How the Hooded Crow got its hood: A tale of two crows and a transposable element

Structural variants provide another clue to the genetic basis of plumage color in crows.

Turning an all-black Carrion Crow (Cornix c. corone) into a grey Hooded Crow (C. c. cornix) might be as easy as flipping a genetic switch. Extensive studies of a European hybrid zone between these species have uncovered many details about the genetic underpinnings of these plumage patterns. Let me quickly recap our understanding so far. A genome-wide association study found three genomic regions associated with plumage color: a big region on chromosome 18 and two smaller regions on chromosomes 1 and 1A. The region on chromosome 1 contains the candidate gene NDP, which also regulates plumage patterns in pigeons. Differential expression of this gene in developing feathers could thus explain the evolution of different plumage patterns in both pigeons and crows. A recent study in the journal Nature Communications might have found the mechanism that explains this differential gene expression in crows.

 

Structural Variants

Matthias Weissensteiner and his colleagues decided to take a closer look at structural variation in the genomes of several crow species. Structural variation refers to a panoply of mutations, such as deletions, insertions, duplications and inversions (you check out this blog post on the role of inversions in avian evolution). These types of mutations have been very difficult to characterize because you need highly contiguous genome assemblies that have only recently became available. Indeed, most bird genome assemblies are far from complete. Using the latest technologies in genome sequencing, the researchers managed to generate high-quality, contiguous assemblies for several crow species. The search for structural variants can begin.

An overview of the different crow species in the study. The numbers indicate the technologies used to generate the sequences: short read (SR), long read (LR) and optical mapping (OM). From: Weissensteiner et al. (2020) Nature Communications.

 

Retrotransposon

The analyses resulted in a total of of 220,452 insertions, deletions and inversions. I will not discuss them all. That would result in a very long and boring blog post. Instead, I will focus on one particular insertion: a LTR retrotransposon on chromosome 1. Retrotransposons are a type of genetic parasites that jump through the genome using a copy-and-paste mechanism. The LTR in their name stands for “Long Terminal Repeats” because these genetic sequences are flanked by long stretches of repetitive DNA. This particular LTR retrotransposon inserted itself about 20,000 nucleotides from the gene NDP (you can feel where this is going).

It turned out that all Hooded Crows in the study were homozygous for the LTR retrotransposon (i.e. they carried the insertion on both copies of chromosome 1). This observation suggests that there has been strong selection for this insertion in the Hooded Crow population. Could it be related to the activity of NDP? Further analyses confirmed this hunch: the expression of NDP was significantly lower in birds that were homozygous for the insertion. It thus seems that the insertion of the LTR retrotransposon affected the expression of NDP, giving rise to the hooded phenotype. This plumage pattern consequently came under strong sexual selection because crows prefer to mate with birds of the same plumage type. Another piece in the plumage pattern puzzle.

The insertion of the LTR retrotransposon (figure a) is homozygous in hooded crows (figure b) and affects the expression of the NDP-gene (figure c). From: Weissensteiner et al. (2020) Nature Communications.

 

References

Weissensteiner et al. (2020). Discovery and population genomics of structural variation in a songbird genus. Nature communications, 11(1), 1-11.

Featured image: Hooded Crow in Berlin © Pelican | Wikimedia Commons

 

This paper has been added to the Corvidae page.

A genomic continuum from feral to wild Red Junglefowl in Singapore

The admixed nature of the population raises several conservation issues.

Hybridization and the consequent exchange of genetic material (i.e. introgression) is not limited to wild populations. Domesticated animals or plants regularly interbreed with their wild relatives and genes flow both ways. These hybridization events can be accidental. After the disaster at the Fukushima Nuclear Power Plant in 2011, for example, several domestic pigs (Sus scrofa) escaped into the Japanese nature and hybridized with local wild boars. In other cases, captive animals are intentionally released into the wild, such as the restocking of European partridge populations with the non-native Chukar Partridge (Alectoris chukar) for hunting purposes. Unsurprisingly, the introduced partridges interbred with the local birds. Another example of hybridization between domestic and wild birds concerns chickens (Gallus gallus) in Singapore and was recently described in the journal Evolutionary Applications. Time for a trip to Asia!

 

Museum Samples

Wild chickens – the Red Junglefowl – were thought to be extinct in Singapore until they were rediscovered on the island Ubin in 1970. These birds probably crossed the 800 meter wide sea channel from the neighboring island Johor (part of Malaysia). Years later, Red Junglefowl also roamed the main island of Singapore. This recolonization was accompanied by an increase in domestic chickens (whether intentionally released or escaped remains uncertain) that occasionally hybridized with their wild relatives. This situation leads to an interesting discussion: are the Red Junglefowl populations on Singapore really wild? Or are they a mixture of wild and domesticated birds? Meng Yue Wu and her colleagues turned to genomic data to solve this mystery.

