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Sequencing Studies Implicate 'Supergene' in Distinct Male Morphs of Bird Species

ruff male morphs

NEW YORK (GenomeWeb) – Studies by two independent research teams reporting in Nature Genetics suggest that a single inversion containing dozens of genes is behind the dramatically different phenotypes found in males from the ruff species Philomachus pugnax, a wading sandpiper bird that makes its home on shores in parts of Eurasia.

The ruff is known for its three behaviorally and physically distinct male morphs. The most common of these is a group of colorful "independent" males with elaborate plumage and head tufts, which defend ruff territories called leks that are used for elaborate breeding rituals.

But a smaller proportion of ruff males fall into either "satellite" or "faeder" morphs. The former morph is smaller and more submissive with white rather than colored ruffs and head tufts, while males in the least-common faeder morph show female-like coloring and size patterns.

For one of the studies, researchers from Uppsala University, BGI-Shenzhen, and elsewhere put together a high-quality genome for a captive ruff from the Helsinki zoo before resequencing 15 independent males, nine satellite males, and one faeder male sampled over more than a decade from an island in the Baltic Sea.

Their initial ruff genome assembly, comprised of Illumina HiSeq 2000 reads, spanned some 1.25 billion bases of the genome to an estimated average depth of around 114-fold coverage.

The team used the same sequencing instrument to resequence satellite ruff male representatives to average sequencing depths of around eight-fold. The faeder male's genome was sequenced to an average depth of 30-fold.

When they compared sequences from each morph to one another, the researchers narrowed in on a 4.5 million base inversion in males from the satellite morph. PCR-based screening experiments uncovered heterozygous forms of the inversion in all of the satellite males tested and in the faeder male, they reported, though it was typically missing in independent males, which carried an ancestral version of the allele.

That 3.8 million-year-old inversion, together with more recent recombination events, apparently produced a collection of 90 or more genes that have since evolved in a set, producing the alternative alleles found in satellite and faeder male morphs.

"We think that this evolutionary process started with the occurrence of the inversion … and that the inversion in itself altered the regulation of one or more genes affecting the metabolism of sex hormones," co-senior author Leif Andersson, a researcher affiliated with Uppsala University, the Swedish University of Agricultural Sciences, and Texas A&M, said in a statement. "[T]his created a primitive alternative male morph, which has been further improved step by step by the accumulation of many genetic changes."

Another international team led by investigators in the UK and Canada came to similar conclusions when it generated and analyzed a 1.17 billion base genome assembly for a captive independent ruff male using a combination of Illumina short reads and Pacific Biosciences long reads.

To that, the group added RNA sequence data from male and female ruff tissues as well as profiles for more than a million SNPs identified in hundreds of captive and wild ruffs that were tested by reduced-representation restriction site-associated DNA sequencing.

With the help of genetic mapping, a genome-wide association analysis on a few dozen male ruffs, and resequencing data for one independent, two satellite, and two faeder males, the researchers linked heterozygous forms of the same chromosome 11 inversion to male morph determination.

Their results suggested the region contains 125 protein-coding genes, including those with ties to distinctive features in the satellite and faeder morphs.

"The special feature of the supergene is that it allows lots of genes that are next to each other on a chromosome — which in this case determine multiple traits including hormones, feathering, color, and size — to evolve together and create two distinct behavioural traits," University of Sheffield animal and plant sciences researcher Terry Burke, senior author on that study, said in a statement.

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