Salty Genes: Hybridization between saltmarsh and Nelson’s sparrow results in exchange of adaptive genes

Genomic study uncovers candidate genes for adaptive introgression in saltmarsh and Nelson’s sparrow.

Hybridization can work as an evolutionary stimulus. For example by transferring beneficial genetic variants from one species to another. This process, adaptive introgression, has been described for numerous taxa, such as butterflies and snowshoe hares. However, examples in birds are quite rare. A recent study in the journal Evolution provides evidence for adaptive introgression between two sparrow species.

 

Hybrid Zone

Jennifer Walsh (Cornell University) has published a nice series of papers on between saltmarsh sparrow (Ammodramus caudacutus) and Nelson’s sparrow (A. nelsoni) that hybridize along the coast of New England (see the Emberizidae page for an overview). The saltmarsh sparrow is a specialist of – you guessed it – saltmarshes, whereas Nelson’s sparrow has a broader ecological niche that includes grasslands and brackish marshes. Using microsatellites, she was able to document gene flow between these species. But could this exchange of genetic material be adaptive? Time to bring out the big guns: genome sequences!

saltmarsh sparrow.jpg

A saltmarsh sparrow (from: https://www.audubon.org/)

 

Salty Genes

By comparing the genomes of 36 individuals, Jennifer and her colleagues were able to pinpoint several genomic regions that have been exchanged between the sparrows. Further exploration of these regions uncovered several genes that could be important for life in the saltmarshes.

[Sixteen] of these 24 putative candidate genes confer potential adaptations to tidal marsh environments, including genes with links to osmotic regulation, response to salt stress, response to water deprivation, and muscle development. The remaining 8 candidates include additional regions, including four genes related to DNA repair and several genes with a range of putative adaptive functions (visual perception, response to pH).

It can be tempting to tell an adaptive story for each gene, but it is important to keep in mind that these are “candidate genes” for adaptation. They should be the starting point for further research, not the final answer. So, you can expect more sparrow studies in the near future.

 

References

Walsh, J., Kovach, A.I., Olsen, B.J., Shriver, W.G. & Lovette, I.J. (2018) Bidirectional adaptive introgression between two ecologically divergent sparrow species. Evolution

 

This paper has been added to the Emberizidae page.

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Where did all these fish come from?! A genomic perspective on the explosive diversification of cichlids

Cichlids provide important insights into the drivers of explosive speciation.

There are more than 1700 species of cichlid fishes, 90% of which can be found in the Great Lakes of East Africa. Since the 19th century, biologists have been visiting the Lakes Victoria, Malawi and Tanganyika to explore the diversity of cichlid species. In 1931, Woltereck introduced the term ‘Artexplosion’ (now known as explosive speciation) to describe the situation. In a recent review paper, Walter Salzburger (University of Basel) puts the cichlid explosion into perspective:

To put cichlid radiations into a temporal context, during the evolutionary time span of our own species, starting with the split between chimpanzees and humans some 5–7 million years ago, approximately 2,000 species of cichlid fish evolved in East Africa, the geographic region where the chimpanzee–human split initially occurred. Within the time span that it took for 14 species of Darwin’s finches to evolve on the Galapagos archipelago, about 1,000 cichlid species evolved in Lake Malawi alone. In addition, since the last ice age, which is when sticklebacks began to diverge into replicate species pairs in the Northern hemisphere, hundreds of cichlid species evolved in Lake Victoria.

 

It’s complicated

To sum up the introductory paragraph of this blog post: that is a lot of fish in a short amount of time. Reconstructing the evolutionary history of such rapidly diversifying species groups is challenging. There are multiple biological processes that hamper the construction of phylogenetic trees. Figure 3 in Salzburgers review paper provides a nice overview of these processes (honestly, one of the best pictures I have come across). The most important ones to keep in mind are incomplete lineage sorting (d) and introgression (e). Incomplete lineage sorting occurs when lineages fail to coalesce in the ancestral population (I have explained this process in more detail previously), while introgression refers to the exchange of genetic material by means of hybridization and backcrossing (see practically all posts on this website…).

fish phylogenetics.jpg

Several biological processes that can complicate the estimation of phylogenetic trees (from: Salzburger 2018 Nature Reviews Genetics)

 

Untangling Tanganyika

Because of these processes, it has been difficult to produce a completely resolved phylogenetic tree of cichlid fish. However, Iker Isarri, Pooja Singh and colleagues managed to disentangle the relationships between all cichlid species of Lake Tanganyika. In addition, they uncovered introgression that the base of this explosive radiation, suggesting that ‘hybridization might have facilitated these speciation bursts.’

