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

Abstract

Background: Nearly 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. Results: Using 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.Conclusions: These 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.

No Signs of Genetic Erosion in a 19th Century Genome of the Extinct Paradise Parrot (Psephotellus pulcherrimus)

“…Although the genome-wide level of heterozygosity in the Paradise Parrot genome is not as high as in the abundant Australian Budgerigar, it is almost twice as high as in the now endangered New Zealand Kea (Table 2). It is also higher than the genome-wide level of heterozygosity found in almost all endangered and vulnerable species listed by [47]. It is within the range of what is found for species falling in the IUCN category "least concerned".…”

“…Li et al [47] found that threatened species, of which some had gone through severe population bottlenecks, on average had considerably lower genome-wide levels of heterozygosity than common and abundant species. Although the genome-wide level of heterozygosity in the Paradise Parrot genome is not as high as in the abundant Australian Budgerigar, it is almost twice as high as in the now endangered New Zealand Kea (Table 2).…”

Little Adaptive Potential in a Threatened Passerine Bird

“…The levels of molecular genetic diversity found in this study are consistent with a depleted diversity compared to other passerine species (Figure 1). Comparison of individual heterozygosity in pairs of threatened and non-threatened bird species [15] similarly showed a diversity roughly two to five times lower in threatened birds. Our average level of individual heterozygosity (0.00069; see Figure S1) falls well within the range observed by [15] for threatened bird species (0.0004-0.00091).…”

Towards inclusion of genetic diversity measures into IUCN assessments: a case study on birds

“…Furthermore, birds in the orders Gaviiformes and Ciconiiformes have been affected by changes in land use and degradation of freshwater systems because of their high dependence on aquatic habitats (Arzel et al, 2015), vulnerability to pathogens (Silva et al, 2010), and exposure to pollutants derived from aquatic contamination (Fontenelle, 2006). There are strong examples in the literature suggesting that populations of many Ciconiiformes have undergone genetic bottlenecks as evidenced by the loss of genetic diversity and an increase in deleterious mutations (Li et al, 2014) due to inbreeding, climate change, habitat loss, hunting and environmental pollution, especially by agrochemicals (e.g., Zhang et al, 2004;Miño et al, 2009). Significant correlations were observed between the number of loci used and the estimates of H O and H E .…”