Genetic study reveals how four different sparrow species adapted to life in the salt marshes

If you put butter and salt on it, it tastes like salty butter.”

– Terry Pratchett (Moving Pictures)

Salt marshes are a relatively new feature in the North American landscape. The expansion of these habitats occurred only a few thousand years ago. In this short time span, several bird species have quickly adapted to living in these salty conditions. Adaptations include a larger bill to facilitate heat exchange in these open environments and an altered kidney structure to cope with the salty drinking water. Members of the bird family Passerellidae seem to have an inordinate fondness for salt marshes, four lineages have independently colonized this habitat. A recent study in the journal Evolution Letters investigated whether these birds used the same genetic tricks to thrive in this new environment.


A singing Savannah Sparrow © Cephas | Wikimedia Commons


Parallel Evolution

Jennifer Walsh and her colleagues compared the genomes of four salt marsh specialists with their upland cousins (see list below). They wanted to know whether the salt-adapted subspecies survive in the salt marshes due to parallel evolution, which they define as “shared [genomic] regions of elevated differentiation between multiple upland-salt marsh pairs.” Alternatively, differentiated regions that are only found in one subspecies pairs are an example of lineage-specific evolution.

  • Savannah Sparrows (Passerculus sandwichensis nevadensis and Passerculus sandwichensis beldingi)
  • Nelson’s sparrows (Ammospiza nelsoni nelsoni and Ammospiza nelsoni subvirgatus)
  • Song Sparrows (Melospiza melodia gouldii and Melospiza melodia pusillula)
  • Swamp Sparrows (Melospiza georgiana georgiana and Melospiza georgiana nigrescens).

The researchers found no regions of elevated differentiation that were shared by all four subspecies pairs. However, some differentiated regions were shared among two or three pairs. In total, the analyses yielded 33 candidate regions that contained 16 genes with a putative role in adaptation to salt marshes.


A Nelson’s Sparrow © Andy Reago & Chrissy McClarren | Wikimedia Commons



Most of the candidate genes were involved in osmoregulation (i.e. maintaining the fluid balance and the concentration of salts to keep the body fluids from becoming too diluted or concentrated). This makes sense because salty environments can disturb the osmotic balance of cells. Interestingly, different osmoregulation genes were under selection in different subspecies pairs.

In Savannah Sparrows, the researchers found WNK2 under selection. This gene plays an important role in regulating cell volume in response to osmotic stress. In Nelson’s Sparrows, MMP17 showed signs of selection. This gene has been linked to drinking behavior and kidney function in mice. In Song Sparrows, yet another gene popped up: MYOF, which is differentially expressed when fish are transferred from fresh to salt water. And in Swamp Sparrows, SLC9A3 has been under selection, a gene that is involved in sodium transport across the cell membrane.

These examples suggest that “these [osmoregulation] pathways are common targets of selection, but the specific genic targets of selection within the pathways differ among species.”


A Song Sparrow © Mdf | Wikimedia Commons


Gene Flow

The researchers also reconstructed the demographic histories of all subspecies pairs. They did this to rule out any demographic factors that might influence their search for differentiated regions. These analyses revealed continuous gene flow between each pair of subspecies. This observation raises the question whether introgression of beneficial alleles might have facilitated adaptation to salt marshes. Indeed, a previous study on Nelson’s Sparrows identified several candidate genes for adaptive introgression. Whether this also occurred in the other lineages remains to be determined.


A Swamp Sparrow © Cephas | Wikimedia Commons



Walsh, J., Benham, P. M., Deane‐Coe, P. E., Arcese, P., Butcher, B. G., Chan, Y. L., … & Shriver, W. G. (2019). Genomics of rapid ecological divergence and parallel adaptation in four tidal marsh sparrows. Evolution Letters.


This paper has been added to the Passerillidae page.


Adventures in the Andes: The Tantalizing Tale of the Torrent Duck

Molecular and morphological analyses uncover three distinct lineages in the Torrent Duck.

