Abstract
Restoration of lost species ranges to their native distribution is key for the survival of endangered species. However, reintroductions often fail and long‐term genetic consequences are poorly understood. Alpine ibex (Capra ibex) are wild goats that recovered from <100 individuals to ~50,000 within a century by population reintroductions. We analyzed the population genomic consequences of the Alpine ibex reintroduction strategy. We genotyped 101,822 genomewide single nucleotide polymorphism loci in 173 Alpine ibex, the closely related Iberian ibex (Capra pyrenaica) and domestic goat (Capra hircus). The source population of all Alpine ibex maintained genetic diversity comparable to Iberian ibex, which experienced less severe bottlenecks. All reintroduced Alpine ibex populations had individually and combined lower levels of genetic diversity than the source population. The reintroduction strategy consisted of primary reintroductions from captive breeding and secondary reintroductions from established populations. This stepwise reintroduction strategy left a strong genomic footprint of population differentiation, which increased with subsequent rounds of reintroductions. Furthermore, analyses of genomewide runs of homozygosity showed recent inbreeding primarily in individuals of reintroduced populations. We showed that despite the rapid census recovery, Alpine ibex carry a persistent genomic signature of their reintroduction history. We discuss how genomic monitoring can serve as an early indicator of inbreeding.
Highlights
Many species experienced near-extinction events in their demographic history
We showed that despite the rapid census recovery, Alpine ibex carry a persistent genomic signature of their reintroduction history
We aimed to identify the population genomic consequences of the Alpine ibex reintroduction strategy using Iberian ibex and domestic goat (Capra hircus) as a reference
Summary
Many species experienced near-extinction events in their demographic history. Habitat protection and reintroductions are the main strategies for species conservation. The first stage is the transfer of individuals and successful reproduction in a new area; such events were causing founder effects in reintroduced populations with a likely loss of genetic diversity. Conservation management can prevent inbreeding depression by translocating individuals from genetically distant populations. As all individuals used for the captive breeding originated from the same source population (Gran Paradiso), the zoo-bred population likely started with no genetic subdivisions. Despite effective management and hunting restrictions across the European Alps, some Alpine ibex populations recently declined in size. We aimed to identify the population genomic consequences of the Alpine ibex reintroduction strategy using Iberian ibex and domestic goat (Capra hircus) as a reference. We addressed the following questions: (i) What was the loss of genomewide diversity due to the reintroduction of Alpine ibex from a single source population? We addressed the following questions: (i) What was the loss of genomewide diversity due to the reintroduction of Alpine ibex from a single source population? How do the levels of genetic diversity compare with the major Iberian ibex populations? (ii) Did the stepwise reintroduction strategy of primary and secondary populations lead to a stepwise increase in genetic subdivision with subsequent rounds of reintroductions? (iii) Did the reintroductions lead to genomewide signatures of recent inbreeding? we discuss how genomewide data can be used to assess the long-term viability of reintroduced species
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