Selection on metabolism and memory in a moving Chickadee hybrid zone

Genetic study confirms experimental work on black-capped and Carolina chickadee.

Hybrid zones are rarely static. In a recent review, Ben Wielstra stated that “the commonality of contemporary hybrid zone movement—with shifts in hybrid zones tracked over years to decennia—cannot be disputed, given the many examples available.” An excellent example of a moving hybrid zone can be found in North America where populations of black-capped (Poecile atricapillus) and Carolina (P. carolinensis) chickadee interbreed. Genetic studies indicated that this hybrid zone is moving northward in response to climate change. As the minimum daily winter temperature increased, Carolina chickadees can expand their range to the north where they meet the closely related black-capped chickadees. This hybrid zone is quite narrow (less than 60 kilometres), which suggests strong selection against hybrids.

But what kind of selection is acting on the hybrids? A quick look at several experimental studies provides some possible answers. Physiological experiments indicated that hybrids have higher basal metabolic rates, which may be due to metabolic inefficiency. And other experiments revealed that hybrids also exhibit deficiencies in learning and memory (you can read the entire story in this blog post). If you were to scan the genomes of these species for genes under selection, you can expect to find genes related to metabolism and brain function to pop up.


A Carolina chickadee © Dan Pancamo | Wikimedia Commons


Metabolism and Memory

We now have some straightforward hypotheses to test. This is a refreshing approach to speciation genomics. A lot of studies just data-mine a genomic data set for genetic outliers and build a story around these. Although this approach can be fruitful, you run the risk of telling just-so stories. In the chickadee case, however, there have clear predictions: the genetic outliers should be involved in metabolism or brain function. Dominique Wagner and his colleagues analyzed genomic data for 154 individual birds to put these predictions to the test. They published their findings in the journal Evolution.

And lo and behold: the researchers found what they were looking for! They write that “our results suggest that genes underlying metabolic and neural signaling pathways may experience consistent selection across the chickadee hybrid zone.” The analyses pointed to a significant over-representation of genes involved in “regulation of metabolic process” and “catabolic process”. This suggests that hybrids might encounter deficiencies in metabolic processes due to genetic incompatibilities. In addition, several genetic outliers play a role in learning and memory function. For example, one set of genes is classified as “glutamatergic synaptic transmission”. Interestingly, glutamate is known to affect learning capacity in rats and mice. This is clearly a good candidate for further research to elucidate the exact mechanism behind this hybrid breakdown.


The genomic analyses in this study confirmed the findings from earlier genetic work, showing that the hybrid zone move northwards. From: Wagner et al. (2020) Evolution



The findings of this study make intuitive sense if you know the biology of these small songbirds. Chickadees are able to overwinter in cold environments, partly by caching food for winter. To survive the cold winters, they have to efficiently regulate their metabolism and remember where they hid their food. Hybrids experience metabolic issues and have bad memory, which probably compromises their chances of survival.

Interestingly, the selective pressures on hybrids seem to vary over time. Although the main biological processes were consistently under selection, the genetic outliers varied between years. This suggests that different metabolic and cognitive pathways are selected depending on the environmental conditions of the season. Perhaps a year with heavy snowfall favors birds that can locate their food stash despite a homogeneous white landscape, while an extremely cold year puts more strain on a particular metabolic pathway. As always more research is needed to figure this out. The ornithologists will keep working and the hybrid zone will keep moving.



Wagner, D. N., Curry, R. L., Chen, N., Lovette, I. J., & Taylor, S. A. (2020). Genomic regions underlying metabolic and neuronal signaling pathways are temporally consistent in a moving avian hybrid zone. Evolution.


This paper has been added to the Paridae page.

Surprisingly high genetic diversity in an island species: What happened to the Raso Lark?

The estimation of genetic diversity is extra complicated due to some special sex chromosomes.

Birds have two sex chromosomes: Z and W. A bird with one of each (ZW) will be female and a bird with two Z-chromosomes will be male. Simple, right? But biology wouldn’t be biology if there weren’t any exceptions. Members of the avian superfamily Sylvioidea have weird sex chromosomes. Some sections of other chromosomes – namely 4A, 3 and 5 – have fused with the traditional sex chromosomes, giving rise to enlarged neo-sex chromosomes (you can read the details in this blog post).  A recent study in the journal Biology Letters added another chromosomes to the mix: in the zitting cisticola (Cisticola juncidis) part of chromosome 4 is now part of a sex chromosome. 

Apart from making the evolution of avian sex chromosomes more complicated (and more interesting), these findings also have implications for population genomic studies. For example, if you want to calculate the genetic diversity of a population, these neo-sex chromosomes can wreak havoc. Female birds have only one member of a sex chromosome pair instead of the usual two (i.e. they are hemizygous). The same goes for the sections on other chromosomes that fused with the sex chromosomes. If you don’t know that these chromosome-sections are now also hemizygous and you treat them as “normal” autosomes (i.e. the non-sex chromosomes), you will make errors in calculating genetic diversity.


