Evolutionary distances were derived from sequence-pair dissimilarities calculated as implemented in MEGA, using Kimura's DNA substitution model [Kimura 1980].
The evolutionary distances were derived from the sequence-pair dissimilarities, calculated as implemented in MEGA using the DNA substitution model reported by Kimura (1980).
The aligned matrix was formatted for BEAST using BEAUti with the data partitioned to allow specification of DNA substitution models for each partition (see BI analysis above).
Prior to the analysis, DNA substitution models for each partition were selected by MrModeltest (Nylander2004) based on the Akaike information Criterion (AIC).
Synonymous DNA substitution rates in the plant chloroplast genome are generally relatively slow and lineage dependent.
Different nested models of DNA substitution and associated parameters were estimated using Modeltest [49].
MrBayes ver. 3.1.2 [74], [74] was used to infer the phylogeny using the models of DNA substitution indicated by BIC.
It has been argued before that certain morphological, physiological, and life history traits influence DNA substitution rates.
Comparisons between DNA regions in mitochondria can be useful for differentiating between genome-specific factors such as DNA substitution rates and gene-specific factors such as selection [6].
Phylogenetic trees were inferred using RAxML [30] under the general time-reversible (GTR) model [31] of DNA substitution with a gamma distribution and 100 replicate bootstrap analyses.
The DNA substitution models as well as the parameter settings for each tree constructed are described in detail in the legend of the respective figure.
