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I think, looking back at the story those records tell, that it might have been something as simple as things just starting to sound different to them, their ears tuning themselves to different, more parental frequencies.
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After using pure parental frequency to estimate the location of Eos/ Ste mutations in the genome, we then filtered the sequence data for candidate mutations within the region of interest (see Materials and Methods).
This procedure inevitably results in the correct estimation of parental allele frequencies but exaggerates the error in estimating allele frequency in the offspring pools as this contains the error from both samples.
For each of these sets of actual parental allele frequencies, I performed estimation under each set of parental allele frequencies as an assumption.
In particular, putative "parental" genotype frequencies were 34% in Guinea Bissau and 73% in The Gambia, while the corresponding frequencies of potential "F1" genotypes (SINE-XMS-3LMS) were 7.1% and 1%.
Therefore any errors in estimating the parental allele frequencies are incorporated in the estimate of k with the result that the estimates of allele frequencies in offspring include the measurement errors from both samples.
These simulations use parental allele frequencies to generate pseudo-offspring that are then re-allocated.
STRUCTURE provides estimates of ancestry that incorporate uncertainty about parental allele frequencies.
To briefly illustrate the consequences of inaccurate assumptions about parental allele frequencies, I simulated ten generations of admixture in small populations (N = 50) with different sets of actual parental allele frequencies, and then estimated S and H I for each individual under different assumed parental allele frequencies.
Here, I generalize his method to jointly estimate S and H I (the interclass heterozygosity index) for individual hybrid genotypes given parental allele frequencies.
My implementation of the estimators for S and H I depends on prior estimates of parental allele frequencies taken as known constants.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com