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Abstract
The traditional knowledge in textbooks indicated that cephalochordates were the closest
relatives to vertebrates among all extant organisms. However, this opinion was challenged
by several recent phylogenetic studies using hundreds of nuclear genes. The researchers
suggested that urochordates, but not cephalochordates, should be the closest living
relatives to vertebrates. In the present study, by using data generated from hundreds
of mtDNA sequences, we revalue the deuterostome phylogeny in terms of whole mitochondrial
genomes (mitogenomes). Our results firmly demonstrate that each of extant deuterostome
phyla and chordate subphyla is monophyletic. But the results present several alternative
phylogenetic trees depending on different sequence datasets used in the analysis.
Although no clear phylogenetic relationships are obtained, those trees indicate that
the ancient common ancestor diversified rapidly soon after their appearance in the
early Cambrian and generated all major deuterostome lineages during a short historical
period, which is consistent with "Cambrian explosion" revealed by paleontologists.
It was the 520-million-year's evolution that obscured the phylogenetic relationships
of extant deuterostomes. Thus, we conclude that an integrative analysis approach rather
than simply using more DNA sequences should be employed to address the distant evolutionary
relationship.