The Torrent Duck (Merganetta armata) surely lives up to its name. These beautiful ducks – the males have a striking black and white head and a fire-red bill – fearlessly dive into the rapid waters of the Andes. They have a wide distribution, ranging from southern Chile all the way up to Venezuela. Their widespread occurrence and affinity for wild waters raises an important question: How do the Andean river networks shape the population structure of this species? On the one hand, rivers could promote dispersal and gene flow between distant populations. On the other hand, rivers could act as barriers to gene flow, leading to population differentiation. A recent study in the journal Zoologica Scripta tackled this question and assessed the population structure of this widespread species.


Three Groups

Natalia Gutiérrez-Pinto and her colleagues analyzed the mitochondrial control region of 198 Torrent Ducks. These analyses uncovered three distinct lineages that correspond to previously described subspecies. A Northern Andes group (colombiana) with birds from Colombia, Ecuador, and northern Peru. A Central Andes group (leucogenis) that covers Peru and northwestern Bolivia. And a Southern Andes group (armata) with individuals living in southeastern Bolivia and Argentina.


Analyses of the mitochondrial control region uncovered three distinct lineages that correspond to previously described subspecies of the Torrent Duck. From: Gutiérrez-Pinto et al. (2019) Zoologica Scripta



The distribution of these three groups seems to match the geographic regions delineated by Jon Fjeldså: Páramo, Puna and Southern Andes. The main geographical barriers between these regions are the North Peruvian Low (between Páramo and Puna) and the Bolivian Altiplano (between Puna and Southern Andes). In case of the Torrent Ducks, the Bolivian Altiplano appears to be an effective barriers between the Central and Southern Andes groups. The high elevations of the Tunari mountain range separate both groups.

The role of North Peruvian Low, however, is less clear. This region was not densely sampled in the study, preventing the researchers from assessing potential gene flow across this barrier. Moreover, the North Peruvian Low has a complex topography which might provide Torrent Ducks with small watersheds that connect the Northern with the Central Andes group. More research in this area is needed to characterize this barrier.


A pair of Torrent Ducks in Colombia © Alejandro Bayer Tamayo | Wikimedia Commons



As mentioned above, the three mitochondrial lineages correspond to three previously described subspecies. A morphological analysis of these birds showed that the Northern Andes group (colombiana) is highly differentiation from the other two groups. The differences between the Central (leucogenis) and the Southern (armata) groups is more subtle. Possibly, these birds represent the extremes of a range of phenotypes. There might even be a hybrid zone at some location. Denser sampling is required to figure this out. If it turns out that they hybridize, you will definitely read it on this blog.



Gutiérrez‐Pinto, N., McCracken, K. G., Tubaro, P., Kopuchian, C., Astie, A., & Cadena, C. D. (2019). Molecular and morphological differentiation among Torrent Duck (Merganetta armata) populations in the Andes. Zoologica Scripta.


This paper has been added to the Anseriformes page.

These two White-eye species should be hybridizing, but they don’t…

Despite their recent divergence, Solomons White-eye and Kolombangara White-eye don’t interbreed.

When closely related species come into secondary contact, they often hybridize. In 2002, Trevor Price and Michelle Bouvier estimated that after, on average, 5 million years of divergence birds tend to produce sterile hybrids. After about ten million years of independent evolution, the hybrids are not viable anymore. Hence, it would be surprising to find species pairs markedly younger than 5 million years to show complete reproductive isolation. But that is exactly what two researchers describe in a recent paper in the journal Evolution.


The two species of White-eye in this study. © Sarah Cowles |



Sarah Cowles and Albert Uy investigated a contact zone between the Solomons White-eye (Zosterops kulambangrae) and the Kolombangara White-eye (Z. murphyi) on Kolombangara Island in the Solomon Archipelago. These species diverged about two million years ago and are thus expected to be able to hybridize. However, the genetic analyses (based on 20,000 SNPs) revealed no evidence for gene flow. This suggests that the reproductive isolation between these two passerines is complete.

The researchers searched the literature for other such cases. They found that these White-eyes represent the youngest known case of complete reproductive isolation in sympatric birds tested within a genomic context.