The Raso Lark © Justin Welbergen | Wikimedia Commons


Genetic Diversity

In a recent paper in Proceedings of the Royal Society B, Elisa Dierickx and her colleagues illustrated the dangers of these neo-sex chromosomes using the Raso Lark (Alauda razae). This species is endemic to the small uninhabited island of Raso in Cape Verde. Latest estimates suggest that the population has been fluctuating between about 50 and 1,500 individuals. The researchers estimated the genetic diversity of this island population. When they accounted for the neo-sex chromosomes, genetic diversity (calculated as average nucleotide diversity, π) was 0.001. This means that there is, on average, one difference in DNA sequence every 1000 base pairs when comparing two individuals. When neo-sex chromosomes are included in the calculations, this estimate almost doubles to 0.0019. That is a huge change, given that these sections only represent 12% of the genome.


The proportion of heterozygous sites on several chromosomes are extremely high in females  (red lines) compared to males (blue lines). This pattern indicates the formation of neo-sex chromosomes. From: Dierickx et al. (2020) Proceedings of the Royal Society B


Population Size

Island species tend to have lower population sizes than mainland species, resulting in lower levels of genetic diversity. And indeed, the genetic diversity of the Raso Lark is lower compared to a mainland species, such as the Eurasian skylark (Alauda arvensis) with π equal to 0.0114. However, when we transform the genetic diversity of the Raso Lark to an effective population size, we end up with an intriguing result. Effective population size (Ne) is a quite abstract concept in population genetics. For now, just envision it as a measure for the historical population size. Doing the calculation, we find an effective population size of 50,000. That is much higher than the census population size of maximum 1,500 individuals. What is going on here?

To understand this fascinating finding, the researchers ran several demographic analyses. It turns out that the population size of the Raso Lark was much larger in the past, after an expansion about 110,000 years ago. Recently, the population experienced a dramatic decrease in population size that seems to coincide with the settlement of Cape Verde by humans in 1462. This recent population bottleneck failed to eliminate the high genetic diversity of the large population. The following analogy explains the process. Imagine you have a jar with 50,000 colorful marbles, representing 10,000 distinct colors. If you now sample 1,500 marbles randomly, you will still end up with a very diverse set of marbles because there are so many distinct colors. The Raso lark might not be a very flamboyant bird, but its evolutionary history is definitely quite colorful.


Two demographic analyses indicated a population expansion about 110,000 years ago and a very recent bottleneck. From: Dierickx et al. (2020) Proceedings of the Royal Society B



Dierickx, E. G., Sin, S. Y. W., van Veelen, H. P. J., Brooke, M. D. L., Liu, Y., Edwards, S. V., & Martin, S. H. (2020). Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark. Proceedings of the Royal Society B287(1922), 20192613.

Genetic bridges: Medium ground finch functions as a conduit for gene flow between two other Darwin’s Finches

Recent study highlights the evolutionary potential of multispecies hybridization.

“Hybridization is not always limited to two species; often multiple species are interbreeding.” This is the opening sentence of my recent review paper on multispecies hybridization in birds. Throughout this paper, I explored different evolutionary and ecological consequences of hybridization between multiple species. One of my favorite ideas concerns “genetic bridges” where one species functions as a conduit for gene flow between two other species that are not interbreeding. You can imagine my excitement when a study by Peter and Rosemary Grant appeared in the journal PNAS where they provide some evidence for this scenario.


A common cactus finch © Mike’s Birds | Wikimedia Commons



The extensive dataset of Darwin’s Finches from Daphne Major island (Galapagos Islands) allowed the Grants to retrace the interactions between three species: the medium ground finch (Geospiza fortis), the small ground finch (G. fuliginosa) and the common cactus finch (G. scandens). Between 1975 and 2011, the number of hybrids between these species was meticulously noted down. It turned out that the medium ground finch occasionally interbred with the resident cactus finch and the immigrant small ground finch. Hybrids between cactus finch and small ground finch were never observed on Daphne Major. However, genetic analyses did uncover some admixed individuals between these species. They might be the outcome of extra-pair copulations or backcrosses with other hybrids.


The frequency of hybrids on Daphne Major increased over time. The letters on the vertical axes indicate the different species combinations: medium ground finch (fortis, F), cactus finch (scandens, S) and small ground finch (fuliginosa, f). From: Grant & Grant (2020) PNAS


Hybrid Fitness

The production of hybrids between these three species is just the first step of the process. For interspecific gene flow to occur, these hybrids need to survive and continue breeding. Further observations showed that survival rates of hybrids were similar to those of pure individuals and confirmed the existence of three-way hybrids (referred to as trihybrids in the paper). Together, these results suggest that gene flow among these three species is occurring.

