Sentence examples for dataset saturation from inspiring English sources

For the COII dataset, saturation levels were tested for the whole data matrix, for each codon position separately, and for the two first codon positions together.

Finally, five of the eight analyses inferred the same topology, with the remaining three tree resulting form less complete datasets (nucleotide substitution saturation analysis was also added in additional file 3) differing at a few nodes, which indicates that the mt-genome is an effective data source for resolving phylogenetic problems within Nepomorpha at the superfamily level.

Potential saturation in the datasets was explored by plotting the number of substitutions versus the divergence (TN93) with the program DAMBE [20].

We subjected the individual aligned datasets to a substitution saturation test (as implemented in DAMBE) to assess the phylogenetic potential (plots shown in Figure S2).

This last observation is especially important, since combined datasets began to reach saturation at 15,000 to 16,000 genes, which is at least 2000 to 3000 more genes than were covered using PEAT; 5000 to 6000 more genes were covered than using PEAT when only considering high confidence PEAT peaks filtered based on the criteria used in [ 3].

Finally, COI shows saturation in our dataset and is therefore suboptimal as molecular clock.

In order to assess the degree of substitution saturation in our dataset, we used a substitution saturation test implemented in DAMBE (Data Analysis in Molecular Biology and Evolution) [ 46, 47].

There is significant incongruence between the ages recovered by the mtDNA and nDNA datasets, likely due to mutational saturation occurring in the mtDNA loci.

Coding genes were translated into amino acid sequences to check for stop-codons or frame shifts and datasets were checked separately for saturation at each codon position.

We assessed saturation in the mitochondrial dataset by plotting the transition/transversion ratio against uncorrected genetic distance for the combined mitochondrial dataset.

DAMBE did not reveal significant saturation in the 12SrDNA dataset.