Dating with different techniques: Consilience of divergence times between Bean Goose species

Several methods suggest that Taiga and Tundra Bean Goose diverged about 2.5 million years ago.

One of the strongest arguments for evolution is consilience, the principle that evidence from independent, unrelated sources converges upon the same conclusions. Numerous lines of evidence, from genetic analyses and comparative morphology to biogeography and embryology, all point to the same unescapable conclusion: life on Earth evolved over billions of years. Doubting evolution would just be silly.

The principle of consilience can also be applied to smaller questions. In my own work on the evolution of geese, I uncovered a nice example of consilience: the divergence between Taiga Bean Goose (Anser fabalis) and Tundra Bean Goose (A. serrirostris). Using different dating techniques, I always converged upon the same answer: these species diverged around 2.5 million years ago.

mtDNA vs. Genomics

Before we delve into my goose work, we start with a study in the Journal of Evolutionary Biology. In 2000, Minna Ruokonen and her colleagues compared about 1000 base pairs of the mitochondrial DNA for seven goose species. Although they only included a sample of the Tundra Bean Goose (and not the Taiga Bean Goose), we can still compare this species with other closely related goose species, such as the Pink-footed Goose (A. brachyrhynchus). Based on the level of genetic divergence in the mtDNA, the researchers provided “a rough estimate for the timing of speciation events of Anser species […] within approximately 2–2.5 million years.”

More than 15 years later, during my PhD at Wageningen University, I used genomic data to unravel the evolutionary history of these goose species. After constructing a phylogenetic tree (based on 6,630,626 base pairs), I ran a molecular clock analysis with the software MCMCtree. First, I estimated a mean substitution rate based on previous studies. Next, the split between the two goose genera – Anser and Branta – was constrained between 4 and 20 million years, the time period for which we have reliable goose fossils. And finally, the MCMCtree analyses were run multiple times to check for convergence of the results. Using this approach, the divergence between Taiga Bean Goose and Tundra Bean Goose was estimated ca. 2.5 million years ago. Very similar to the mitochondrial result by Minna Ruokonen and her colleagues.

Genomic data suggested that the Taiga Bean Goose (in green) and the Tundra Bean Goose (in orange) diverged around 2.5 million years ago. From: Ottenburghs et al. (2016).

Demographic Models

So, now we have two independent lines of evidence for the divergence time between Taiga Bean Goose and Tundra Bean Goose. But it gets even better. During my postdoc at Uppsala University, I focused on the evolution of these two species (and later adding the Pink-footed Goose to the mix). To understand their evolutionary dynamics, I opted for a demographic modelling approach with genomic data. Using the software package DADI, I compared different demographic scenarios, ranging from strict isolation to secondary contact with asymmetrical gene flow.

DADI simulates the change in allele frequencies using a diffusion equation, similar to gas molecules moving through a room. Depending on the interplay of genetic drift, selection and migration, genetic variants spread through a population at different speeds. The end result can be visualized in a square with different populations on the horizontal and vertical axes (in my case, the two Bean Goose species). Genetic variants that are unique for one of the species can be found in the lower left corner, whereas variants shared by both species are found in the top right corner. Gene flow between the populations mixes things up. Different demographic models lead to different squares which can be compared to the actual data.

My genomic analyses pointed to a scenario of allopatric divergence (about 2.5 million years ago) followed by recent secondary contact (about 60,000 years ago). Another independent line of evidence for the divergence time between Taiga Bean Goose and Tundra Bean Goose.

DADI uses a diffusion equation to simulate how genetic variants spread through a population. The result can be visualized in a square and compared with the actual data. For the Bean Geese, the close match between the data and the model suggested a scenario of allopatric divergence with secondary contact. From: Ottenburghs et al. (2020).

Consilience

And there you have it. Three independent analyses that all converge upon the same conclusion. It does not matter if you use a simple calculation based on mitochondrial divergence, a molecular clock calibrated with fossils, or a demographic model using diffusion equations. The conclusion is always the same: Taiga Bean Goose and Tundra Bean Goose diverged ca. 2.5 million years ago. Now, that is consilience.

References

Ottenburghs, J., Megens, H. J., Kraus, R. H., Madsen, O., van Hooft, P., van Wieren, S. E., Crooijmans, R. P. M. A., Ydenberg, R. C., Groenen, M. A. M. & Prins, H. H. T. (2016). A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese. Molecular Phylogenetics and Evolution, 101, 303-313.

Ottenburghs, J., Honka, J., Müskens, G. J., & Ellegren, H. (2020). Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation. Heredity, 125(1-2), 73-84.

Ruokonen, M., Kvist, L., & Lumme, J. (2000). Close relatedness between mitochondrial DNA from seven Anser goose species. Journal of Evolutionary Biology, 13(3), 532-540.

Featured image: Taiga Bean Goose (Anser fabalis) © Marton Berntsen | Wikimedia Commons

The reticulated evolution of the Bean Goose complex

Hybridization partly erased the phylogenetic patterns of three goose taxa.

Different genes tell different stories. This simple statement is probably the most important lesson that I have learned while working with genomic data. Sexual reproduction is accompanied by recombination, the shuffling of chromosomal segments during meiosis. That is why your genome is a complex mixture of your parents’ DNA. Different genomic regions can thus be traced back to your father or mother. If you extend this reasoning back across multiple generations, you will quickly understand why different genes tell different stories. Each genomic segment follows its own trajectory into the past.