This suggestion was supported by further analyses, revealing that several genes related to key innovations in cichlids, such as dietary adaptations and color vision, showed signs of positive selection and introgression. This is nicely illustrated by the opsin-genes, which shape the visual system of these fish. In cichlids that feed on plankton the UV-sensitive opsin sws1 shows faster evolution, facilitating foraging because plankton is more visible under UV-light. Fish that graze on green algae, on the other hand, show faster evolution in the green-sensitive opsin rh2α-α.

cichlid phylogeny.jpg

The resolved cichlid phylogeny. Check out the original paper for a higher quality image: Irisarri et al. (2018) Nature Communications

 

Multiple Opportunities

So, does that answer our question? Did we get all these fish because of introgressive hybridization? It is definitely one of the factors that has fueled cichlid speciation, but other factors also need to be taken into account, such as ecological opportunity: the African Great Lakes are conducive for diversification by providing a plenitude of ecological niches to fill. Genomic analyses of several cichlids also revealed that the genomes of these fish have certain features that could potentially facilitate explosive speciation (I cannot go into great detail here, but I have provided links to relevant literature for interested readers):

  1. Accumulation of standing genetic variation before the radiation (partly supplied by introgressive hybridization)
  2. Increased rate of gene duplications which speeds up the process of genes acquiring new functions (i.e. neo-functionalization)
  3. Greater dynamics in gene regulatory processes compared to other fish species (check out this review if you want to know more about gene regulation and speciation).
  4. Elevated levels of coding sequence evolution (see examples of opsin-genes above)
  5. Three waves of transposable element expansion that might have sped up cichlid evolution (see these recent reviews the role of transposable elements in speciation and adaptation)

Clearly, the explosive diversification of cichlids is a complex interplay of several factors. Disentangling these processes – and possibly discovering new ones – will likely fuel the research community for some time.

 

References

Irisarri, I., Singh, P., Kolbmuller, S., Torres-Dowdall, J., Henning, F., Franchini, P., Fischer, C., Lemmon, A.R., Lemmon, E.M., Thalinger, G.G., Sturmbauer, C. & Meyer, A. (2018) Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes. Nature Communications 9, 3159.

Salzburger, W. (2018) Understanding explosive diversification through cichlid fish genomics. Nature Reviews Genetics,

 

 

The eagle has landed: Tracking the migration of hybrids between lesser and greater spotted eagles

Following hybrid eagles to their wintering grounds in Africa.

Bird migration is on of the big mysteries in biology. How do birds know where to fly to each winter? For small songbirds, a genetic basis for migration strategies has been uncovered, perhaps regulated by a so-called ‘migratory gene package‘. In larger birds that travel in flocks, such as geese and cranes, social factors are probably more important as birds learn the migration routes from their parents and relatives.

 

Hybrid Migration

But how to disentangle genes from culture? To answer this nature-vs-nurture question on bird migration, you can turn to hybrids. One of the first studies to use this strategy focused on European blackcap warblers (Sylvia atricapilla). These small passerines migrate either southwest or southeast. Hybrids between birds that use different migratory strategies direct their migration intermediate, namely south. Similar studies have been conducted on other bird species, such as Swainson’s trush (Catharus ustulatus) and willow warbler (Phylloscopus trochilus).

lesser spotted eagle.jpg

A lesser spotted eagle (from: http:/www.wikipedia.com/)

 

Tracking Eagles

But what about birds of prey? Researchers have suggested that these big soaring birds learn their migration routes although they usually migrate alone. As the work on passerines indicates, just check the migration of hybrids. And that is exactly what Ülo Väli and his colleagues did: they tracked the migration routes of 62 lesser spotted eagles (A. pomarina), greater spotted eagles (A. clanga) and their hybrids.

