Data from: Beyond abundance: The impact of sampling design on effective population size estimates in capercaillie

Effective population size (Ne) is a useful parameter to evaluate the
long-term viability of populations. While obtaining enough field data from
wild populations to estimate Ne directly is challenging, molecular
techniques applied to non-invasive samples provide an appealing
alternative. However, Ne estimates may be biased by both ecological and
sampling-related factors. In polygamous species, the monopolization of
mating tends to reduce the ratio between the effective population and the
census population (Ne: Nc) compared to idealized populations. Ne estimates
may also be affected by sample size, spatial structure, and relatedness,
factors that are often overlooked in studies of wild populations. We
investigated how sample size, spatial structure, and relatedness impact Ne
estimates in an endangered population of a polygynous forest grouse, the
Cantabrian capercaillie, inhabiting the mountains of north-western Spain.
We studied  135 capercaillie individuals based on DNA extracted
from droppings and shed feathers. We estimated contemporary Ne based on
linkage disequilibrium. Ne estimates stabilized at sample sizes of ~20
individuals, with confidence intervals markedly narrowing beyond 30
individuals, i.e., at 23 to 35% of the estimated population size. Samples
taken in specific valleys yielded consistently lower Ne values compared to
similar-sized random samples from the entire study area, indicating that
the spatial structure of the sampling design also affected Ne. We observed
a negative correlation between Ne and relatedness, which highlighted the
need to account for kinship structure in sampling design. Our estimated
Ne: Nc ratio (~15%) was not as low as expected for a polygynous species
with male-biased sex ratios and inhabiting a fragmented habitat. However,
the absolute Ne values were extremely small. We showed the relevance of
integrating field-based observations of demography and spatial ecology
into DNA-based estimates of Ne to improve its interpretation and
usefulness in conservation efforts.