How did the Ground Tit get its long beak?

Genomic analyses lead to a list of candidate genes, including one with a major effect.

The Ground Tit (Pseudopodoces humilis) is a peculiar species. Based on its morphology – specifically its long, curved beak –  ornithologists thought this small songbird belonged to the family Corvidae (crows, ravens, jays and their relatives). Hence, they referred to it as Hume’s Ground Jay or Tibetan Ground jay. Molecular analyses, however, showed that the Ground Tit is the largest member of a completely different bird family: the Paridae (tits, chickadees, and titmice). A good reminder that morphology is not always a reliable guide in taxonomy. Correctly classifying this species raised an intriguing question: Where did this long, curved beak come from? The shape of the beak seems to be an adaptation to foraging on the open grasslands of the Qinghai-Tibet Plateau. As its name suggests, the Ground Tit collects its food on the ground, eating a wide range of arthropods. Although it also searches rock crevices and holes for a tasty grub. A recent study in the journal Molecular Biology and Evolution tried to unravel the genetic underpinnings of this long beak.

 

Beak Morphology

In a previous blog post and a YouTube-video, I discussed the genetic basis of beak morphology. Analyses of 72 bird genomes indicated that coding and non-coding regions work together to create the spectacular diversity of avian beaks. And although there are some common underlying developmental pathways (such as Wnt signalling pathway and the ESC pluripotency pathways), it seems that different protein-coding genes are under selection in different species. For example, in Darwin’s Finches several genes are associated with beak morphology (e.g., BMP4, CALM1, ALX1 and HGMA), while a different gene (COL4A5) determines the beak morphology of Great Tits (Parus major). So, what about its relative, the Ground Tit?

To answer this question, Yalin Cheng and his colleagues compared the genome of the Ground Tit with 13 short-beaked parid species. The researchers applied two methods to identify genomic regions that differed between these species. First, they calculated Z-transformed FST-values for different genomic regions. FST is a measure for genetic differentiation and can be standardized with a Z-transformation, which allows for easier comparison between species. Next, they compared genetic outliers with beak lengths using a partial Mantel test. These analyses resulted in 25 genomic regions, containing 23 candidate genes.

Genome-wide FST analysis between long-beaked Ground Tit and short-beaked parids (upper panel) and partial Mantel tests (lower panel) pointed to several candidate genes. The ones identified by both analyses are indicated in red. From: Cheng et al. (2020) Molecular Biology and Evolution.

 

Natural Selection

Among these 23 candidate genes were two genes (FZD3 and ROR1) involved in the Wnt signalling pathway, highlighting the importance of common developmental pathways in the evolution of beak morphology. To narrow down the list of candidates, the researchers performed several tests to detect signatures of selection (such as Tajiima’s D and Fu & Li’s D). These tests showed the strongest positive selection in the gene COL27A1. Interestingly, this gene is homologous to COL4A5, which is associated with the elongated beak of Great Tits as a response to supplementary feeding at bird feeders. A closer look at the genetic code of COL27A1 indicated several mutations under positive selection, including two in a particular domain of the protein that probably changed its biological function. This finding suggests that COL27A1 has a major effect on the extreme beak evolution in the Ground Tit.

Two mutations in the COL27A1 gene of the Ground Tit (Q and L on the top row) probably changed the function of the protein, resulting in the long beak of this species. From: Cheng et al. (2020) Molecular Biology and Evolution.

 

References

Cheng, Y., Miller, M. J., Zhang, D., Song, G., Jia, C., Qu, Y., & Lei, F. (2020). Comparative genomics reveals evolution of a beak morphology locus in a high-altitude songbird. Molecular biology and evolution37(10), 2983-2988.

Featured image: Ground Tit (Pseudopodoces humilis) © Dibyendu Ash | Wikimedia Commons

The speciation cycle of Taiga and Tundra Bean Goose

Are these bean geese merging into one species or not?

“I’ve been following your progress into the world of bird speciation and I wondered whether you’d be interested in a proposal.” This was the first sentence of an e-mail from Joe Tobias that I received in December 2019. He had been invited to write a review on bird diversification for the journal Annual Reviews in Ecology, Evolution, and Systematics and was looking for co-authors to write some sections. The only catch: the deadline was approaching fast (19th of January 2020). I did not have to think long about my decision, this was a great opportunity to work with one of the leading scientists in avian research and publish in one of my favorite journals. Moreover, I enjoy writing and I am always up for a challenge. A few days later, Alex Pigot joined the writing team and together we produced an extensive review that recently appeared online: “Avian Diversity: Speciation, Macroevolution, and Ecological Function“.