The genetic analyses showed that these White-eyes are clearly distinct. From: Cowles & Uy (2019) Evolution


Isolation Mechanisms

But what is preventing these birds from interbreeding? It could be that these species do not recognize each other as potential partners. They produce different songs and calls. And the size of the white eye-ring is significantly different. Whether the birds use these traits in species recognition remains to be investigated. Another possibility is that the hybrids are not viable due to genetic mismatches. A genomic study in 2015 suggested that White-eyes have elevated rates of genomic evolution, which could result in the rapid accumulation of such genetic mismatches. Clearly, more research is needed here.


Both species produce clearly different song and calls. Could this prevent hybridization? From: Cowles & Uy (2019) Evolution


The Paradox of the Great Speciator

This study might provide a solution to a paradox raised by Jared Diamond and his colleagues. They wondered how these White-eyes (the family Zosteropidae) can diversify so quickly while colonizing a vast geographical range. You would expect that incipient species come into secondary contact during their colonization. Then hybridization and consequent gene flow would prevent further divergence and effectively reverse the speciation process. However, in just two million years, the White-eyes diversified into more than 100 species while spreading to Africa, Asia, Australia and throughout the Indo-Pacific. How can this happen?

Solomons White-eye and Kolombangara White-eye might hold the answer to this paradox: lineages with high dispersal capacities can have high speciation rates if they evolve complete reproductive isolation more rapidly than other lineages. Testing this idea with other pairs of White-eyes will be necessary to see if the solution is correct.


A drawing of Solomons White-eye. © John Gerrard Keulemans | Wikimedia Commons



I wanted to cover this story earlier. The paper was gathering dust at the top of my writing list for some time now. But I waited for the publication of another paper, namely my digest of this study. The journal Evolution provides the opportunity to write short news articles (so-called digests) about selected original research. I wrote one about the White-eye study, which you can read here (although it is a more technical story that covers the same ground as this blog post). Apart from my Avian Hybrids blog, these digests are a great way to spread the latest findings about hybridization in birds. Even if the species under investigation don’t hybridize…



Cowles, S. A., & Uy, J. A. C. (2019). Rapid, complete reproductive isolation in two closely‐related Zosterops White‐eye bird species despite broadly overlapping ranges. Evolution.

Ottenburghs, J. (2019) Digest: White‐eye birds provide possible answer to the paradox of the great speciator. Evolution


This paper has been added to the Zosteropidae page.

Genetic study uncovers a deep split within the Hooded Pitta species complex

A clear split between eastern and western groups with signatures of gene flow between different subspecies.

In the 18th century, the French naturalist Georges-Louis Leclerc, Comte de Buffon published Planches Enluminées D’Histoire Naturelle, a collection of drawings from animals all around the world. One of these drawings depicted the “Merle des Philippines” (the Blackbird of the Philippines). Modern ornithologists know this species as the Hooded Pitta (Pitta sordida). This small passerine, which occurs from India to New Guinea, was generally considered a single species, but the phenotypic variation among different populations suggests this might not be the case. A recent study in the journal BMC Evolutionary Biology provides some genetic support for this idea.


Buffons drawing of the Hooded Pitta, which he called the “Blackbird of the Philippines”.


Plumage Variation

The Hooded Pitta complex is comprised of numerous populations on different Indo-Pacific islands. These populations differ in several plumage traits, such as the color of the forehead and the crown, the amount of red, black and blue on the flanks and the belly, and the size of a white wing patch. Per Ericson and his colleagues tried to reconstruct the evolutionary history of these populations. They sampled the 13 recognized subspecies across the range of this species complex and sequenced their DNA. For interested readers, the genetic analyses were based on mitogenomes, 23 nuclear genes and about 2.1 million SNPs.


A Hooded Pitta in Thailand © J.J. Harrison | Wikimedia Commons


Wallace Line

Reconstructing the evolutionary history of these colorful birds revealed two distinct groups that diverged about 2 million years ago. This split coincides to the Wallace Line, which highlights the striking differences in fauna and flora in the eastern and western parts of the Indo-Australasian archipelago. However, the origin of Wallace Line is much older than the split between the groups within the Hooded Pitta. The most likely scenario is that some birds dispersed across the Wallace Line during the Pleistocene (between 2.5 million and 11.000 years ago) when sea levels were lower.



