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See below the argument for our choice of the root position for the purpose of reconstruction.
If no outgroup is included, BEAST will automatically sample rooted trees, and the most plausible root position for the data analyzed under a molecular clock model, is indicated.
To obtain an accurate root position for our EFL tree, we included related subfamilies of the GTPase translation factor superfamily: EF-1α, eukaryotic release factor 3 (eRF3), heat shock protein 70 subfamily B suppressor (HBS1) and archaebacterial EF-1α sequences in our analyses.
However, in our trees, F. angustifolia resides in the root position for both clade A and clade B (ML = 100, BI = 100), and this modification is consistent with the same number of layers (8 layers) of leaf ground tissue observed in F. angustifolia and two C3 species: F. cronquistii and F. robusta [ 12].
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Uncertainties regarding the root positions for gene trees make direct inferences regarding the nature of donors difficult.
Each of the three unrooted trees (A-C, see Figure 4) has five possible root positions, for 15 possible rooted trees.
The maximum clade compatibility tree from the BEAST analysis found different intraspecific root positions for N. sericea and A. strepitans, compared to the ML results.
Because of the variety of possibly confounding biases that could affect mitochondrial genomes concurrently, strong outgroup effects should be expected and have been observed (Cameron et al. 2004, Rota-Stabelli and Telford 2008), with different outgroups suggesting alternative equally well-supported rooting positions for ingroup taxa.
Kinaesthetic learners - when beginning Satie's Gymnopedie III, consistently using the Left Hand finger pattern 5-3-1 for root position chords (like A-C-E) and first inversion chords (like C-E-A), but using fingers 5-2-1 for second inversion chords (like A-D-F) can be of enormous help to kinaesthetic learners in achieving accuracy.
While the exact ML position of the root is poorly supported, there is very high support for a root position within the MDH portion of the tree, somewhere near the center.
Nevertheless, there is strong support for a root position within the central MDH section of the tree and outside of the five identified clades, including the canonical LDH clade (confidence level >0.99985 according to the aLRT), indicating that the canonical LDHs evolved from an ancestral MDH.
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