Breaking Barriers: Low levels of gene flow among subspecies of the Grey Shrike-thrush

How the Pleistocene climate shaped the distribution of an Australian songbird.

The Pleistocene, the geological epoch that lasted from about 2.5 million to 11,700 years ago, is often referred to as the Ice Age. Large parts of Eurasia and North America were covered by ice sheets, pushing bird populations into separate refugia where they consequently diverged into different (sub)species, see for example the Ground Tit in Asia and the Red-bellied Woodpecker in North America.

Australian biologists, however, would refrain from referring to the Pleistocene as the Ice Age. During this period, Australia remained practically ice-free. Instead, cycles of aridity and sea-level fluctuations resulted in biogeographical barriers that shaped the avifauna of this continent. A recent study in the journal Heredity focused on the Grey Shrike-thrush (Colluricincla harmonica). How did the “Pleistocene Dry Age” influence this species?

Colluricincla harmonica

The Grey Shrike-thrush © John Manger, CSIRO | Wikimedia Commons


Five Subspecies

Currently, there are five subspecies of the Grey Shrike-thrush, corresponding to five regional populations across Australia: rufiventrisbrunnea, superciliosa, harmonica and strigata. These populations are separated by particular biogeographic barriers. For example, subspecies rufventris and brunnea do not overlap in western Australia due to the Canning Barrier. To test which barriers have influenced the current populations structure, Annika Mae Lamb and her colleagues sequenced several genetic markers (mtDNA, nuclear introns and microsatellites) and reconstructed the evolutionary history of the Grey Shrike-thrush.

The genetic analyses revealed five genetic clusters that correspond to the five subspecies. As expected, the timing of the splits corresponds to the emergence of the different biogeographical barriers. This suggests that these barriers did indeed drive the divergence of the five subspecies.


Evolutionary relationships between the subspecies (based on mtDNA) and their distribution across Australia. From: Lamb et al. 2019 Heredity


Explaining Disagreement

There was, however, some disagreement between the genetic markers. The evolutionary relationships based on mtDNA differed from ones using nuclear markers. This indicates that hybridization might have influenced the history of these subspecies. Indeed, at locations where populations overlapped, the researchers detected low levels of gene flow. These patterns can be explained by two – not mutually exclusive – processes: sex-biased dispersal or adaptive introgression.

First, male birds might disperse further than females and mate with members from the neighboring subspecies. This will lead to the exchange of nuclear genes (which are passed on by both sexes), but not of mtDNA (which is only passed on by females). Because females stay loyal to their geographical location, population structure based on mtDNA will correspond to geographical distributions. Nuclear genes, on the other hand, will follow the dispersal patterns of the males. Second, certain mitochondrial variants might provide an advantage in harsh, arid climates. When such a variant is exchanged by hybridization, it will quickly spread through the population. It is thus possible that climate-driven selection drove adaptive introgression of mtDNA.

Colluricincla harmonica2

A Grey Shrike-trush enjoying its meal with a free drink. © Patrick_K59 | Wikimedia Commons



Further research is needed to figure out which of these processes – male dispersal or adaptive introgression – has been more important. The researchers thus conclude that “this and other studies should trigger a genome-wide investigation into sex-biased population processes including dispersal, mitochondrial introgression and mitonuclear evolution.”



Lamb, A.M., da Silva, A.G., Joseph, L., Sunnucks, P. & Pavlova, A. (2019) Pleistocene-dated biogeographic barriers drove divergence within the Australo-Papuan region in a sex-specific manner: an example in a widespread Australian songbird. Heredity


This paper has been added to the Pachycephalidae page.


Is the Great White Heron a distinct species?

A population in Florida holds the key to answer this question.

A species is a population of organisms that actually or potentially interbreed in nature, right? I wish it was that simple. This Biological Species Concept is just one of the many concepts that have been put forward to decide what is a species. Recently, more and more taxonomists are using an integrative approach in which they evaluate different species concepts before making a decision. In some cases, all concepts point in the same direction and the decision is easy. In other cases, different concepts lead to different taxonomic arrangements, resulting in heated debates. A recent study in the journal The Auk on the species status of the Great White Heron (Ardea herodias occidentalis) concerns the second scenario. Is it a distinct species or not?


A Great White Heron in Cuba © Charles J. Sharp | Wikimedia Commons.


