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Positive selection analysis was performed by comparing the different Branch maximum likelihood codon substitution models using the improved test 2, which tests for different dN/dS (nonsynonymous/synonymous substitutions) ratios along given branches of the tree [76], [77].

With the codon alignment and the corresponding unrooted ML protein tree, we implemented several Markov models of codon evolution (which describe the substitution process between 61 of the 64 codons) to statistically estimate the selective pressures acting over all codon sites, specific branches, and sites within given branches of the Epd protein family phylogeny.

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Another consequence of successful logicist reduction of a given branch of mathematics is that mathematical certainty (within that branch) is of a piece with certainty about logical truth.

Professional papers in evolutionary biology continue to host expressions in agreement with the pre-evolutionary metaphor of the scala naturae (the great chain of being), when contrasting 'lower' to 'higher' representatives of a given branch of the tree of life.

A guild restricted those in a given branch of the culinary industry to operate only within that field.

Low Ka/Ks ratios for a given branch of the tree therefore imply that GC-D was functional for all, or at least a substantial part, of the time represented by that branch of the tree.

The number of mutations overlaid onto given branch of the pedigree is proportional to its length.

Rejecting a stochastic birth-death model implies that a non-neutral process governs the evolutionary fate of duplicate genes on a given branch of a phylogeny.

Recently, a number of extensions of the MKT have been proposed to control for these confounding factors when trying to estimate the proportion of adaptive changes along a given branch of the phylogeny.

In our dataset, the low level of polymorphism along any given branch of the tree (the majority of inferred mutated genes contain only a single polymorphism specific to the pathotype branch) does not provide enough power to estimate selective constraints accurately in a pathotype-specific manner [ 49].

At least five parameters might affect the fixation rate of retroposons in a population in a given branch of the phylogenetic tree: (I) the promoter activity of the master gene, (II) the overall availability of enzymatic retroposition machinery and (III) its affinity to the master RNA, (IV) the population size, and (V) the branch length.

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