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However many of these placements are among the most weakly supported branches of the resulting phylogenetic trees (Fig. 1).
This filter, which removes the most weakly supported clusters, retained 188 (39 %) and 157 (46 %) MIWI2-dependent 3' UTR clusters in liver and spleen, respectively (Figs. 5a, b).
In addition to being highly variable, the placement of L. albirostris has typically been one of the most weakly supported [ 21, 26, 27].
Edges in this consensus network were removed if 1) the edge was involved in a loop, and 2) the edge was the most weakly supported of all edges making up the loop.
It is notable that both for the ordered and unordered character state approach the Testudines-Sauria tree is among the shortest and that the archosaurian hypothesis is among the most weakly supported ones (Table S6 and S7).
In this consensus network, an edge was removed if 1) it was involved in a loop, and 2) it was the most weakly supported of all edges making up the loop.
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Unfortunately gene trees may not be able to resolve this problem because relationships (clades) beyond the family level of ANTP genes (e.g. the Gsx, NK6, Evx etc. family) are, in most cases, weakly supported (e.g. Figure S1 & S2; cf. [4], [5]).
Most nodes are weakly supported.
In the mt trees, the most basal nodes are weakly supported, while the relationships between the other Alpine endemics are well resolved: O. fuchsi, endemic to the Northern Calcareous Alps, is the sister group of a highly supported clade comprising O. austriaca, O. gularis, O. pseudodolium and O. tolminensis.
An ML tree built using only translations of the most conserved pseudogenes showed weakly supported but consistent association of the human pseudogenes with HSPD1 from primates, whereas pseudogenes from mouse and rat all associated with murid Hspd1 sequences, also indicating their relatively recent origin.
Our trees show broad concordance with previous morphological hypotheses of ditrysian phylogeny, although most relationships among superfamilies are weakly supported.
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Justyna Jupowicz-Kozak
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