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Despite its popularity, phylogenetic inference based on complete mt genomes has important analytical challenges.
Phylogenetic relationships within Caenogastropoda were also analyzed based on complete mt genome nucleotide sequence data (allnuc data set).
Phylogenetic analyses based on complete mt genome data resolved a higher number of internal branches of the caenogastropod tree than individual mt genes.
Here we report the first estimates of divergence time among Crassostrea species based on complete mt sequences and the complete conservation in gene order among the six Asian Crassostrea species.
Two innovative and important recent studies [ 3, 6] inferred phylogenetic relationships among snakes based on complete mt genome sequence data for 10 and 11 species (and genera) respectively, and used this framework to examine mt genome evolution.
Phylogenetic analyses based on complete mt sequence data have proved to enhance resolution, and statistical confidence of inferred phylogenetic trees in vertebrates when compared with analyses based only on partial mt genes [ 25- 27].
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In fact, in some previous studies, Ursidae phylogenies based on the combined analysis of a few mt genes have also, to a degree, demonstrated the potential valuable information as those based on complete genome analysis [ 8, 12].
Our results increase the number of caenogastropod mt genomes sequenced to 20, substantially increase the sampling of mt genomes outside the Neogastropoda, and present the first direct evidence of major gene order rearrangements within the Littorinimorpha based on complete genome sequences.
Results are based on complete cases only.
All analyses based on complete data.
In-group frog species were largely chosen based on available complete mt genomes, and to allow direct comparison and combination of mt and nuclear data.
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