DOI: 10.5061/dryad.2ngf1vj28
title: Data from: Beyond abundance: The impact of sampling design on effective population size estimates in capercaillie

description: 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.
description: # Data from: Beyond abundance: The impact of sampling design on effective
 population size estimates in capercaillie Dataset DOI:
 [10.5061/dryad.2ngf1vj28](10.5061/dryad.2ngf1vj28) ## Description of the
 data and file structure This file contains microsatellite data for the 135
 Cantabrian capercaillie individuals (listed in column INDV) included in
 the study "Beyond abundance: the impact of sampling design on
 effective population size estimates in capercaillie" (DOI:
 10.1002/wlb3.01520). ### Files and variables #### File:
 WB_capercaillie_Ne_dataset.xlsx **Description:** The dataset provides
 genotypes at nine microsatellite loci (BG15, BG10, TUD4, TUT1, TTD6, TUD5,
 TTD2, TUT3, TUD2), with alleles coded in a three-digit format, together
 with sex information for each individual (column SEX_INDV; M = male, F =
 female, ? = unknown). For spatial analyses, each individual was assigned
 to one or more of the three main valleys in the study area (Muniellos,
 Degaña, Hermo). Valley assignment is indicated with a "1" in the
 corresponding column, while "0" denotes absence from that
 valley. In some cases, individuals are assigned to more than one valley,
 reflecting detections in multiple locations.