Back from the brink of extinction: The remarkable recovery of the Crested Ibis

The severe bottleneck has left its footprints in the genomes of these birds.

Seven. There were only seven individuals of the Crested Ibis (Nipponia nippon) in 1981. China and Japan started extensive captive breeding programs to save this species from extinction. Currently, the Crested Ibis is still endangered but the population has increased to over 2,000 individuals. A remarkable recovery. However, the severe bottleneck has left its traces in the genome of the Toki (its Japanese name). A study in the journal Current Biology documented the genetic legacy of this history by comparing contemporary samples with historical ones.


A crested Ibis in the Xi’an QinLing Wildlife Park (China)  © Danielinblue | Wikimedia Commons


Low Genetic Diversity

An international group of scientists sequenced the genomes of 57 historical samples (dating between 1841 and  1922) and eight contemporary birds. These genomes revealed that the historical samples clustered according to their geographic origin. The contemporary samples formed a separate group, indicating that they can be traced back to a few individuals.

The clustering analyses suggests that a lot of genetic diversity has been lost over time. Indeed, nucleotide diversity is considerably lower in the contemporary samples. Moreover, several genetic loci that were polymorphic (i.e. had multiple variants) in the historical samples have gone to fixation (i.e. only one variant is left) in present-day birds. You can compare this situation with a pool filled with differently colored balls. Over time, more and more colors disappear until you are left with only one color. A dramatic loss in diversity.


Nucleotide diversity across the genomes of historical (blue) and contemporary (red) samples. From: Feng et al. (2019) Current Biology


Inbreeding Depression

These results point to high levels of inbreeding. Not that surprising, given that the population was reduced to only seven individuals. To quantify the severity of this inbreeding, the researchers counted the number of homozygous deleterious mutations in the genomes of these birds. Homozygous indicates that both chromosomes have the same variant and deleterious refers to the negative effect on the fitness of the individual. Several diseases are caused by this type of mutation. This analysis revealed that the number of these mutations has doubled in less than 100 years. That is a severe bottleneck.

The seriousness of this situation is nicely exemplified by the Major Histocompatibility Complex (MHC). This set of genes is essential for the immune response that protects individuals from harmful bacteria and viruses. Ideally, the MHC is very variable, allowing it to swiftly react to a broad range of pathogens. In the Crested Ibis, however, the MHC has experienced a drastic decrease in genetic diversity. This makes these birds susceptible for different diseases.


The genetic diversity of MHC is drastically reduced in contemporary birds (outer ring), as shown by the large stretches of low diversity regions (dark-blue). From: Feng et al. (2019) Current Biology



Although the Crested Ibis has made a remarkable recovery, the footprints of the severe bottleneck are still visible in their genomes. The low genetic diversity renders these birds vulnerable to future perturbations. It is thus essential to continue the conservation efforts to ensure the survival of this beautiful bird.



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 Biology29(2), 340-349.

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