These two raptors – that breed in eastern Europe – have very different migration routes. Greater spotted eagles migrate over short distances to winter in southern Eurasia and northeast Africa. The lesser spotted eagle, on the other hand, is a long distance migrant that flies all the way to southern Africa.

greater-spotted-eagle.jpg

A greater spotted eagle (from: http://KuwaitBirds.org/)

 

Mixed Strategies

The results, based on GPS-telemetry, indicated that the timing of the hybrids was similar to lesser spotted eagles while the wintering destinations were similar to greater spotted eagles. The map below shows the migration routes of lesser spotted eagles (blue), greater spotted eagles (yellow) and their hybrids (red). These mixed patterns suggests that there is some genetic influence on the migration strategy of these eagles. But this doesn’t mean that it is all genetics, the researchers write: ‘these results suggest a strong genetic influence on migration strategy via a trait-dependent dominance effect, although we cannot rule out the contribution of social interactions.’

migration eagles

the migration routes of lesser spotted eagles (blue), greater spotted eagles (yellow) and hybrids (red). From: Väli et al. (2018).

 

References

Väli, U., Mirski, P., Sellis, U., Dagys, M. & Maciorowski, G. (2018) Genetic determination of migration strategies in large soaring birds: evidence from hybrid eagles. Proceedings of the Royal Society B 285,20180855.

 

This paper has been added to the Accipitriformes page.

Wall lizards form hybrid swarms in German cities

Genetic study reveals extensive mixing of wall lizard lineages in German cities.

Lately, I have been writing quite a lot about hybridization in South America, featuring among others jacamars, siskins, and ruddy ducks. But you don’t need to venture into the dense jungle of Colombia or Bolivia to see hybrids. Sometimes you can find them right under your nose, in the city for example. A recent study in Proceedings of the Royal Society explored hybrid lizards in German cities.

 

Wall Lizards

Apart from pigeons and jackdaws, you can also find reptiles in cities, such as the common wall lizard (Podarcis muralis). Joscha Beninde and his colleagues collected no less than 826 of these little critters in four German cities: Trier, Saarbrucken, Freiburg and Mannheim. They genotyped all of these individuals using a mitochondrial marker (cytochrome b) and 17 microsatellites.

PA030019.JPG

A picture of a wall lizard that I took myself in 2014 during a conference on Speciation Genomics in Fribourg (Switserland).

 

Hybrid Swarms

The wall lizard comprises a number of distinct genetic lineages that originated from multiple regions in the Mediterranean and spread across Europe. The researchers wanted to know how many lineages can be found in each of the cities and if individuals from different lineages are interbreeding.

Each city houses a native lineage (the so-called ‘Eastern France’ lineage), but in several cities you can also find some non-native lineages. In Mannheim, for instance, the researchers found representatives of the Southern Alps and the Venetian lineages. More detailed genetic analyses revealed that these lineages are mixing, giving rise to hybrid swarms (i.e. a population comprised of two or more genetic lineages).

 

Railways

The researchers also applied some landscape genetic analyses, to explore how cityscape structures influence patterns of gene flow. Water bodies turned out to be strong barriers, whereas railway tracks are conducive to gene flow. Surprising, only the genes of the admixed populations flow along railway tracks. It thus seems that non-native lizards are spreading by railway, not by taking the train but by travelling along the railway enbankments.

It will be interesting to see how the genetic make-up of lizards in these cities will develop. Indeed, the authors conclude that: ‘cities are likely to become major playgrounds for hybridization.’

railway.jpg

The ideal habitat for non-native wall lizards?

 

References

Beninde, J., Feldmeier, S., Veith, M. & Hochkirch, A. (2018) Admixture of hybrid swarms of native and introduced lizards in cities is determined by the cityscape structure and invasion history. Proceedings of the Royal Society B 285, 20180143.

Pinpointing the position of a parrot hybrid zone in eastern Australia

A genomic perspective on an Australian hybrid zone.

Ever heard of Julian Ford? During the 1970s, this Australian ornithologist studied numerous hybrid zones across Australia. His 1987 Emu paper “Hybrid Zones in Australian Birds” lists about 100 contact zones. At the time, molecular techniques were in their infancy, so Ford relied on morphological descriptions. With the advent of genetic – and later genomic – data, some researchers are revisiting these hybrid zones. A recent study in Heredity focuses on two rosella species.

Ford - Hybrid Zones.jpg

An overview of contact zones between different bird species in Australia. Can you spot the rosella hybrid zone? – from: Ford (1987) Emu.

 

A Moving Hybrid Zone?

Hybrid parrots are pretty common in captivity (see this recent series of photos), but these colorful birds also interbreed in the wild. Ashlee Shipham and her colleagues revisited a hybrid zone between pale-headed rosella (Platycercus adscitus) and eastern rosella (P. eximius), which has previously been described using phenotypic data. They sequenced the DNA of 139 birds, collected across the contact zone in eastern Australia.

