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Phylogenetic analysis revealed two major clades corresponding generally to southern France and northern Spain, respectively.
The tree divided all 23 proteins into 3 major clades corresponding to ClpB, ClpC and ClpD proteins.
Based on a concatenated alignment of 2851 orthologous core genes shared by the 9 taxa, the best maximum likelihood (ML) tree identified two major clades corresponding to species.
Phylogenetic analysis shows three well-supported major clades corresponding to polymerases from 1) eukaryotes and three viral groups; 2) archaeans, Myoviridae and a halovirus; 3) and the WSSV and WSSV-like polymerases (Fig. 6).
The ML phylogenetic analyses of integrin α sequences (Fig. 5A) are broadly consistent with previous studies; the resolution of bilaterian sequences into two major clades corresponding to the major ligand classes RGD (PS2) and laminin (PS1) is strongly supported.
According to the ITS tree, rooted with three outgroup species, P. arguta was monophyletic (with MP/ML bootstrap values of 100/100%) and consisted of two major clades corresponding to var.
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The two major clades corresponded with the geographical distributions of S. m. fuscus and S. m. palmatus in the region.
Like those of the QS proteins, trees of TraA, TraG and TrbE divide into two major clades, precisely corresponding to the Group I and Group II organizational patterns (fig. 4 A– C).
Among crinoids, myzostomids are recorded to infect seven major clades (roughly corresponding to taxonomic families), of which four are feather stars (all represented here) and three are stalked crinoids (Bathycrinidae not represented here).
The ML estimate of phylogeny for the mature inhibin/activin protein is consistent with an origin of three major β-subunit clades (corresponding to the mammalian βA, βB, and βC/βE groups) early in vertebrate evolution (Fig. 1B), probably during the WGD [29] (Fig. 1A).
The tree showed three major clades, one each corresponding to ClpB, ClpC and ClpD proteins.
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