Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species

Abstract

BackgroundNearly one-quarter of all avian species is either threatened or nearly threatened. Of these, 73 species are currently being rescued from going extinct in wildlife sanctuaries. One of the previously most critically-endangered is the crested ibis, Nipponia nippon. Once widespread across North-East Asia, by 1981 only seven individuals from two breeding pairs remained in the wild. The recovering crested ibis populations thus provide an excellent example for conservation genomics since every individual bird has been recruited for genomic and demographic studies.ResultsUsing high-quality genome sequences of multiple crested ibis individuals, its thriving co-habitant, the little egret, Egretta garzetta, and the recently sequenced genomes of 41 other avian species that are under various degrees of survival threats, including the bald eagle, we carry out comparative analyses for genomic signatures of near extinction events in association with environmental and behavioral attributes of species. We confirm that both loss of genetic diversity and enrichment of deleterious mutations of protein-coding genes contribute to the major genetic defects of the endangered species. We further identify that genetic inbreeding and loss-of-function genes in the crested ibis may all constitute genetic susceptibility to other factors including long-term climate change, over-hunting, and agrochemical overuse. We also establish a genome-wide DNA identification platform for molecular breeding and conservation practices, to facilitate sustainable recovery of endangered species.ConclusionsThese findings demonstrate common genomic signatures of population decline across avian species and pave a way for further effort in saving endangered species and enhancing conservation genomic efforts.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-014-0557-1) contains supplementary material, which is available to authorized users.

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

“…Note that this figure is similar to that observed in a highly inbred domestic cat (121 SNPs/Mb) and lower than those of other highly endangered mammals [43] (Fig. 4d) or birds [44], including the endangered crested ibis ( Nipponia nippon ; 430 SNPs/Mb) or the white-tailed eagle ( Haliaeetus albicilla ; 400 SNPs/Mb) [44]. Accordingly, we also observed values of average genome-wide nucleotide diversity and synonymous nucleotide diversity that are to our knowledge the lowest reported for any organism [50] (Table 1; Additional file 1: Sections 20 and 21).…”

Understanding and monitoring the consequences of human impacts on intraspecific variation

“…Such species are typically of intense interest and are therefore frequently monitored for various aspects of intraspecific variation. As one example, a comparative genomic study across avian species discovered that both the loss of genetic variation and the accumulation of deleterious mutations of protein‐coding genes contributed to major genetic defects in endangered species (Li et al., 2014). They also implied that some sets of genes could contribute to averting extinction or enhancing recovery in endangered crested ibis ( Nipponia nippon ) populations.…”

Avian genomics: fledging into the wild!

“…Actually, the Avian Genomics papers from December 2014 offer a first example of how true genomic information fosters more applied fields of research, long waiting for large-scale genomic information: conservation genomics (Allendorf et al 2010;Ouborg et al 2010;Piertney 2006;Shafer et al 2015). Li et al (2014b) characterised important baseline data in the genome of the crested ibis regarding processes such as near-extinction and subsequent rescue.…”