Regarding the performed FDG-PET/CT studies, the acquired functional and morphological datasets were read separately.
The lengths of the branches of the morphological datasets were calculated using a Euclidean distance matrix (SAS Procedure DISTANCE SASS version 9.1.3).
However, the estimated K-scores indicated that the three distance-optimized trees based on the different morphological datasets were almost congruent in topology and branch lengths, implying similar changes on nodes between the trees.
Despite their different and largely non-overlapping taxon sampling schemes, the molecular and morphological datasets were congruent in their placement of T. pseudonana as sister to Cyclotella.
We show that the combination of well-resolved phylogenies obtained by phylogenomic analyses and well-documented extensive morphological datasets is an appropriate basis for reconstructing complex morphological transformations and for the inference of evolutionary histories.
The patristic distances calculated for each morphological dataset were significantly correlated with those of the ML tree estimated from the molecular dataset based on Pearson correlation or Mantel tests (Table 4).
Several patterns regarding higher-level relationships inferred from the present morphological dataset are also noteworthy.
The morphological dataset was combined with the 20.1kb molecular supermatrix of Beck [10]-which comprises DNA sequence data from 7 nuclear genes (APOB, BRCA1, IRBP, PGK1, P1, RAG1, and VWF) and 15 mitochondrial loci (12S rRNA, 16S rRNA, tRNA valine, and 12 H-strand protein-coding genes -and analysed usingenes -and3.1.2 [37].
However, our morphological dataset was not constructed to solve this issue, since it relies on larval characters only.
Phenotypic variation in our morphological dataset is affected by both genetics and environment, whereas fish from the kinematic dataset would have been less influenced by environment.
The morphological dataset was analyzed using unordered parsimony with 1,000 random addition TBR branch swapping replicates using PAUP* [ 41], and we conducted 1,000 bootstrap replicates.
