DOI: 10.5061/dryad.68kk0
title: Data from: Estimating demographic contributions to effective population size in an age-structured wild population experiencing environmental and demographic stochasticity

description: 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.
description: Data for demographic
 estimation of NeThis file contains data
 required for the estimation of effective population size (Ne) from
 population- and individual-level demographic data from a population of
 red-billed chough on Islay, Scotland, UK. Each row provides data on
 sex-age-year specific breeding success and survival to the following
 year.data
 for demographic estimation of
 Ne.txtData for LD genetic
 estimation of NeThis file contains the
 raw microsatellite genotype data required for the estimation of effective
 population (Ne) of the Islay red-billed chough population, using linkage
 disequilibrium (LD) in the program NeEstimator v2.01 (Waples & Do
 2008).data
 for LD genetic estimation of
 Ne.txtData for ONeSAMP genetic
 estimation of NeThis file contains the
 raw microsatellite genotype data required for the estimation of effective
 population (Ne) of the Islay red-billed chough population, using
 approximate Bayesian computation (ABC) in the program ONeSAMP (Tallmon et
 al. 2008).data for ONeSAMP genetic
 estimation of Ne.txtData for survival
 analysisThis file contains the
 encounter histories required for estimation of mean age-specific survival
 probabilities using capture-mark-recapture models in program MARK (White
 & Burnhman 1999).data for survival
 analysis.txt