A phylogenetic study indicated that past hybridization has resulted in the exchange of mtDNA between these parrot species (see this recent blog post on mitochondrial capture in another system). The present study revealed that hybridization is still ongoing, and that ‘contemporary hybridization extends beyond the recently defined limits of the hybrid zone.’ Indeed, the position of the hybrid zone uncovered in this study does not correspond to that reported in previous studies. This discrepancy can be due to observer bias in past studies or the hybrid zone has actually moved over time. More research is needed to figure this out.

Eastern-Rosella.jpg

An eastern rosella (Platycercus eximius) – from: http://www.wikipedia.com/

 

Respecting Species Boundaries

Interestingly, there were no first generation hybrids in the dataset. All admixed individuals were multi-generational or back-crossed birds. This suggests that there is some degree of reproductive isolation between pale-headed and eastern rosella. The exact nature of this isolation mechanism remains to be uncovered, but it could include assortative mating based on plumage, vocalizations or odor (yes, parrots can use smell to recognize each other).

Finally, there was a strong correlation between genomic data and morphology. It thus seems feasible to identify hybrids and back-crosses based on plumage patterns (something that is not always straightforward, see for example hybrids between Saltmarsh Sparrow and Nelson’s Sparrow). This provides great opportunities for further research into this interesting hybrid zone.

pale-headed rosella.jpg

Pale-headed rosella (P. adscitus)

 

References

Shipham, A., Joseph, L., Schmidt, D.J., Drew, A., Mason, I. & Hughes, J.M. (2018) Dissection by genomic and plumage variation of a geographically complex hybrid zone between two Australian parrot species, Platycercus adscitus and Platycercus eximiusHeredity.

 

The paper has been added to the Psittaciformes page.

Ancient DNA study sheds light on domestication history of geese in Russia

Ancient DNA analyses of goose fossils in Russia lead to some surprising results.

Geese are amazing guard dogs. According to the historian Livy, geese alarmed the Roman soldiers when the Gauls tried to invade the Capitoline hill. This story indicates that geese were already domesticated in Roman times. The exact time and locations of goose domestication, however, is unknown. There are some indications that it happened in Egypt during the Old Kingdom (2686-1991 BCE) or in Mesopotamia (2900-2350 BCE). In general, not much is known about the domestication history of geese. A recent study in the journal Genes focuses the medieval period (4th – 18th century) in Russia by sequencing fossils from archaeological sites.

Meidum-geese.jpg

The Meidum Geese – Ancient Egyptian Art*

 

Three Groups

In Russia, a large collection of domestic goose bones has been found in several archaeological sites. It is, however, challenging to discriminate between wild and domestic geese based on the excavated bones. Therefore, Johanna Honka (University of Oulu) and her colleagues sequenced part of the mitochondrial DNA of these fossils. The genetic analyses revealed three main groups: the D-group with domestic greylag geese, the F-group with both domestic and wild greylag geese, and group comprising another species, the taiga bean goose.

Domestic_Goose.jpg

A domestic goose of the Emden breed (from: http://www.wikipedia.com/)

 

Hybridization?

The D-group unequivocally points to domesticated greylag geese. But what about the mixed F-group? Several scenarios are possible here: they could represent a mixture of domestic and hunted wild birds or there could have been hybridization between domestic and wild geese.

The presence of taiga bean geese was a surprising finding. It could be bones from wild birds that were hunted. Or maybe the Russians were starting to domesticate bean geese? Or could it point to hybridization between domestic greylag geese and wild bean geese? There are still many questions on goose domestication waiting to be answered.

Taiga Bean Goose.JPG

A Taiga Bean Goose (from: http://www.gobirding.eu/)

 

Chinese Goose

In Europe, the domestic geese are descended from wild greylag geese (Anser anser). The pink coloration of the bill suggests that it was likely the eastern subspecies rubirostris that was domesticated. Geese have also been domesticated in southeast Asia, but these birds are derived from another species, the Swan Goose (A. cygnoides). Some European breeds have been crossed with the Asian ones, but the present study did not find any evidence for this in their analyses.

chinese goose

A Chinese Goose – domesticated form of Swan Goose (from: http://www.wikipedia.com/)

 

References

Honka, J., Heino, M.T., Kvist, L., Askeyev, I.V., Shaymuratova, D.N., Askeyev, O.V., Askeyev, A.O., Heikkinen, M.E., Searle, J.B. & Aspi, J. (2018) Over a Thousand Years of Evolutionary History of Domestic Geese from Russian Archaeological Sites, Analysed Using Ancient DNA. Genes 9, 369.

