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As dataset size increased, branch length misestimation decreased.
The exonic tree showed a greatly increased branch length (>7×) on the branch leading to C. americanum and T. caeruleum relative to the intronic tree.
Above this range, branch lengths are progressively underestimated with increased branch length; below this range, branch lengths are progressively overestimated.
Our study required 3-D analysis, because microglial cells in the cortex gray matter showed greater overlap of processes (reflected by their increased branch length and tree area).
However, if this were the case, we would expect deterioration of phylogenetic signal with increased branch length – we did not observe this pattern.
Similar(55)
Due to the artificially increased branch lengths in the simulated data, this approach provides an extremely conservative test for positive selection.
Two recombination events were simulated as well as a 100 bp region of increased branch lengths of the topologies as shown in Figure 2. Full details of the simulation are given in Husmeier (2005).
The NJ tree with polymorphisms treated as character states (see Methods) had increased branch lengths leading to heteroplasmic species (Fig. 4; minimum evolution score 3.0905), resulting in stronger identification confidence for H. dimidiatus, H. kukui, and H. connectens and H. haleakalae populations as determined by BS support values (Fig. 5).
The trend in the relationship between crown biomass and branch diameter and length was similar but the variability in biomass increased with increasing branch length (Figure 1).
The pattern of increasing branch length misestimation with increasing branch lengths was consistent regardless of dataset size.
Increasing underestimation with increasing branch length is consistent with the expected effects of site saturation - multiple hits are counted as single substitutions.
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