Mixed Breeding Pairs

The Great White Heron used to treated as a separate species. But in 1973, the American Ornithologists’ Union decided to consider it a subspecies of the Great Blue Heron (A. herodias). This decision was based on several studies that reported the occurrence of mixed breeding pairs between Great White Heron and Great Blue Heron in Florida. However, these studies were largely based on anecdotal evidence. Nobody actually quantified the frequency of mixed pairs in this population. Therefore, Heather McGuire and her colleagues decided to study this population in greater detail. They collected data on morphology, genetics and breeding behavior to assess the species status of the Great White Heron.


Morphology and Genetics

Apart from the clear distinction in color, there were no significant differences in morphology between individuals with blue or white plumage. However, there were several individuals with intermediate gray plumage – often referred to as Wurdemann’s Herons – which could be hybrids between Great White Heron and Great Blue Heron. This conclusion is supported by genetic data. Based on a set of 13 microsatellites, the researchers uncovered two genetic groups: one consisting of three subspecies of the Great Blue Heron (fannini, herodias and wardi) and the other consisting of the Great White Heron. Moreover, intermediate individuals showed admixture from these two groups.


A Great Blue Heron flying over Rockport Beach Park, Texas © Alan D. Wilson | Wikimedia Commons.


Assortative Mating

The most convincing line of evidence comes from the breeding behavior. The researchers surveyed 114 nests in the Florida population. Most nests were occupied by pairs with the same color (white-white or blue-blue). Only a few nests contained mixed breeding pairs (white-blue). The observed pattern was significantly different from random mating. It seems that these herons choose their partner based on similar plumage color. In other words, they mate assortatively.

In addition, the blue and white herons breed at different times. This could explain the occurrence of some mixed pairs. Blue herons are relatively rare in the Florida population and might settle for a less desired partner instead of not breeding at all.


The Verdict

So what would you say? Based on the data described above, are the Great White Heron and the Great Blue Heron separate species? The authors believe that the weight of evidence tilts the scale to the Great White Heron as a separate species. They apply the General Lineage Concept of Kevin de Queiroz, which states that a species is a metapopulation with its own evolutionary trajectory separate from other such metapopulations. Indeed, the Great White Heron is separated from the Great Blue Heron by the following features:

  • diagnostic plumage (white vs. blue)
  • behavior (mate choice and timing of breeding)
  • habitat (saltwater vs. fresh/brackish water)

The only issue is some gene flow between blue and white herons. But as this website shows, that shouldn’t be a problem…



de Queiroz, K. (2007) Species concepts and species delimitation. Systematic Biology, 56:879-886.

Eisenmann, E., Amadon, D., Banks, R.C., Blake, E.R., Howell, T.R., Johnson, N.K., Lowery, G.H., Parkes, K.C. & Storer, R.W. (1973) Thirty-Second Supplement to the American Ornithologists’ Union Check-List of North American Birds. The Auk, 90:411-419.

McGuire, H.L., Taylor, S.S. & Sheldon, F.H. (2019) Evaluating the taxonomic status of the Great White Heron (Ardea herodias occidentalis) using morphological, behavioral and genetic evidence. The Auk, 136(1):uky010.


This paper has been added to the Pelecaniformes page.

Species in the making: Genomic analyses reveal incipient speciation in the Ground Tit

Isolation in glacial refugia and the subsequent differentiation in habitat and morphology shaped the evolution of the Ground Tit.

Many bird species have adapted to life at the Qinghai-Tibet Plateau, about 4500 meters above sea level. Most of these species are endemic to this area and show no genetic structure. In technical terms, they are panmictic. A notable exception is the Ground Tit (Pseudopodoces humilis). This small passerine is comprised of two distinct populations, one in the central region of the Qinghai-Tibet Plateau and one in the east margin. A recent study in the journal Zoological Scripta reconstructed the evolutionary processes that shaped these two populations.

ground tit.jpg

A Ground Tit on the lookout in Nyingtri Prefecture, Tibet, China. © Cherry Wong | Oriental Bird Images


Desert or Ice Ages?

Previous genetic work on the Ground Tit uncovered two distinct lineages. But the origin of these populations was unclear. One study – using the mitochondrial control region – estimated the divergence of these lineages at ca. 1 million years ago. This would indicate that the separation was driven by the desertification of the Qaidam Basin. Another study – based on two mitochondrial genes – calculated that these populations diverged about 300,000 years ago. This date points to a glacial refugia scenario in which these populations became isolated in separate areas during the Pleistocene ice ages. To determine which scenario is more likely, a group of Chinese scientists sequenced the genomes of these birds and performed a suite of genetic and ecological analyses.


