crows composite

By GirlScientist

Photo Carrion crow (Corvus corone) and (right) hooded crow (Corvus cornix) are the same species, Leander Khil & Bob O’Hara

Although they look dramatically different, carrion crows and hooded crows are almost indistinguishable genetically, and hybrid offspring are fertile, but the two forms remain distinct mostly due to the dominant role of plumage color in mate choice

If you’ve ever visted or lived in Germany, as I have, you simply must visit the River Elbe. This river is the location of the most remarkable division between two bird species that I’ve ever seen. On the western shore lives the the jet-black carrion crow, Corvus corone, whilst the grey-bodied hooded crow, C. cornix, predominates on the eastern shore.

Scientists have been fascinated by this remarkable natural boundary too, because the two crow species are genetically indistinguishable, yet even a casual human observer would agree that they look dramatically different. The crows agree too: the two forms almost never interbreed, but yet, when they do, they produce fertile hybrid offspring. These fascinating peculiarities have made these two crows a popular model amongst scientists who study evolution and how new species arise.

“Defining speciation as the buildup of reproductive isolation, carrion crows and hooded crows are in the process of speciation”, said Jochen Wolf, a professor at Ludwig Maximilian University of Munich (LMU-Munich). Professor Wolf specializes in using a variety of technologies to decipher the interplay between phenotypic divergence and natural selection at the molecular level.

Previous studies by Professor Wolf and his collaborators have suggested that the dramatic differences in plumage color strongly limit hybridization between the two crow species. But now, Matthias Weissensteiner, who was a graduate student in Professor Wolf’s lab when he conducted this study, and his collaborators have identified a genetic mutation associated with the grey-bodied plumage color in hooded crows. Further, their findings suggest that ancestral corvids started out being clad in a uniformly funereal black.

Where and when did these two crow species arise?

When the onset of glaciation in the Late Pleistocene forced European birds to shelter in either southwestern (Iberian peninsula) or eastern (Balkan peninsula) refugia, ancestral crows ended up sheltering in one of these two locations — and began to diverge into separate lineages. In short, they were in the process of speciating. However, when the planet warmed and the glaciers retreated, the crows re-colonized their original range throughout Europe. But by this time, the two populations of crows looked so different that they rarely viewed members of the other group as being the same species. After living apart for millennia, they had become almost completely reproductively isolated from each other.

The southwestern crows gave rise to the carrion crow, which are entirely black, whereas the eastern crows gave rise to the grey-bodied hooded crow. The area where the two forms come into contact and where they occasionally mate with each other is known as the ‘hybrid zone’. Hybrids can be visually identified by their intermediate color and patterning between their two parents.

As hybrid zones go, this one is remarkably stable and narrow: it’s only 20 to 50 km (12-31 miles) wide and, in Germany, it basically follows the River Elbe. This stark boundary between the two crows suggests that individuals of both color forms carefully choose life partners that look just like themselves, a practice known as assortative mating.

“Within this narrow zone, there is a low incidence of interbreeding. The progeny of such crosses have plumage of an intermediate color”, Professor Wolf explained.

Despite their dramatic differences in plumage color, these crows still have similar habits and morphologies, so ornithologists long considered them to be geographic races of just one species. However, after careful observations, experts concluded in 2002 these two crows really are different species because they very rarely hybridized and the hybrid offspring were less fit than either parent (ref) — both hallmarks of speciation. But paradoxically, the two species cannot be distinguished based on their genetics.

A map of Europe indicating the distribution of the carrion and hooded crows on either side of a … [+] Cruithne9 via a Creative Commons license

“Only two major effect genes, which together encode the feather color, differ sharply on either side of the hybrid zone — the gray alleles are not found to the west of the zone and the black allele is absent in the eastern region”, Professor Wolf said.

Major effect genes are those that have fundamental control over a particular trait. A modification in a major effect gene can rapidly and profoundly alter the trajectory subsequent evolution. In this situation, both crow species are demonstrating strong assortative mating on the basis of plumage color, which makes it extremely difficult for hybrids to find a mate.

“The fact that this zone is so clearly defined implies that hybrid progeny are subjected to negative selection.”

New technologies illuminate small details of genomes

Ever since it was first discovered that the two crows were genetically the same, Professor Wolf and his collaborators have been working on gaining a clearer understanding for the genetic basis for reproductive isolation in these birds. They published an earlier study that necessarily ‘skimmed the surface’ by identifying single-base pair (bp) differences at sites within the two species’ genomes.

“However, we have never been able to directly determine the functional effects of such single-base variations on plumage color”, said the lead author of the recent study, Dr Weissensteiner, who now is a postdoctoral researcher at Pennsylvania State University. “Even when we find an association between a single-base variant and plumage color, the mutation actually responsible for the color change might be located thousands of base-pairs away.”

Clearly, a more exhaustive (and much more expensive) effort was required to better understand what they were seeing. To follow up on earlier studies, the research team addressed the same question but used a much more rigorous and technically demanding method to find differences in vast stretches of DNA. Such undetected differences in previously hidden regions of the genome are known as structural variations and could include deletions, insertions or inversions of large blocks of genomic DNA.

“Up until recently, high-throughput sequencing technologies could only sequence segments of DNA on the order of 100 bp in length, which is not long enough to capture large-scale structural mutations”, Professor Wolf said. “Thanks to the new methods, we can now examine very long stretches of DNA comprising up to 150,000 base pairs.”

