Publication: Mean d2 and divergence time: transformations and standardizations

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Title Mean d2 and divergence time: transformations and standardizations
Authors/Editors* Bryan D. Neff
Where published* Journal of Heredity
How published* Journal
Year* 2004
Volume 21
Number 6
Pages 165-171
The fitness consequences of inbreeding and outbreeding have intrigued biologists for a long time. Recently a measure of relatedness of parental haplotypes has been proposed called mean d2. This measure is based on a stepwise mutational process and therefore is tailored to microsatellite genetic markers. Theoretical work suggests that mean d2 typically is less suited for measuring fitness consequences due to close inbreeding rather than heterozygosity. However, mean d2 may be more appropriate than heterozygosity for measuring divergence times over longer time scales and thus for detecting outbreeding depression. Here, simulations are used to (1) identify appropriate standardization coefficients and transformations for mean d2, and (2) evaluate mean d2 as a measure of divergence time of parental lineages over time scales up to 10,000 generations. Results show that mean d2 is a linear predictor of divergence time. The coefficient of variation of mean d2 approaches a constant value with increasing divergence time and therefore logarithm transformation is appropriate to restore homoscedasticity. When mutation rates and sizes are known for each locus they can be incorporated into a standardization coefficient to increase the precision of mean d2. As few as 10 loci can explain more than 70% of the variation in divergence time between lineages. While heterozygosity outperforms mean d2 at detecting differences in divergence time over relative short time periods (1000 generations), mean d2 can outperform heterozygosity at detecting differences over longer time periods (1000 generations). However, gene flow of as little as 1% per generation can significantly reduce the ability of either mean d2 or heterozygosity to estimate divergence time.
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