Effective population sizes and adaptive genetic variation in a captive bird population
Captive populations are considered a key component of ex situ conservation programs. Research on multiple taxa have shown the differential success of maintaining demographic versus genetic stability and viability in captive populations. In typical captive populations, usually founded by few or related individuals, genetic diversity can be lost and inbreeding can accumulate rapidly, calling into question their ultimate utility for release into the wild. Furthermore, domestication selection for survival in captive conditions is another concern. Therefore, it is crucial to understand the dynamics of population sizes, particularly the effective population size, and genetic diversity at non-neutral, at adaptive loci in captive populations.\n\nIn this study, we assessed effective population sizes and genetic variation at both neutral microsatellite markers, as well as SNP variants from the MHC-B locus of a captive Red Junglefowl population. This population is a rare instance of a well-documented history in captivity, and also following a realistic chain-of-custody, unlike captive lab populations. Our analysis of 27 individuals that comprise the entirety of one captive population. Our results show very low neutral and adaptive genetic variation, as well as low effective sizes, which are surprising in spite of the known demographic history. Finally, our study also shows the divergent impacts of small effective size and inbreeding in captive populations on microsatellite versus adaptive genetic variation in the MHC-B locus. Our study provides insights into the difficulties of maintaining adaptive genetic variation in small captive populations.