But how are the genes flowing? Is one species functioning as a genetic bridge? To answer this question we need to take a closer look at the hybrid patterns. The authors write that “secondary admixtures occur through interbreeding of G. scandens and Ff hybrids [i.e. G. fortis x fuliginosa] or backcrosses.” This indicates that fuliginosa genes are flowing into G. fortis (through the production of hybrids) and consequently to G. scandens (through interbreeding with these hybrids). In other words, the medium ground finch is acting as a genetic bridge between small ground finch and cactus finch.


Survival curves from different Darwin’s Finches and their hybrids. These findings indicate no obvious differences in survival between pure individuals and hybrids. From: Grant & Grant (2020) PNAS


An Evolutionary Stimulus

These patterns of genetic exchange also affect the morphology of the Darwin’s Finches. Both two-way and three-way hybrids showed increased variance in certain traits, such as beak morphology. The surplus in morphological and genetic variation provides the fuel for further evolutionary changes. This can be particularly important in current events with human-induced habitat changes and rapid climate change. Hybridization might be the key to cope with these challenges. In the 1950s, the botanists Anderson and Stebbins already argued that introgressive hybridization can act as an evolutionary stimulus. The Grants echo this conclusion and write that “Hybridizing species may therefore be disproportionately successful in coping with a changing environment in the future, as in the past”


Patterns of gene flow between the three Darwin’s Finches. The medium ground finch (G. fortis) acts as a genetic bridge between the other two species. From: Grant & Grant (2020) PNAS



Grant, P. R., & Grant, B. R. (2020). Triad hybridization via a conduit species. Proceedings of the National Academy of Sciences117(14), 7888-7896.

This paper has been added to the Thraupidae page.

The curious case of the Vaurie’s nightjar

Genetic and morphological analyses shed light on the identity of this illustrious bird.

Time for an ornithological mystery. In September 1921, Frank Ludlow collected a peculiar nightjar in western China. Initially, it was considered an Egyptian nightjar (Caprimulgus aegyptius). A few decades later, however, Charles Vaurie described it as a new species: the Vaurie’s nightjar (C. centralasicus). And that is all we know about this species. Several expeditions to the Taklamakan Desert in Central Asia (in the 1970s, 1990s and 2004) failed to find any trace of this nightjar. Did the species go extinct? Was it even a distinct species?

These circumstances are reminiscent of species that turned out to be hybrids, such as Rawnsley’s Bowerbird (Ptilonorhynchus rawnsleyi) or Imperial Pheasant (Lophura imperialis). Perhaps Vaurie’s nightjar is a hybrid? A recent study in the Journal of Ornithology tried to solve this mystery.


The only specimen of Vaurie’s nightjar. From: Schweizer et al. (2020) Journal of Ornithology


Morphology and Mitochondria

Manuel Schweizer and his colleagues retrieved the only known specimen of Vaurie’s nightjar from the Natural History Museum in Tring for detailed morphological and genetic analyses. They sequenced one mitochondrial gene (COI) and compared it to other nightjar species. The DNA sequence from the Vaurie’s nightjar specimen turned out to be identical that that of several European nightjars (C. europaeus). Could it be an abnormal specimen of this widespread species?

Next, the researchers turned to morphology. They contrasted the Vaurie’s nightjar with numerous other nightjar species. These comparisons indicated that we are not dealing with Nubian nightjar (C. nubicus) or Sykes’s nightjar (C. mahrattensis). And we can also rule out the Egyptian nightjar, the species it was first confused with. The plumage coloration of Vaurie’s nightjar does match that of European nightjar, but the specimen is much smaller than this species. The researchers suspect that it might represent a not fully grown fledgling.


The haplotype network of the mitochondrial gene COI shows that the Vaurie’s nightjar (lightblue) clusters with the European nightjars (darkblue). From: Schweizer et al. (2020) Journal of Ornithology


Mystery Solved?

Did we solve the mystery of the Vaurie’s nightjar? In the conclusion section of the paper, we read the following: “Based on the combined evidence from molecular genetics and morphology, we recommend that Caprimulgus centralasicus is better considered a synonym of Caprimulgus europaeus, belonging genetically to the eastern mtDNA clade of this widespread Palearctic species.”

Case closed! Well, not entirely. The authors admit that they cannot rule out the possibility that the Vaurie’s nightjar is a hybrid. That would require more than just one mitochondrial marker. I am looking forward to the genomic study!



