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The genomic footprint of the crested ibis

Dr. Friederike Woog, curator of the bird collection at the Stuttgart State Museum of Natural History.

During guided tours through the museum’s bird collection, I keep emphasizing that our over 150,000 bird objects can be regarded as a DNA bank. It is possible to extract genetic material from a small skin sample. Especially in the case of species threatened with extinction with small remnant populations, it is important to know whether the species’ genetic variation is sufficient for the population to survive. This is especially important for reintroduction projects. If animals are too closely related, inbreeding can occur. Inbreeding may result in low fertility and even in sterile birds that cannot produce young.

Possible inbreeding effects can only be reliably tested if one is familiar with the genetic diversity of the past. Examining historical specimens from scientific collections can help to clarify this. When I was asked by Tom Gilbert, Professor of Paleogenomics at the University of Copenhagen, if we had samples of the threatened Crested Ibis (Nipponia nippon), I had no idea what would follow. I often decline these sorts of requests of tissue to safeguard our specimens, but in this case I decided the request would be justified. According to the IUCN, there are only 300 adult birds of this enigmatic ibis species left in the wild, in two localities in Shaanxi Province in China. Formerly they also occurred in Japan, South and North Korea, Taiwan and Russia, but they are now thought to be extinct there.

Crested Ibis (Nipponia nippon) in the SMNS bird collection, collected in 1882 in Japan (Photo: Ulrich Schmid / SMNS).
Crested Ibis, painted in 1838 (Wikimedia commons).

The world population of this species in breeding programs in zoos is approximately 2000 individuals. Reintroduction efforts have already been partially successful. However, it was not known to what extent the breeding programs made sense from a genetic point of view.

This is why inquiries to various museums with large historical collections, including the Stuttgart Natural History Museum, were successful. We carefully took skin samples from our two historical specimens and sent them to Copenhagen. In total, Tom Gilbert’s team received 57 historical samples from eight museums around the world (USA, England, Germany, Austria, Netherlands, Denmark), which had been collected between 1841 and 1922. The samples, which geographically covered large parts of China, Korea, Japan and Russia, are diverse enough to allow statistically reliable statements.

Instead of just comparing individual gene segments from historical finds from museums with animals still living in the wild, the entire genomes of these rare birds were examined. It turned out that the genetic diversity today is only half as great as in the 19th and early 20th centuries. The extant population shows strong inbreeding with a genome that has many harmful mutations — a clear “bottleneck effect”. The population bottleneck caused random losses (“genetic drift”) and in connection with inbreeding this led to a massive decline in the original genetic diversity.

Even if it doesn’t look so good for the Crested Ibis from a genetic point of view, it could still recover if it continues to be strictly protected. This has been shown for some species that live on islands with strong ecological fluctuations. In poor conditions they almost die out entirely, but can then recover again and sometimes in better condition—despite genetic bottlenecks. This study is an example that genomic information from museum samples can be an important basis for the conservation of threatened species.


References

Feng, S., Fang, Q., Barnett, R., Li, C., Han, S., Kuhlwilm, M., Zhou, L., Pan, H., Deng, Y., Chen, G., Gamauf, A., Woog, F., Prys-Jones, R.., Marques-Bonet, T., Gilbert, M.T.P., Zhang, G. 2019. The genomic footprints of the fall and recovery of the crested ibis. Current Biology 21; 29(2):340-349

https://www.sciencedirect.com/science/article/pii/S0960982218316099

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