Studying introgression in chickens is challenging because there has been gene flow between several species and breeds (as explained in this blog post). To obtain a genomic reference for the wild Red Junglefowl, the researchers used two museum samples that were collected about 150 years ago on Malaysia. Next, they sequenced the DNA of 70 free-roaming birds from Singapore. The genomic analyses revealed a continuum from domestic to wild chickens with varying levels of introgression. There were no clear spatial patterns, suggesting that the wild and domestic chickens are freely mixing in Singapore (although most wild-type birds seem to cluster around Singapore’s largest national park).

Genomic analyses revealed a continuum from domestic (orange) to wild (blue) birds in Singapore. Each column represents an individual and the colors indicate the percentage of wild and domestic ancestry in the genome. The museum samples are indicated with stars in figure a. The three graphs represent different analyses: (a) all genomic samples, (b) all genomic samples without museum specimens, and (c) all genomic samples + additional RADseq samples. From: Wu et al. (2020) Evolutionary Applications.

 

Conservation

These findings result in a conservation conundrum. On the one hand, managers might warn that the wild Red Junglefowl on Singapore have been “genetically contaminated” by domestic genes. On the other hand, the exchange of genetic material might lead to higher genetic diversity and could potentially speed up adaptation.

Morphological analyses of the Singaporean chickens indicated that a handful of traits (tarsus and primary feather coloration for females and tail feather, primary feather, and lappet coloration for males) can be used to confidently discriminate between wild and domestic chickens. It is thus feasible to detect and remove “introgressed” individuals from the population. Should we intervene or not? I will not try to answer this question here, but feel free to share your thoughts in the comments below.

The researchers studied several traits to see whether it is possible to tell the difference between wild, domestic and mixed individuals. From: Wu et al. (2020) Evolutionary Applications.

 

References

Wu, M. Y., Low, G. W., Forcina, G., van Grouw, H., Lee, B. P. Y. H., Oh, R. R. Y., & Rheindt, F. E. (2020). Historic and modern genomes unveil a domestic introgression gradient in a wild red junglefowl population. Evolutionary Applications, 13(9), 2300-2315.

Featured Image: © Seng Alvin | Singapore Bird Group

 

This paper has been added to the Galliformes page.

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 evolution, 37(10), 2983-2988.

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

Solving the genetic mystery of the mosaic canary

Which genes are responsible for this peculiar plumage pattern?

Good scientific research resembles a thrilling mystery novel. Gathering clues, testing potential leads and critical thinking enable both detectives and scientists to solve the challenging questions. A recent study in the journal Science nicely illustrated this approach. The mystery: the genetic basis of mosaic plumage coloration in captive canaries. These red canaries are the result of crossing the Common Canary (Serinus canaria) with the Red Siskin (Spinus cucullatus). Bird breeders have selected for this color pattern – commonly known as the mosaic phenotype – by consecutive backcrossing the hybrids with “pure” Common Canaries. Over time, the genome of resulting red canaries is largely Common Canary-DNA with a dash of Red Siskin. And this dash of DNA probably contains the genes responsible for the red plumage color.

Consecutive backcrossing between the Common Canary x Red Siskin hybrid and “pure” Common Canaries results in a genome that mainly consists of Common Canary DNA (light green) with a bit of Red Siskin-DNA (dark green). From: Gazda et al. (2020) Science.

Zooming in

Using a series of genomic techniques, the researchers zoomed in on the Red Siskin-DNA in the mosaic canaries. They narrowed the search down to a genomic region (on scaffold NW_007931177) with 52 genetic variants that were different between canaries with yellow and red feathers. The mosaic phenotype is a recessive trait, meaning that mosaic birds have the same genetic variant on both chromosomes (in other words, they are homozygous). This insight provides another important clue to solve the mystery. Which of the 52 genetic variants are homozygous for the Red Siskin in the mosaic canaries? Focusing on these homozygous variants pointed to a genomic region of about 36,000 DNA-letters, containing three genes: PTS (6-pyruvoyltetrahydropterin synthase), BCO2 (b-carotene oxygenase 2), and TEX12 (testis-expressed protein 12).

The genetic basis of red coloration is homozygous for Red Siskin DNA. This knowledge allowed the researchers to zoom in on a particular region with homozygous variants (highlighted in the black box). From: Gazda et al. (2020) Science.

Gene Expression

Now that we have three main suspects (PTS, BCO2 and TEX12) we can explore a next lead: differential gene expression. Mosaic males and females show distinct plumage patterns. Males accumulate more red pigment in their feathers than females. Hence, we can expect that the genes controlling red color are differently expressed in males and females. The researchers took a closer look at the expression patterns of PTS, BCO2 and TEX12 in regenerating feather follicles. One gene showed decreased expression in males compared to females: BCO2. Did we find the culprit?!

