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Although the control region was the greatest source of character conflict, removal of this data partition impeded phylogenetic resolution.
The ribosomal DNA sequences, the principal source of character data in the present study, vary considerably in length, creating uncertainty in the inference of nucleotide-level homology.
For example, the removal of the control region, the putative source of character conflict, produced spurious results with inconsistencies among and within topologies from parsimony and Bayesian analyses.
The number of synapomorphies contributed by the nuclear DNA data partitions did not change between independent and simultaneous analyses (data not shown), which indicated they were not a source of character conflict.
For example, we have evidence that the dloop is a source of character conflict, and the deviation of the expected results from the linear regression analysis may be an additional indicator of this conflict.
For example, the removal of the control region, the putative source of character conflict, produced spurious results with inconsistencies among and within topologies from parsimony and Bayesian analyses, and these inconsistencies were not trivial.
Similar(54)
Our results show that introns 4 and 5 in AP3/DEF-like genes are a valuable source of characters for phylogenetic studies at the infrageneric level.
Sequencing errors and orthology determination pose challenges to the use of ESTs as a source of characters for systematics.
Sequencing errors and orthology determination are the major problems when using ESTs as a source of characters for systematics.
Progress with resolving avian phylogeny and thus identification of morphological/behavioral convergence has been enhanced by the use of molecular data that provides a source of characters independent of morphology.
See Additional file 1 for additional information on character descriptions, methods, and sources of character data.
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