Sentence examples for using the phylogenetic analyses from inspiring English sources
By using the phylogenetic analyses of mtDNA sequence data, molecular diagnostic sites and phenotypic morphometric traits, we uncovered two previously undetected species whose distributions contradict the two existing biogeographic models.
We selected the appropriate model of sequence evolution to be used in the phylogenetic analyses using jModeltest [ 70], and we reconstructed the ML phylogeny using TreeFinder (version of 2008) [ 71].
The evolutionary model used for the phylogenetic analyses was determined using ModelTest v3.0 with Akaike information criterion (AIC) [ 66].
The alignments used were similar to the one used for the phylogenetic analyses but some sequences were added to encompass all of the calibration points and some were removed to reduce complexity.
In this instance the molecular characters used in the phylogenetic analyses confirmed the shell-based morphological characters used to identify different terebrid species.
Each primary aligned sequence was realigned using ProAlign ver. 0.5 [ 45] and those regions with posterior probabilities ≥70% used in the phylogenetic analyses.
The alignment and the concatenation of sequences, as well as the selection of the best partition scheme and evolutionary models, were the same as what were used in the phylogenetic analyses.
Minimum evolution, parsimony, and likelihood methods were used for the phylogenetic analyses of mt SSU rDNA sequences from Botryosphaeria species and related taxa.
Regions with posterior probabilities of >70% were used in the phylogenetic analyses.
GenBank accession numbers of the analyzed sequences are listed in Table S2, the number of amino acid positions used for the phylogenetic analyses are listed in Table S3.
The amino acid alignments were used as a guide to obtain the corresponding nucleotide alignment and only the nucleotide positions corresponding to amino acid positions with a score greater than 3 were used in the phylogenetic analyses.
