Hybrid zones help to unravel the genetics of bird coloration

Studying hybrid zones can provide important insights into the genetic basis of plumage coloration in birds.

Why is a Blackbird (Turdus merula) black and a Yellow Warbler (Setophaga petechia) yellow? This might seem like a trivial question, but the genetic basis of plumage color in birds is an active field of research. In general, the color differences between bird species can be traced back to several pigments: melanins, caroteniods and porphyrins. For example, carotenoids are responsible for the bright red plumage of the Northern Cardinal (Cardinalis cardinalis). But which genes regulate how birds use these pigments to create the colorful variety we see in nature?


northern cardinal.jpg

Carotenoids are responsible for the bright red color of the Northern Cardinal (http://www.thespruce.com/)


Studying Hybrid Zones

To investigate the genetic control of plumage colors, researchers make use of hybrid zones. In these areas, different bird species come into contact and interbreed. The resulting hybrids are often a mixture of both species. Some feathers are colored like one species, while other feathers have the color of the second species. By comparing these patterns with the genes of the hybrids, ornithologists can figure out which genes belong to which plumage pattern.



Two recent studies have applied this approach to disentangle the genetics of bird coloration. In the first study, published in Current Biology, David Toews and his colleagues focused on Golden-winged Warbler (Vermivora chrysoptera) and Blue-winged Warbler (V. cyanoptera), two species that hybridize in eastern North America. They found six small genomic regions that housed genes involved in feather development and pigmentation. One feature, throat coloration, was associated with the promotor region (the on/off-switch, if you will) of a gene called agouti.


winged warblers.jpg

The difference in throat coloration between Blue-winged (left) and Golden-winged Warbler is related to the agouti gene. (http://www.allaboutbirds.com/)


Alan Brelsford and his colleagues turned their attention to the western part of North America and took a closer look at two other interbreeding passerines: Audubon’s Warbler (Setophaga coronata auduboni) and Myrtle’s Warbler (S. c. coronata). For several plumage traits, they found associations with genomic regions, which harboured genes related to keratin filaments that build feathers. Two melanin-based traits – eye line and eye spot – could even be traced back to a single genomic region.


coronata warblers

Myrtle (left) and Audubon’s Warbler have different eye lines, which can be traced back to one genomic region (http://www.tringa.com/)


These two studies provide a long list of candidate genes involved in bird coloration. Now, researchers can set out to unravel the biochemical pathways underlying these traits. In the end, I might be able to tell you precisely why a Blackbird is black and a Yellow Warbler yellow. In the meantime, let us just enjoy our colorful feathered friends.



Brelsford, A., D. P. L. Toews and D. E. Irwin (2017). Admixture mapping in a hybrid zone reveals loci associated with avian feather coloration. Proceedings of the Royal Society B: Biological Sciences 284(1866).

Toews, D. P., S. A. Taylor, R. Vallender, A. Brelsford, B. G. Butcher, P. W. Messer and I. J. Lovette (2016). Plumage genes and little else distinguish the genomes of hybridizing warblers. Current Biology 26(17): 2313-2318.


Both papers have been added to the Parulidae page.

Disentangling the Evolutionary History of Towhees in Mexico

Highly heterogenous patterns of genetic differentiation between two Towhee species.

Take two closely related species that are hybridizing. Collect some samples and sequence their genomes (which is relatively cheap nowadays). Next, compare those genomes. You will notice that some genomic regions are drastically different between both species. Why is this? There are multiple possible explanations. Perhaps, the species are living in distinct habitats and the genomic differences are the outcome of different selection pressures. Or could it be that the genomic regions are involved in reproductive isolation. In hybrids, a particular genomic region might lead to infertility. So, this region is not exchanged between the species and becomes different over time. Or could it be a combination of both?


Hybrid zones

Sarah Kingston and her colleagues explored this conundrum in two Towhee species: Spotted Towhee (Pipilo maculatus) and Collared Towhee (P. ocai). Why these two species? Because they interbreed in not one, but two Mexican hybrid zones! One zone runs from north to south along the Tezuitlán gradient, while the other zone is orientated east-west along the Transvolcanic gradient. On the one hand, genetic differences that occur in both hybrid zones probably reflect historical divergence and reproductive isolation. On the other hand, genetic differences that are specific to a hybrid zone point to stochastic processes or environment-dependent selection.


spotted towhee

A Spotted Towhee (from: http://www.hbw.com/)


Genomic Clines

There are various ways to characterize genetic differentiation between two species. This study, published in Journal of Evolutionary Biology, relied on a fixation index (Fst) and genomic cline analyses. The latter method should not be confused with geographical cline analysis (you can read more about that method here). I will not go into the details of genomic cline analyses, but interested readers can check out this paper. In short, you compare numerous genes against a model that describes the genomic background of the interbreeding species. Two parameters (alfa and beta) can be estimated to find genes that deviate from this null model. These genes are likely under divergent selection or involved in reproductive isolation.



