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Otherwise, offspring genotypes were compared to all possible parents and the most likely parent was chosen.
Finally, we used the most likely parent pairs identified in this analysis to estimate family contributions in pooled samples of DNA from the progeny.
Furthermore, to avoid bias in relative RS estimates as a result of the 'aunt and uncle effect,' we made parentage assignments based on absolute LOD score rather than a threshold relative to the next most likely parent (Ford and Williamson 2010).
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"Most likely parents may have been influenced by the beliefs often consistent with alternate medicine," Greene, who wasn't involved with the study, said by email.
The LOD threshold for assigning parentage was readily apparent by inspection of the LOD scores for the most likely parents for each potential offspring.
The highest LOD score indicates the most-likely parent [ 34].
Briefly, the most-likely parents and parent pairs were detected using log-likelihood ratios (LOD-scores) [ 31, 32] and population allele frequencies estimated from the whole dataset (n = 581).
In addition, Cervus calculates the difference in LOD scores ("delta") for the two most-likely parents, and uses computational simulations of the population genotypes to evaluate a critical delta against which a confidence estimate is obtained [ 54, 55].
Furthermore, for the vast majority of potential offspring that were not assigned to any parents, the most likely single parent had many mismatching loci (median = 4).
Critical Delta criteria [defined as the difference in LOD (the natural log of the overall likelihood ratio) scores between the most likely paternal parent and the second most likely paternal parent] were obtained from simulations and used as a criterion for assignment of parentage.
To resolve conflicts posed by multiple potential parent genes, we initially took the simple approach of labeling as the most likely true parent the gene with the highest percent identity to the retrocopy.
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