Demographic and Ecological Modelling

The genomic data confirmed the existence of two distinct lineages. Demographic modelling supported a scenario where these populations diverged about 100,000 years ago and subsequently continued exchanging genes. Gene flow was primarily from the edge to the platform population. This result suggests that the two populations have been isolated in separate refugia.

To validate this hypothesis, the researchers turned to ecological niche modelling. Reconstructing the range of the Ground Tit revealed that during the Last Glacial Maximum (about 20,000 years ago) both populations were smaller and resided in distinct margins of the plateau.


A pair of Ground Tits near Hongyuan (Tibetan Plateau), Sichuan, China. © Ulrich Weber | Oriental Bird Images


Current Differentiation

A detailed look at the current populations shows that they are also differentiated in habitat and morphology. The platform population is restricted to higher altitudes and colder climates compared to the edge population. Regarding morphology, the populations differ in body weight, wing length and tail length. Putting everything together, the researchers nicely summarize their findings.

Our results based on genome‐wide data revealed an incipient speciation with unidirectional gene flow from the edge to platform populations, suggesting that both refugial isolation and the subsequent habitat differentiation and morphological
divergence have contributed and maintained the incipient speciation pattern between the platform and edge populations of the Ground Tit.



Jiang, Z.Y., Gao, B., Lei, F.M. & Qu, Y.H. (2019) Population genomics reveals that refugial isolation and habitat change lead to incipient speciation in the Ground tit. Zoologica Scripta, Early View.

Qu, Y. H. & Lei, F.M. (2009) Comparative phylogeography of two endemic birds of the Tibetan plateau, the white-rumped snow finch (Onychostruthus taczanowskii) and the Hume’s ground tit (Pseudopodoces humilis). Molecular Phylogenetics and Evolution, 51:312-326.

Yang, S.J., Yin, Z.H., Ma, X.M. & Lei, F.M. (2006) Phylogeography of ground tit (Pseudopodoces humilis) based on mtDNA: Evidence of past fragmentation on the Tibetan Plateau. Molecular Phylogenetics and Evolution, 41:257-265.


This paper has been added to the Paridae page.

Museum specimens reveal phenotypic introgression in a Scrub-Jay contact zone

By Devon DeRaad

The Blue Jay (Cyanocitta cristata) is a classic charismatic backyard bird of Eastern North America, but it’s lesser known cousins have recently stolen the show, at least scientifically. Closely related to the well-known Blue Jay, the genus Aphelocoma is comprised of the Scrub-Jays, Mexican Jays, and Unicolored Jays, which inhabit Western North America and Mexico. While not the most flashy “blue jays” in North America, this genus has received extensive scientific attention over the past decade, and has quickly become a model for understanding the processes of allopatric lineage diversification, local environmental adaptation, and hybridization upon secondary contact.


Three Distinct Groups

The former Western Scrub-Jay was a classic example of a polytypic species, with close to a dozen subspecies recognized across Western North America and Mexico. However, DNA sequence data indicated that among this multitude of locally adapted forms, there were three genetically distinct groups, corresponding with the previously described California Scrub-Jay, Woodhouse’s Scrub-Jay, and Sumichrast’s Scrub-Jay. The California Scrub-Jay was thusly described as a unique species, while Woodhouse’s and Sumichrast’s were lumped as Woodhouse’s Scrub-Jay, due to a lack of information about the degree of phenotypic differentiation and genetic introgression between the two forms.


A Woodhouse’s Scrub-Jay perched on Joshua tree, Red Rock Canyon, southern Nevada © Stan Shebs | Wikimedia Commons


Contact Zone

The Moore Laboratory of Zoology, where I worked as an Occidental College undergraduate researcher, has an extensive collection of Woodhouse’s Scrub-Jay specimens from throughout Mexico. Using this valuable series of specimens, and extra specimens from near the contact zone, which we loaned from other natural history museums from around the country, we set out to discover exactly what was going on between Woodhouse’s and Sumichrast’s Scrub-Jays. We used digital calipers to take careful measurements of the tail, wing chord, tarsus, bill length, bill width, and bill depth, of 133 specimens from throughout Mexico, and used light spectroscopy to quantify the color of the back feathers of each specimen.