On an evolutionary timescale, this process is nicely illustrated by the Bean Goose complex – a group of goose taxa that is currently classified into three species: the Taiga Bean Goose (Anser fabalis, with three subspecies), the Tundra Bean Goose (Anser serrirostris, with two subspecies) and the Pink-footed Goose (Anser brachyrhynchus, monotypic). Depending on which genes you analyze, different phylogenetic patterns arise. For example, mitochondrial DNA clusters the Taiga and Tundra Bean Goose whereas genomic data places the Pink-footed Goose next to the Tundra Bean Goose. Again, different genes tell different stories. So, which genes should we follow? Which genes show the “true” species tree?

Differentiation Islands

To find the “true” species tree, a recent study in the journal BMC Ecology and Evolution (published by yours truly) focused on highly differentiated sections in the genome. Some scientists have argued that these genomic regions of increased divergence (i.e. differentiation islands) reflect the species tree. However, several phylogenomic studies found that these regions can produce misleading results due to selection or introgression (see for example this blog post). We should thus be cautious and carefully examine the phylogenetic patterns in regions of high genetic differentiation.

To explore the reliability of these differentiation islands for phylogenetics, we constructed gene trees for highly differentiated regions across the genomes of the three goose species. As a control, we sampled random genomic regions (which mainly represent the undifferentiated sections of the genome) and again constructed gene trees. The resulting phylogenetic patterns followed our expectations.

This approach [i.e. random selection of genomic regions] did not resolve the Bean Goose complex, but resulted in a monophyletic A. brachyrhynchus clade nested within a mixed cluster of A. fabalis and A. serrirostris. In contrast, phylogenetic analyses of differentiation islands converged upon a topology of three monophyletic clades in which A. brachyrhynchus is sister to A. fabalis, and A. serrirostris is sister to the clade uniting these two species.

A closer look at the gene trees in the differentiation islands revealed one dominant phylogenetic arrangement in which the Pink-footed Goose is most closely related to the Taiga Bean Goose. It seems unlikely that species-specific selective sweeps or ancient introgression events have impacted all these differentiation islands in the same way. Hence, we are confident that we have found the “true” species tree.

Species tree for (a) a random selection of genomic windows and (b) highly differentiated genomic windows. The different goose taxa are highlighted in different colors. The gradient of colors for A. fabalis, A. serrirostris and A. brachyrhynchus in figure a indicates the mixed nature of this clade. From: Ottenburghs et al. (2023).

Introgression

But our story does not end here. In a previous study – published in Heredity and covered in this blog post – we found extensive introgression between Taiga and Tundra Bean Goose. When we tested for introgression in the current study (using D-statistics), we found that no less than 21.9% of the genetic variants showed signatures of introgression between these two species. Clearly introgressive hybridization plays an important role in the evolutionary history of the Bean Goose complex.

Putting all the phylogenetic puzzle pieces together, we came up with the following scenario. After the divergence between the Taiga and the Tundra Bean Goose, a population of Taiga Bean Goose became geographically isolated on several islands (e.g., Svalbard, Greenland or Iceland). These populations evolved into the Pink-footed Goose. Later on, extensive hybridization between the Taiga and the Tundra Bean Goose erased the phylogenetic branching pattern between these taxa, resulting in a mixed clade of the Taiga and the Tundra Bean Goose containing a monophyletic Pink-footed Goose. Differentiation islands were largely unaffected by homogenizing introgression – perhaps because they contained loci involved in reproductive isolation – and maintained the phylogenetic patterns that reflect the species tree. A plausible scenario that requires further investigation.

Within the differentiation islands the topology grouping Taiga Bean Goose (A. fabalis) and Pink-footed Goose (A. brachyrhynchus) occurred most often. The gene trees uniting Taiga Bean Goose and Tundra Bean Goose (A. serrirostris) can be partly explained by recent introgression. Asterisks (*) indicate gene trees that were not observed in the data. From: Ottenburghs et al. (2023).

Trees or Networks?

These findings raise an intriguing conundrum: How should we depict the evolutionary history of the Bean Goose complex? The answer depends on the message you want to convey. If you are focused on reconstructing the order of speciation events, you can settle for a bifurcating tree. If you want to quantify the impact of introgression, a network approach will be more suitable. The evolution of the Bean Goose complex can certainly be depicted as a simple bifurcating tree, but this would ignore the role of introgressive hybridization. Hence, we advocated that the evolutionary relationships between these taxa are best represented as a phylogenetic network. But feel free to disagree.

What is the best way to depict the evolutionary history of the Bean Goose complex: a tree or a network? From: Ottenburghs et al. (2023).

References

Ottenburghs, J., Honka, J., Heikkinen, M.E., Madsen, J., Müskens, G.J.D.M. & Ellegren, H. (2023) Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex. BMC Ecology and Evolution 23, 2.

Featured image: Taiga Bean Goose (Anser fabalis) © Marton Berntsen | Wikimedia Commons

How different are Mallards and Chinese Spot-billed Ducks on a genetic level?

A recent study detected minor differences on the sex-chromosomes.