Using this new power, the team sequenced DNA from 31 individual corvids from eight species, and searched for large structural variations that differentiate the genomes of carrion crows from hooded crows. Dr Weissensteiner and his collaborators did uncover many variants — quite a few which did not have any (immediately obvious) relationship with color — but the only structural variations that they uncovered were involved in plumage color. Specifically, they found a 2.25-kb insertion mutation in a gene in the hooded crow genome that affects plumage color by interacting with another, distant, gene, and changing its expression pattern.

Basically, a difference in just 2,250 DNA letters, out of a total of about 1.2 billion or so may be all that separates these two species. Although there are several genes involved in producing plumage color in corvids, this one insertion mutation next to just one gene probably created these dramatic differences in plumage color.

Dr Weissensteiner and his collaborators’ genomic comparisons also revealed that the common ancestor to carrion and hooded crows was jet black, whereas the hooded crow plumage color variant popped up approximately 530,000 years ago.

But what allowed this color variant to sweep through the entire population of Balkan crows? Although they’re not certain what the selective agent is, behavioral data show clear evidence for assortative mating in the hybrid zone. The novelty of this grey-bodied mutation could have made it popular in the ancestral eastern crows’ dating scene.

“The new color variant seems to be quite attractive, because it was able to establish itself very quickly, and therefore must have been positively selected”, Professor Wolf mentioned. “This is also what we modeled in this biorRxiv paper [ref]”, he added in email.

The mutation may have been advantageous, too. The grey-bodied mutation may have been adaptive for hot regions because the color reduces water loss by reflecting sunlight. But whether this plumage color mutation was selected through mate choice (attractiveness) or by natural selection (by reducing water loss in hot environments) has not yet been established, and remains a question for future investigations, no doubt.

Are hooded crows’ dramatic colors created by selfish “jumping genes”?

But natural selection can only act on what’s present, which raises the question: what genetic process actually created the hooded crows’ dramatic departure from their ancestral ebony black? It could have resulted from the effects of jumping genes, which are short stretches of selfish DNA that serve no purpose outside of peppering the genome with copies of themselves, an event that can create molecular havoc by, say, interfering with the production of black plumage color, or with the production of any number of other traits, depending upon where they land.

Once present in the genome, the grey-bodied trait then became entrenched in the ancestral hooded crow population through random genetic drift, which is a process where rare genes rise to prominence throughout a population (this phenomenon is most often observed in small isolated populations). But neither genetic drift nor selfish genes are mutually exclusive developments and both can, in fact, work in concert.

“Once it had reached a certain frequency within the local population, it would have been able to spread because parental imprinting, which enables nestlings to recognize their parents, also causes mature birds to choose mates that resemble their parents in appearance”, Professor Wolf explains.

Jumping genes are extraordinarily common. For example, they are so successful at inserting copies of themselves throughout a genome that we’ve found that half of the human genome is composed of a variety of them.

The researchers identified that the DNA insertion was one sort of selfish gene, a transposable element, which basically, does nothing, but is notorious for messing with the expression of whatever host gene it implants itself next to, by either up-regulating or down-regulating it.

“[I]magine the genome as an ecosystem for selfish genes where one copy accidentally inserts next to a host gene”, explained co-author Alexander Suh, an assistant professor at Uppsala University and a lecturer at the University of East Anglia. Professor Suh’s research investigates the evolution of transposons and viruses in animal genomes.

“Imagine this host gene normally gives black feathers but now gives grey feathers because of the sequence information the nearby selfish gene contains”, Professor Suh elaborated in email. “Selection can then act on this new phenotype that started as a within-genome accident caused by a selfish gene.”

“[J]ust imagine the endless forms of gene regulation that can happen simply because selfish genes deposit regulatory elements everywhere in the genome”, Professor Suh added in email.
Mutations caused by selfish “jumping genes” are quite common

Although selfish genes are common, they remain undiscovered in most organisms. However, considering this study’s findings in two crow species, it’s likely that selfish genes will be found everywhere that we look. And where ever selfish genetic elements pop up, they can act as an important mechanism that drive rapid evolutionary changes in natural populations. Despite accelerating evolutionary changes, they also raise important questions about what exactly is a species. Is a species the result of larger changes throughout the genome or just a few, strategically located, changes?

This fascinating study into the lives — and the genes — of two crow species neatly exemplifies the old proverb that ‘birds of a feather flock together’ by describing the genetics underlying what these crows do naturally, because the only genes that differ significantly between the two species are those involved in determining the color of their plumage.

Sources for your reading pleasure:

Matthias H. Weissensteiner, Ignas Bunikis, Ana Catalán, Kees-Jan Francoijs, Ulrich Knief, Wieland Heim, Valentina Peona, Saurabh D. Pophaly, Fritz J. Sedlazeck, Alexander Suh, Vera M. Warmuth and Jochen B. W. Wolf (2020). Discovery and population genomics of structural variation in a songbird genus, Nature Communications, 11:3403 | doi:10.1038/s41467-020-17195-4

Ulrich Knief, Christen M. Bossu, Nicola Saino, Bengt Hansson, Jelmer Poelstra, Nagarjun Vijay, Matthias Weissensteiner and Jochen B. W. Wolf (2019). Epistatic mutations under divergent selection govern phenotypic variation in the crow hybrid zone, Nature Ecology & Evolution, 3:570–576 | doi:10.1038/s41559-019-0847-9

Matthias H. Weissensteiner (2019). Doctoral thesis: Evolutionary genomics in Corvids: From single nucleotides to structural variants, ISBN: 978-91-513-0550-9 | Permanent link

via Do ‘Birds Of A Feather’ Speciate Together?