Data from: Inbreeding and selection shape genomic diversity in captive populations: implications for the conservation of endangered species

Captive breeding programs are often initiated to prevent species
extinction until reintroduction into the wild can occur. However, the
evolution of captive populations via inbreeding, drift, and selection can
impair fitness, compromising reintroduction programs. To better understand
the evolutionary response of species bred in captivity, we used nearly
5500 single nucleotide polymorphisms (SNPs) in populations of white-footed
mice (Peromyscus leucopus) to measure the impact of breeding regimes on
genomic diversity. We bred mice in captivity for 20 generations using two
replicates of three protocols: random mating (RAN), selection for docile
behaviors (DOC), and minimizing mean kinship (MK). The MK protocol most
effectively retained genomic diversity and reduced the effects of
selection. Additionally, genomic diversity was significantly related to
fitness, as assessed with pedigrees and SNPs supported with genomic
sequence data. Because captive-born individuals are often less fit in wild
settings compared to wild-born individuals, captive-estimated fitness
correlations likely underestimate the effects in wild populations.
Therefore, minimizing inbreeding and selection in captive populations is
critical to increasing the probability of releasing fit individuals into
the wild.