 

Road Trip along the Speciation Cycle

The resulting review paper centered around the concept of the speciation cycle (see figure below) which involves a series of evolutionary and ecological events. First, populations become geographically isolated and diverge in allopatry. When these populations establish secondary contact, several scenarios are possible. They might be reproductively isolated and transition into sympatry (and the cycle can start again). Or they might still be able to hybridize and establish a hybrid zone. The dynamics in these hybrid zones consequently determine the next phase in the speciation cycle. If hybrids are unfit – for instance, sterile or unable to find a mate – selection against hybrids can lead to character displacement, leading to further differentiation between the hybridizing species that eventually transition to sympatry. Alternatively, hybridization levels are so high that the populations collapse into one species. Regardless of the outcome (sympatry or collapse), the cycle can start again.

The different phases of the speciation cycles. The colored circles surrounding the diagram indicate different fields of research that are relevant to specific phases. From: Tobias et al. (2020) Annual Review in Ecology, Evolution, and Systematics.

 

Crossroads

The review paper elaborates on numerous interesting aspects of the speciation cycle. In this blog post, however, I want to focus on one particular point in this cycle: the crossroads at the hybrid zone phase. Will the populations transition into sympatry or will they merge into one species? One of my recent papers, published in the journal Heredity, provides a nice case study of this situation. During my postdoc at Uppsala University (Sweden), I studied the evolutionary history of the taiga bean goose (Anser fabalis fabalis) and the tundra bean goose (Anser fabalis serrirostris). Using whole genome resequencing data, I reconstructed their evolution history and tried to understand the genetic make-up of these birds.

It turned out that these geese diverged about 2.5 million years ago in allopatry and came into secondary contact ca. 60,000 years ago. Their genomes are largely undifferentiated but a few genomic regions – so-called ‘islands of differentiation’ – stand out. These islands might contain genes that contribute to reproductive isolation. For example, we found the gene KCNU1 which is involved in spermatogenesis. However, other evolutionary forces, such as background selection, can also give rise to these islands of differentiation. These results raise an important question: Are taiga and tundra bean goose now merging into one species?

A strolling taiga bean goose © Marton Berntsen | Wikimedia Commons

 

Merging or Diverging?

Which path of the speciation cycle the bean geese will follow, is difficult to predict. I suspect that these two populations have been stuck in a cycle of merging and diverging for thousands of years. With the genomic analyses, we managed to capture the latest merging event about 60,000 years ago. More powerful techniques might be able to find evidence for older hybridization events. In the future, taiga and tundra bean goose might start diverging again, possibly driven by the differences in the genetic islands of differentiation that we uncovered. However, if levels of hybridization increase, they might collapse into one species. Clearly, they are at an important crossroads in their evolution and future studies will reveal which turn they eventually took.

The current situation complicates the taxonomy of the bean geese. Should they be considered separate species or are they better classified as subspecies? Personally, I find this discussion nonsensical and uninteresting. Taiga and tundra bean goose are obviously in the grey zone of the speciation continuum where subjective taste determines their taxonomic status. Although I was a bit reluctant to enter this discussion, my co-authors and the reviewers advised me to discuss the taxonomy of the bean geese in the paper. So, based on low genetic differentiation, considerable morphological variation and incomplete reproductive isolation, we argued that taiga and tundra bean goose should be treated as subspecies.

A tundra bean goose flying over Sweden. © Stefan Berndtsson | Wikimedia Commons

 

Trivial Taxonomy

This conclusion struck a chord with some birdwatchers, who reacted furiously to the taxonomic recommendations (even though they were only a minor part of the study) on Twitter. One random birder – who would not recognize a DNA-sequence if it hit him in the face – even had the audacity to question how the paper made it through peer review. Just because you disagree with a certain conclusion, doesn’t mean that you should trash the entire study. To use a common saying: Don’t throw the baby out with the bathwater! Instead of reacting in the same manner as the birdwatchers, I did not lower myself to their level and politely explained the reasoning behind my conclusions (which you can also find in the paper).

