When 1 + 1 = 3: Hybrid speciation in birds

Exploring the origin of hybrid bird species.

Whenever an interesting hybrid combination is reported, people ask the question: Will this hybrid evolve into a new species? The answer is almost always a resounding no. The origin of a new species through hybridization – hybrid speciation – requires very specific conditions. First of all, you need several hybrid individuals that can breed with each other. In some cases, hybridization is too rare to sustain a population of hybrids. And the hybrids should be reproductively isolated from their parental species, allowing the hybrids to carve out their own independent evolutionary trajectory. But despite these restrictions, hybrid speciation does occur. Hybrid life finds a way.

Three Criteria

How to recognize a hybrid species? In 2014, Molly Schumer and her colleagues put forward three criteria to show that a species is of hybrid origin, namely (1) reproductive isolation of hybrid lineages from the parental species, (2) evidence of hybridization in the genome, and (3) evidence that this reproductive isolation is a consequence of hybridization. A survey of the literature revealed that only four species (three sunflowers and one butterfly) fulfilled all three criteria. The main bottleneck was the third criterion. The first two criteria make intuitive sense, but the third one does seem too strict. Why should hybridization directly lead to reproductive isolation before we can talk about a hybrid species? Other evolutionary mechanisms could lead to reproductive isolation between the hybrids and their parental species.

Several researchers indicated that the third criterion was too strict, leading to the exclusion of potentially interesting cases of hybrid speciation. In 2018, I proposed a possible solution to this clash of criteria by discriminating between two types of hybrid speciation: type I where reproductive isolation is a direct consequence of hybridization and type II where it is the by-product of other processes. Applying this approach to birds revealed that the majority of putative hybrid species belongs to the type II group. Specifically, reproductive isolation often evolved when the hybrid population became geographically isolated from the parental species. A combination of hybrid speciation and classic allopatric speciation.

An overview of how many putative hybrid species follow the three criteria of Schumer et al. (2014).

Italian Insights

This academic debate about criteria sounds rather abstract. Let’s explore an actual case to make it more tangible: the Italian Sparrow (Passer italiae). Morphologically, this small passerine resembles a cross between House Sparrow (P. domesticus) and Spanish Sparrow (P. hispaniolensis). Indeed, Jo Hermansen and his colleagues noted that:

Male Italian sparrows have a chestnut-coloured crown and nape, and white cheeks similar to the Spanish sparrow (house sparrows have a broad, grey band on the crown and nape, and grey cheeks), but a small bib and a brown-streaked back similar to the house sparrow (Spanish sparrows have a large black bib that extends all along the body flanks and a black- and yellow-streaked back). Interestingly, male F1-hybrids between house sparrows and Spanish sparrows resemble Italian sparrows.

The morphological intermediacy of the Italian Sparrow was confirmed by genetic analyses. As expected, the genome of the Italian Sparrow is a mixture of the House Sparrow (ca. 60%) and the Spanish Sparrow (ca. 40%). The hybrid speciation event probably occurred less than 10,000 years ago when House Sparrows expanded across Europe and came into contact with the Spanish Sparrow. The resulting hybrid population became geographically isolated on the Italian peninsula and adjacent islands, eventually evolving into the Italian Sparrow. A nice example of a type II hybrid species.

Genomic analyses of the Italian Sparrow revealed that it is a mixture of House Sparrow (blue) and Spanish Sparrow (red). The origin of this hybrid species probably involved geographical isolation on the Italian Peninsula and neighboring islands. From: Elgvin et al. (2017).

Big Bird

A scenario of hybrid speciation with an allopatric phase is not only limited to the Italian Sparrow. Another example concerns the Audubon’s Warbler (Setophaga auduboni), a hybrid between Myrtle Warbler (S. coronata) and Black-fronted Warbler (S. nigrifrons). And there is the Golden-crowned Manakin (Lepidothrix vilasboasi), a hybrid between Opal-crowned Manakin (L. iris) and Snow-capped Manakin (L. nattereri). Does this mean that all hybrid bird species belong to the type II group? Well, there is always an exception that proves the rule.

A beautiful example of a type I hybrid bird species – where reproductive isolation is directly caused by hybridization – is the so-called “Big Bird” on the Galapagos Islands. In 1981, a large Cactus Finch (Geospiza conirostris) arrived on the island Daphne Major and mated with a female Medium Ground Finch (G. fortis). The resulting offspring only bred with each other and as such established a new hybrid lineage on the island. The hybrids have an intermediate beak morphology and produce a distinctive song. These traits contribute to reproductive isolation from at least one parental species (G. fortis) because of differences in song and beak morphology. Reproductive isolation is thus directly due to hybridization.

