The use and abuse of genetic marker‐based estimates of relatedness and inbreeding

Genetic marker‐based estimators remain a popular tool for measuring relatedness (rxy) and inbreeding (F) coefficients at both the population and individual level. The performance of these estimators fluctuates with the number and variability of markers available, and the relatedness composition and demographic history of a population. Several methods are available to evaluate the reliability of the estimates of rxy and F, some of which are implemented in the program COANCESTRY. I used the simulation module in COANCESTRY since assess the performance of marker‐based estimators of rxy and F in a species with very low genetic diversity, New Zealand's little spotted kiwi (Apteryx owenii). I also conducted a review of published papers that have used COANCESTRY as its release to assess whether and how the reliability of the estimates of rxy and F produced by genetic markers are being measured and reported in published studies. My simulation results show that even when the correlation between true (simulated) and estimated rxy or F is relatively high (Pearson's r = 0.66–0.72 and 0.81–0.85, respectively) the imprecision of the estimates renders them highly unreliable on an individual basis. The literature review demonstrates that the majority of studies do not report the reliability of marker‐based estimates of rxy and F. There is currently no standard practice for selecting the best estimator for a given data set or reporting an estimator's performance. This could lead to experimental results being interpreted out of context and render the robustness of conclusions based on measures of rxy and F debatable. The performance of genetic marker‐based estimators of relatedness and inbreeding is known to be highly variable and repeated calls have been made for researchers using these tools to assess their likely performance for the marker set in question before implementing them; software such as COANCESTRY facilitates this a priori assessment. Using empirical allele frequencies from a species of conservation concern with low genetic variation, I demonstrate the pitfalls of relying on marker‐based relatedness and inbreeding estimates. I also review the scientific literature and demonstrate that, though marker‐based estimators of relatedness and inbreeding are widely used, the majority of studies fail to assess or report the likely reliability of their estimates, leaving their conclusions open to question. I suggest that a standardised format for evaluating the reliabilit