Morphologically, Mallards (Anas platyrhynchos) and Chinese Spot-billed Ducks (A. zonorhyncha) are easy to tell apart. First of all, the sexes of the Mallard are drastically different whereas male and female Chinese Spot-billed Ducks look alike. In addition, the Chinese Spot-billed Duck can be recognized by its pale head which is marked by a whitish eyebrow and two black stripes. And it sports a yellow spot on the bill from which it derives its name. Interestingly, these morphological differences do not extend to the genetic level. Analyses of mitochondrial DNA and several nuclear markers could not discriminate between these species.

The observation of clear morphological disparity without genetic divergence is not uncommon in birds. I have covered several cases on this blog, such as redpolls and warblers. A mismatch between morphology and genetics can often be explained by a few differentiated genomic regions that underlie the phenotypic differences. Hence, Irina Kulikova and her colleagues took another look at the genetic make-up of the Mallard and the Chinese Spot-billed Duck. Did they find any genetic differences?

Genetic Outliers

The researchers scanned the genomes of 23 Spot-billed Ducks, 29 Mallards and 3 hybrids. In the end, they obtained more than 3000 genetic loci: 3130 on the autosomes and 194 on the Z-chromosome (i.e. one of the sex-chromosomes in birds). Most of the genetic variants at these loci were shared between the two species, confirming previous work that they are genetically similar. However, genetic differentiation was about 4.5 times higher on the Z-chromosome compared to the autosomes. A more detailed look at this sex-chromosome revealed three loci that were significantly different between Mallard and Chinese Spot-billed Duck. Moreover, these loci popped up when the researchers tested for signatures of divergent selection. There are thus genetic differences between these duck species. We just had to look really hard to find them.

The Z-chromosome is highly differentiated between Mallards and Chinse Spot-billed Ducks. It contains three clear outlier (depicted as triangles) that might underlie the morphological differences. From: Kulikova et al. (2022).

Future Work

Finding the genetic differences between these duck species is only the first step. Now, the researchers want to find out whether these genetic outliers directly contribute to the morphological differences that we observe. We know that genes regulating plumage coloration and bill color often reside on the sex-chromosomes (see this review by Darren Irwin). Mallards and Spot-billed Ducks might be another example. But this hypothesis remains to be tested with more fine-scale genomic analyses. Nonetheless, the researchers are confident that they are on the right track:

Whether these regions are involved in phenotypic differences between the species and sexual dimorphism is the prospect of future work. We believe that whole-genome sequencing along with plumage analyses will shed light on phenotypic evolution and help to identify speciation mechanisms in Mallard and Chinese Spot-billed Duck.

References

Kulikova, I. V., Shedko, S. V., Zhuravlev, Y. N., Lavretsky, P., & Peters, J. L. (2022). Z‐chromosome outliers as diagnostic markers to discriminate Mallard and Chinese Spot‐billed Duck (Anatidae). Zoologica Scripta.

Featured image: Chinese Spot-billed Duck (Anas zonorhyncha) © Alpsdake | Wikimedia Commons

Adaptive introgression between two high-altitude duck species

Genetic analyses suggest exchange of hemoglobin genes.

Last week, Svante Pääbo was awarded the Nobel Prize in Physiology or Medicine “for his discoveries concerning the genomes of extinct hominins and human evolution.” Together with many colleagues, he discovered how Neanderthals and Denisovans have contributed to the evolutionary story of humans. Hybridization appears to have been quite common, leading to genetic exchange among archaic humans and these extinct species. Building on this work, Emilia Huerta-Sánchez and her colleagues documented introgression from Denisovans into Tibetans, allowing the latter to adapt to life at high altitudes. Specifically, the gene EPAS1 – which plays an important role in dealing with low oxygen conditions – was transferred between these ancient hominins. A beautiful example of adaptive introgression.

Similar examples have been reported in animal species that live at high altitudes, such dogs and cattle (see this blog post). However, these cases do not feature humans and thus received less attention from the media. Luckily, there are some science websites – such as this blog – that put the spotlight on some hidden gems in the vast scientific literature on hybridization. Recently, Allie Graham and her colleagues investigated whether adaptive introgression also occurred in two South American duck species: the Speckled Teal (Anas flavirostris) and the Yellow-billed Pintail (A. georgica). Their findings were published in the journal Heredity.

D-statistics

Both duck species are widespread across South America and can be found at high altitudes in the Andes. These mountain populations are thus interesting study systems to understand adaptation to high altitude. Given the examples of adaptive introgression in other high-altitude animals and the high incidence of hybridization in ducks, it seems reasonable to look for evidence of adaptive introgression in these two species. The researchers focused on 31 genes that are involved in the production of hemoglobin and the physiological reaction to low oxygen conditions (i.e. the HIF pathway).

A commonly used test for introgression is the D-statistic, also known as the ABBA-BABA test. The rationale behind this test is quite straightforward: it considers ancestral (‘A’) and derived (‘B’) alleles across the genomes of four taxa. Under the scenario without introgression, two particular allelic patterns ‘ABBA’ and ‘BABA’ should occur equally frequent. An excess of either ABBA or BABA, resulting in a D-statistic that is significantly different from zero, is indicative of gene flow between two taxa. Applying this approach to the two duck species revealed significant D-statistics for the β-globin genes, but not for any of the other genes in the study (i.e. α-globin genes and the HIF pathway).

