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Finally, to allow for a direct comparison of performance between gene order data and sequence data over the same taxa, we conducted maximum parsimony analyses of ITS and rbcL data.
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This conclusion rejects some previous claims based on mitochondrial gene order data of close relationships between Arthropoda and Tardigrada (Ryu et al. 2007).
HC participated in the analysis of gene order data.
We used CRex [ 50] to analyse gene order data.
The gene content and gene order data sets were merged together to produce a data set of combined structural data.
AdM, LP and CB performed phylogenetic analysis of sequence data, LP analyzed gene order data.
This unexpected conflict between gene order and gene phylogenies is difficult to explain.
As more data become available, especially protist TPX2 genes and more gene-order data, this question may be resolvable.
The evidence for a sister relationship between Mesostigma and Chlorokybus is particularly compelling considering that analyses of gene order and sequence data independently support this relationship.
Pairwise genomic comparisons reveal very little conservation of gene order with other species (data not shown).
Among these instances of disagreement between weakly supported nodes, there is no general pattern of disagreement between the sequence data and the gene order analyses.
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