Our results show that Sumichrast’s Scrub-Jay is significantly larger in overall body size, and has brown back feathers, as opposed to the blue back feathers of the Woodhouse’s Scrub-Jays in northern Mexico. Our results align with Pitelka’s description of Sumichrast’s Scrub-Jay from his seminal 1951 work on the genus ‘Speciation and ecologic distribution in American jays of the genus Aphelocoma’. Additionally, our results shed new light on the contact zone between Woodhouse’s and Sumichrast’s Scrub-Jays, where Pitelka described intermediate specimens as ‘scant’. By accessing specimens unavailable to Pitelka and analyzing them with modern methods, we reveal phenotypic introgression between the groups, with clinal transitions in body size and back color centered concurrently near Mexico City. These results indicate that the transition between these forms is likely a case of introgression upon secondary contact, following a period of divergence in geographic and genetic isolation.


The clines across the phenotypic hybrid zone between subspecies of the Woodhouse’s Scrub-Jay (from DeRaad et al. 2019 The Auk)


Speciation in Action

This new discovery is exciting because the existence of a contact zone between these two divergent forms creates a natural experiment, where we can study speciation in action. In the future we hope to collect modern specimens from the contact zone and use genetic sequencing to identify whether hybridization is occurring and if so, at what frequency. These future genetic studies will help us understand the genomic architecture of introgression between divergent populations that have come back into contact, and will help us make more informed taxonomic decisions about how to recognize Woodhouse’s and Sumichrast’s Scrub-Jays.


Woodhouse’s and Sumichrast’s Scrub-Jays © Maggie Schedl



DeRaad, D. A., Maley, J. M., Tsai, W. L. E., & McCormack, J. E. (2019). Phenotypic clines across an unstudied hybrid zone in Woodhouse’s Scrub-Jay (Aphelocoma woodhouseii). The Auk, 136(2).

Gowen, F. C., Maley, J. M., Cicero, C., Peterson, A. T., Faircloth, B. C., Warr, T. C., & McCormack, J. E. (2014). Speciation in Western Scrub-Jays, Haldane’s rule, and genetic clines in secondary contact. BMC evolutionary biology, 14(1), 135.

Pitelka, F. A. (1951). Speciation and ecologic distribution in American jays of the genus Aphelocoma. University of California Press. Berkeley and Los Angeles, CA.


Do you want to write a guest post for Avian Hybrids? Just write me at the contact page.

The Niches of the Nuthatch: How local adaptation and competition have shaped the present-day distribution of the Eurasian Nuthatch

Different lineages of the Eurasian Nuthatch have different evolutionary histories.

When you see a bird crawling head down on a tree, it is probably the Eurasian Nuthatch (Sitta europaea). This small passerine is found throughout Europe and Asia across a wide range of climatic niches. Surprisingly, the number of distinct lineages in this species is unknown. A recent study in the journal Molecular Ecology explored this mystery.


The Eurasian Nuthatch © Paweł Kuźniar | Wikimedia Commons


Six Lineages

Yu-Chi Chen, Masoud Nazarizadeh and their colleagues collected samples across Eurasia and sequenced several molecular markers to reconstruct the evolutionary history of the Eurasian Nuthatch. The genetic analyses revealed six distinct lineages corresponding to different geographical regions, namely Europe, North Asia, East Asia, Caucasus, Northern Iran and Southwestern Iran.

The geographical distributions of these six lineages are immediately adjacent to each other but do not significantly overlap (i.e. parapatric distributions). To understand why these lineages do not mix, the researchers turned to Ecological Niche Modelling. These models predict the past geographical distribution of a species based on environmental data. These analyses indicated that different lineages of the Eurasian Nuthatch have been influenced by different ecological and evolutionary histories.

The northern lineages (Europe and North Asia) experienced frequent range contractions and expansions driven by the fluctuating climate during the ice ages. The southern lineages (East Asia, Caucasus, Northern Iran and Southwestern Iran), on the other hand, show a more stable history.

nuthatch tree.jpg

The six parapatric lineages in the Eurasian Nuthatch, based on the mitochondrial ND2 gene (from: Chen et al. 2019 Molecular Ecology).


No Mixing

The parapatric distribution of these lineages raises an intriguing question: why did the lineages not merge? The researchers think that different processes are preventing the mixing of lineages in the north and the south. Northern lineages have been geographically isolated during the ice ages. During this separation, they adapted to different climatic conditions. When they came into secondary contact, they could not invade the range of the other lineage. This is an example of local adaptation.