Schweizer, M., Etzbauer, C., Shirihai, H., Töpfer, T., & Kirwan, G. M. (2020). A molecular analysis of the mysterious Vaurie’s Nightjar Caprimulgus centralasicus yields fresh insight into its taxonomic status. Journal of Ornithology, 1-16.

Colorful females, dull males and everything in between: the complex evolution of plumage patterns in the Pacific Robin

A recent study reconstructed the evolutionary history of this island radiation.

Male birds are colorful and female birds are dull. If the plumage colors of males and females are different, you can generally expect this pattern (which biologists refer to as sexually dichromatic). However, several species don’t show these sex-specific differences and it is difficult to tell males and females apart (i.e.they are monochromatic). Especially island species tend to exhibit a reduction in sexual dichromatism. This is nicely exemplified by the the Pacific robin (Petroica multicolor) species complex. The taxa in this complex vary from completely sexually dichromatic to almost monochromatic. Interestingly, some monochromatic taxa have ‘feminine’ dull brown feathers while others have ‘masculine’ black and red plumage patterns. A recent study in the Journal of Avian Biology tried to figure out how this mosaic of sexual plumage coloration evolved.


A Pacific robin (Petroica multicolor) on Norfolk Island © Paul Balfe | Wikimedia Commons


Four Lineages

The Pacific robin species complex contains sixteen distinct taxa, which have been divided into three species. The Norfolk robin (P. multicolor) is endemic to Norfolk Island while the red-capped robin (P. goodenovii) can be found on mainland Australia. The third species (P. pusilla) inhabits several islands, including the Solomon Islands, Vanuatu, Fiji and Samoa (the figure below gives a good overview). As explained above, the taxa in this species complex differ in their sexual plumage patterns. For example, populations on Fiji show clear sexual dichromatism, whereas male and females birds on Somoa are all brightly colored.

Anna Kearns and her colleagues collected samples from each island and reconstructed the evolutionary history of these birds using several genetic markers. They found evidence for four distinct lineages that correspond to particular island groups. There were clear differences between two already recognized species: the Norfolk robin (on Norfolk Island) and the red-capped robin (on Australia). Next, the researchers showed that populations from the Solomon Islands and populations from three other islands (Vanuatu, Fiji and Somoa) diverged about 400,000 years ago and should be considered distinct species.


Distribution and plumage patterns of all taxa within the Pacific robin species complex. Genetic analyses pointed to four distinct lineages: the red-capped robin (RC), the Norfolk robin (NI), the Solomon lineage (SOL) and the VFS-lineage. From: Kearns et al. (2020) Journal of Avian Biology


A Colorful Ancestor

Establishing the phylogenetic framework allowed the researchers to reconstruct the evolutionary history of sexual plumage patterns. The analyses suggested that the ancestor of this species complex was sexually dichromatic and that this trait was lost and regained several times on the Pacific islands. For instance, colorful monochromatism evolved three times independently, on Vanuatu, Samoa and the Solomon Islands.

The exact mechanism behind these evolutionary dynamics remains to be determined. A reduction in sexual dichromatism can be explained by several processes that are not mutually exclusive. First, depending on the environmental conditions, natural selection can drive a population to monochromatism. Second, a relaxation in sexual selection might reduce the selective pressures on colorful males, leading to monochromatism. Third, perhaps a founder effect – where only a subset of a larger population colonizes an island – resulted in the random selection of individuals that happened to be more monochromatic. Fourth, genetic drift in small island populations can lead to the fixation of genes involved in monochromatism. Understanding the genetic basis of these plumage patterns will allow ornithologists to unravel the exciting evolutionary history of these robins in more detail.


The evolution of sexual plumage patterns across the phylogeny of the Pacific robin. The ancestor was probably sexually dichromatic (indicated in red) and this trait was subsequently lost in certain taxa (white = dull monochromatic, black = colorful monochromatic). From: Kearns et al. (2020) Journal of Avian Biology


Kearns, A. M., Joseph, L., Austin, J. J., Driskell, A. C., & Omland, K. E. (2020). Complex mosaic of sexual dichromatism and monochromatism in Pacific robins results from both gains and losses of elaborate coloration. Journal of Avian Biology51(4).

Complicated Cotingas: Can we resolve any phylogeny by just adding more data?

A recent genetic study tried to resolve the phylogeny of two bird genera by generating more data.

Time for a trip down memory lane. In 2012, I started my PhD at the Wageningen University in the Netherlands. The topic of my research project: unraveling the evolutionary history of the True Geese (genera Anser and Branta). To my surprise, there was no resolved phylogeny at the time. Several researchers had tried to determine the phylogenetic relationships between the different goose species, but they all ran into polytomies and branches with low bootstrap support. How could we ever solve this conundrum? My solution was quite straightforward: just use more data! So, I sequenced the whole genomes of all goose species and released several phylogenomic tools on the terabytes data. A few years later, I proudly published a resolved phylogenetic tree for the True Geese (you can find the paper here). A recent study in the journal Molecular Phylogenetics and Evolution applied a similar approach to determine the phylogeny of two tropical bird genera.


