For the simulated data, we implemented estimators of the genealogical coancestry based on molecular coancestry (equations (5) or (9)) and molecular covariance (equations (6) or (10)), using the true or estimated frequencies.
Estimators of genealogical coancestry based on molecular data are easy to derive.
As mentioned above, the performance of management based on molecular coancestry relative to that based on genealogical coancestry increased with decreasing N e, except when the density of SNPs was very low.
The rationale to compare and estimate genealogical coancestries based on molecular empirical coancestries or covariances has been shown for any outbred or inbred population, and different estimators have been developed which account for variation in allele frequencies between loci.
Several estimators of coancestries based on molecular information have been proposed, including recent estimators that are designed to deal with a large number of markers [ 2- 7].
In conservation genetics, coancestry coefficients are used to optimize genetic management in a conservation program and several estimators of coancestries based on molecular information have been proposed, e.g., [ 32, 33].
However, these results differed significantly from those obtained using microsatellites [ 2, 8] in which case management based on genealogical coancestry always outperformed that based on molecular coancestry.
For low densities (generally, d < 500), management based on genealogical coancestry resulted in higher diversity than management based on molecular coancestry and the difference in EH between these two strategies increased across generations.
However, with d = 500, the EH maintained with management based on molecular coancestry, i.e. 90% and 99% of the initial EH for N e = 20 and N e = 160, respectively, exceeded that with management based on molecular coancestry, i.e. 87% and 98% for N e = 20 and N e = 160, respectively.