The distribution of the Hooded Pitta subspecies and their evolutionary relationships. Notice the deep split between eastern and western populations. From: Ericson et al. (2019) BMC Evolutionary Biology


Gene Flow

The researchers could not find consistent patterns within the two groups. It seems that recent gene flow between different populations from the same subspecies has partly erased any geographic patterns in the genetic data. During the Pleistocene, fluctuations in sea levels resulted in occasional land-bridges between the different islands, allowing birds to hop from one island to the next. The consequent bursts of gene flow prevented island populations from diverging from one another.

There has also been some gene flow between different subspecies. One individual from the subspecies forsteni, which lives in the eastern part, showed signatures of gene flow from the western part. In addition, samples in the western clade, bangkana from Bangka Island and palawanensis from Palawan, exhibited signs of admixture. The bangkana individual appears to be admixed between the migratory population on the Asian mainland (cucullata) and nearby populations on Sumatra and Borneo (mulleri). The subspecies palawanensis harboured DNA from sordida and mulleri.


A Hooded Pitta in Singapore © Darren Bellerby | Wikimedia Commons



Ericson, P. G., Qu, Y., Rasmussen, P. C., Blom, M. P., Rheindt, F. E., & Irestedt, M. (2019). Genomic differentiation tracks earth-historic isolation in an Indo-Australasian archipelagic pitta (Pittidae; Aves) complex. BMC Evolutionary Biology19(1), 151.


This paper has been added to the Pittidae page.

High levels of gene flow between different populations of North American Scoters

A genetic study finds weak population structure in three Scoter species.

Some bird species are difficult to study. Take, for instance, the Scoters (genus Melanitta). These black ducks spend most of their time at sea where they aggregate in big flocks. Several breeding colonies and wintering areas have been found, but ornithologists don’t know how these populations are structured. Do birds switch between breeding areas or do they stay loyal to one location? These questions can be answered using genetic data, as shown by a recent study in the journal Ecology and Evolution.


A Surf Scoter © Alan D. Wilson | NaturesPicsOnline


Five (or three) species

Sarah Sonsthagen and her colleagues focused on three North American: the Black Scoter (M. americana), the Surf Scoter (M. perspicillata) and the White-winged Scoter (M. deglandi). They also analyzed samples from two European species: the Common Scoter (M. nigra, which is sometimes considered conspecific with the Black Scoter) and the Velvet Scoter (M. fusca, which is sometimes seen as conspecific with the White-winged Scoter). So, depending on your taxonomic preference, there are three or five species of Scoter in this study. The researchers used a combination of ddRAD-seq and microsatellites to probe the genetic population structure of these Scoters.


A White-winged Scoter © Matt MacGillivray | Flickr



The three North American species showed weak population structure, indicating high levels of gene flow between different locations. In birds, this pattern is mostly attributed to male-biased dispersal. Males choose a partner at the wintering grounds and follow her back to the breeding area. However, female Surf Scoters and White-winged Scoters can occasionally switch between migration routes. For example, the White-winged Scoters that nest in central Canada are a mixture of birds wintering on the Atlantic and the Pacific coast. There is evidence for a female using different wintering areas in different years.

Black Scoters showed some population genetic structure that coincides with their breeding distribution. There appears to be a barrier – behavioral of physical – between birds from Alaska and the Atlantic region.


A Black Scoter © Peter Massas | Flickr


Gene Flow

The three North American species were clearly differentiated from their European cousins. There was no evidence for gene flow between different continents. The pattern is most likely driven by the use of distinct wintering areas.

In addition, the researchers found no signs of gene flow between species. Hybrids between several species (e.g., White-winged Scoter x Surf Scoter) have been observed. However, such hybridization events are probably too rare to influence the genetic structure of these species. The courtship and copulation displays of different Scoter species are quite distinct and could serve as a behavioral barrier.



Sonsthagen, S. A., Wilson, R. E., Lavretsky, P., & Talbot, S. L. (2019). Coast to coast: High genomic connectivity in North American scoters. Ecology and Evolution9(12), 7246-7261.