We know that BCO2 codes for an enzyme that plays an essential part in the degradation of carotenoids, the pigments responsible for red coloration. In mosaic males, this enzyme is not very active and does not break down many carotenoids, resulting in the accumulation of red pigment in the feathers. The mosaic phenotype is thus the outcome of sex-specific differences in BCO2-activity, suggesting that it is controlled by other regulatory sequences (the genetic on-and-off switches). These regulatory elements remain to be identified. We might have found the murderer, but we are still looking for the brains behind the crime.

Two genes (PTS and TEX12) did not show significant differences in gene expression between males and females (top boxes). The third gene (BCO2), however, was less active in males compared to females. Interestingly, the difference in gene expression was only apparent in feather follicles (lower left box) and not in the liver (lower right box). From: Gazda et al. (2020) Science.

References

Gazda, M. A. et al. (2020). A genetic mechanism for sexual dichromatism in birds. Science, 368(6496), 1270-1274.

Featered image: A mosaic canary © Fernando Zamora Vega | Shutterstock

Should I stay or should I go? Patterns of gene flow across land bridges in Southeast Asia

Land bridges can promote gene flow. But do the birds cross them?

The genetic patterns in present-day bird populations can often be explained by the glacial dynamics of the ice ages (during the Pleistocene, between 2.5 million and 11,000 years ago). On the Northern Hemisphere, huge ice sheets covered large parts of North America and Eurasia. These glaciers formed formidable barriers between plant and animal populations, which could not exchange genes any longer and started to diverge genetically. Hence, divergence times often align with glacial maxima on the northern half of our planet.

On the Southern Hemisphere, however, conditions were quite different, especially on Southeast Asian islands. The growth of expansive ice sheets in the north requires a lot of water, leading to a significant decrease in sea level. In the western part of the Indonesian archipelago, this drop in sea level resulted in the formation of land bridges between islands. These connections might allow previously isolated island populations to exchange genetic material. A recent study in the journal Molecular Ecology took a closer look at five bird species (two babblers and three bulbuls) on Singapore, Sumatra and Borneo to determine whether land bridges promoted gene flow between these island populations.

The Indonesian archipelago now comprises several islands, but during glacial maxima these islands were connected by land bridges (indicated in grey). Did this result in gene flow between bird populations on the different islands? From: Cros et al. (2020) Molecular Ecology

 

Five Species

To infer whether gene flow occurred during the ice ages, Emilie Cros and her colleagues generated DNA sequences for the following five species:

• Chestnut-winged Babbler (Cyanoderma erythropterum)
• White-chested Babbler (Trichastoma rostratum)
• Olive-winged Bulbul (Pycnonotus plumosus)
• Asian Red-eyed Bulbul (Pycnonotus brunneus)
• Cream-vented Bulbul (Pycnonotus simplex)

Genetic analyses indicated that the island populations of these species diverged well before the Last Glacial Maximum (ca. 20,000 years ago). However, two species did show signatures of recent gene flow, namely the Asian Red-eyed Bulbul and the Olive-winged Bulbul. What can explain these different gene flow patterns?

Each circle is an individual bird and the color represents its genetic make-up. There is clear genetic divergence between the islands populations (most obvious in C. erythropterum here). In some species, however, there are signatures of recent gene flow. This is nicely illustrated by P. plumosus where different islands share genetic variation. Adapted from: Cros et al. (2020) Molecular Ecology.

 

Ecology Matters

A closer look at the ecology of these species reveals a striking pattern. The babbler species reside in the understory of the forest, while the bulbuls can be found in the canopy. A study in South America showed that canopy species have lower genetic divergence values compared to understory birds. The researchers attributed this difference to higher dispersal propensity of the canopy species. The same reasoning applies to the birds in Southeast Asia: the understory babblers might not have dispersed far during the ice ages and rarely crossed the land bridges between the islands.

In addition to the position in the forest (canopy vs. understory), other habitat features explain the gene flow patterns. Forest specialists, such as the Cream-vented Bulbul, do not venture outside the forest and thus need forested areas to disperse. The land bridges probably consisted of open habitats, including swamps, woodlands and savannas. Not the ideal habitats for forest specialists. More generalist species, such as the Olive-winged Bulbul, could survive in these non-forested areas and travel between islands. This ecological explanation is reflected in genetic patterns: the generalist (Olive-winged Bulbul) showed higher levels of gene flow compared to the habitat specialist (Cream-vented Bulbul). Ecology matters!

 

References

Cros, E., Chattopadhyay, B., Garg, K. M., Ng, N. S., Tomassi, S., Benedick, S., Edwards, D. P. & Rheindt, F. E. (2020). Quaternary land bridges have not been universal conduits of gene flow. Molecular Ecology, 29(14): 2692-2706.

Featured image: Red-eyed Bulbul (Pycnonotus brunneus) © Lip Kee | Wikimedia Commons

 

This paper has been added to the Pycnonotidae page.