Sentence examples for base composition bias in from inspiring English sources
This leads to underestimation of dup,pu with MCU, a bias similar to MP. ML inference for data simulated under the exact parameterization of the HKY85 model showed no bias in dup,pu, even under strong base composition bias in a 2× tree (Figure 6).
However, this position was generally weakly supported and has been discussed as a possible result of base composition bias in Appendicularia and Mogulidae, a family of Stolidobranchia [ 27].
We assessed base composition bias in the nucleotide data set (ntAll) by conducting a chi-square test using PAUP* v.4.0b10 [ 162] to determine if the base frequencies across taxa were homogeneous.
To what extent this incongruence can be explained by limited taxon sampling or biases in the molecules used to infer divergence dates (e.g., strong base composition bias in Anophelinae; Table 4), is presently unknown.
We tested all multiple sequence alignments (MSAs) for evidence of significant levels of amino acid composition bias and base composition bias in each lineage using the TreePuzzle software [ 15].
One possible explanation could be that the base composition in the mitochondrial inserts is less AT rich than in the rest of the plastome (55% compared to 61%) as the PCR step during Illumina library preparation has been shown to introduce base composition bias in fragments [ 44].
Even among closely related lineages at equilibrium base composition, biases in ancestral inference can generate patterns consistent with a genome-wide decline of MCU.
PCR amplification, however, has been shown to be the major source of artifacts and base-composition bias in library fragments.
Results of the amino acid composition and nucleotide base composition bias tests, are shown in the A.A. Comp Bias and Base Comp Bias columns respectively.
On the other hand, obvious nucleotide substitution saturation and base composition bias have been observed in the mitochondrial loci.
The accuracy of ancestral inference, even among relatively closely related species, has a complex dependence on branch lengths, the location of lineages within a phylogeny, rate heterogeneity among mutation classes (levels of base composition bias) and among lineages (changes in base composition).
