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.

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