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The likelihood values of inferred trees were recalculated from the non-coding portions of the plastid DNA matrix (excluding trnS, trnL and trnF) with and without enforcing a molecular clock and the likelihood ratio test was used to determine whether the data evolved at a homogenous rate [34].
Conversely we start observing the d-HSCs after 24 hours (stage 2) since they have now been activated, but since they are dividing at an increased rate (most likely close to the a-HSC rate) it still appears as if there is a homogenous rate of BrdU uptake.
The earliest and easiest method was to assume a strict molecular clock (i.e. homogenous rate among lineages).
Two assumptions were made when adjusting the rate: (1) the subset tested is a representative specimen of AMES cases, and (2) there was a homogenous rate of infection within a given prefecture, age group, and initial clinical diagnosis stratum.
Two models of codon substitution (M2a and M8) that allow for heterogeneous selection pressures among sites were compared to null models (homogenous rate among sites, models M1a and M7) as described in Data S2.
We thus decided to use the approach of Sperling et al. (2009) in which sites are partitioned into quartiles and only those from the two internal ones (i.e., those with the most homogenous rate of substitution) are used for phylogenetic analyses, with the very slow and very fast sites analyzed for comparison.
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Generally, it can be proposed that homogenous rates of tadpole growth and development will reflect appropriate culture and testing conditions.
After the deletion of all alignment gaps, each pairwise distance was calculated from 1000 bootstrapped datasets using the JTT substitution matrix, assuming homogenous rates among lineages.
High survival rates, homogenous rates of development, relatively short times to completion of metamorphosis of control animals, and concentration-dependent effects of E2 treatment on gonadal development were achieved using appropriate testing conditions.
Each gene in the core was tested under two models, one assuming homogenous rates (rooted model, n − 1 branch length are estimated) and the other assuming different rates for each branch (unrooted model, 2 n − 3 branch length should be estimated).
An equation for the selectivity of the primary electrode reaction product is derived as a function of the limiting degree of conversion of substrate and of the kinetic parameter expressing the ratio of the intervening homogenous reaction rate constant and of the rate constant of electrolysis.
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