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While phylogenetic reconstruction with the cone opsin genes SWS1 and M/LWS generated a species tree in accord with expectations, the RH1 gene tree united Pteropodidae (Old-World fruit bats) and Yangochiroptera, with very high bootstrap values, suggesting the possibility of convergent evolution.
Phylogenetic analysis of the comparatively long groEL gene sequence showed highly significant clustering of the samples into 3 groups supported by high bootstrap values, suggesting the existence of at least 3 types of Candidatus N. mikurensis sequence variants.
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The bootstrap values suggest the occurrence of distinct families, indicated in the figures by different colours.
This tree supported by high bootstrap values suggested the following steps for evolution of PAD genes in craniates: PADs' common ancestor was present as far back as in the last common ancestor of Teleostean and Mammals.
The deep nodes of the tree were supported by very low bootstrap values, suggesting that the information supplied by the 31 model parameters was highly heterogeneous.
The analysis of the HisD phylogenetic tree obtained using all the available eukaryotic sequences with their prokaryotic counterparts revealed that it is consistent with the eukaryotic species phylogeny and supported by very high bootstrap values, suggesting a vertical inheritance for hisD in Fungi and Plants.
The Adh genes from the Solanaceae, Brassicaceae, Anacardiaceae, and Fabaceae were monophyletic with high bootstrap values, suggesting that duplication events leading to these Adh genes occurred independently after diversification of these plant families.
The bipartite separation of Lbx sequences was supported by high bootstrap values, suggesting that in all extant Osteichthyes, only Lbx1 and Lbx2 type genes were maintained, with teleosts harbouring duplicates of Lbx1.
In our analysis, the Type III PIK4CB and Type II PIK4B proteins of Plasmodium sp. cluster with plant orthologs with significant posterior probabilities and high bootstrap values suggesting a plant or cyanobacteria origin for those kinases.
High bootstrap values suggest their close relationship to the AG subtype of Uzbek origin.
This clade's strong support (96%% bootstrap value) suggests another spurious instance of BonBMT described by Bouvier and co-workers [ 12] (Additional file 2: Figure S3).
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