The situation in the south was slightly different. These lineages were not geographically isolated and could thus freely mix. Why didn’t this happen? The answer could be competitive exclusion, which refers to the situation where two species competing for the same limiting resource cannot coexist. In this case, the limiting resource might be tree holes which Nuthatches use as nesting sites. More research is needed to test this hypothesis.

In summary, the parapatric distribution of the Eurasian Nuthatch lineages have been shaped by local adaptation in the north and competitive exclusion in the south. Whether this is a common pattern among Eurasian bird species remains to be determined.


An Eurasian Nuthatch in a nesting cavity © Jente Ottenburghs



Chen Y., Nazarizadeh, M., Lei, F., Yang, X., Yao, C., Dong, F., Dong, L., Zou, F., Drovetski, S.V., Liu, Y., Huang, C. & Hung, C. (2019) The niches of nuthatches affect their lineage evolution differently across latitude. Molecular Ecology, 28(4): 803-817.

An Egyptian Goose is not a goose

But what is it?

The names of bird species can be misleading. For example, several North American species called sparrows, such as White-crowned Sparrow (Zonotrichia leucophrys) or Fox Sparrow (Passerella iliaca), are actually buntings. These “American Sparrows” are more closely related to Old World buntings (family Emberizidae) than they are to the Old World sparrows (family Passeridae). A similar case concerns the Egyptian Goose (Alopochen aegyptiaca). Despite its name, it is not a goose. But then, what is it?


The Egyptian Goose is not a goose. © Andreas Trepte | Wikimedia Commons


The True Geese

First of all, what are “true geese”? This group of waterbirds comprises two genera – Anser and Branta – in the subfamily Anserinae. The genus Anser contains the grey geese and the white geese (sometimes placed in a separate genus, Chen), while the genus Branta houses the black geese. Below you can see all the species in this subfamily. The tree in the middle depicts the evolutionary relationships between the species, based on my own work (you can find the original paper here or read the summary here).

Goose Circle with names.jpg

The evolutionary relationships among the True Geese. Adapted from Ottenburghs et al. 2016 Molecular Phylogenetics and Evolution)


Where does the Egyptian Goose fit in?

The Egyptian Goose does not occur in the circle above. When you reconstruct the evolutionary history of the family Anatidae (ducks, geese and swans), The Egyptian Goose ends up in a group with several shelducks, such as Common Shelduck (Tadorna tadorna) and Australian Shelduck (Tadorna tadornoides). This nicely illustrates that the Egyptian Goose is not a goose, but a duck!

Anseriformes phylogeny.jpg

The evolutionary position of the Egyptian Goose (green) shows that it does not belong to the True Geese (red). Adapted from Donne-Goussé et al. 2002 Molecular Phylogenetics and Evolution.



So, there you have it: the Egyptian Goose is actually a duck (and probably a shelduck). But I can understand the confusion. With its long neck it does resemble a true goose. Moreover, Egyptian Goose has hybridized with several goose species, such as Greylag Goose (Anser anser) and Canada Goose (Branta canadensis). However, hybridization is very common among waterfowl and Egyptian Goose has interbred with numerous other – not so closely related – species, including Muscovy Duck (Cairina moschata) and Mallard (Anas platyrhynchos). You can find an overview of all known Egyptian Goose hybrids here.

To conclude, you can keep using the name Egyptian Goose but just keep in mind that it is actually a duck…

egyptian goose x tadorna hybrid.jpg

An Egyptian Goose x Ruddy Shelduck hybrid  (left) with Egyptian Goose and Ruddy Shelduck. © Joern Lehmhus |

Mallard x Egyptian Goose.JPG

An Egyptian Goose x Mallard hybrid © Dave Appleton |



Donne-Goussé, C., Laudet, V., & Hänni, C. (2002). A molecular phylogeny of anseriformes based on mitochondrial DNA analysis. Molecular Phylogenetics and Evolution, 23:339-356.

Ottenburghs, J., Megens, H.-J., Kraus, R.H.S., 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.

Combinatorial Speciation: Reassembling of old genetic variation facilitates rapid speciation and adaptive radiation

A fresh way of looking at the origin of species.

The origin of new species – or speciation – is a slow process that takes thousands to millions of years. In general, populations become geographically isolated and slowly accumulate incompatible mutations. There are numerous examples of such allopatric speciation events, see for example this blog post on hummingbirds and crombecs. But what about rapid speciation events and adaptive radiations where numerous species arise in the evolutionary blink of an eye? These scenarios seem incompatible with the slow accumulation of mutations. A recent paper in the journal Trends in Ecology & Evolution provides a possible solution to this paradox: combinatorial speciation!


