideas. As I worked my way through the chapters, I became inspired to write a series of blog posts related to The Origin of Species, each starting from a specific quote or concept and developing it in light of our current understanding of evolution. This first blog post focuses on a striking comparison in Chapter V, “Laws of Variation,” where Darwin draws parallels between domesticated pigeon breeds and several species within the horse genus.

Multiple Ancestors

Before we can compare pigeons and horses, we first need to understand the origin of domesticated pigeon breeds. In Darwin’s time, most naturalists believed that each pigeon breed descended from a distinct wild species. Darwin challenged this view in the first chapter (“Variation Under Domestication”), where he presented compelling evidence that “all our domestic breeds are descended from the rock-pigeon or Columba livia with its geographical sub-species.” Let’s briefly review the main arguments supporting this single-ancestor hypothesis.

First, Darwin argues that it is extremely unlikely that each domestic pigeon breed descended from a distinct wild species. This scenario would require the existence of seven or eight separate ancestral species. If this were the case, where are these wild ancestors today? Have they all gone extinct? As Darwin himself notes, “the supposed extermination of so many species having similar habits with the rock-pigeon seems a very rash assumption.” Moreover, many of the distinctive traits found in domestic pigeon breeds have no counterparts in any known wild species.

We may look in vain through the whole great family of Columbidae for a beak like that of the English carrier, or that of the short-faced tumbler, or barb; for reversed feathers like those of the Jacobin; for a crop like that of the pouter; for tail-feathers like those of the fantail.

Accepting multiple wild ancestors would therefore require us to assume not only that early humans deliberately (or accidentally) selected a series of exceptionally abnormal species, but also that all of these species subsequently became extinct or remain entirely unknown. Taken together, this chain of assumptions is highly implausible.

An overview of different pigeon breeds. From: Karl Wanger (1909) Meyers Großes Konversations-Lexikon | Wikimedia Commons

Fertile Hybrids

In addition to arguing against multiple ancestral species, Darwin also offers positive evidence in support of a single-ancestor hypothesis. In particular, he draws on observations of both the fertility and morphology of hybrids produced by crossing different pigeon breeds. Based on his own experiments, Darwin reports that “the hybrids or mongrels from between all the breeds of the pigeon are perfectly fertile,” a finding that strongly suggests close relatedness among the breeds.

Morphological evidence further reinforces this statement. Darwin observed that hybrid offspring often display traits characteristic of the ancestral rock pigeon, even when these traits are absent in the parent breeds. He concluded that “we can understand these facts, on the well-known principle of reversion to ancestral characters, if all the domestic breeds are descended from the rock-pigeon.”

Counting Stripes

The final argument supporting a single ancestral origin for pigeon breeds – reversion to ancestral characters – also plays a pivotal role in Darwin’s comparison with horses. In Chapter V, “Laws of Variation,” Darwin extends this reasoning to patterns of variation in both wild and domesticated equine species. He begins with a detailed survey of asses and horses that exhibit striping on the legs or along the back. Rather than reviewing all of his examples here, I will focus on a representative passage that nicely illustrates Darwin’s determination to amass as much empirical evidence as possible.

With respect to the horse, I have collected cases in England of the spinal stripe in horses of the most distinct breeds, and of all colours; transverse bars on the legs are not rare in duns, mouse-duns, and in one instance in a chestnut; a faint shoulder-stripe may sometimes be seen in duns, and I have seen a trace in a bay horse. My son made a careful examination and sketch for me of a dun Belgian carthorse with a double stripe on each shoulder and with leg-stripes. I have myself seen a dun Devonshire pony, and a small dun Welsh pony has been carefully described to me, both with three parallel stripes on each shoulder.