 

* There has been some discussion whether the “Meidum Geese” are a fake. You can read about it here and here.

Got your mtDNA! Mitochondrial capture in Amazonian Jacamars

A case of mitochondrial capture in jacamars.

I guess you have probably heard the phrase ‘Mitochondria are the powerhouse of the cell.’ And indeed they are, these small organelles generate the energy (in the form of ATP) that keeps our cells going. Inside these sausage-shaped structures lies a circular piece of DNA – mitochondrial DNA or mtDNA – that became the most popular molecular marker of the 1990s (thanks to John Avise).

 

Got you nose mtDNA!

When you construct a phylogenetic tree based on mtDNA, chances are that it will differ from tree based on nuclear DNA. This phenomenon – known as mitonuclear discordance – has troubled biologists for decades, because several biological processes can explain this pattern. You can check out this recent paper by Timothée Bonnet and colleagues for an overview, but I would like to focus on one of these processes: mitochondrial capture.

When two species are hybridizing , mtDNA can be exchanged. In the simplest case you have two variants – or haplotypes – of mtDNA, one for each species. If one variant is superior over the other (i.e. better adapted to local conditions), it will increase in frequency until all individuals of both species share the same haplotype. In technical terms, we say that the variant went to fixation. At this point, one species has captured the mtDNA of the other: mitochondrial capture!

bronzy_jacamar

A bronzy jacamar (from: http://www.hbw.com/)

 

Jacamars

This process probably occurred between species of jacamar (genus Galbula) in the Amazon region. Mateus Ferreira and his colleagues collected samples of two species: bronzy jacamar (G. leucogastra) and purplish jacamar (G. chalcothorax). Next, they sequenced the DNA of these birds and constructed phylogenetic trees for mtDNA and nuclear DNA. As you might have guessed, the trees looked different. The nuclear genes nicely separated the species into two distinct groups, while the mtDNA mixed the two species. Specifically, G. leucogastra specimens from the Madeira clade clustered together with their geographical neighbours G. chalcothorax. The authors state:

Our hypothesis for this incongruence is that an ancient event of hybridization between G. chalcothorax and the Madeira lineage of G. leucogastra caused the introgression of the Madeira lineage mtDNA into the G. chalcothorax lineage, replacing its “original” mtDNA lineage. This mitochondrial capture may have been influenced by the populational and ecological context of differentiation within WSE.

 

White Sands

What is this WSE they mention? WSE stands for white-sand ecosystems, a unique type of habitat within Amazonia which consists of patches of ‘differentiated habitats scattered across the landscape and isolated by the forest matrix.’ Surprisingly, the different patches have distinct geological origins. In the northeast, these patches are the result of podzolization, in which nutrients are leached away from the top layers of soil, leaving only sand. In other regions, the white sands are the result of river deposits.

The distribution of these patches within a forest matrix resembles an island setting. And researchers have been curious how this peculiar environment has shaped the animals that live in it. The geological and climatic history of the white sands might have facilitated contact between the jacamar species at some point, leading to the capture of mtDNA. The authors could not reconstruct the exact scenario, but I bet it will be a ‘captiviting’ story when they figure it out.

purplish-jacamar12.jpg

A purplish jacamar (from: http://www.hbw.com/)

 

References

Ferreira, M.; Fernandes, A.M., Aleixo, A., Antonelli, A., Olsson, U., Bates, J.M., Cracraft, J. & Riba, C.C. (2018) Evidence for mtDNA capture in the jacamar Galbula leucogastra / chalcothor-ax species-complex and insights on the evolution of white-sand ecosystems in the Amazon basin. Molecular Phylogenetics and Evolution

 

The paper has been added to the Piciformes page.

Fascinating Finches: Patterns of Gene Flow in South American Siskins

Multiple hybridization events in South American siskins.

