Data from: Population genomics analyses of European ibex species show lower diversity and higher inbreeding in reintroduced populations

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 genome-wide 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 step-wise
reintroduction strategy left a strong genomic footprint of population
differentiation, which increased with subsequent rounds of
reintroductions. Furthermore, analyses of genome-wide 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.