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However, we cannot yet provide precise guidelines about where this distinction occurs in biological systems, although we empirically observe that the model produces equal estimates of pool proportions across all lineages and high tree uncertainty when confronted with very highly mixed samples.
For the DPGP2 data set, nucleotide diversity was largely consistent with the previous estimates of Pool et al. (2012), although estimates for the newly assembled sequences were generally slightly higher (Table S9), perhaps due to the improved coverage of more diverse regions.
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For one of our experiments, 1M-Duo Batch 2, we observed unusually high estimates of pool-construction variance and low estimates of array variance (see Figure 6).
As well, some estimates of pool-construction variance were negative, and these were set to zero, which would lead to overestimation of pool-construction variance.
These estimates of pooling variance are very similar to those seen for pools on the 1M-Single array; however, the estimates of pool-construction variance are higher (see Additional File 3, Table S3 for all values).
For these pools the estimates of pooling variance are nearly 2-3 fold higher than those of batch 1 but the array variance remained low at 2.4 × 10-4, leading to high estimates of pool-construction variance (see discussion).
Most of our estimates of pool-construction variance were based on values from Type C comparisons, and for these var econstruction) usually fell between 20 and 40% of the pooling variance.
Var epooling-2) estimates followed the same pattern, larger estimates of pooling Var epooling-2ool-construction variancestimatesot shown).
Our purpose is to calculate empirical estimates of pooling variance and array variance, and then to estimate pool construction variance by subtraction.
Recapture-rate estimates of pooled families by cross type at each site, and pooled families by cross type in each river, were generated using weighted binomial generalized linear models (glm).
In addition, the between-chip variance for these arrays was much higher than observed in the 1M-Duo Batch 1 dataset, which lead to large estimates of pooling and pool-construction variance overall.
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