Gray-winged cotinga (Tijuca condita) © Joao Quental | Flickr



Deep within the bird family Cotingidae, you can find the genera Lipaugus (7 species) and Tijuca (2 species). Most of these species are restricted to montane habitats, where they occur along narrow elevational ranges, whereas two species reside in the lowlands. Previous genetic work on the Cotingidae family revealed that these genera are closely related. Interestingly, one Tijuca species – the black-and-gold cotinga (T. atra) – was embedded with the other genus. The reliability of this finding was uncertain, because the relationship had low statistical support. The study only used six genetic markers, so perhaps more data could provide some clarity.

Amie Settlecowski and her colleagues revisited this situation with more data. First, they repeated the previous analysis with the six markers (but including more species). This exercise confirmed the relationships uncovered before, but again with low statistical support. In addition, three nodes in the tree could not be resolved. Next, the researchers generated a large dataset of more than 1,000 ultraconserved elements (UCEs). These conserved sequences are shared among divergent animal genomes and are probably involved in controlling gene expression. Analyses of these elements resulted in a completely resolved phylogeny with high statistical support for all nodes. It turned out that the two Tujica species are indeed embedded with the genus Lipaugus. Moreover, they are not even sister species!


A few genetic markers generated with Sanger sequencing could not resolve the phylogeny. Adding more data with ultraconserved elements revealed that the Tujica species are embedded within the genus Lipaugus. From: Settlecowski et al. (2020) Molecular Phylogenetics and Evolution


Problem solved?

What can we learn from my goose story and this study: If you cannot solve a phylogenetic tree, just add more data? Not necessarily. More data can help to resolve some contentious relationships, but it is not a guarantee for success. Take the attempts to reconstruct the complete avian phylogeny, for example. Erich Jarvis and his colleagues used whole genome sequences from 48 species and could not confidently determine the branching order at the base of the tree. Clearly, more data is not always the answer.

If we cannot fix a phylogenetic problem with more data, we run into a heated debate. Some scientists will argue that we will be able to resolve the issue in the future (with even more data or with better methods), while others will say that the problem cannot be fixed (the uncertainty reflects reality). In the latter case, the situation cannot be captured in a simple bifurcating tree. A network approach might then be more suitable to depict complex dynamics, such as high levels of hybridization. It is important to keep in mind that each phylogenetic solution – whether it is a tree or a network – is just a provisional hypothesis. And hypotheses can be rejected with new data…

Lipaugus vociferans

Screaming piha (Lipaugus vociferans) © Hector Bottai | Wikimedia Commons



Settlecowski, A. E., Cuervo, A. M., Tello, J. G., Harvey, M. G., Brumfield, R. T., & Derryberry, E. P. (2020). Investigating the utility of traditional and genomic multi-locus datasets to resolve relationships in Lipaugus and Tijuca (Cotingidae). Molecular Phylogenetics and Evolution, 106779.

Loss of migration leads to speciation in the Fork-Tailed Flycatcher

The establishment of sedentary populations has several consequences for genetics, morphology and behavior.

Numerous bird species migrate. Occasionally, a migrating population “decides” to stop their annual trips and become sedentary. These migratory drop-offs have been documented in several taxa and often result in morphological and physiological changes. But can they also drive speciation? Theoretically, it is certainly possible that differences in morphology and genetics start to accumulate between migratory and sedentary populations, ultimately resulting reproductive isolation and the origin of new species. A recent study in the journal Current Biology tested this idea in the Fork-Tailed Flycatcher (Tyrannus savana).

Tyrannus savana

A Fork-Tailed Flycatcher © Charles J. Sharp | Wikimedia Commons


Four Subspecies

The Fork-Tailed Flycatcher contains four subspecies. One subspecies (savanna) is a long-distance migrant that breeds from central Brazil to Argentina and spends the non-breeding season in northern South America. The other three subspecies (monachus, sanctaemartae, and circumdatus) are sedentary in Central and South America. This system provides the ideal circumstances to test the idea that loss of migration can result in speciation. If this idea holds true, you would expect clear differences in genetics, morphology and behavior between the migratory and sedentary subspecies. And that is exactly what Valentina Gómez-Bahamón and her colleagues found. Time for a quick overview!