Calculating the D-statistic indicated an excess of shared alleles between the high-altitude populations of the Yellow-billed Pintail and the Speckled Teal. This pattern can be due to introgression. From: Graham et al. (2021).

Convergent Evolution?

However, a significant D-statistic does not necessarily mean introgression. The same pattern can be the outcome of other evolutionary processes, such as convergent evolution. Perhaps the high-altitude populations of Yellow-billed Pintail and the Speckled Teal independently acquired the same mutations in the β-globin genes? To rule out this explanation, the researchers took a closer look at the genomic region containing these genes. Interestingly, the β-globin gene cluster showed very low genetic differentiation between the high-altitude populations. This reduced differentiation was not limited to the genes, but extended across the whole genomic region. In addition, a phylogenetic network of the β-globin genes revealed a clearly separate cluster of haplotypes that contained introgressed alleles that were identified in a previous study. Together, these patterns indicate that the β-globin gene variants are not the result of parallel mutations, but are identical by descent. Introgression is thus the most likely explanation.

Two lines of evidence suggest that the β-globin gene cluster was introgression. The top figure shows that the genomic region has low genetic differentiation between the high-altitude duck populations. And the lower figure reveals a separate cluster (highlighted in red) with the introgressed genetic variants. Adapted from Graham et al. (2021).

Faster Evolution

All in all, this study provides convincing evidence for introgression of β-globin genes between the two duck species. Moreover, demographic modelling revealed that the genes flowed from Speckled Teal into the Yellow-billed Pintail. This finding allowed the researchers to sketch a possible scenario:

Thus, the yellow-billed pintail received these variants through hybridization and may not have waited for de novo mutations to adapt to the high-altitude environment, but rather acquired beneficial alleles from the standing variation, albeit via another species with a similar genetic background, leading to faster evolution.

Although adaptive introgression seems likely, it remains to be explicitly tested if the exchange of these genes was indeed adaptive. One possible analysis could be performed with the so-called VolcanoFinder. This approach scans the genome for certain genetic patterns that look like volcanos when plotting pairwise genetic differences. In such an analysis, the β-globin gene cluster should be a clearly visible peak, similar to the Andean mountains where these duck species reside.

References

Graham, A. M., Peters, J. L., Wilson, R. E., Muñoz-Fuentes, V., Green, A. J., Dorfsman, D. A., Valqui, T. H., Winker, K. & McCracken, K. G. (2021). Adaptive introgression of the beta-globin cluster in two Andean waterfowl. Heredity, 127(1), 107-123.

Featured image: Yellow-billed Pintail (Anas georgica) © Brian Ralphs | Wikimedia Commons

Recent and ancient hybridization among sea duck species, including a potential hybrid species

Genomic analyses point to several bouts of past gene flow.

Waterfowl hybridize like there is no tomorrow. Between 30% and 40% of ducks, geese and swans are known to interbreed. For some species combinations, hybrids are regularly observed because they are easy to recognize and occur close to humans. A nice example concerns Greylag Goose (Anser anser) x Canada Goose (Branta canadensis) hybrids in the Netherlands. The aberrant morphology of these crosses allows for easy identification and they reside around several Dutch cities (see this paper for more details). But what about sea ducks? This group of waterfowl – classified in the tribe Mergini – spend most of their lives at sea, making them difficult to observe. Some hybrids have been reported, such as Barrow’s Goldeneye (Bucephala islandica) x Common Goldeneye (B. clangula). However, the incidence of hybridization among the 15 species in this tribe remains largely unknown. A recent study in the journal Molecular Phylogenetics and Evolution addressed this knowledge gap with genomic data. Sampling more than 350 individuals, the researchers searched for genetic signatures of hybridization.

Recent Hybrids

Before starting their quest for sea duck hybrids, the researchers needed to be sure that they could confidently discriminate between all species. A principal component analysis pointed to three main groups: (1) Harlequin Ducks (Histronicus histronicus), (2) eider species and Long-tailed Ducks (Clangula hyemalis), and (3) Bufflehead (Bucephala albeola), scoters, mergansers, and goldeneyes. Within these three groups, population assignment analyses (using ADMIXTURE) could identify the different species and even provided some insights into more fine-scale population structure within certain species.

Now, we can explore the dataset for possible hybrids. The ADMIXTURE results indicated a first-generation hybrid between Barrow’s Goldeneye and Common Goldeneye. Moreover, there were 18 individuals with signs of ancestry from several species, suggesting possible backcrosses. The ADMIXTURE analyses had too low resolution to pinpoint the species involved, so the researchers turned to a more powerful co-ancestry analysis (using fineRADstructure). Here is an overview of the uncovered hybrids with number of individuals between parentheses:

• Barrow’s Goldeneye x Common Goldeneye (1)
• Barrow’s Goldeneye backcrossed with Bufflehead (1)
• Bufflehead backcrossed with White-winged Scoter (3)
• Common Eider backcrossed with Common Goldeneye (1)
• Common Eider backcrossed with Harlequin Duck (3)
• Harlequin Duck backcrossed with Common Merganser and Bufflehead (2)
• King Eider backcrossed with Surf Scoter (1)
• Long-tailed Duck backcrossed with Black Scoter (1)
• Long-tailed Duck backcrossed with Bufflehead (2)
• Long-tailed Duck backcrossed with Harlequin Duck and a scoter species (1)
• Long-tailed Duck backcrossed with eider species (1)
• Red-breasted Merganser backcrossed with King or Spectacled Eider (1)

A principal component analyses uncovered three main groups among the sea duck species (described in the text). From: Lavretsky et al. (2021).