Darwin next considers the “effects of crossing the several species of the horse genus.” Once again, he marshals numerous examples of hybrids that exhibit striping on different parts of the body. In one striking anecdote, he recalls, “I once saw a mule with its legs so much striped that anyone might have thought that it was a hybrid zebra.” He further describes striping in hybrids between an ass and a zebra (“whose legs were much more plainly barred than the rest of the body”) as well as in crosses between a chestnut mare and a male quagga, and between an ass and a hemionus (now known as the onager).

A hybrid between an ass and a zebra. From: ArtsCult.com | Wikimedia Commons

A Common Parent

Now, we are finally in a position to directly compare pigeons and horses. By invoking the principle of reversion to ancestral characters, Darwin builds a compelling case for the common ancestry of all species within the horse genus. He explicitly draws the reader’s attention back to domestic pigeon breeds, which (despite their striking diversity) are known to descend from a single ancestral species. In that case, the occasional reappearance of ancestral traits in particular individuals or in hybrids is readily explained by shared descent. Darwin argues that the same logic applies to horses: the recurrence of striped patterns reflects common ancestry as well, although unfolding over longer evolutionary timescales.

Call the breeds of pigeons, some of which have bred true for centuries, species; and how exactly parallel is the case with that of the species of the horse genus! For myself, I venture confidently to look back thousands on thousands of generations, and I see an animal striped like a zebra, but perhaps otherwise very differently constructed, the common parent of our domestic horse (whether or not it be descended from one or more wild stocks) of the ass, the hemionus, quagga, and zebra.

A Mere Mockery and Deception

It is fascinating to see how Darwin weaves together multiple lines of evidence (each grounded in a wealth of careful observations) to make a compelling case for the common descent of morphologically diverse species. For me, his writing offers a masterclass in how to construct a rigorous argument for or against a scientific hypothesis. At the end of Chapter V, Darwin contrasts his explanation with the prevailing view of the time (independent creation), underscoring the power of his reasoning. It is a fitting and powerful conclusion to both the chapter and this blog post.

He who believes that each equine species was independently created, will, I presume, assert that each species has been created with a tendency to vary, both under nature and under domestication, in this particular manner, so as often to become striped like the other species of the genus; and that each has been created with a strong tendency, when crossed with species inhabiting distant quarters of the world, to produce hybrids resembling in their stripes, not their own parents, but other species of the genus. To admit this view is, as it seems to me, to reject a real for an unreal, or at least for an unknown cause. It makes the works of God a mere mockery and deception; I would almost as soon believe with the old and ignorant cosmogonists, that fossil shells had never lived, but had been created in stone so as to mock the shells now living on the seashore.

References

Darwin, C. (1997). On the origin of species. Wordsworth Editions. (Original work published 1859)

Featured image: Common Pigeon (Columba livia) © Satdeep Gill | Wikimedia Commons

One gene to rule them all: Reshuffling of genetic variants explains plumage patterns in wheatears

Introgression drives parallel evolution of plumage coloration.

Several years ago, I wrote a blog post on the parallel evolution of plumage patterns in Oenanthe wheatears, based on a genetic study showing that distantly related species display remarkably similar coloration. However, the underlying mechanism driving this parallel evolution remained unresolved. In that blog post, I outlined several possible explanations and wondered “whether hybridization has influenced the evolution of plumage patterns in these species.”

Unrelated species might use genetic material that was already present in a distant ancestor. Or traits might be transferred from one species to another by hybridization. Or similar mutations might have arisen independently. Unfortunately, the present study cannot confidently discriminate between these scenarios.

A new study published in Science has now provided a clear answer. Through an impressive amount of work, Dave Lutgen and his colleagues unraveled the genetic basis of several plumage traits, demonstrating how hybridization has shuffled the relevant genetic variation across several species. This process accounts for the strikingly parallel plumage patterns among distantly related wheatears.

