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Consequently the lack of the tritocerebral appendage as possible synapomorphy for insects and myriapods was often, and obviously with some justification, understated in phylogenetic discussions (e.g. [ 54, 55]).
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As a consequence of the strong topological agreement between the concatenated dataset and single partitions, phylogenetic discussion will be based on the tree resulting from the combined dataset.
We have based our phylogenetic discussion in the all-genes topology, which was the most solved and supported tree and summarizes the information of all analyzed genes.
The most recent of these by Desai et al. (2013) used whole genome data from 21 individuals, 11 within S. enterica subsp. enteria, and two from each of the other five S. enterica subspecies, although the phylogenetic discussion focused mainly on subspecies relationships.
Both systems may contribute to phylogenetic and systematic discussions.
In contrast, the spirochete-chlamydia clade might reflect a deep phylogenetic relationship (see discussion below).
We thank Callum Brandon for technical assistance and David Bryant for discussions regarding phylogenetic congruence testing.
The authors would like to express sincere thanks to Allyson M. Fenwick and Haakon M. Kalkvik for many helpful discussions regarding phylogenetic analyses.
RC performed the phylogenetic analyses and appended discussions.
Thank you to Marc Cadotte, Ammon Corl, Christy Hipsley, Emma Goldberg, Kathleen Kay, Susan Mazer, Don Miles, Johannes Mueller, and Jim Regetz for helpful discussions on phylogenetic analyses and software.
The PhAT was conceived during a meeting of the Tree Reasoning in Evolution Education (TREE Working Groupp at the National Evolutionary Synthesis Center (NESCent) in May 2008, which included leading experts in all aspects of phylogenetic trees and extensive discussions of how students interact with and interpret phylogenetic trees.
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