A Collares Towhee (from: http://www.hbw.com/)


A Complex History

Applying these two methods (Fst and genomic clines), Sarah Kingston and her colleagues found several genomic regions (6-20 percent) that are different between the Towhee species in both hybrid zones. But there were also many regions that are specific to each hybrid zone. They conclude that “these results are consistent with a history in which reproductive isolation has been influenced by a common set of loci in both hybrid zones, but where local environmental and stochastic factors also lead to genomic differentiation.” A similar pattern was uncovered by a study comparing several crow hybrid zones (see here). I guess the Towhees (and the crows) can change their Facebook-status to ‘it is complicated…’



Kingston, S. E., T. L. Parchman, Z. Gompert, C. A. Buerkle and M. J. Braun (2017). Heterogeneity and concordance in locus-specific differentiation and introgression between species of towhees. Journal of Evolutionary Biology 30(3): 474-485.


This paper has been added to the Emberizidae page.

OMG (Owls, Migration and Genetics)! A Heteropatric Speciation Model for Northern Saw-whet Owls

Two owl subspecies might be the outcome of a peculiar speciation model.

Open a standard textbook on the origin of new species and you will probably come across three main speciation models: allopatric, sympatric and parapatric speciation. In short, allopatric speciation occurs when two populations become geographically isolated leading to a sudden break in gene flow. Over time these populations diverge genetically into different species. Alternatively, during sympatric speciation, populations diverge even though they live in the  same habitat. Parapatric speciation, finally, entails the differentiation of two neighbouring populations that still exchange some genes in the process.



Three different speciation models in a standard textbook.


Mixing the Models

Besides this Mayrian triumvirate (as German biologist Ernst Mayr popularized these models), several other modes of speciation are possible. One of these is heteropatric speciation, in which populations occur in the same area at some times during the year, but are geographically separated at other times (in a sense a hybrid between allopatric and sympatric speciation). This model nicely applies to birds where one population is migratory while the other is sedentary. You can read Kevin Winkers’ excellent review on this process in Ornithological Monographs.


The Origin of Owl Subspecies

Two subspecies of the Saw-whet Owl (Aegolius acadicus) might have diverged in a heteropatric fashion. One subspecies brooksi remains sedentary on the island of Haida Gwaii (British Columbia) while the other subspecies acadicus is migratory. During fall and winter both subspecies co-occur, but during the rest of the year they are far apart. Are they still interbreeding and exchanging genes when they meet?

To figure this out, Jack Withrow, Spencer Sealy and – not surprisingly – Kevin Winker sequenced mitochondrial and nuclear DNA (AFLPs) from both subspecies. The analyses revealed that the subspecies are genetically differentiated with extremely low levels of gene flow. In fact, it seems likely that there is no gene flow at all (a genomic approach is necessary to be sure).


saw-whet owl.jpg

A Northern Saw-whet Owl (from http://www.hwb.com)


Ice Ages

Nonetheless, the most plausible scenario is that an ancestral acadicus population colonized the Haida Gwaii about 16,000 years ago when this island was a refugium during the ice ages. This population became sedentary (and who could blame them, wouldn’t you like to live on an island?) and started diverging from the migratory mainland population. A nice example of heteropatric speciation?



Withrow, J. J., S. G. Sealy and K. Winker (2014). Genetics of divergence in the Northern Saw-whet Owl (Aegolius acadicus). The Auk 131(1): 73-85.


The paper paper has been added to the Strigiformes page.

From the Rainforest to the Savannah: Ecological Speciation in the Little Greenbul?