Demographic analyses using genomic data indicated that the migratory and sedentary populations diverged about 1.08 million years ago. There was no sign of gene flow between these populations after the initial split, suggesting that the loss of migration happened only once. This finding is supported by a phylogenetic analyses that shows the sedentary populations nested within the migratory subspecies. The researchers conclude that “[the genomic] patterns are consistent with the hypothesis that migratory and sedentary fork-tailed flycatchers are on separate evolutionary trajectories.”


The genetic data indicated that the sedentary populations are nested within the migratory subspecies (Figure A), suggesting a single loss of migration. Moreover, there were no signs of gene flow between the sedentary and migratory subspecies, as shown by the clear separation in the admixture plots (Figure B). From: Gómez-Bahamón et al. (2020) Current Biology


More Differences

The genetic patterns are corroborated by morphological and behavioral data from the field. The researchers reported morphometric divergence between migratory and sedentary birds in traits associated with flight performance, such as the shape of the wings and tails. In line with previous studies, migratory birds had longer, more pointed wings for powered flight, while sedentary birds had shorter and more rounded wings to enhance maneuverability. The populations also exhibited differences in the timing of breeding (see figure below), contributing to reproductive isolation.

Taken together, these findings indicate that “migratory and tropical sedentary fork-tailed flycatchers are reproductively isolated due to spatial and temporal separation in breeding activities as a result of changes in migratory behavior leading to alternative strategies.”


The migratory (blue) and sedentary (yellow) subspecies breed at different times, contributing to their reproductive isolation. From: Gómez-Bahamón et al. (2020) Current Biology


Genetic Assimilation

The genetic data show that a small section of the migrating population became sedentary: both the demographic modelling and several measure of genetic diversity (e.g., heterozygosity and Tajima’s D) point to a reduction in effective population size. In a sense, this event can be seen as a founder event speciation. But how did this event happen? Migration is a complex trait that is influenced by numerous genes. A single genetic mutation cannot simply overturn migratory behavior and lead to sedentary individuals.

The researchers speculate that the change in migration strategy was due to behavioral plasticity. Some individuals switched to a sedentary lifestyle and were exposed to new selection pressures, leading to the accumulation of genetic differences between the sedentary and the migratory populations. Later on, the plasticity was lost when the new sedentary behavior was “assimilated” into the genome. An interesting hypothesis that needs further investigation.

Regardless of the mechanism behind the establishment of sedentary populations. It seems that loss of migration might be a common road to speciation. A macroevolutionary analysis of the family Tyrannidae shows that several species have lost the ability to migrate. Interestingly, speciation rates were higher for migratory and partially migratory lineages than those of sedentary lineages. Migration is thus an important factor to take into account if we want to understand the origin of bird species.


A macroevolutionary analysis of the Tyrannidae showed that migration has been lost in several species (migration = blue, partial migration = green, sedentary = yellow). The dynamic nature of migratory behavior is an important factor in avian speciation. Gómez-Bahamón et al. (2020) Current Biology



Gómez-Bahamón, V., Márquez, R., Jahn, A. E., Miyaki, C. Y., Tuero, D. T., Laverde-R, O., Restrepo, S. & Cadena, C. D. (2020). Speciation associated with shifts in migratory behavior in an avian radiation. Current Biology.

Do plumage patterns support the eleven subspecies of the Velazquez’s Woodpecker?

Recent study maps the geographic phenotypic variation in a highly variable woodpecker.

Biologists try to classify the living world into neat little boxes (which is not always possible). Some get carried away and grasp any opportunity to draw lines between supposed species or subspecies. A few feathers with a slightly different color can be used to define a new subspecies. Devising a realistic and biologically relevant classification for variable species can be tricky. The Velazquez’s Woodpecker (Centurus santacruzi), for example, exhibits striking variation in plumage and size across its range, which runs from northeastern Mexico to Nicaragua. Subdividing this diversity has resulted in at least 11 recognized subspecies. But how meaningful is this taxonomic arrangement? A recent study in the Journal of Ornithology took a closer look.

Golden-fronted Woodpecker

A Velazquez’s Woodpecker in Mexico © Becky Matsubara | Wikimedia Commons



Pilar Benites and her colleagues collected specimens from all 11 subspecies (for interested readers: grateloupensis, veraecrucis, dubius, polygrammus, santacruzi, huglandi, pauper, leei, insulanus, canescens, and turneffensis). Based on extensive analyses of morphometrics and plumage patterns, the researchers uncovered three basic morphs:

  1. red nape/red belly with higher barring frequency and lower barring ratio
  2. red nape/yellow belly with intermediate barring frequency and intermediate barring ratio
  3. yellow nape/yellow belly with lower barring frequency and higher barring ratio

A closer look at the distribution of the 11 subspecies shows that they do not reflect the variation in morphology and plumage patterns. A taxonomic revision might thus be warranted here.


