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The sequencing of multiple loci provides a balance between technical feasibility and resolution.
Particularly when implemented with multiple calibrations in a Bayesian framework, the simultaneous analysis of multiple loci provides independent constraints on the evolutionary model, thereby avoiding potential biases associated with a single gene or genome [ 64].
This is almost certainly an indication of complex, multigenic control processes regulating energy metabolism and homeostasis, and the identification of large numbers of multiple loci provides an important documentation of genes involved in complex metabolic pathways.
The dosage model operates when possessing multiple loci provides a beneficial increase in gene product [ 3, 92]; this model seems inappropriate as well, as RH2aβ opsin expression is generally quite low in both Oreochromis niloticus and Lake Malawi haplochromine cichlids [ 42, 44], and as the paralogs are known to be functionally divergent, contrary to model predictions.
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Such studies using mice harboring mutations at multiple loci provide great insight into common and distinct functions of transcriptional regulators and their downstream actions.
Theoretical work suggests that data from multiple nuclear loci provide better estimates of population genetic parameters than do single loci, but just how many loci are needed and how much sequence is required from each has been little explored.
Hence, even though multiple loci would provide greater precision in a single model run, for reasons of computational tractability, genetic structure was modeled by using only one locus with 10 alleles.
Array-based comparative genomic hybridization (aCGH) measures copy number variations at multiple loci simultaneously, providing an important tool for studying genomic alterations associated with cancer, developmental disorders, and germline copy number polymorphisms.
Although an extensive barcode study for 31 Carex species suggested that a single locus or even multiple loci cannot provide a resolution of greater than 60%, it did not include some of the new markers (atpF-atpH and psbK-psbI) [ 19].
Consistent patterns of evolution over time (i.e., the relative frequency and rate of substitutions at particular nodes) among multiple loci can provide evidence that variation in branch lengths among regions of a topology represent the actual evolutionary history of a lineage.
The epistatic model presumes multiple loci bear alleles providing partial virulence that act synergistically to amplify an individual gene's adaptive potential when held in combination.
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