Ecological gradients might drive speciation in an African songbird

Ever heard of Wakwa, Ngaoundaba Ranch or Betare Oya? These are sites in Central Africa where Ying Zhen and colleagues collected samples of a small passerine bird: the Little Greenbul (Andropadus virens). You can find this songbird in the rainforest, but also as you walk towards the savannah. This transition from rainforest to savannah is characterized by less trees and less rainfall compared to the rainforest habitat. Biologists refer to such transitions as ecotones and think that they can play a crucial role in the origin of new species.



A Little Greenbul (from http://commons.wikimedia.com/)


Genomic Tools

Many authors have speculated that rainforest-savannah ecotone in Central Africa has been driving speciation in the Little Greenbull by means of natural selection. However, previous genetic studies (based on “old-school” mtDNA and microsatellites) could not differentiate between ecotone and rainforest populations. Now, in a paper published in Molecular Ecology, researchers use the newest genomic tools to revisit this African species. Based on almost 50,000 genetic markers (Single-Nucleotide Polymorphisms or SNPs), they were able to discriminate between different Greenbul populations.


More Than Distance Alone

A first look at the data revealed that more distant populations were genetically more different. This pattern – known as isolation-by-distance – points to a neutral model of evolution, contrary to the expectation that natural selection is driving genetic divergence in Greenbuls. However, further analyses revealed that geographic distance alone cannot explain the observed genetic differentiation. Other processes, such as local adaptiation by means of natural selection, are also at work here.

Comparing SNPs between rainforest and ecotone populations uncovered several outliers that are probably under selection. These outliers include EDIL3, a calcium-binding protein that is involved in the formation of eggshels and MLXIPL, a protein that plays a role in fat deposition. It is tempting to speculate about possible roles for these genes in the different habitats, but one quickly threads into the dangerous territory of ‘Just-so-stories’. The message to take away here is that several genes seem to be under divergent natural selection, possibly driven by ecological differences.


Ecological Speciation?

In the end, these patterns are in line with a model of ecological speciation, where ‘natural selection caused by shifts in ecology can promote speciation.’ As evolutionary biologists interested in speciation, we surely live in interesting times.



Zhen Y, Harrigan RJ, Ruegg KC, Anderson EC, Ng TC, Lao S, Lohmueller KE, Smith TB. (2017). Genomic divergence across ecological gradients in the Central African rainforest songbird (Andropadus virens). Molecular Ecology. 26:4966-4977.


This paper has been added to the Pycnonotidae page.



Hybridization as the Engine of Adaptive Radiation

Hybridization can promote adaptive radiation.

Adaptive radiation is the process in which organisms rapidly diversify to fill empty ecological niches. A textbook example is the radiation of Darwin’s Finches on the Galapagos Islands. These birds diversified in beak morphology occupying different ecological feeding niches. A similar story unfolded on the Hawaiian islands where Honeycreepers evolved into endless forms most beautiful. And it will get even better when you add hybridization to the mix!



A Multitude of Hawaiian Honeycreepers (From: http://www.hdouglaspratt.com/)


Mathematical Model

Several biologists have proposed that hybridization between evolutionary lineages can cause rapid diversification of ecological phenotypes, thereby facilitating adaptive radiations. This plausible hypothesis has not been tested theoretically. Sounds like a challenge for Kotaro Kagawa and Gaku Takimoto, who constructed a mathematical model to simulate how hybridization can impact adaptive radiations.

Their mathematical model is quite, well, mathematical. So, I will focus on the outcomes. If you are interested in the actual model, you can read all about it in Ecology Letters. One of the key parameters in these analyses is the creation of new phenotypic variation by hybridization. This phenomenon is known as transgressive segregation. See, for instance, the unique colors and shapes of hybrid orchids or the extreme size of lion x tiger crosses.



Hercules the Liger (From: http://www.liger-hercules.com/)


Transgressive Segregation

However, the amount of phenotypic variation introduced by hybridization has important consequences for the outcome of the model. Too much variation and the fitness of the hybrids decreases (i.e. they are too different from their parents), ultimately leading to the collapse of hybrid populations. But if the amount of phenotypic variation in hybrids increases fitness, a hybrid population might florish and give rise to a hybrid species. With regard to adaptive radiations, hybrids with extreme phenotypes might reach new ecological niches that are inaccesable to other species. In a sense, hybridization allows populations to jump over fitness valleys onto distant adaptive peaks. In other words, hopping hybrids.