Unfortunately, the unnuanced and emotional responses of these birdwatchers reflect the current level of discourse in our society, especially on social media. When someone doesn’t agree with the statement of a particular person, they immediately vilify everything about that person. I hope this style of discussion does not find its way into science and we can continue to carefully consider each others arguments, culminating in a strong consensus or at least politely agree to disagree.

But to end on a positive note: there was also a nice discussion on the website Dutch Birding about the taxonomy of the Bean Geese. In contrast to the blunt messages on Twitter, several birders provided constructive feedback. It is possible!

An online posting guide that the birdwatchers should have followed…

 

References

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

Tobias, J.A., Ottenburghs, J. & Pigot, A. (2020) Avian Diversity: Speciation, Macroevolution, and Ecological Function. Annual Review of Ecology, Evolution and Systematics. Early View.

Are we missing something? Exploring the diversity of white-eye species on the African mainland

Most white-eye species have been found on islands, but what about the diversity on the mainland?

When I say white-eyes, you say islands (if you are an ornithologist). About 90 percent of described white-eye species – the bird family Zosteropidae – occurs on islands. This bias is also apparent on the Avian Hybrids blog: all the papers about white-eyes that I covered took place on islands, such as the interactions between Solomons white-eye (Zosterops kulambangrae) and Kolombangara white-eye (Z. murphyi) on Kolombangara Island (see here) and the evolution of the Reunion grey white-eye (Z. borbonicus) on the small island of Reunion (see here). Could this focus on islands distort our perspective on these small passerines? What about the species diversity on the mainland? A recent study in the journal Molecular Phylogenetics and Evolution explored the diversity of white-eye species on the African mainland.

Cape white-eye (Zosterops virens) © Alandmanson | Wikimedia Commons

 

A Single Colonization Event

Frederico Martins and his colleagues collected genetic material from the 14 white-eye species and 18 subspecies that are currently recognized on the African mainland. Comparing these specimens with species from Asia revealed that the African mainland was colonized about 1.3 million years ago. After this single colonization event, the white-eyes spread to different African oceanic islands (for example, in the Gulf of Guinea) and several ecological sky-islands in the mountains. There, they diversified into a range of new species and subspecies. This begs the question: how many species are there on the African mainland?

The distribution of white-eyes on the African continent. The colors indicate the main species groups. From: Martins et al. (2020) Molecular Phylogenetics and Evolution

 

Species Boundaries

A species delimitation analysis based on mitochondrial DNA indicated that several taxa should be elevated to species level, resulting in 27 African white-eye species (remember, we started with 14). However, the researchers realize that this analysis relies on just one molecular marker. Clearly, there is more to a species than mitochondrial DNA (see this blog post on species concepts), indicating that more detailed studies are needed to describe all the white-eye species on the African continent. Nonetheless, this study shows that we are probably underestimating the diversity of white-eye species on the mainland.

 

References

Martins, F. C., Cox, S. C., Irestedt, M., Prŷs-Jones, R. P., & Day, J. J. (2020). A comprehensive molecular phylogeny of Afrotropical white-eyes (Aves: Zosteropidae) highlights prior underestimation of mainland diversity and complex colonisation history. Molecular Phylogenetics and Evolution149, 106843.

Blackcaps help to unravel the genetic basis of bird migration

An extensive study on Eurasian blackcaps indicates that there are multiple genetic ways for birds to become migratory.

Bird migration has a genetic basis. Ornithologists reached this conclusion by studying European blackcaps (Sylvia atricapilla) with some clever experiments. Blackcaps orient their migration either southwest or southeast, depending on their migration routes. Hybrids between birds that use different migratory strategies direct their migration intermediate, namely south. This simple set-up suggests a genetic basis for bird migration. But which genes underlie this complex trait that integrates morphology, physiology and behavior? Several researchers have searched the genomes of various bird species for these “migration genes”. Different studies found different genomic regions related to migration (among others in thrushes, willow warblers and Vermivora warblers). The discrepancies between these species indicates that there are multiple genetic ways to a migratory lifestyle. A recent study in the journal eLife returned to the bird species that started it all – the Eurasian blackcap – and continued the search for migration genes.

A Eurasian blackcap in Germany © Kathy Büscher | Wikimedia Commons

 

Whole Genomes

Kira Delmore and her colleagues assembled the whole genome for this iconic species. This genome provided the backbone for genomic sequences that were generated for 110 individual birds. This huge dataset covered the entire spectrum of migratory behavior, from exclusively migratory populations in the north to short distance and partially migratory populations in the Mediterranean, and including non-migratory, or resident, populations from the European continent (Iberian Peninsula) and the Atlantic islands.

