Data from: Dealing with assumptions and sampling bias in the estimation of effective population size: A case study in an amphibian population

Accurately estimating effective population size (Ne) is essential for
understanding evolutionary processes and guiding conservation efforts.
This study investigates Ne estimation methods in spatially structured
populations using a population of moor frog (Rana arvalis) as a case
study. We assessed the behaviour of Ne estimates derived from the linkage
disequilibrium (LD) method as we changed the spatial configuration of
samples. Moor frog eggs were sampled from 25 breeding patches (i.e.,
separate vernal ponds, ditches or parts of larger fens) within a single
population, revealing an isolation-by-distance pattern and a local spatial
genetic structure. Varying buffer sizes around each patch were used to
examine the impact of sampling window size on the estimation of effective
number of breeders (Nb). Our results indicate a downward bias in LD Nb
estimates with increasing buffer size, suggesting an underestimation of
Nb. The observed bias is attributed to LD resulting from including
genetically divergent individuals (mixture-LD) confounding LD due to
drift. This emphasises the significance of considering even subtle spatial
genetic patterns. The implications of these findings are discussed,
emphasising the need to account for spatial genetic structure to
accurately assess population viability and inform conservation efforts.
This study contributes to our understanding of the challenges associated
with Ne estimation in spatially structured populations and underscores the
importance of refining methodologies to address population-specific
spatial dynamics for effective conservation planning and management.