Three Traits, One Gene

The plumage patterns of wheatears can be distilled into a combination of three color traits: throat, mantle, and neck. Using nearly 400 genome sequences, the researchers were able to pinpoint the genetic basis of each trait. The white throat coloration traces back to mutations in the ASIP gene and the presence of an LTR retrotransposon (a mobile genetic element that “jumps” around the genome). According to the authors, “the throat LTR up-regulates ASIP expression, whereas the protein-changing throat SNP variation determines throat coloration.” Interestingly, this LTR–ASIP combination is absent in the white-throated vittata subspecies of the Pied Wheatear (Oenanthe pleschanka), suggesting that a different genetic variant must regulate ASIP expression in these birds.

Mantle coloration is controlled by a cluster of genetic variants (referred to as the “mantle loci”) located roughly 45,000 base pairs upstream of ASIP. These variants display an additive architecture, meaning their effects accumulate to shape the final phenotype. Put simply: the more “white” variants a bird carries, the whiter its mantle will be. Analyses of neck coloration revealed associations with the same set of genetic variants (albeit more weakly), indicating that neck coloration is largely an extension of mantle coloration.

The combination of mutations in the ASIP-gene and the insertion of a LTR retrotransposon explains the occurrence of a white throat in some wheatear species. Interestingly, the LTR retrotransposon is absent in the vittata taxon, even though it shows a white-throated phenotype. From: Lutgen et al. (2025).

Cointrogression

Now that we understand the genetic underpinning of these traits, we can explore their evolutionary history. Time for hybridization to enter the picture. A suite of sophisticated population genetic analyses uncovered the following scenario.

Originally, all members of the species complex appear to have had black throat and mantle coloration. White mantle coloration first evolved in the Eastern Black-eared Wheatear (O. melanoleuca) through mutations located upstream of ASIP, which became fixed under positive selection. Once this white-mantled genetic background was established, additional protein-coding changes in ASIP, combined with the insertion of an LTR retrotransposon upstream of the gene, produced the white-throated phenotype in this species.

White throat coloration later introgressed into the Western Black-eared Wheatear (O. hispanica), where it is maintained as a balanced polymorphism. Because these throat-associated variants are genetically linked to the mantle region, the white mantle variation probably cointrogressed into Western Black-eared Wheatear. In the Pied Wheatear, hybridization with the Eastern Black-eared Wheatear resulted in the introgression of white coding variation at ASIP, but without the accompanying exchange of the “mantle loci” located upstream of ASIP. The outcome is a white-throated species with a black mantle.

The evolutionary story of plumage coloration in wheatears. The white plumage traits originated in O. melanoleuca (red) and introgressed into O. hispanica (yellow) and O. pleschanka (blue). From: Lutgen et al. (2025).

Mosaic Phenotypes

Understanding the genetic architecture of these plumage traits also provides insights into the diversity of phenotypes in hybrid zones. Ongoing hybridization and backcrossing culminate in the recombination of the genetic variants in and around the ASIP-gene. One of my favorite figures in the paper nicely illustrates how different haplotypes map onto different plumage phenotypes. Take your time to go through these examples and appreciate the wonderful variation in plumage patterns. All you need is one gene and some hybridization.

An overview of the relationship between different plumage phenotypes and the underlying genetics. The ovals represent the black and white “mantle loci” whereas the red colors correspond to the ASIP-variants and the LTR retrotransposon. From: Lutgen et al. (2025).

References

Lutgen, D., Peona, V., Chase, M. A., Kakhki, N. A., Lammers, F., de Souza, S. G., … & Burri, R. (2025). A mosaic of modular variation at a single gene underpins convergent plumage coloration. Science, 390(6770), eado8005.

Schweizer, M., Warmuth, V., Alaei Kakhki, N., Aliabadian, M., Förschler, M., Shirihai, H., Suh, A. & Burri, R. (2020). Parallel plumage colour evolution and introgressive hybridization in wheatears. Journal of Evolutionary Biology, 32(1), 100-110.

Featured image: Eastern Black-eared Wheatear (Oenanthe melanoleuca) © Frank Vassen | Wikimedia Commons