The extensive pedigree of the hybrid lineage on the island Daphne Major. Hybridization between a female Medium Ground Finch (green) and a male Cactus Finch (blue) gave rise to a population of hybrids that only mated among themselves. From: Lamichhaney et al. (2018).

Extreme Hybrids

The hybrid species discussed above show intermediate morphology. The Italian Sparrow has plumage patterns of both parental species, and the “Big Bird” lineage sports an intermediate beak. In some cases, however, hybrids exhibit extreme phenotypes that surpass the range of the parental species. Think of the excessive size the hybrid ligers compared to their parents, lions and tigers.

Some researchers have used this phenomenon – known as transgressive segregation – to pinpoint potential hybrid species. Two intriguing examples concern the Steller’s Eider (Polysticta stelleri) and the Red-breasted Goose (Branta ruficollis). Both species have exceptional plumage patterns and show signs of past hybridization with other species. The Steller’s Eider shares genetic variation with Long-tailed Ducks (Clangula hyemalis) and several eider species. And the Red-breasted Goose might have originated through hybridization between Brent Goose (Branta bernicla) and the ancestor of the white-cheeked geese (a group which includes among others, the Canada Goose, B. canadensis).

There is, however, an alternative explanation for the genetic make-up of the Steller’s Eider and the Red-breasted Goose. These birds might have hybridized with several species at different times during their evolutionary history, picking up genetic variants in each of these hybridization events. The resulting mixture looks like a hybrid species, but developed along a different evolutionary path (see figure below). Discriminating between successive hybridization events and hybrid speciation requires more detailed genetic analyses. Clearly, we need more that a handful of criteria to identify a hybrid species.

The difference between hybrid speciation and successive hybridization events can be difficult to tease apart. In the right figure, hybridization repeatedly occurs between species A and B, but more species might be involved. From: Ottenburghs (2018).

References

Elgvin, T. O., Trier, C. N., Tørresen, O. K., Hagen, I. J., Lien, S., Nederbragt, A. J., Ravinet, M., Jensen, H. & Sætre, G. P. (2017). The genomic mosaicism of hybrid speciation. Science advances, 3(6), e1602996.

Hermansen, J. S., Sæther, S. A., Elgvin, T. O., Borge, T., Hjelle, E., & Sætre, G. P. (2011). Hybrid speciation in sparrows I: phenotypic intermediacy, genetic admixture and barriers to gene flow. Molecular Ecology, 20(18), 3812-3822.

Lamichhaney, S., Han, F., Webster, M. T., Andersson, L., Grant, B. R., & Grant, P. R. (2018). Rapid hybrid speciation in Darwin’s finches. Science, 359(6372), 224-228.

Lavretsky, P., Wilson, R. E., Talbot, S. L., & Sonsthagen, S. A. (2021). Phylogenomics reveals ancient and contemporary gene flow contributing to the evolutionary history of sea ducks (Tribe Mergini). Molecular Phylogenetics and Evolution, 161, 107164.

Nieto Feliner, G., Álvarez, I., Fuertes-Aguilar, J., Heuertz, M., Marques, I., Moharrek, F., Piñeiro, R., Riina, R., Rosselló, J. A., Soltis, P. S. & Villa-Machío, I. (2017). Is homoploid hybrid speciation that rare? An empiricist’s view.

Ottenburghs, J., Megens, H. J., Kraus, R. H., Van Hooft, P., van Wieren, S. E., Crooijmans, R. P., Ydenberg, R. C., Groenen, M. A. M. & Prins, H. H. (2017). A history of hybrids? Genomic patterns of introgression in the True Geese. BMC Evolutionary Biology, 17(1), 1-14.

Ottenburghs, J. (2018). Exploring the hybrid speciation continuum in birds. Ecology and Evolution, 8(24), 13027-13034.

Schumer, M., Rosenthal, G. G., & Andolfatto, P. (2014). How common is homoploid hybrid speciation?. Evolution, 68(6), 1553-1560.

Featured image: Italian Sparrow (Passer italiae) © Omar Bariffi | Wikimedia Commons

Does mitochondrial introgression also impact the nuclear genome?

Looking for nuclear-encoded mitochondrial genes in Audubon’s Warbler.

Some individuals of the Audubon’s Warbler (Setophaga [coronata] auduboni) have acquired mitochondrial DNA from the closely related Myrtle Warbler (S. [c.] coronata). The transfer of this circular DNA might even have conferred an advantage on the receiving species. In 2014, David Toews and his colleagues found that Myrtle-type mitochondria were metabolically more efficient than ancestral ones. Moreover, these variants might be linked to changes in migratory behavior. Having a cellular powerhouse that produces more energy is certainly an asset during migration.

