Assessing evolutionary processes over time in a conservation breeding program: a combined approach using molecular data, simulations and pedigree analysis

Captive breeding for conservation is widely used to prevent extinction, however these programs face many challenges due to small population size, founder effects, lack of migration and potential adaptation to captivity. Together these influence how selection, genetic drift and gene flow shape the genetic makeup of small populations, so examining these in a captive setting is valuable for appropriate biodiversity management. We have quantified the effects of selection, drift and gene flow in 503 individuals across five generations from the Tasmanian devil insurance population. To determine whether different processes were acting in different settings, we separately analysed animals housed under individual-based management, versus those that were released to an island site. We found that a greater proportion of alleles were lost over time in the smaller island population than in captivity and propose that genetic drift is the most likely process influencing this result. We found that the captive population became more heterozygous over time, while the island population stayed constant. Our molecular measure of inbreeding found a decrease over generations in captivity that is not captured by pedigree-based analysis. As management of breeding interactions only takes place in the captive population, our results are consistent with gene flow through managed breeding in captivity minimising inbreeding over time. Gene flow was also evident through changes to population structure in the captive population. Our findings serve as an example of how conservation managers can assess the impact of evolutionary processes on managed populations and adapt management practices if required.