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The strict consensus of minimum length trees is fairly well resolved (Figure 2).
Characters were optimized onto all minimum length trees using the map characters option in TNT [37].
If the unstable positions of these taxa are ignored, relationships for the remaining 72 taxa in the analysis are consistent across all 20 minimum length trees.
According to minimum length trees for the combined data, these character states were independently derived within Cetaceamorpha and in †Mesonychia (Figure 3A).
These include Cetacea, Hippopotamidae, Cetancodonta, Ruminantia, Cetruminantia, Suina, Camelidae, and Artiodactyla (Table 1), which are found in all minimum length trees (even if the strict consensus is sometime unresolved due to unstable fossils).
Instead we find minimum length trees in which †Mesonychia is the sister group to a large clade composed of Artiodactyla (including Cetacea), Perissodactyla, †Hyopsodus, †Protungulatum, †Phenacodus, and †Eoconodon (Figure 2 and 3A).
Similar(38)
Under this setting, iterations were run until the minimum length tree was found in 500 separate replicates, to try to hit as many islands of trees as possible [71].
The magnitude of ddBS scores provides a measure of the degree to which the supermatrix contradicts these suboptimal topologies; following Lee [ 146], Templeton/Wilcoxon rank sum tests [ 147] were conducted on each pair-wise comparison between a suboptimal topology and each minimum length tree to assess the significance of ddBS values.
The rectilinear Steiner tree problem in the plane is to construct a minimum-length tree interconnecting a set of points (called terminals) consisting of horizontal and vertical line segments only.
Trees of minimum length were found at least three times.
To avoid numerical instability and focus on branches of topological relevance, we computed DFs only for branches with a minimum length (>0.0004) in the source tree, which included 91 96% of branches in the complete gene tree for each gene family.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com