Old Genetic Variants

The genomic approach to speciation has revealed that many genetic variants that underlie speciation events are often much older than the actual time when the species originated. Take, for instance, the apple maggot species complex (Rhagoletis pomonella). These species emerged in about 200 years, whereas the genomic variation responsible for their origin dates back to about 1.6 million years ago. Similarly, genetic variation associated with adaptation to different food sources predates the radiation of Darwin’s Finches on the Galapagos Islands.

But where did this genetic variation come from? David Marques, Joana Meier and Ole Seehausen propose two main sources: standing genetic variation and hybridization. In their paper, the authors provide several cases. I will complement their list with some examples from the Avian Hybrids blog.

darwin's finches.jpg

The genetic variation that fueled the diversification of Darwin’s Finches was already present (from: Grant 1991 – Scientific American)


Standing Genetic Variation

Standing genetic variation refers to ancestral variation that is already present in the population and can be utilized immediately. An example of using old genetic variants concerns the vinous-throated parrotbill (Sinosuthora webbiana). This small songbird occurs on the Asian mainland and the island of Taiwan. There, it lives up to 3100 meters above sea level. A recent genomic study compared island populations from the lowlands and the highlands to understand how these birds adapted to living at high altitude. The analyses revealed that most genetic variants under selection in the highland populations are also present in birds from the mainland. This suggests that these variants are not new mutations but represent old genetic variants that proved to be useful in a high altitude setting. In other words, adaptation from standing genetic variation. You can read the whole story in this blog post.

vinous-throated parrotbill

The vinous-throated parrotbill (from:


Introgressive Hybridization

The second source of old variants is introgressive hybridization. Gene flow between different species can fuel the rapid origin of new species. Indeed, I have written before about hybridization as the engine of adaptive radiation. The authors provide several reasons for why hybridization is a powerful source for rapid speciation.


Filtered Genetic Variation

Hybridization will immediately augment genetic variation, the fuel for adaptive evolution. A classical example is the radiation of cichlid fishes in the African lakes. Moreover, the genes that are acquired by hybridization have already been filtered by selection in the donor species. Hence, deleterious alleles are less likely to be exchanged between species. New mutations, on the other hand, are often (slightly) deleterious.

A nice example of this process concerns subspecies of the White Wagtail (Motacilla alba) which are characterized by different head patterns. Some ornithologists think that these patterns are the outcome of a few genes that are being shuffled around by hybridization. You can read more about this interesting system here.


Different head patterns of the White Wagtail (from:


Extreme Phenotypes

Interactions between divergent genes can result in transgressive segregation, namely extreme phenotypes that lie outside the range of the interacting species. These novel phenotypes can facilitate adaptation to particular ecological niches. The likelihood of transgressive segregation partly depends on the divergence between the hybridizing species. In highly divergent species, there are more ways in which old variants can be reordered into new combinations.

Hybridization between recently diverged taxa is less likely to drive the rapid origin of new species. However, it can facilitate parallel speciation, the recurrent evolution of similar species. This has been documented in threespine sticklebacks where marine populations have repeatedly colonized freshwater habitats. It might also explain the recurrent evolution of plumage patterns in Wheatears (see here for the complete story of these birds).


Male eastern black-eared wheatear at Ipsilou Monastery, Lesvos, Greece © Mark S Jobling | Wikimedia Commons


Sorting of incompatibilities

Incompatible mutations are unlikely to arise in a single population because they will be weeded out by selection. But these mutations could arise in separate lineages and consequently be brought together by hybridization, leading to the rapid origin of new species. This probably happened in the Italian Sparrow (Passer italiae), a hybrid species between House Sparrow (P. domesticus) and Spanish Sparrow (P. hispaniolensis). The title of this paper Hybrid speciation through sorting of parental incompatibilities in Italian sparrows – is quite clear about the underlying process. If you are interested in this case, you can read more about it here and here.

italian sparrow

The Italian Sparrow (from


Large Effects

Introgression can result in the transfer of large-effect haplotypes that contain multiple coadapted genes. These regions of large phenotypic or ecological effect can help populations respond quickly to new challenges. Inversions – regions in the DNA that have been flipped around and contain numerous genes – are a good example of such large-effect haplotypes. Classic examples of important inversions in birds include the Ruff (Calidris pugnax) and the White-throated Sparrow (Zonotrichia albicollis). See this blog post for an overview of inversions in avian evolution.