The paper has been added to the Anseriformes page

Central-American Wood-partridges are older than expected

They probably diverged in the Pliocene, about 3.6 million years ago.

The origin of new species is mostly linked to particular environmental conditions in the past. In my own research on the evolutionary history of geese, for example, I showed that the diversification within two genera (Anser and Branta) happened about 2 million years ago, coinciding with the glacial cycles during the Pleistocene. In fact, conditions during the Pleistocene – commonly known as the ice ages – have been called upon to explain the origin of numerous species around the world.

Let’s have a look at the situation in Central America. Here, the Isthmus of Tehuantepec represents an important geographical barrier.  In 2010, Brian Barber and John Klicka found that several avian species pairs diversified across the Isthmus during the Pleistocene. They linked this diversification to the habitat fragmentation that occurred during the ice ages. Does this scenario hold for all birds in this area?


Long-tailed Wood-partridge © Nick Athanas | Flickr


Three Species

A recent study in the journal Molecular Phylogenetics and Evolution explored the evolutionary history of the Dendrortyx Wood-partridges. These birds occur in the highlands of Central America. Three species have been described: the Bearded Wood-partridge (D. barbatus), the Buffy-crowned Wood-partridge (D. leucophrys) and the Long-tailed Wood-partridge (D. macroura). Whitney Tsai and her colleagues extracted DNA from several specimens of these species and included Elegant Quail (Callipepla douglasii) as an outgroup.

The genetic analyses – based on 1516 SNPs – showed that these three species started diverging about 3.6 million years ago. This estimate predates the Pleistocene ice ages and suggests that other environmental factors have driven the evolution of Wood-partridges in Central America. The researchers think that tectonic activity in the late Miocene and early Pliocene might have played a role. But it is difficult to exclude other influences, such as climate change.


The evolutionary history of the Wood-partidges extends back more than 3 million years ago. From: Tsai et al. (2019) Molecular Phylogenetics and Evolution



This study also highlights the importance of museum specimens. In some cases, it is impossible or unethical to collect samples, because the species under investigation are endangered or extinct. Museum specimens provide an excellent solution. The authors nicely summarize this implication in the conclusions-section:

In these particular cases, DNA from museum specimens offers the only way to assess biodiversity by leveraging the efforts of collectors over the last several hundred years. In this study, the legacy of these collectors reveals previously undescribed phylogenetic diversity in the Mesoamerican Highlands and shows that both the Pleistocene ice ages and events in the Pliocene were important to diversification of cloud forest birds.


Buffy-crowned Wood-partridge © David Rodríguez Arias | Flickr



Barber, B. R., & Klicka, J. (2010). Two pulses of diversification across the Isthmus of Tehuantepec in a montane Mexican bird fauna. Proceedings of the Royal Society B: Biological Sciences, 277(1694), 2675-2681.

Tsai, W. L., Mota-Vargas, C., Rojas-Soto, O., Bhowmik, R., Liang, E. Y., Maley, J. M., Zarza, E. & McCormack, J. E. (2019). Museum genomics reveals the speciation history of Dendrortyx wood-partridges in the Mesoamerican highlands. Molecular Phylogenetics and Evolution, 136, 29-34.

Off-color Orioles: Hybrids or abnormal plumage patterns?

A high frequency of aberrantly plumage orioles in Australia and New Guinea. 

Occasionally ornithologists come across a bird with aberrant plumage. Abnormal plumage patterns can be the result of problems with feather growth or issues with pigmentation. Alternatively, aberrant plumage can point to hybridization. In some cases, the bird shows characteristics of both parents. But how can you confidently discriminate between these explanations? One way is to sequence the DNA of the bird in question. And that is exactly what Leo Joseph and his colleagues did when they stumbled upon some orioles (genus Oriolus) with peculair plumage. Their findings recently appeared in the journal Emu – Austral Ornithology.