Ancient Gene Flow

The results described above nicely fit with general hybridization patterns in birds: rare on an individual basis (only 18 out of 363 individuals), but common at a species level (just count the number of species in the list). But the sea duck story does not end here. Next, the researchers explored the genomes of the sea duck species for signs of ancient introgression. These analyses suggested gene flow between the ancestors of scoters and mergansers, and between the ancestors of scoters and goldeneyes. However, it is difficult to pinpoint the exact species involved in these ancient introgression events. It could entail hybridization between the ancestors of extant species, or between extinct lineages that left their genetic signature in present-day species (i.e. ghost introgression). Regardless of the details, introgression clearly played a pivotal role in the evolutionary history of sea ducks.

A phylogenetic tree of sea ducks. However, their evolutionary history might be better represented as a network given the signatures of ancient introgression. From: Lavretsky et al. (2021).

A Hybrid Species?

And then there is the Steller’s Eider (Polysticta stelleri). The genetic analyses indicated that this species contains genetic ancestry from Long-tailed Ducks and several eider species. Specifically, 94-98% of genetic variation in the Steller’s Eider came from three other eider species, while the remaining 2-6% was assigned to Long-tailed Ducks. These patterns raise the possibility that the Steller’s Eider is a hybrid species. If that is the case, its unique plumage might be the result of transgressive segregation (i.e. hybrids showing extreme phenotypes). However, the hybrid species hypothesis remains to be tested with more detailed analyses. There is still the possibility that the genetic make-up of the Steller’s Eider is the outcome of several, independent hybridization events (similar to the situation in Red-breasted Goose, Branta ruficollis). Indeed, the researchers indicate that “while we cannot definitively identify the source of the shared genetic variation, we provide strong evidence for a complex evolutionary history of shared variation between true Eiders, long-tailed ducks, and Steller’s eider that will require additional sampling of individuals and genomes to fully understand.” To be continued.

References

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.

Featured image: Steller’s Eider (Polysticta stelleri) © Ron Knight | Wikimedia Commons

Some peculiar duck hybrids provide insights into the evolution of sexual dichromatism

A closer look at captive hybrids between the Chiloé Wigeon and the Philippine Duck.

The Avian Hybrids Project officially started in 2015 with the publication of a short paper in Ibis. My main goal was to gather the scientific literature on avian hybridization in one place. Later on, I started publishing blog posts on a wide range of bird-related topics, summarizing many scientific publications. The blog post you are currently reading is number 400. An important milestone for the Avian Hybrids Project. To celebrate this achievement, I decided to cover one of my own recent papers that was recently published in the journal Ecology and Evolution. In this paper, Jan Harteman and I describe some interesting hybrids between the Chiloé Wigeon (Mareca sibilatrix) and the Philippine Duck (Anas luzonica).

Plumage Patterns

Let’s start from the beginning. In the spring of 2020 Jan contacted me with an intriguing story. A female Chiloé Wigeon had mated with a male Philippine Duck, producing four hybrids. He asked me if these hybrids would be interesting to study in more detail. We decided to let them grow up to see how their plumage patterns would develop. And we were in for a surprise! Chiloé Wigeon and Philippine Duck are both sexually monochromatic (i.e., both sexes look alike). But the hybrids showed clear sexual dichromatism. The males exhibited the iridescent green head pattern of the Chiloé Wigeon, whereas the females developed the dark crown and eye stripe of the Philippine Duck.

This observation triggered me to dive into the literature and learn more about the genetic and developmental mechanisms of sexual mono- and dichromatism in ducks. It turns out that the showy male plumage is the default state in both sexes, while the production of estrogen culminates in the development of cryptic female-type plumage. The plumage patterns in the hybrids were probably the outcome of different levels of estrogen production. Chiloé Wigeon and Philippine Duck belong to different branches on the evolutionary tree, diverging about 13 million years ago. It is thus likely that sexual monochromatism arose independently in these species, with different modifier genes controlling the production of estrogen. More detailed genetic analyses will be needed to identify these genes.

In addition, the hybrids formed two pairs, of which one pair produced a clutch of six unfertilized eggs. It is difficult to pinpoint the exact reason for infertility of these eggs. One of the sexes (or both) might be sterile, or fertilization was unsuccessful due to genetic incompatibilities between sperm and egg cells. Another interesting question to explore further.

Pictures of the parental species – (a) Chiloé Wigeon and (b) Philippine Duck – and their hybrids (c–d). © Jan Harteman.

Documenting Hybrids

This study takes me back to the basis of the Avian Hybrids Project: documenting hybridization in birds. In the current scientific climate of big grants and fancy genomic tools, it is easy to forget about the simple description of interesting observations. Other notable examples include the pairing between between a Cerulean Warbler and a Black-throated Blue Warbler in Indiana (see this blog post) or the reports of several fairywren hybrids (see this blog post). The disdain for such descriptive studies by some researchers was nicely illustrated by one of the reviewers who wrote that “there is not really a whole lot here.” Luckily, the other reviewer and the editor were enthusiastic about our work, resulting in a swift acceptance.