The three ruff phenotypes (faeder, satellite & territorial) are caused by an inversion (from:


Combining Views

In summary, the reassembly of old genetic variants into new combinations can facilitate adaptive radiation and rapid speciation. How common this combinatorial speciation is, remains to be determined. However, it seems like a plausible mechanism to explain numerous radiations.

While reading this paper, I remembered playing around with similar ideas during my PhD. Searching through my dusty PhD-archive, I came across this figure (which didn’t make it into the final version of the dissertation). I was on the right track but didn’t synthesize it into a common framework. To put it in Thomas Henry Huxley’s words when he read Darwin’s book On the Origin of Species: “How extremely stupid not to have thought of that.”

Adaptive Potential

Some thoughts from my PhD work…



Marques, D.A., Meier, J.I. & Seehausen, O. (2019) A Combinatorial View on Speciation and Adaptive Radiation. Trends in Ecology & Evolution.

Mastering Malaria: The Hawaiian ‘Amakihi uses a variety of genes to combat avian malaria

Genetic analyses reveal selection for certain gene classes, but not the same genes.

Malaria is not only a human problem, birds have to cope with it too. Avian malaria,  caused by the parasite Plasmodium, occurs globally and is spread by mosquitoes. One of these mosquito vectors Culex quinquefasciatus has been introduced on Hawaii where avian malaria has impacted the radiation of Hawaiian Honeycreepers. At least seven extinction events and the population declines of the surviving species can be attributed to avian malaria. Birds have several strategies for dealing with malaria. They can try to avoid it or adapt to it. Hawaiian honeycreepers have done both: some populations moved to higher elevations where the mosquitoes cannot survive, while other populations remained in the lowlands and developed immunity to the disease.



A few members of the Hawaiian honeycreeper radiation (from:


Adapting ‘Amakihi

A recent study in the journal Molecular Ecology focused on the ‘Amakihi (Chlorodrepanis virens) which consists of both susceptible populations at high altitude and tolerant populations in low elevation. Loren Cassin-Sackett and her colleagues wanted to pinpoint the genetic changes responsible for the tolerance of these birds. Therefore, they probed the genomes of the ‘Amakihi populations for genes under positive selection using a suite of statistical tests.


The ‘Amakihi © Bettina Arrigoni | Wikimedia Commons


MHC and others

The analyses revealed some predicted genes, such as the major histocompatibility complex (MHC). This set of genes codes for cell surface proteins essential for the immune system to recognize pathogens, such as bacteria and viruses. The MHC molecules bind to the pathogens (specifically their antigens) and present them on the cell surface for recognition by the appropriate T-cells that consequently eliminate the pathogens.

In addition, several candidate genes popped up. Most of them are other infection- and immune-related genes, such as Toll-like receptors and interferons. An interesting candidate gene that is not involved in the immune response codes for an erythrocyte membrane protein. This protein is used by Plasmodium (the pathogen causing malaria) to cause cells to aggregate so it can easily infect more red blood cells. In the ‘Amakihi, this gene might be under positive selection to prevent the formation of such aggregations.


The ‘Amakihi © Sharif Uddin | eBird


Selection on gene classes, not specific genes

I have written before that it is always dangerous to tell just-so-stories based on a collection of outlier genes. The researchers are aware of this and state that “genes inferred with these approaches should be treated not as conclusive genes involved in malaria protection, but as candidates for further studies.” However, the fact that some of these candidate genes were found in multiple analyses suggests that they might be more than just candidates.

Comparing the candidate genes between different immune populations revealed an interesting pattern. Different genes were under selection in different populations. These genes, however, did belong to the same classes, namely infection- and immune-related genes. This finding nicely illustrates that evolution is partly predictable (selection on the same gene classes) and partly contingent on population-specific variation (selection on specific genes). Selection works with the available material to help individuals overcome challenges. In this case, the ‘Amakihi birds needed to fend off malaria and it didn’t matter which genes they used to do it. As long as it works…



Cassin-Sackett, L., Callicrate, T.E. & Fleischer, R.C. (2019) Parallel evolution of gene classes, but not genes: Evidence from Hawai’ian honeycreeper populations exposed to avian malaria. Molecular Ecology, 28:568-583.