Ghost populations explain how the Red-billed Chough reached the Canary Islands

Genetic analyses point to a ghost population on the African coast.

Island populations originate when small sections of the mainland population colonize remote archipelagos. So, just look for the closest mainland population and you have identified the source population. This reasoning sounds logical, but it ignores one important issue: species distributions change over time. The current range of a species does not necessarily represent the situation when the islands were colonized. The populations that fueled the island colonization might have disappeared. It is thus important to consider the possibility of these “ghost populations”. A recent study in the Journal of Biogeography investigated whether ghost populations played a role in the establishment of the Red-billed Chough (Pyrrhocorax pyrrhocorax) on the Canary Islands.

Colonization Scenarios

I have always associated the Red-billed Chough with alpine environments, so I was surprised to learn that this corvid also occurs on the Canary Islands. The population on the island of La Palma is even one of its strongholds in the western Palearctic with an estimated 2800 individuals. But how did the Red-billed Chough reach La Palma? When we look at its current distribution on the mainland, we can narrow it down to two source populations: Iberia (Spain and Portugal) or the Atlas Mountains in Morocco. Both populations are quite far from the Canary Islands: a trip from Iberia covers about 1200 kilometers, while the distance between Morocco and La Palma amounts to 800 kilometers. Red-billed Choughs are not known to travel such large distances, so long-distance dispersal seems unlikely.

Another possibility is that there has been suitable habitat for choughs along the North African coast. This scenario is supported by paleoclimatic studies, revealing that the Sahara has experienced periods of a wet, subtropical climate. Today, the nearest distance between the coast and the closest island (Fuerteventura) is 96 km, and during ice ages this distance would be even shorter due to drops in sea level. Francisco Morinha, Borja Milá and their colleagues used genetic data to test these scenarios (long-distance dispersal vs. ghost populations) and reconstruct the colonization history of the Red-billed Chough.

Different island colonization scenarios for the Red-billed Chough (a) Current distribution of Red-billed Choughs in Iberia, inland Morocco and La Palma (Canary Islands), with sampling sites indicated by star symbols. (b) The long-distance colonization hypothesis proposes that choughs colonized La Palma through a transoceanic flight from Iberia or from current populations in inland Morocco. (c-d) The ghost population hypothesis proposes that colonization of La Palma Colonization from a coastal Morocco (ghost) population that has since gone extinct as habitat desertified and became unsuitable for choughs. From: Morinha et al. (2020) Journal of Biogeography.

Genetic Evidence

The genetic analyses of mitochondrial DNA and ten microsatellites indicated that Red-billed Choughs from La Palma are most closely related to the Iberian population. That still leaves the question whether these birds flew all the way from Iberia or if they originate from ghost populations that were connected to Iberia. The researchers discard the long-distance dispersal scenario for several reasons:

  1. Red-billed Choughs are non-migratory and do not disperse far (a few 100 kilometers at most)
  2. These is no fossil evidence of choughs on other islands, such as the Azores or Madeira, that lie between Iberia and the Canary Islands.
  3. The mtDNA shows no signs of a genetic bottleneck which would be expected if a small population from Iberia colonized the Canary Islands.

These are all reasonable arguments, but disproving the long-distance dispersal scenario does not automatically validate the ghost population scenario (that would be a black-or-white fallacy). So, what about the evidence in favor of the scenario involving a ghost population? The researchers tested this hypothesis using Approximate Bayesian Computation in which they compared different biogeographic models. The results revealed that “the model including a ghost population connecting Iberia and La Palma was more likely than alternative models.” However, the researchers warn that this modelling approach is based on just ten microsatellites, and will need to be validated with genomic data. Nonetheless, based on the current evidence, it seems likely that the Red-billed Chough reached La Palma through a ghost population on the African coast.

An overview of the different models to explain the colonization history of La Palma by the Red-billed Chough. The scenario with the highest probability (figure d) suggests a ghost population (black) connecting Iberia (orange) with La Palma (blue). From: Morinha et al. (2020) Journal of Biogeography.

References

Morinha, F., Milá, B., Dávila, J. A., Fargallo, J. A., Potti, J., & Blanco, G. (2020). The ghost of connections past: A role for mainland vicariance in the isolation of an insular population of the red‐billed chough (Aves: Corvidae). Journal of Biogeography47(12), 2567-2583.

Featured image: Red-billed Cough (Pyrrhocorax pyrrhocorax) © Malte Uhl | Wikimedia Commons

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 communications11(1), 1-11.

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

 

This paper has been added to the Corvidae page.