Data from: Estimating demographic contributions to effective population size in an age-structured wild population experiencing environmental and demographic stochasticity

1.A population's effective size (Ne) is a key parameter that shapes
rates of inbreeding and loss of genetic diversity, thereby influencing
evolutionary processes and population viability. However estimating Ne,
and identifying key demographic mechanisms that underlie the Ne to census
population size (N) ratio, remains challenging, especially for small
populations with overlapping generations and substantial environmental and
demographic stochasticity and hence dynamic age-structure. 2.A
sophisticated demographic method of estimating Ne/N, which uses
Fisher's reproductive value to account for dynamic age-structure, has
been formulated. However this method requires detailed individual- and
population-level data on sex- and age-specific reproduction and survival,
and has rarely been implemented. 3.Here we use the reproductive value
method and detailed demographic data to estimate Ne/N for a small and
apparently isolated red-billed chough (Pyrrhocorax pyrrhocorax) population
of high conservation concern. We additionally calculated two single-sample
molecular genetic estimates of Ne to corroborate the demographic estimate
and examine evidence for unobserved immigration and gene flow. 4.The
demographic estimate of Ne/N was 0.21, reflecting a high total demographic
variance (σ2dg) of 0.71. Females and males made similar overall
contributions to σ2dg. However, contributions varied among sex-age
classes, with greater contributions from 3 year-old females than males,
but greater contributions from ≥5 year-old males than females. 5.The
demographic estimate of Ne was ~30, suggesting that rates of increase of
inbreeding and loss of genetic variation per generation will be relatively
high. Molecular genetic estimates of Ne computed from linkage
disequilibrium and approximate Bayesian computation were approximately 50
and 30 respectively, providing no evidence of substantial unobserved
immigration which could bias demographic estimates of Ne. 6. Our analyses
identify key sex-age classes contributing to demographic variance and thus
decreasing Ne/N in a small age-structured population inhabiting a variable
environment. They thereby demonstrate how assessments of Ne can
incorporate stochastic sex- and age-specific demography and elucidate key
demographic processes affecting a population's evolutionary
trajectory and viability. Furthermore, our analyses show that Ne for the
focal chough population is critically small, implying that management to
re-establish genetic connectivity may be required to ensure population
viability.