Comparing the genomes of all the populations revealed that migratory and resident populations went their separate ways about 30,000 years ago. This divergence led to some genetic differentiation between the distinct migration strategies. The perfect set-up to find migration genes. Indeed, the researchers did not hide their enthusiasm in the paper: “Evidence for limited population differentiation combined with dramatic differences in the migratory behaviour of blackcaps is ideal for identifying genomic regions that are associated with this focal trait.”

The genomic analyses revealed significant differences between the resident and the migratory populations. From: Delmore et al. (2020) eLife

 

Candidate Genes

The researchers ran several analyses to pinpoint putative migration genes under selection. The search resulted in a short list of candidate genes, including SDC1. This gene codes for a transmembrane protein in the Wnt-pathway which is involved embryonic development. Perhaps a change in this pathway affects morphological traits important in migration, such as the shape of the wings? At the moment, we can only speculate about the possible roles of candidate genes. More research is obviously needed here.

Interestingly, none of the genes under selection in blackcaps overlapped with genomic regions in other migratory species, such as a region on chromosome 4 in Swainson’s thrushes (Catharus ustulatus) and regions on chromosomes 1 and 5 in willow warblers (Phylloscopus trochilus). As I mentioned in the beginning, there seem to be multiple genetic ways to a migratory lifestyle.

A scan of the genome revealed several genes under selection in migratory populations, including SDC1. From: Delmore et al. (2020) eLife

 

Regulating Residents

Apart from scanning the genomes for migration genes, the researchers also investigated the transition from migratory to resident. These analyses uncovered strong selection on a few genomic regions. A closer look at these regions showed that the genetic variants under selection were located in non-coding sections of the DNA. This suggests that changes in gene regulation underlie the transition to a resident lifestyle. Whether this finding can be extrapolated to other species remains to be determined, but it might indicate that a shift in migratory behavior can occur relatively quickly. In fact, a recent study on tyrannid flycatchers showed that a migratory strategy was lost multiple times during the evolution of this bird family. Could it all be regulatory changes?

 

References

Delmore, K., Illera, J. C., Pérez-Tris, J., Segelbacher, G., Ramos, J. S. L., Durieux, G., Ishigohoka, J. & Liedvogel, M. (2020). The evolutionary history and genomics of European blackcap migration. Elife9, e54462.

How many members of the Lesser Whitethroat complex breed in Iran?

And is the taxon zagrossiensis valid?

Just because you see a bird in a certain country doesn’t mean that it breeds there. It could be passing through. Or perhaps it is a lost migrant, blown off course by strong winds. In Iran, you can observe several species of the lesser whitethroat complex (Sylvia curruca). Ornithologists are quite certain that the nominal species (S. curruca) and Hume’s whitethroat (S. althaea) breed in this Middle-Eastern country. But the jury is still out on some other members of this widespread species complex. For example, some researchers argue that the desert whitethroat (S. minula) breeds in northeastern Iran, while others think it just visits the area in winter. A recent study in the Journal of Ornithology sampled more than 30 individuals across Iran to solve this mystery.

A lesser white-throat © Imran Shah | Wikimedia Commons

 

Mitochondrial DNA

The latest molecular studies divide the lesser whitethroat complex into six geographical groups (based on mitochondrial DNA): althaea, blythi, halimodendri, margelanica, curruca and minula. Raziyeh Abdilzadeh and his colleagues compared the genetic make-up of the Iranian birds with these six groups. This analysis revealed that all samples could assigned to three groups: curruca, althaea and halimodendri. The samples of halimodendri – which is considered a subspecies of Hume’s whitethroat – were collected in February and represent wintering or migrating birds. Moreover, none of the samples were members of the minula group. There is thus no evidence that the desert whitethroat breeds in Iran.

The genetic analyses pointed to three groups in Iran, of which halimodrendi is migratory. From: Abdilzadeh et al. (2020) Journal of Ornithology

 

Another taxon?

This study also sheds some light on another mystery: the taxon zagrossiensis. In 1911, Sarudny considered the birds in the Zagros mountains to be a distinct taxon, classified as S. althaea zagrossiensis. Birds from this area are slightly darker compared to the nominal lesser white-throat. The current analyses do not support this classification. Indeed, the researchers note that “Our data suggest that birds inhabiting the mountains of western Iran and the central Zagros mountains, at least as far east as Shiraz, sometimes recognized as caucasica and zagrossiensis, respectively, belong to the curruca clade sensu Olsson et al. (2013), based on mitochondrial haplotypes.” The origin of the darker plumage of these birds remains to be investigated. Did they acquire it through hybridization with another member of this species complex?