Kagawa, K. & Takimoto, G. (2017). Hybridization can promote adaptive radiation by means of transgressive segregation. Ecology Letters. http://onlinelibrary.wiley.com/doi/10.1111/ele.12891/full

Hybrid Bird Species: A Big Bird on the Galapagos Islands and a Small Manakin in the Amazon Basin

Hybrid speciation in birds: a fresh perspective on an old case and a new addition to the list.

Let me start with a joke. What do you call a cross between en bulldog and a shitzu? Wait for it… a bullshit! Hilarious as this may be, hybridization between two closely related species can lead to something completely different, occasionally even a new species. This phenomenon – hybrid speciation –  is quite controversial in birds. Many putative hybrid species have failed to pass the test. Some well-documented cases include the Italian Sparrow (Passer italiae) and the Audubon’s Warbler (Setophaga auduboni). Recently, two studies on hybrid speciation appeared. One providing a genomic perspective on an old case, the other presenting a new hybrid species in the Amazon basin. Let’s dive right in (the papers, not the Amazon…).


Big Bird Revisited

In 2009, Peter and Rosemary Grant presented a peculiar case of putative hybrid speciation. They reported that a male hybrid between Medium Ground Finch (Geospiza fortis) and Common Cactus Finch (G. scandens) arrived on the Galapagos Island of Daphne Major. This bird – which they nicknamed ‘Big Bird’ – mated with a female Medium Ground Finch. The offspring of this couple started interbreeding amongst each other for several generations, resulting in a hybrid lineage that is reproductively isolated from its parental species.

Now, Sangeet Lamichhaney and his colleagues (including the Grants) revisited this hybrid lineage using genomic data. They showed that the Grants were partly wrong. The male that ended up on Daphne Major was not a hybrid, but a Large Cactus Finch (G. conirostris) from Espanola, an island  more than 100 km from Daphne Major. Nevertheless, the offspring of this male and his Medium Ground Finch partner did interbreed amongst each other, which culminated in an increasing inbreeding coefficient.

Further analyses of the beak morphology of this lineage indicated that it is ecologically distinct from its parental species. And in 2009, the Grants already established that it is reproductively isolated from the Medium Ground Finch (if it is also isolated from the other parental species, which lives on another island, has not been tested yet). All in all, strong evidence for hybrid speciation.

large cactus finch.jpg

A Large Cactus Finch (Geospiza conirostris)


A Memorable Manakin

The Golden-crowned Manakin (Lepidopthrix vilasboasi) had not been seen since the 1950’s until it was rediscovered in 2002. Alfredro Barrera-Guzman and his colleagues took advantage of this rediscovery and sequenced several individuals from an isolated population between the Tapajós and the Jamanxim rivers. When they compared the DNA sequences with two closely related species – Snow-capped Manakin (L. nattereri) and Opal-crowned (L. iris), they were in for a surprise. The Golden-crowned Manakin turned out to be a hybrid species! Detailed genetic analyses (including coalescent modelling) reinforced this finding.

There is, however, one intriguing observation. Recent hybrids between Snow-capped and Opal-crowned Manakin still occur in the Amazon Basin. But these hybrids do not have the striking yellow crown patches of the Golden-Crowned Manakin. Were the authors wrong? Did they jump to conclusions too quickly? No, further investigations into the nanostructure of these crown patches provided some clues.

The researchers studied the keratin matrix of the crown feathers using electron microscopy. This revealed that the matrix of the hybrids is intermediate between the parental species (no surprise there). But the same goes for the Golden-crowned Manakin. So where does the yellow color come from? In the hybrid species – which originated about 260,000 years ago – the crown patch has been thinkened by carotenoids, which explains the yellow color. The accumulation of carotenoids probably compansated for the loss of brightness (a feature that the parental species use to attract females). Apparently, female Golden-crowned Manakins have a weak spot for yellow. And who could blame them?

golden-crowned manakin.jpg

A Golden-crowned Manakin (Lepidothrix vilasboasi)



Barrera-Guzmán, A. O., Aleixo, A., Shawkey, M. D. & Weir, J. T. (2017). Hybrid speciation leads to novel male secondary sexual ornamentation of an Amazonian bird. Proceedings of the National Academy of Sciences, 201717319.

Lamichhaney S, Han F, Webster MT, Andersson L, Grant BR, Grant PR. (2017). Rapid hybrid speciation in Darwin’s finches. Science:eaao4593.


These papers have been added to the Thraupidae and the Pipridae pages.