Although hybridization is a widespread phenomenon in birds, detecting gene flow between species (i.e. introgression) is still challenging. In my Avian Research review – “Avian Introgression in the Genomic Era” – I provided an overview of several methods that can be used to infer genetic exchange between species. Most of these methods assume that you know the evolutionary relationships between the species under investigation. In other words, these methods are dependent on a resolved phylogeny. Unfortunately, this information is not always readily available, especially in recent radiations. A recent study in Molecular Ecology tries to circumvent this phylogenetic uncertainty and shows that you can infer introgression without a proper phylogeny.

hooded siskin

Hooded siskin (Spinus magellanicus) – from: http://www.wikipedia.com/

 

Siskins

South American siskins (genus Spinus) are a group of 11 species that diversified about 550,000 years ago. Previous work indicated that species in the same area share identical mitochondrial haplotypes. This sharing might be due to rapid speciation or hybridization. To figure this out, Elizabeth Beckman and her colleagues focused on four species: hooded siskin (Spinus magellanicus), black siskin (S. atratus), thick-billed siskin (S. crassirostris), and yellow-rumped siskin (S. uropygialis).

black siskin.jpg

Black siskin (Spinus atratus) – from: http://www.hbw.com/

 

Testing for Introgression 

The evolutionary relationships between the siskin species are uncertain. To deal with this uncertainty, the researchers did the following. First, they assessed the population structure of the siskins and delineated particular groups based on their geographical distribution. Next, they generated a phylogenetic tree based on 45,000 SNPs. Finally, they conducted several tests for introgression on a collection of smaller trees that were compatible with the main phylogenetic tree. Using this approach, they were able to pinpoint introgression between the following species:

  • Hooded siskin (from Peru) and thick-billed siskin
  • Hooded siskin (from Peru) and yellow-rumped siskin
  • Hooded siskin (from southern Peru) and black siskin
  • Hooded siskin (from Bolivia) and black siskin

Most of these introgression events probably occurred in the past, around the time these species diversified. However, there might also be recent introgression in Bolivia between hooded siskin and black siskin.

yellow-rumped siskin.jpg

Yellow-rumped siskin (Spinus uropygialis) – from: http://www.hbw.com/

 

Network Analysis

One caveat of this study – as the authors discuss themselves – is that they did not assess these introgression events in a single analysis. Here, a promising approach could be the implementation of phylogenetic networks, which deviate from the classical bifurcating trees by allowing for reticulations. I have actually argued for these networks before, here are the final sentences from my 2016 paper in The Auk:

[I]n birds, phylogenetic networks will provide a powerful tool to display and analyze the evolutionary history of many bird groups. The genomic era might thus result in a paradigm shift in avian phylogenetics from trees to bushes.

tick-billed siskin

Thick-billed siskin (Spinus crassirostris) – from: http://www.flickr.com/ – picture by Pablo Caceres Contreras

 

References

Beckman, E.J., Benham, P.M., Cheviron, Z.A. & Witt, C.C. (2018) Detecting introgression despite phylogenetic uncertainty: the case of the South American siskins. Molecular Ecology.

 

This paper has been added to the Fringillidae page.

 

On the Origin of Pigeon Plumage Patterns: A Role for Hybridization

“Believing that it is always best to study some special group, I have, after deliberation, taken up domestic pigeons.”

– Charles Darwin (1859)

If you have difficulty sleeping at night, grab the Origin of Species by Charles Darwin and turn to the section “On the Breeds of Domestic Pigeons”. His seemingly endless description of various pigeon breeds is bound to make your eyes close. But all joking aside, as Darwin already knew, pigeons are an excellent study system to answer numerous biological questions. This is exemplified by a recent study in the journal eLife that explored the genetic basis of plumage patterns in domestic pigeons (Columba livia).

 

Four Phenotypes, One Locus

There are over 350 breeds of domestic pigeon, showing a variety of plumage pigmentation patterns. Classic experiments have shown that the pigmentation of the wing is determined by variation at a single locus that results in four phenotypes: T-check, checker, bar and barless (see pictures below). Darwin already deduced that bar is the ancestral state. However, checker and T-check are common in feral populations, suggesting an adaptive advantage for these plumage patterns in cities.