The geographical distribution of subspecies (left) does not match the three morphs uncovered in this study. Adapted from: Benites et al. (2020) Journal of Ornithology


Local Adaptation

The patterns uncovered by this study raise an additional question: What environmental factors underlie this morphological variation? The researchers reported a significant correlation between plumage patterns and precipitation seasonality. However, because precipitation co-varies with numerous other environmental variables (e.g., habitat type) it is difficult to pinpoint the exact driver of this phenotypic diversity. Despite this uncertainty, it seems plausible that the plumage patterns are caused by local adaptation.

Genetic work on the Velazquez’s Woodpecker reported weak population structure, indicating that “divergence in the phenotypic traits probably evolved faster than neutral genetic markers.” Most likely, the plumage patterns in these birds are encoded by a few genes, similar to other woodpecker species. For instance, the genetic differences between three Sphyrapicus woodpeckers are due to 19 small genomic regions, one of which contains a candidate gene for plumage variation. Will a genomic analysis of the Velazquez’s Woodpecker reveal comparable patterns?



Benites, P., Eaton, M. D., García-Trejo, E. A., & Navarro-Sigüenza, A. G. (2020). Environment influences the geographic phenotypic variation in Velazquez’s Woodpecker (Centurus santacruzi). Journal of Ornithology, 1-14.

Ready, set, speciate: The role of sex chromosomes in the divergence of Reunion grey white-eye morphs

Genomic analyses find evidence for sex-linked diversification of island populations.

Sex chromosomes can drive speciation. From a genetic point of view, the origin of new species can be seen as the slow accumulation of genetic mismatches – so-called Bateson-Dobzhansky-Muller incompatibilities – between populations. These genetic mismatches often arise on sex chromosomes for several reasons (reviewed by Darren Irwin in this excellent paper). For example, important reproductive isolation mechanisms, such as male sterility, male plumage traits, and assortative mating, have all been linked to sex chromosomes. If these chromosomes are involved in the build-up of reproductive isolation, you expect genomic regions on the sex chromosomes to be more divergent compared to other chromosomes (i.e. the autosomes). A recent study in the journal Molecular Ecology tested this idea for the Reunion grey white-eye (Zosterops borbonicus).

Zosterops borbonicus

The Reunion grey white-eye © David Monniaux | Wikimedia Commons


Color Morphs

I have written about the Reunion grey white-eye before (see this blog post from 2017). On the small island of Reunion, this small passerine occurs in several populations with distinct plumage patterns. In the lower parts of the island, you can find a brown-headed brown (BHB), a grey-headed brown (GHB), and a brown-naped brown form (BNB). A fourth form is restricted to the highlands (between 1,400 and 3,000 m) and comprises two very distinct color morphs. Previous genetic work uncovered narrow hybrid zones between several populations and suggested that these color morphs are separated by a few genomic regions. Unfortunately, the resolution of genetic markers (microsatellites) was too weak to pinpoint the exact genomic regions that might be involved in reproductive isolation. Recently, Yann Bourgeois and his colleagues used genomic data to fill this gap in our knowledge on the Reunion grey white-eye.


A map of Reunion showing the different Zosterops populations. From: Bourgeois et al. (2020) Molecular Ecology


Sex-linked Genes

The results were in line with an important role for sex chromosomes in the early stages of speciation on Reunion. First, the autosomal markers could only discriminate between lowland and highland populations, whereas the sex-linked markers uncovered more fine-grained population structure within the lowland morphs. Second, the researchers contrasted demographic models with autosomal and sex-linked markers. The models with sex-linked markers pointed to lower levels of gene flow between the different populations compared to models based on autosomal markers. This suggests that some genomic regions on the sex chromosomes are not being exchanged between the populations and might harbor genes involved in reproductive isolation.

To identify candidate genes for reproductive isolation, the researchers searched the genomes for divergent regions. These analyses uncovered several promising genomic locations, including a clear outlier on chromosome 4A. Wait a minute, you might say, chromosome 4A is not a sex chromosome! Well, recent studies reported the existence of special sex chromomes in the Sylvioidea superfamily, to which the Reunion grey white-eye belongs. Several genomic locations – including part of chromosome 4A – have fused with fused with the existing sex chromosomes, giving rise to neo-sex chromosomes (you can read the entire story in this blog post).


Scanning the genomes of the white-eyes for divergent regions uncovered a clear peak on chromosome 4A, which has fused with the traditional sex chromosome. From: Bourgeois et al. (2020) Molecular Ecology


Plumage Patterns

Additional analyses revealed two interesting candidate genes that are involved in plumage coloration: TYRP1 and WNT5A. Interestingly, WNT5A is known to regulate the expression of TYRP1. These findings “suggests that a large part of plumage colour variation between the geographical forms of the Reunion grey white-eye may be controlled by a set of a few loci of major effect. More detailed studies of hybrid zones between the different lowland forms may help to characterize the exact association of alleles that produce a given plumage color phenotype.” Other studies have already taken advantage of hybrid zones to pinpoint specific plumage genes, such crows and warblers. Hopefully, the Reunion grey white-eye can be a new addition to this list.