In addition, this paper highlights the importance of reporting avian hybrids in the scientific literature. If Jan had not contacted me, these hybrids might have gone unnoticed. Getting an overview of all known avian hybrids is a daunting task. Eugene McCarthy has produced a nice overview of hybridization in birds with his “Handbook of Avian Hybrids of the World”. However, several hybrid records in this book are unreliable and require further investigation (a quest that I have recently started with by checking the reliability of tinamou hybrids). The description of hybrids in peer-reviewed papers is sorely needed to obtain a better overview of the incidence of hybridization in birds. And who knows? Maybe some hybrids might even provide some crucial insights into fundamental scientific questions, such as the evolution of sexual mono- and dichromatism in ducks.

References

Ottenburghs, J. & Harteman, J. (2021) Sexually dichromatic hybrids between two monochromatic duck species, the Chiloé wigeon and the Philippine duck. Ecology and Evolution.

Featured image: Hybrids between the Chiloé wigeon (Mareca sibilatrix) and the Philippine duck (Anas luzonica) © Jan Harteman.

How often do Barrow’s Goldeneye and Common Goldeneye hybridize?

A genetic study detected only one hybrid individual.

Estimating the incidence of hybridization on an individual level is extremely challenging. Recently, Nicholas Justyn and his colleagues used data from the citizen science database eBird to investigate how often birds hybridize in North America. They found that 0.064% of the reported sightings were hybrids. This estimate can probably be regarded as a lower bound, because birdwatchers tend to under-report common hybrids (as I argued together with David Slager in a response to this study, and see also this paper by Hannah Justen and her colleagues). These papers highlight the difficulty of estimating hybridization rates in wild birds, even if you are focusing on just two species. In some cases, hybrids might be difficult to identify morphologically or the study species live in remote areas. Here, genetic data can be a valuable asset (see for example this blog post on penguin hybrids).

A recent study in the Journal of Avian Biology attempted to estimate the incidence of hybridization between Barrow’s Goldeneye (Bucephala islandica) and Common Goldeneye (B. clangula). Field observations suggest that these sea ducks occasionally interbreed (see the Anseriformes page for an overview), but the exact proportion of hybrids in their populations remains unknown.

Gene Flow

Joshua Brown and his colleagues followed a genetic approach and took a closer look at the DNA of 61 individuals. Using two different genetic markers (microsatellites and ddRAD-seq), they found evidence for one hybrid individual. Additional demographic analyses pointed to an evolutionary model of allopatric speciation with secondary contact. The migration rate, however, amounted to less than one migrant per generation in both directions. In other words, an extremely low estimate of gene flow due to hybridization. These findings indicate that hybrid goldeneyes are a rare sighting. The authors attribute this low occurrence of hybridization to “assortative mating, differences in habitat preferences and territorial behaviors exhibited during mate pairing.”

The genetic analyses, based on ddRAD-seq (figure b) and microsatellites (figure c), detected one hybrid individual (indicated with an arrow). Barrow’s Goldeneye (black) and Common Goldeneye (grey) are clearly genetically distinct. From: Brown et al. (2020) Journal of Avian Biology.

Population Structure

In addition to quantifying hybridization, the researchers also investigated population structure in both species. Previous work reported clear population structure in terms of mitochondrial DNA, suggesting that females rarely disperse between breeding grounds (mtDNA is inherited through the female line). The same study also found no overlap in winter band recoveries among individuals marked in Alaska and British Columbia. Based on these patterns, the researchers expected to find some population structure in the nuclear DNA as well.

Surprisingly, there was no discernable population structure in the microsatellites or the ddRAD-seq data. This lack of nuclear population structure might be explained by dispersal of males between colonies. However, Barrow’s Goldeneye shows a high level of breeding site fidelity in both sexes, with the average yearly return rate of males (67%) roughly identical to that of females (63%). The situation in Common Goldeneyes is unknown due to lack of data. But not all males are equal. It is known that subadult males return to natal nesting grounds significantly less often than subadult females and are thus much more likely to disperse between colonies. Hence, the authors argue “that homogeneity across the nuclear genome most likely results from high levels of juvenile male dispersal despite high mtDNA structure.”

Low levels of genetic differentiation between populations of Barrow’s Goldeneye and Common Goldeneye, indicating a lack of population structure in nuclear DNA. From: Brown et al. (2020) Journal of Avian Biology.

References

Brown et al. (2020). High site fidelity does not equate to population genetic structure for common goldeneye and Barrow’s goldeneye in North America. Journal of Avian Biology, 51(12).

Featured image: Common Goldeneye (Bucephala clangula) © Becky Matsubara | Wikimedia Commons

This paper has been added to the Anseriformes page.

A mallard mystery: Unraveling the genetic basis of green egg color

A series of experiments narrows the mystery down to one candidate gene.

You might not think about it when you prepare eggs for breakfast, but the color of an egg is an important ecological trait. The eggshell color is mainly determined by a mixture of three types of pigments: protoporphyrin-IX, biliverdin-IX and biliverdin zinc chelate. These pigments provide protection against damaging solar radiation and play a role in thermoregulation, creating the ideal conditions for embryonic development. Moreover, egg color is often a crucial factor in brood parasites that mimic the egg color of their unsuspecting hosts. In some species, the color of eggs is even used as a signal for female quality (see for example this blog post on hoopoes).