This interesting discovery was, however, limited to mitochondrial DNA. In the 2014 paper, the authors did speculate about potential patterns in the nuclear genome: “Are there small portions of the nuclear genome that covary with mtDNA, consistent with a pattern of cryptic genomic regions of isolation between individuals with the two mitochondrial types?” Indeed, some nuclear genes still interact with mitochondrial ones during energy production, and might thus show genetic signs of coevolution. A recent study in the journal Molecular Ecology finally put this idea to the test.

Nuclear Genes

Stephanie Szarmach and her colleagues compared whole genome sequences for Audubon’s Warblers that carried different mitochondrial variants. For clarity, the Myrtle-type mitochondria were referred to as “northern haplotypes” whereas the ancestral mitochondria were called “southern haplotypes.” If certain nuclear genes coevolved with these mitochondrial variants, they might show genetic differentiation between the northern and southern haplotypes. And indeed, the researchers reported “three previously unidentified regions that were moderately differentiated (FST > 0.2) between Audubon’s warblers that had mitochondrial haplotypes from the introgressed northern clade versus those from the ancestral southern clade.” Interestingly, one of these genomic regions houses the gene NDUFAF3, which is a nuclear-encoded mitochondrial gene. Exactly what you would expect.

A differentiated region on chromosome 12 contained the nuclear-encoded mitochondrial gene NDUFAF3. From: Szarmach et al. (2021).

Comparing Techniques

Apart from this biological investigation, the researchers also asked a more technical question: Would you be able to find these differentiated regions with less powerful sequencing techniques? As the saying goes, to pose the question is to answer it (apparently this figure of speech is known as hypophora). So, the researchers compared three genomic sequencing techniques: Whole Genome Sequencing (WGS), Genotyping-by-Sequencing (GBS) and double-digest restriction-site associated DNA (ddRAD). These three approaches differ dramatically in the amount of data that they produce. In the warblers of this study, the average number of reads varied accordingly: 0.6 million per individual for ddRAD, 4.8 million per individual for GBS, and 31.0 million per individual for WGS.

When the researchers scanned the data for regions of genetic differentiation, they noticed that “the reduced representation approaches [GBS and ddRAD] were much less effective at identifying regions with elevated FST at the fine scale and do not provide the same detailed picture of the landscape of divergence that is found using WGS.” This result might not be that surprising – it has been found in other study systems, such as Sporophila seedeaters and Colaptes woodpeckers – but it does lead to an intruiging insight. If you are mainly interested in characterizing the genomic landscape of differentiation, it will be worthwhile to directly opt for WGS instead of first exploring the genome with reduced representation approaches.

Exploring the genomic landscape of differentiation with different sequencing techniques revealed that WGS is far superior compared to reduced representation approaches (GBS and ddRAD). From: Szarmach et al. (2021).

References

Szarmach, S. J., Brelsford, A., Witt, C. C., & Toews, D. P. (2021). Comparing divergence landscapes from reduced‐representation and whole genome resequencing in the yellow‐rumped warbler (Setophaga coronata) species complex. Molecular Ecology, 30(23), 5994-6005.

Toews, D. P., Mandic, M., Richards, J. G., & Irwin, D. E. (2014). Migration, mitochondria, and the yellow‐rumped warbler. Evolution, 68(1), 241-255.

Featured image: Audubon’s Warbler (Setophaga [coronata] auduboni) © Pterzian | Wikimedia Commons

What is the most diverged avian hybrid?

Genetic analysis of a putative hybrid between species that diverged 65 million years ago.

In 1956, the Brazilian ornithologist Augusto Ruschi acquired a peculiar bird: a putative hybrid between Helmeted Guineafowl (Numida meleagris) and Rusty-margined Guan (Penelope superciliaris). These species belong to different bird families – Numididae and Cracidae, respectively – and diverged about 65 million years ago, making this cross the most divergent hybrid ever documented.

Early Skepticism

At a conference in South Africa, Dean Amadon – Chairman of the Department of Ornithology at the American Museum of Natural History in New York City – shared this case with his colleagues, generating some controversy. Especially, the French ornithologist Jacques Berlioz was skeptical and noted that “owing to differences in the structure of the cloacas, it is anatomically impossible for guans and guineafowl to mate – it would be almost equivalent to crossing a fowl and a duck.”

After Ruschi sent the preserved skin to the American Museum of Natural History, Amadon reconsidered his opinion, suggesting that it might be a hybrid between Helmeted Guineafowl and Chicken (Gallus gallus). Nonetheless, this hybrid combination still circulates in the scientific literature, such as the Handbook of Avian Hybrids of the World (which contains some other dubious records). How reliable is this hybrid record?