An Olive-backed Oriole © Patrick_K59 | Wikimedia Commons


Noticeable, aberrant plumage

During field work in Papua New Guinea, three researchers (Leo Joseph, Ian Mason and Alex Drew) were collecting orioles. They captured four individuals, representing two species: the Olive-backed Oriole (O. sagittatus) and the Green Oriole (O. flavocinctus). Three of them were “unremarkable” members of their species. The fourth, however, caught the attention of its captors. This specimen, that received the name ANWC B56219, was “an adult female also from Bensbach [with] an easily noticeable, aberrant plumage unknown in Oriolus.”



What could explain this remarkable plumage pattern? There are several explanations: (1) it could be a new, undescribed taxon, (2) an individual with aberrant plumage, or (3) a hybrid. Regarding the hybrid hypothesis, there were three possible species involved: the two species collected in the area (Olive-backed Oriole and Green Oriole) and a third species, the Brown Oriole (O. szalayi). To solve this mystery, the researchers sequenced the mitochondrial gene ND2, which has been shown to be diagnostic for the three species, for the aberrant specimen.


A Green Oriole © Francesco Veronesi | Wikimedia Commons


Specimens A and B

The analyses revealed that ANWC B56219 had the ND2-gene of Olive-backed Oriole. The plumage trait resembled Green Oriole in the front and Olive-backed Oriole in the back. You can compare this bird in the large figure below (marked as specimen A) with the other species. Together, these observations point to a hybrid. Because of the mitochondrial gene (which is passed on through the female line), we can deduce that this bird is probably the result of hybridization involving a female Olive-backed Oriole followed by several generations of backcrossing with Green Orioles.

The genetic analyses also incovered an unexpected result. An unremarkable Olive-backed Oriole carried the mtDNA of Green Oriole. Close inspection of the plumage indicated that the dorsal parts (crown and mantle) do indeed resemble Green Oriole. Here, we have a bird that is the result of hybridization between a female Green Oriole and a male Olive-backed Oriole. It is marked as specimen B in the figure below.


An overview of all two hybrids (Specimens A and B) in comparison to the “pure” species. From: Joseph et al. (2019) Emu – Austral Ornithology


More Hybrids?

A search through several museums uncovered more noticeable orioles. In the American Museum of Natural History (ANHM), they found an aberrant Olive-backed Oriole from 1937. The label indicated that it was a female from “Bugi, 3 miles east of mouth of Mai Kussa River.” The Port Moresby (PM) collection housed a bird that was previously described as a rare grey morph of the Green Oriole. Are these two specimens also hybrids? The plumage characteristics of the 1937 specimen suggest a hybrid origin. The grey morph, however, seems to be an aberrant individual and not a hybrid. Unfortunately, genetic data is missing for these birds. Perhaps they will figure it out in the future. And then you can read all about it at the Avian Hybrids Project.



Joseph, L., Dolman, G., Iova, B., Jønsson, K., Campbell, C. D., Mason, I., & Drew, A. (2019). Aberrantly plumaged orioles from the Trans-Fly savannas of New Guinea and their ecological and evolutionary significance. Emu-Austral Ornithology, 1-10.


This paper has been added to the Oriolidae page.

Pecking in the Pyrenees: No gene flow across a hybrid zone between Eurasian and Iberian Green Woodpecker

Genetic study finds few admixed individuals in the contact zone.

Today I learned a new word: yaffling. It refers to the sound a Eurasian Green Woodpecker (Picus viridis) makes when it flies off (click here to listen to it). I have heard this loud “laughter” during countless forest walks. Indeed, this distinctive call echoes throughout most of the European forests because this species occurs from northern Sweden all the way down to southern France. When you cross the Pyrenees into Spain, however, you will meet another woodpecker species – the Iberian Green Woodpecker (P. sharpei) – that produces a similar call. A recent study in the Journal of Ornithology explored a contact zone between these two woodpeckers.


Eurasian Green Woodpecker © MoniqueWN | Wikimedia Commons


Le Pic Vert

The Iberian and Eurasian Green Woodpecker might sound alike, they differ by several plumage features. The color of the face is most obvious: the Iberian birds have a grey face whereas the face is black in Eurasian woodpeckers. In the Pyrenees, which we crossed in the introduction of the blog post, individuals with intermediate plumage have been observed. Already in the 1920s, Jouard asked if there was “une nouvelle forme de Pic Vert” in the Pyrenees (For my non-French-speaking readers: a new form of Green Woodpecker).