Bourgeois, Y. X., Bertrand, J. A., Delahaie, B., Holota, H., Thébaud, C., & Milá, B. (2020). Differential divergence in autosomes and sex chromosomes is associated with intra‐island diversification at a very small spatial scale in a songbird lineage. Molecular Ecology29(6), 1137-1153.


This paper has been added to the Zosteropidae page.

Crossbills show there is more to evolution than natural selection

What explains the fit between beak morphology and pine seeds in a Spanish population?

A common misunderstanding about evolutionary theory is equating evolution to natural selection. However, evolution is much more than natural selection. Evolution refers to the change of populations over time (often phrased in terms of allele frequencies), while natural selection is just one mechanism underlying these changes. The idea behind natural selection is simple, but very powerful. It is the logical conclusion of these three premises:

  1. Individuals vary in certain traits
  2. These traits are heritable (they are passed on from parent to offspring)
  3. Variation in these traits leads to differences in survival and reproduction

And that’s it. A quick hypothetical example illustrates the workings of natural selection. Imagine a population of birds with different beak sizes. These birds feed on a tree species that produces seeds hidden inside small cones. Birds with a certain beak size can open these cones and access the seeds inside. These birds will be most successful in surviving (they have plenty of food) and producing offspring (they can feed their young). Because beak morphology is heritable, the young birds inherit beak size from their parents. Each generation, the variation in beak size will be determined by the surviving birds and their offspring from the previous generation. Over time, the average beak size of the population will converge upon the optimal size for cracking the cones.

Loxia curvirostra

A Common Crossbill in Austria © Frank Vassen | Wikimedia Commons



A recent study in the Journal of Avian Biology studied this scenario in common crossbills (Loxia curvirostra) from Spain. These birds show variation in beak size and forage on mountain pines (Pinus uncinata). Using a capture–recapture dataset spanning 27 years, the researchers investigated whether natural selection is driving beak morphology to an optimum size to feed on mountain pines. Between 1988 and 2014, birds were ringed and recaptured. How did beak morphology change over this period?

Statistical models indicated that the population optimum beak width is 11.43 mm. Apparent survival decreased when beak width deviated from this value. I write “apparent survival” because the capture-recapture data only suggest that a bird did not survive. When a bird is not caught again, it could be dead or it could have moved to another location.


For different age classes (juveniles, yearling and adults), apparent survival shows a peak around a beak width of ca. 11 mm. From: Gómez‐Blanco et al. (2019) Journal of Avian Biology


Selecting Environments

This results suggests that natural selection is keeping the population stable around a beak width of 11.43 mm. As I explained above, individual birds with smaller or bigger beaks don’t survive and are thus removed from the population. The reality, however, is not that straightforward. An alternative explanation is that maladapted birds do survive but fly to other locations where they have better access to food. Instead of the environment selection for particular individuals (i.e. natural selection), the individuals are selecting a certain environment.

This phenomenon could partly explain the result in this study. The authors write that “our estimate would be a rather unusually strong measure of stabilizing natural selection. Said otherwise, an unusual number of selective deaths would have to occur because of a phenotypic trait. Therefore, it appears probable that selective dispersal of locally maladapted individuals out of the study area has also contributed in order to produce this high value.” More widespread sampling of neighboring populations is needed to confirm this idea.


The estimated selection gradients from the present study (blue) versus a literature review (grey) indicates from strong selection on crossbills. Perhaps too strong? Gómez‐Blanco et al. (2019) Journal of Avian Biology


Alternative Explanations

This study illustrates that a match between a certain trait and the environment is not always the outcome of only natural selection. There are several alternative explanations that need to tested, such as individuals selecting certain environments. Other possibilities are phenotypic plasticity and adjustment of the environment. Phenotypic plasticity concerns the situation where a trait can vary in different environments (think of a tree growing higher in fertile soil compared to bare soil). Adjustment of the environment is self-explanatory: a population changes the environment to fit its needs, such as beavers building a dam to flood an area.

These alternative explanations highlight that we should be careful in attributing adaptations solely to natural selection and telling unfounded just-so stories (such as my hypothetical example above). Explore all possibilities before your draw conclusions.



Gómez‐Blanco, D., Santoro, S., Borrás, A., Cabrera, J., Senar, J. C., & Edelaar, P. (2019). Beak morphology predicts apparent survival of crossbills: due to selective survival or selective dispersal?. Journal of Avian Biology50(12).