Photograph of the specimen by Peter Capainolo. © American Museum of Natural History.

Whole Genome Sequence

Solely relying on morphology to identify hybrids can be challenging. Genetic analyses are often needed to validate a particular hybrid combination (as I argued before). That is why James Alfieri and his colleagues decided to sequence the complete genome of the specimen that Dean Amadon received from Augusto Ruschi. Comparing the DNA sequences of the specimen with other species revealed that most genomic segments mapped to Helmeted Guineafowl and Chicken. Moreover, the mitochondrial DNA matched with the Helmeted Guineafowl, indicating that this species was the mother (mtDNA is passed down through the maternal line). Hence, the researchers concluded that “the parents of the hybrid were the frequently observed, yet still extremely diverged species pair, G. gallus (sire) and N. meleagris (dam).” Mystery solved.

Genomic segments of the specimen mostly mapped to Helmeted Guineafowl (Numida meleagris) and Chicken (Gallus gallus). From: Alfieri et al. (2023).

Golden Standard

Although the hybrid is not the outcome of mating between Helmeted Guineafowl and Rusty-margined Guan, it is still the most diverged avian hybrid to date. Helmeted Guineafowl and Chicken diverged about 47 million years ago. More importantly, this study highlights the danger of only using phenotypic data to determine the parental species that produced the hybrid. In their paper, the authors rightfully remark that “genetic approaches, such as whole-genome sequencing, remain the gold standard for validating hybridization events.” Amen to that.

References

Alfieri, J. M., Johnson, T., Linderholm, A., Blackmon, H., & Athrey, G. N. (2023). Genomic investigation refutes record of most diverged avian hybrid. Ecology and Evolution, 13(1): e9689.

Ruschi, A., & Amadon, D. (1959). A supposed hybrid between the families Numididae and Cracidae. Ostrich, 30(S1): 440-442.

Featured image: Rusty-margined Guan (Penelope superciliaris) © Luan Faitanin Volpato | Wikimedia Commons

Urbanization promotes hybridization between Common Swift and Pallid Swift

Genetic analyses uncover several hybrids and backcrosses in France.

In 2013, French researchers discovered a mixed pair of Common Swift (Apus apus) and Pallid Swift (Apus pallidus). This observation raised the question how common hybridization is between these two species. Identifying hybrids based on morphological traits is extremely challenging. Indeed, even “pure” Common and Pallid Swifts are difficult to tell apart. That is why Alice Cibois and her colleagues turned to genetic data. They inspected the genetic make-up of almost 500 individuals.

The sampling effort centered around the French town of Bastia (Corsica) where both species are breeding. The researchers noted that “although the two species are known to form mixed colonies at the same natural sites, sympatry predominantly occurs within urban regions where both species breed in buildings.” The chances of finding hybrids are thus highest in these urban areas.

Recent Hybrids and Backcrosses

The mitochondrial gene COI provided the first clue for hybridization. A haplotype network uncovered six Pallid Swift individuals with mitochondrial sequences of the Common Swift. Nuclear markers – a set of nine microsatellites – provided more detailed patterns of hybridization. The analyses suggested four first-generation hybrids and ten backcrosses (indicating that the hybrids are fertile). These findings highlight the power of genetic data to document hybridization between morphologically similar species. The researchers nicely address this topic in the discussion of their paper:

Observers never reported a mixture of phenotypic traits suggestive of a hybrid origin. Genotyping at nuclear markers is thus the only tool available to reliably identify individuals with hybrid origin and to track the dynamics of introgression between the two species.

Haplotype network for Common Swifts (blue) and Pallid Swifts (orange). The circles are proportional to the number of individuals. Asterisks show the six individuals identified as Pallid Swifts that have Common Swift haplotypes. From: Cibois et al. (2022).

Anthropogenic Hybridization

As expected, most of these admixed individuals were found in and around the city of Bastia. This pattern supports the idea that human actions can lead to hybridization. And it is not just limited to swifts. In a previous blog post, for example, I explained how nectar feeders and ornamental plants in gardens might have facilitated hybridization between two subspecies of Allen’s Hummingbird (Selasphorus sasin). Similarly, another recent study reported that hybrids between four species of chickadee (genus Poecile) were more common in urban settings (see this blog post). Urbanization might thus fuel hybridization.

References

Cibois, A., Beaud, M., Foletti, F., Gory, G., Jacob, G., Legrand, N., … & Thibault, J. C. (2022). Cryptic hybridization between Common (Apus apus) and Pallid (A. pallidus) Swifts. Ibis, 164(4), 981-997.

Featured image: Common Swift (Apus apus) © XJochemx.nl | Wikimedia Commons