Despite this variety of roles in ecological and evolutionary processes, the genetic basis of egg color remains largely unknown. A recent study in the journal Molecular Ecology focused on the green egg color of a Chinese domesticated duck breed (the Jinding duck). What genes underlie this peculiar green color?

Comparing Genomes

The researchers performed a series of clever experiments to determine the genetic basis of green egg color (similar to the case of the mosaic canary described in this blog post). First, they compared the genomes of reciprocal crosses between Pekin ducks (with white eggs) and mallards (with green eggs). The genome-wide search identified a broad target region on chromosome 4 that was significantly associated with egg color. This region was explored in greater detail by analyzing the genomes of seven indigenous duck populations that differ in the coloration of their eggshells. The divergence between green-shelled and white-shelled populations could be traced to a small section of the target region, containing two genes: PRKG2 and ABCG2. The second gene (ABCG2) codes for a membrane transporter that carries biliverdin, one of the pigments that contribute to egg shell coloration. Sounds like the perfect candidate gene.

The genome-wide association study (GWAS) pointed to a region on chromosome 4 that might contain the genes underlying green egg color. From: Liu et al. (2021) Molecular Ecology.

Gene Expression

The researchers did not stop at identifying the candidate gene. They performed more detailed analyses to understand how this gene contributes to the green egg color. Eggshell formation takes place in the uterus, so the researchers measured gene expression in uterine tissues from four populations. As expected, ABCG2 was expressed at a higher level in the green-shelled groups compared to the white-shelled groups. Moreover, the data revealed that ABCG2 produces five distinct isoforms (i.e. different proteins that derive from the same DNA sequence). This is achieved by combining different sections of the gene during protein translation. In the mallard case, the third isoform (ABCG2-X3) is expressed most.

Finally, the researchers took a closer look at the DNA sequence of ABCG2. Does it contain genetic differences that clearly separate green-shelled from white-shelled ducks? Using a collection of sophisticated analyses (including ATAC-sequencing and a luciferase assay), the search could be narrowed down to one genetic variant on nucleotide 47,418,074 of chromosome 4. This position is targeted by different transcription factors (ATF and c/EBPα) in white-shelled compared to green-shelled ducks: ATF binds the white-shelled variant, whereas c/EBPα binds the green-shelled variant. The green egg color of the Jinding duck can thus be explained by a regulatory change in the expression of a specific isoform of the ABCG2-gene. The resulting protein is active in the uterus where it transports the pigment biliverdin from the blood onto the developing egg shell. Mystery solved.

A specific isoform of the candidate gene (ABCG2-X3) shows the highest expression level in green-shelled ducks. From: Liu et al. (2021) Molecular Ecology.

References

Liu et al. (2021). A single nucleotide polymorphism variant located in the cis‐regulatory region of the ABCG2 gene is associated with mallard egg colour. Molecular Ecology, 30(6), 1477-1491.

Featured image: Green eggs in the nest of a duck © Smudge9000 | Flickr

The role of hybridization in the domestication of geese

Gene flow patterns between wild and domestic geese changed during the domestication process.

Geese probably saved the Roman empire. The Gauls were secretly climbing the Capitoline Hill when they woke up a flock of geese. The noise of the honking geese alarmed the Romans that managed to fend off the Gaul attack. This story indicates that geese were already domesticated in Roman times. The earliest reliable reference to domestic geese can be traced back even further, to the 8th century BCE in Homer’s Odyssey. But when did humans domesticate geese?

This question is difficult to answer because different domestic goose breeds are derived from two species: the Greylag Goose (Anser anser) and the Swan Goose (Anser cygnoides). In addition, some breeds are probably the outcome of hybridization between these species, and several breeds are known to hybridize with their wild relatives. Marja Heikkinen and her colleagues tried to solve this complex puzzle of hybridization and domestication with genetic data. Their results recently appeared in the journal G3: Genes | Genomes | Genetics.

Gene Flow

The researchers collected samples from wild and domestic geese across Eurasia. Genomic data revealed a clear separation between wild Greylag Geese, European domestic breeds and Chinese domestic breeds. Demographic analyses suggested that the wild and domestic lineages diverged around 14,000 years BCE (although the authors indicate that this divergence time has wide confidence intervals and will need to be confirmed with more detailed analyses). This divergence was followed by several episodes of hybridization and consequent gene flow.

At the onset of domestication, gene flow was primarily from domestic into wild geese. Probably, geese were not intensively managed at that time, allowing domestic geese to interbreed with their wild relatives. Moreover, goose farmers might occasionally restock their flock by collecting eggs from the wild and raising them in captivity. By Medieval times, goose-keeping was a common phenomenon and the escaped birds would regularly mix with wild flocks. This resulted in gene flow in the opposite direction, from the wild into the domestic population. A patterns that is still visible in present-day goose populations.

A principal component analysis indicates a clear separation between wild Greylag Geese (blue), European domestic breeds (green) and Chinese domestic breeds (red). Some locations, such as Turkey, show admixture from different lineages.

Turkish Hybrids?

Interestingly, the amount of gene flow from wild into domestic goose populations differs between countries. In Finland and Norway – where goose rearing is not so popular – the genetic influence of wild birds is relatively low. In the Netherlands, however, the genetic signs of hybridization is more pronounced. This can be explained by the popularity of waterfowl collections in this country and the fact that many Greylag Geese winter in the Dutch fields (and a large proportion is even present year-round). There is thus ample opportunity for domestic geese to interbreed with wild ones.