 

References

Abdilzadeh, R., Aliabadian, M., & Olsson, U. (2020). Molecular assessment of the distribution and taxonomy of the Lesser Whitethroat Sylvia curruca complex in Iran, with particular emphasis on the identity of the contentious taxon, zagrossiensis Sarudny, 1911. Journal of Ornithology, 161:665–676.

What drives avian speciation in the Amazonian floodplains?

Genomic analyses suggest an important role for past climate changes.

The Amazonian floodplains are among the most diverse places on our planet. This collection of habitats covers over 300,000 square kilometres and houses about 10% of endemic tree species and 15% non-aquatic bird species. But where did all this diversity come from? What factors drive the origin of new species on these flooded plains? Numerous studies have attempted to answer these questions. Some researchers pointed to the role of rivers (as you can read in this blog post), while others suggested that climatic events are more important (such as in this blog post). Clearly, the jury is still out on the drivers of avian speciation on the Amazonian floodplains. A recent study in the journal Science Advances revisited this age-old conundrum.

The leaden antwren (Myrmotherula assimilis) © Hector Bottai | Wikimedia Commons


Three Species Complexes

The researchers focused on three species complexes:

  • Ash-breasted antbird (Myrmoborus lugubris)
  • Blackish-grey antshrike (Thamnophilus nigrocinereus) and Castelnau’s antshrike (T. cryptoleucus)
  • Leaden antwren (Myrmotherula assimilis)

They obtained genetic material from all known subspecies in these species complexes and meticulously mapped the genetic patterns across the Amazonian floodplains. These analyses revealed that the three species showed similar genetic population structure across different sections of the floodplains. For example, all species exhibited higher genetic diversity in central portion of the Amazon River, suggesting the existence of hybrid zones. This finding already indicates that these populations have been geographically isolated in the past. Let’s have a closer look at the results.

The three species complexes showed similar genetic population structure. Top: M. lugubris. Middle: T. nigrocinereus/T. cryptoleucus. Bottom: M. assimilis. From: Thom et al. (2020) Science Advances


Patterns and Processes

The uncovered genetic population structure could be explained by three non-mutually exclusive effects: (1) isolation-by-distance in which populations become more genetically divergent the farther they are apart, (2) ecological gradients where different populations adapt to different environmental conditions, and (3) long-term geographic changes to the Amazon River basin.

Although the first two processes – isolation-by-distance and ecological gradients – explain some part of the genetic patterns, the main driver appears to be previous geographic changes to the Amazon Basin. Indeed, the diversification of the three species complexes coincides with the Mid- and Late Pleistocene when major reorganization of Amazonian tributaries occurred and when the current transcontinental Amazon River arose. Specifically, climatic changes affected the sediment dynamics and floodplain structure, isolating bird species adapted to life on the river edges. During the Holocene (less than 11,000 years ago), the floodplains expanded, resulting in the establishment of secondary contact zones in the central part of the distribution.

A female ash-breasted antbird © Hector Bottai | Wikimedia Commons

 

Refugia

This scenario is reminiscent of the “forest refugia hypothesis” that explains the origin of numerous forest species. But instead of forest habitat contracting and expanding, it is now “the contraction or interruption of river edge forest resulting in isolated blocks restricted to the main Amazonian rivers.” This parallel between forest and river habitats suggests that a South American synthesis on the role of climate changes in avian speciation is getting closer.

 

References

Thom, G., Xue, A. T., Sawakuchi, A. O., Ribas, C. C., Hickerson, M. J., Aleixo, A., & Miyaki, C. (2020). Quaternary climate changes as speciation drivers in the Amazon floodplains. Science Advances6(11), eaax4718.

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.

Carolina_Chickadee

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.

chickadee_hybridzone

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

 

Selection

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.

 

References

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.

Razo_lark

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.

lark_chromosomes

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.

larks_Ne

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

 

References

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.

Cactus_Finch

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

 

Geospiza

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.

hybrids_DF

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.

suvival

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”

finches

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

 

References

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.

specimen

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.

network

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!

 

References

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.