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Their strict relationship is supported also by gene order data, given that both species share the unique mitochondrial translocation of the trnS uga from the original position between cob and nad1 to a new location between trnI and trnM [ 16, 73].
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Whereas the former support a position within a clade of platyzoan taxa, mitochondrial data recovers an annelid affinity, which is strongly supported by the gene order data and is congruent with morphology.
We have tested the hypothesis that vertical inheritance of the leukotoxin (lktCABD) operon has occurred from the last common ancestor of genus Mannheimia to any ancestor of the diverging subclades by exploring gene order data.
The "common heritage" hypothesized herein for the Ascaridida and Strongylida to the exclusion of the Spirurida has been supported by previous studies using mt gene order data [ 49] and using concatenated amino acid sequence data inferred from protein-coding mt genes [ 38].
Ancestral gene order data can be inferred by either median computations or the maximum likelihood method.
Gene order in each of these chloroplast genomes was converted to all possible pairs of signed genes (i.e., taking into account gene polarity) and a gene order data set was obtained by coding as binary characters the presence/absence of signed gene pairs in two or more genomes.
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.
As more data become available, especially protist TPX2 genes and more gene-order data, this question may be resolvable.
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