Turkish goose populations showed genetic signatures from both European and Chinese domestic breeds. They might thus be a hybrid population between these independently domesticated breeds. Alternatively, the Turkish geese might represent the ancestral genetic variation of Greylag Geese, supplemented with some gene flow from Chinese breeds. More research is needed to solve this mystery and determine whether the domestication of geese started in Turkey.

References

Heikkinen, M. E., et al. (2020). Long-term reciprocal gene flow in wild and domestic geese reveals complex domestication history. G3: Genes, Genomes, Genetics, 10(9), 3061-3070.

Featured image: Domestic geese © Hippopx

This paper has been added to the Anseriformes page.

Why the “Red-breasted Meidum Goose” is probably not an extinct species

Convincing evidence to consider it an extinct species is currently lacking.

“Extraordinary claims require extraordinary evidence”, said Carl Sagan in the television program Cosmos. This statement came to mind when I read several news articles with bold titles, such as “4,600-Year-Old Egyptian Painting Depicts Extinct Species of Goose” and  “Ancient art reveals extinct goose.” These headlines refer to a recent study on the Meidum Geese, a 4,600-year-old Egyptian painting that historians described as “one of the great masterpieces of the Egyptian animal genre”. It depicts several goose species, including two Red-breased Geese (Branta ruficollis). However, a closer look at these colorful paintings reveals some striking differences with this well-known species. Could the Meidum Geese represent an extinct taxon?

 

Tobias Criteria

To answer this question, Anthony Romilio applied the Tobias criteria to the artwork. This method scores the characters between closely related taxa on a scale of dissimilarity. Low scores indicate that the taxa are very similar and could be classified as a single taxon (e.g., subspecies ), while high scores point to many dissimilarities and possibly distinct species. The first goose on the artwork showed low scores when compared to Greylag Goose (Anser anser) or Bean Goose (Anser fabalis), while the second painted goose most likely corresponds to a Greater White-fronted Goose (Anser albifrons). The third species of the Meidum Geese, however, did not accurately reflect Red-breasted Goose. Romilio writes that “This raises the possibility that the ‘Medium Geese 3′ may illustrate a distinct, yet now extinct goose population as has been suggested previously.”

The Meidum Geese. The top left and bottom right paintings could correspond to Greylag Goose of Bean Goose. The pair in the top right are most likely Greater White-fronted Geese. But what about the Red-breased Geese?

 

Counterarguments

Stating that there was an extinct goose species in ancient Egypt based on a painting is quite an extraordinary claim. In contrast to the news headlines, the paper provides a very balanced analysis of this claim. And although it is a possibility, I would argue that the extraordinary evidence to back this claim is currently missing. I am not convinced for two main reasons:

1. Unique Artwork. The Meidum Geese are the only depiction of a Red-breased Goose in Egyptian art (to my knowledge). This suggests that they might have been seen as rare vagrants, and were later painted from the artists’ memory which can explain the differences. Moreover, if the painting represented an extinct taxon, you could expect independent artwork depicting this colorful bird.
2. Not Accurate Enough. In the paper, the author argues that other species are realistically painted and hence we can assume that the “Red-breasted Meidum Goose” is also realistic. First, this reasoning is contradicted by the analysis of Meidum Goose 1, which could be either a Greylag Goose or a Bean Goose. If the paintings were accurate, you should be able to tell the difference. And second, the other goose species on the artwork belong to the genus Anser, which is not known for its colorful members. These “grey geese” do not leave much room for artistic freedom, in contrast to the colorful patterns on the Red-breasted Goose.

 

Fossils and Genomes

What could convince me that the “Red-breasted Meidum Goose” does represent an extinct species? Another clue might come from the fossil record or genetic analyses. Recently, a goose skull was discovered on Crete that is similar to the Red-breasted Goose. A morphological analysis of this skull might reveal whether it belonged to an unknown species that is closely related to the Red-breasted Goose. In addition, researchers might be able to extract ancient DNA from the skull and perform a proper phylogenetic analysis.

The genomes of present-day goose species might also hold the key to this mystery. Genomic analyses have uncovered signatures of hybridization events with now extinct species in the genomes of extant species, a phenomenon known as ghost introgression. Given the high levels of hybridization in geese, the extinct Egyptian species might have interbred with the Red-breasted Goose or another goose species. If so, we might be able find genetic traces of these ancient hybridization events. And if we are lucky, the introgressed regions might provide some insights into the phenotype of this extinct species. I am aware that this is very speculative and wishful thinking. But it would certainly be extraordinary evidence!

 

A Hybrid Goose?

In a discussion on Twitter, someone proposed the possibility of a hybrid. Although I like this suggestion, I do not think it is likely. If it was a hybrid, there was clearly a Red-breasted Goose involved. And hybrids with this species tend to be “drab” and lose their bright red markings.

A putative hybrid between Red-breasted Goose and Barnacle Goose. © Dave Appleton | Flickr.

 

References

Romilio, A. (2021). Assessing ‘Meidum Geese’ species identification with the ‘Tobias criteria’, Journal of Archaeological Science: Reports 36:102834.