No Gene Flow

This observation, along with more recent ones, suggests that there is a hybrid zone between these Woodpeckers. Jean-Marc Pons and his colleagues collected samples within and outside the putative contact zone. Based on a suite of 19 molecular markers, they characterized the genetic structure in this region. They found “no introgression of nuclear loci in allopatric populations located on both sides of the contact zone, which thus acts as an efficient barrier to gene flow.” This finding contributes to the idea that Eurasian and Iberian Green Woodpecker are distinct species.


Iberian Green Woodpecker © Luis García | Wikimedia Commons


Tension Zone

In the contact zone, the researchers found several individuals that carried DNA from both species. This indicates that although hybridization occurs, the genes are not flowing between the species. There is probably some selection against hybrids. Based on these findings, the contact zone is most likely a so-called tension zone. This particular type of contact zone occurs when the effects of dispersal of parental species into the zone and selection against hybrids balance each other.

Cline analyses revealed that the hybrid zone is about 245 kilometers wide and centered in the area between Béziers and Montpellier (for more on cline theory, you can read this blog post). This seems like the perfect place for a hybrid zone, given that the University of Montpellier is known for its excellent evolutionary research.



Pons, J. M., Masson, C., Olioso, G., & Fuchs, J. (2019). Gene flow and genetic admixture across a secondary contact zone between two divergent lineages of the Eurasian Green Woodpecker Picus viridis. Journal of Ornithology, 1-11.


This paper has been added to the Piciformes page.

Back from the brink of extinction: The remarkable recovery of the Crested Ibis

The severe bottleneck has left its footprints in the genomes of these birds.

Seven. There were only seven individuals of the Crested Ibis (Nipponia nippon) in 1981. China and Japan started extensive captive breeding programs to save this species from extinction. Currently, the Crested Ibis is still endangered but the population has increased to over 2,000 individuals. A remarkable recovery. However, the severe bottleneck has left its traces in the genome of the Toki (its Japanese name). A study in the journal Current Biology documented the genetic legacy of this history by comparing contemporary samples with historical ones.


A crested Ibis in the Xi’an QinLing Wildlife Park (China)  © Danielinblue | Wikimedia Commons


Low Genetic Diversity

An international group of scientists sequenced the genomes of 57 historical samples (dating between 1841 and  1922) and eight contemporary birds. These genomes revealed that the historical samples clustered according to their geographic origin. The contemporary samples formed a separate group, indicating that they can be traced back to a few individuals.

The clustering analyses suggests that a lot of genetic diversity has been lost over time. Indeed, nucleotide diversity is considerably lower in the contemporary samples. Moreover, several genetic loci that were polymorphic (i.e. had multiple variants) in the historical samples have gone to fixation (i.e. only one variant is left) in present-day birds. You can compare this situation with a pool filled with differently colored balls. Over time, more and more colors disappear until you are left with only one color. A dramatic loss in diversity.


Nucleotide diversity across the genomes of historical (blue) and contemporary (red) samples. From: Feng et al. (2019) Current Biology


Inbreeding Depression

These results point to high levels of inbreeding. Not that surprising, given that the population was reduced to only seven individuals. To quantify the severity of this inbreeding, the researchers counted the number of homozygous deleterious mutations in the genomes of these birds. Homozygous indicates that both chromosomes have the same variant and deleterious refers to the negative effect on the fitness of the individual. Several diseases are caused by this type of mutation. This analysis revealed that the number of these mutations has doubled in less than 100 years. That is a severe bottleneck.

The seriousness of this situation is nicely exemplified by the Major Histocompatibility Complex (MHC). This set of genes is essential for the immune response that protects individuals from harmful bacteria and viruses. Ideally, the MHC is very variable, allowing it to swiftly react to a broad range of pathogens. In the Crested Ibis, however, the MHC has experienced a drastic decrease in genetic diversity. This makes these birds susceptible for different diseases.


