The Genomic Footprints of the Fall and Recovery of the Crested Ibis

Summary

Human-induced environmental change and habitat fragmentation pose major threats to biodiversity and require active conservation efforts to mitigate their consequences. Genetic rescue through translocation and the introduction of variation into imperiled populations has been argued as a powerful means to preserve, or even increase, the genetic diversity and evolutionary potential of endangered species [ 1, 2, 3, 4]. However, factors such as outbreeding depression [ 5, 6] and a reduction in available genetic diversity render the success of such approaches uncertain. An improved evaluation of the consequence of genetic restoration requires knowledge of temporal changes to genetic diversity before and after the advent of management programs. To provide such information, a growing number of studies have included small numbers of genomic loci extracted from historic and even ancient specimens [ 7, 8]. We extend this approach to its natural conclusion, by characterizing the complete genomic sequences of modern and historic population samples of the crested ibis ( Nipponia nippon), an endangered bird that is perhaps the most successful example of how conservation effort has brought a species back from the brink of extinction. Though its once tiny population has today recovered to >2,000 individuals [ 9], this process was accompanied by almost half of ancestral loss of genetic variation and high deleterious mutation load. We furthermore show how genetic drift coupled to inbreeding following the population bottleneck has largely purged the ancient polymorphisms from the current population. In conclusion, we demonstrate the unique promise of exploiting genomic information held within museum samples for conservation and ecological research.

Highlights

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  Recent population decline of crested ibis in 10 kya was likely shaped by human activity

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  Modern group has lost almost half of genetic variations in pre-bottleneck ancestors

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  Modern group suffers from a high inbreeding coefficient and deleterious mutation load

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  Ancestral balancing selection is outweighed by genetic drift in the modern group

Abstract

Feng et al. use whole-genome sequencing of contemporary and historic crested ibis, an iconic endangered bird species, to explore how their genetic diversity has changed through time. Their analyses reveal the roles of genetic drift and intensive inbreeding on the loss of genetic diversity in today’s population.