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The extent to which mutational changes have impacted human monogenic diseases with single (SPD) or multiple (SHD) phenotypic defect(s) can be traced by estimating the evolutionary rates of human SHD (defect number ≥ 2) and SPD (defect number = 1) genes considering ND (defect number = 0) genes as the control set.
We tested this idea by estimating the evolutionary rates (using the nucleotide substitution rate as a proxy) between orthologs of S. cerevisiae and other two yeast species from the pre- and post-whole-genome duplication clades namely K. lactis and C. glabrata (supplementary table S3, Supplementary Material online).
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Finally, we tested the agreement between evolutionary and within-population allometries by estimating the angles between evolutionary and within-population regression vectors and comparing the observed angles with a parametric distribution to test the null hypothesis that the vectors have random directions in regression space.
To address these concerns, we estimated the evolutionary processes experienced by the duplicated genes after the 3R-WGD by analyzing the whole-genome data of four teleosts (zebrafish, stickleback, medaka, and Tetraodon) based on teleost phylogeny and their divergence time estimates.
Genomes are identifiable by their signatures and dissimilarity between signatures is used to estimate the evolutionary distance between species [ 4, 6].
These estimates were subsequently used to estimate the evolutionary timescale of SFTSV (see Methods).
Secondly, by estimating evolutionary rates from the primate and rodent pairs separately, we generate estimates of evolutionary rates from primate and rodent lineages.
We also investigated the evolutionary processes of Bathymodiolus mussels by estimating evolutionary divergence times with variable rates over time.
We provisionally hypothesized the evolutionary history of Bathymodilolus mussels by estimating evolutionary time under a relaxed molecular clock model.
This observation is further supported by estimating average evolutionary divergence values (p = 0.251±0.027 substitutions per site) for plant lineages.
The degree of conservation of each amino acid in the ferritin family was analyzed by estimating site-specific evolutionary rates using the ML (maximum likelihood) approach of the ConSurf server [72].
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