The genetic diversity of MHC is drastically reduced in contemporary birds (outer ring), as shown by the large stretches of low diversity regions (dark-blue). From: Feng et al. (2019) Current Biology



Although the Crested Ibis has made a remarkable recovery, the footprints of the severe bottleneck are still visible in their genomes. The low genetic diversity renders these birds vulnerable to future perturbations. It is thus essential to continue the conservation efforts to ensure the survival of this beautiful bird.



Feng, S., Fang, Q., Barnett, R., Li, C., Han, S., Kuhlwilm, M., Zhou, L., Pan, H., Deng, Y., Chen, G., Gamauf, A., Woog, F., Prys-Jones, R., Marques-Bonet, T., Gilbert, M. T. P. & Zhang, G. (2019). The genomic footprints of the fall and recovery of the crested ibis. Current Biology29(2), 340-349.

How many species of Red-shouldered Hawk are there?

Which subspecies deserve a species status?

The taxonomy of raptors can be complicated as shown by several species complexes, such as the Northern Goshawk (Accipiter gentilis) and Palearctic buzzards (genus Buteo). Another example is the Red-shouldered Hawk (Buteo lineatus), a common sit-and-wait predator from North America. Currently, ornithologists recognize five subspecies. One subspecies (elegans) occurs in the west of the US, while the remaining four can be found in the east (alleni, extimus, lineatus, and texanus). Do some of these subspecies actually represent distinct species? A recent study in the journal Ecology and Evolution tried to figure it out.


A Red-shouldered Hawk in Florida © Andy Morffew | Wikimedia Commons


East vs. West

George Barrowclough and his colleagues collected samples across the entire range of the Red-shouldered Hawk. They sequenced the mitochondrial ND2 gene and two nuclear introns. These genes revealed a clear difference between the eastern and western populations. The western birds in California – originally described as a distinct species Buteo elegans by Cassin (1855) – are clearly a separate species. This conclusion is corroborated by morphological data: California birds have a much richer rufous coloration and can be diagnosed using the number and size of tail bands.


Morphological differences between western (elegans) and eastern (lineatus and extimus) populations of the Red-shouldered Hawk. From: Complete Birds of North America, 2006.


Florida Population

What about the four subspecies the eastern part of the range? Three subspecies – alleni, lineatus and texanus – were genetically similar. The fourth subspecies (extimus), however, was genetically distinct from the rest (see haplotype network below). This subspecies, which occurs in Florida, is substantially smaller and paler than the other three subspecies.

Does the Florida population represent a different species? The genetic analyses uncovered extensive gene flow between this population and the northern birds. Following the Biological Species Concept (which emphasizes reproductive isolation), the Florida birds would be a well-differentiated subspecies. However, the authors of the present study argue that the population in Florida should be considered a distinct species:

However, our opinion is that the Florida peninsula population has had a separate evolutionary history from that of the other eastern birds and consequently represents an appropriate unit for studies of diversification and historical biogeography; therefore, it represents a phylogenetic species. This would not be apparent were the taxon to be simply regarded as a subspecies in the B. lineatus complex.

In this regard, they follow the Evolutionary Species Concept, which states that “A species is an entity composed of organisms which maintains its identity from other such entities through time and over space, and which has its own independent evolutionary fate and historical tendencies.” Hence, we can recognize three species in the Red-shouldered Hawk:

  • Red-shouldered Hawk (B. lineatus)
  • California Red-shouldered Hawk (B. elegans)
  • Florida Red-shouldered Hawk (B. extimus)

You can check this recent blog post for a longer discussion on avian species concepts.


Haplotype network of the ND2 gene in the Red-shoulderd Hawk and a map of the geographic distribution of these haplotypes. This analysis suggests three separate species (represented in different colors). From: Barrowclough et al. (2019) Ecology and Evolution



Barrowclough, G. F., Groth, J. G., Mauck, W. M., & Blair, M. E. (2019). Phylogeography and species limits in the red‐shouldered hawk (Buteo lineatus): Characterization of the Northern Florida Suture Zone in birds. Ecology and Evolution, 9(11):6245-6258.


This paper has been added to the Accipitriformes page