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Recent work has suggested that synteny is more common with developmental regulatory genes and maintained due to selection on co-expression (Quijano et al. 2008).
The present work, in addition to other studies, provides useful insights regarding the role of natural selection in determining the nucleotide/amino acid composition of a protein by demonstrating that elevated levels of G+A in NASP are maintained due to selection for alanine and/or glutamic acid/aspartic acid rather than the random mutational biases.
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In the absence of paternal inheritance of Wolbachia, the mutation/s that led to the development of pathogenesis are likely to have arisen as the result of normal errors in genomic replication, and to have been maintained due to relaxed selection for longevity in a fly stock center environment.
Theory suggests that this variation in genotype can change the underlying genetic architecture in spite of the phenotype being maintained due to strong stabilizing selection [32].
The Mnemiopsis genome has 10 full-length photoprotein genes situated within two genomic clusters with high sequence conservation that are maintained due to strong purifying selection and concerted evolution.
However, homozygosity for certain short and medium ROH regions were not maintained due to the absence of selection for any specific alleles; therefore, variants with deleterious effects will be purged by artificial selection.
Meanwhile, low complexity is maintained due to the rapid convergence.
Once deleterious mutations appear in population, they will be maintained at a relatively low frequency due to selection pressures.
Translation-optimized codon usage is well documented in many model organisms (Ikemura 1985), most likely due to selection for maintaining translational accuracy (Stoletski and Eyre-Walker 2007).
It seems plausible, therefore, that during the original screening process the higher efficiency second-generation nitroTyr-RS variants were lost due to selection criteria that maintained unnecessarily stringent fidelity in the absence of nitroTyr, leaving behind only nitroTyr-RSs with strict fidelity but poor efficiency.
Hence, propensity score methods may offer the researcher a useful tool for controlling for potential confounding due to selection bias and maintaining a manageable number of prognostic and predictive covariates.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com