Pigeons.jpg

The four wing patterns in domestic pigeons (from: Vickrey et al. 2018 eLife)

 

A Candidate Gene: NDP

When you study the genetic basis of a particular trait, it is useful to have a target gene in mind. So, Anna Vickrey and her colleagues compared the genomes of bar and checker pigeons to see if there were any significant differences. One genomic region – on scaffold 68 – stood out prominently. This region contains, among others, the gene NDP, which is differentially expressed in crow subspecies (black and hooded crow) that differ in their plumage patterns. The same holds true for these pigeons, experiments showed that NDP is significantly more expressed in checker feathers.

fst peak

Comparing the genomes of checker and bar pigeons uncovered a differentiated region on scaffold 68 (the huge peak on the left) that contains the gene NDP (from: Vickrey et al. 2018 eLife).

 

Speckled Pigeon

Further analyses of the NDP-containing region indicated that it originates from another species: the speckled pigeon (C. guinea). It was probably introduced after the domestication of the rock pigeon, which started about 5000 years ago. Apparently, this result is not that surprising to pigeon breeders:

“Pigeon fanciers have long hypothesized that the checker pattern in the rock pigeon (Columba livia) resulted from a cross-species hybridization event with the speckled pigeon, a species with a checker-like wing pattern”

speckled pigeon.JPG

Pigeon breeders already suspected that the speckled pigeon had something to do with plumage patterns in domestic pigeons (from: http://www.wikipedia.com/)

 

Vision Defects

Finally, there is also a connection with humans here (apart from the domestication of pigeons). In humans, a defect NDP gene can result in Norrie disease, a genetic disorder that primarily affects the eye and almost always leads to blindness. Interestingly, the barless phenotype in pigeons is associated with a defect NDP-gene as well. Moreover, pigeon breeders have known for a long time that barless pigeons often have issues with vision. When the researchers compared the defect NDP genes in humans and barless pigeons, it turned out that in both species there was a nonsense mutation at the start of the protein. Who would have seen that coming!

 

References

Vickrey, A.I., Bruders, R., Kronenberg, Z., Mackey, E., Bohlender, R.J., Maclary, E.T., Maynez, R., Osborne, E.J., Johnson, K.P., Huff, C.D., Yandell, M. & Shapiro, M.D. (2018) Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon. eLife 7, e34803.  DOI: 10.7554/eLife.34803

 

This paper has been added to the Columbiformes page.

Something smells fishy: Exchange of olfactory genes between cichlids

The best way to observe a fish is to become a fish sequence its genome.

– Adapted from Jacques Yves Costeau

 

The speciation of Coptodon cichlids might have been driven by smell.

African cichlids are a textbook example of rapid speciation. In the lakes of East Africa, thousands of species have originated in the geological blink of an eye (check these excellent reviews by Thomas Kocher and Ole Seehausen for more detailed information). A recent study in Molecular Ecology investigated one of the many cichlid radiations and uncovered a peculiar pattern of gene flow.

 

Lake Ejagham

Three isolated lakes in Cameroon house four cichlid radiations. Two of these lakes are crater lakes, while the third one (Lake Ejagham) is probably the result of a meteor impact. The latter lake houses four species of Coptodon cichlids. Previous work found evidence for gene flow from river populations into this lake. Jelmer Poelstra and his colleagues explored the evolutionary history of these cichlids in more detail.

The researchers sequenced the genomes of three species in the lake (C. fusiforme, C. deckerti and C. ejagham) and two riverine species (C. guineensis and the undescribed C. sp. “Mamfé”). The comparison of these genomes confirmed the results from the previous study: there has been gene flow from riverine species into Lake Ejagham.

fish cameroon

The genomes of five species from Cameroon were sequenced. The first three come from lake Ejagham, the other two from rivers (from: Poelstra et al. 2018 Molecular Ecology).

 

‘Smell Genes’

Further analyses revealed that a particular genomic region was transferred from C. sp. “Mamfé” into C. deckerti and C. ejagham. This transfer happened just before the divergence of the latter two species. Could this genomic region have initiated a speciation event?

Interestingly, this genomic regions contained a cluster of eight olfactory receptor genes. Olfactory receptors – “smell genes” if you will – have often been linked to the origin of new species. Several fish species use smell to recognize members from their species. Whether smell has also been important in the Coptodon radiation remains to be investigated, but it seems like a plausible scenario.

Coptodon deckerti

A specimen of Coptodon deckerti (from: https://www.nvcweb.nl/)

 

References

Poelstra, J.W., Richards, E.J. & Martin, C.H. (2018) Speciation in sympatry with ongoing secondary gene flow and a potential olfactory trigger in a radiation of Cameroon cichlids. Molecular Ecology.