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. 2015 Aug;5(15):3140-50.
doi: 10.1002/ece3.1541. Epub 2015 Jul 14.

The Use and Abuse of Genetic Marker-Based Estimates of Relatedness and Inbreeding

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Free PMC article

The Use and Abuse of Genetic Marker-Based Estimates of Relatedness and Inbreeding

Helen R Taylor. Ecol Evol. .
Free PMC article

Abstract

Genetic marker-based estimators remain a popular tool for measuring relatedness (r xy ) 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 r xy 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 r xy 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 r xy 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 r xy 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 r xy 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 r xy and F debatable.

Keywords: COANCESTRY; estimators; inbreeding; relatedness.

Figures

Figure 1
Figure 1
Spread of relatedness coefficients estimated by TrioML in COANCESTRY for simulated dyads in six true relationship categories using simulated genotypes based on the Long Island and Zealandia microsatellite marker sets. Boxes represent the upper and lower quartiles, divided by the median. The 10 and 90 percent quartiles are depicted by lines and dots represent the outliers. Dashed horizontal lines mark true rxy coefficients of 0.5 (parents-offspring (PO) and full siblings (FS)), 0.25 (half siblings/avuncular/grandparent-grandchild (HS)), 0.125 (first cousin (FC)), 0.01325 (second cousin (SC)) and 0 (unrelated (U)).
Figure 2
Figure 2
Regression line (solid) versus 1:1 line (dashed) for regressions of inbreeding coefficients estimated using TrioML in COANCESTRY versus true inbreeding coefficients for simulated individuals with genotypes based on the Long Island and Zealandia microsatellite marker sets. Long Island β = 0.85, r2 = 0.61, F = 3260, P < 0.001. Zealandia β = 0.88, r2 = 0.67, F = 4257, P < 0.001.

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