Effective population sizes and adaptive genetic variation in a captive bird population

Abstract

Captive populations are considered a key component of ex situ conservation programs. Research on multiple taxa has 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 and adaptive loci in captive populations. In 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 represents a rare instance of a population with a well-documented history in captivity, following a realistic scenario of chain-of-custody, unlike many captive lab populations. Our analyses, which included 27 individuals comprising the entirety of one captive population show very low neutral and adaptive genetic variation, as well as low effective sizes, which correspond with 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.

Keywords: Birds; Bottleneck; Captive population; Effective population size; Junglefowl; Major histocompatibility complex; Microsatellites.

Figure 1. A flowchart showing the known demographic history of the Richardson’s Red Junglefowl.

A graphical representation of the known population history of the Richardson’s Red Junglefowl population in captivity and chain of custody. The red rimmed box denotes released populations that ultimately failed to take hold, and experienced extinction in their new habitat. The blue shaded boxes show the history of the populations that trace back to Isaac Richardson’s flock.

Figure 2. LD plot generated based on recombination frequencies across the MHC-B locus as characterized by the SNP panel.

A linkage map based on the 90 SNP loci on chromosome 16, generated from genotype data for the study population. The map shows pairwise estimates of linkage disequilibrium between markers. Red colored blocks suggest high linkage disequilibrium (D′) values of 1, implying little to no recombination between markers.

Figure 3. A haplotype network based on genetic distances between the five haplotypes identified in the study population.

A haplotype network of the the five (phased) haplotypes detected in the study population. Only three of the five unique haplotypes were found at a frequency of over 10% in the population (I, III, and V).