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Genetic analysis of the global diversity of CTVT cancers has indicated that the lineage has achieved considerable heterogeneity, with substantial lineage diversity present worldwide (Murgia et al., 2006; Rebbeck et al., 2009).
A recent molecular-based phylogeny suggests a different topology for this phylogeny, as well as substantial lineage and dietary diversification, particularly the adoption of plant and detritus-based diets, upon a single historical invasion of fresh water environments by euryhaline-marine terapontids [ 45].
Since protein-coding gene sequence divergence between species is considered as insufficient to account for substantial lineage- and species-specific phenotypes, much more attention has been paid to regulatory sequence divergence, gene amplifications, gene loss, and lineage-specific protein-coding genes [ 28, 50, 51].
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Taking this paradigm shift from a phylogenomics perspective, we have previously reported that duplications played a prominent role in the divergent evolution of BCL-2 homologous genes and contributed to the generation of substantial lineage-specific diversity in the BCL-2 complement of extant metazoans.
This topology differed greatly from the 'Minimize Deep Coalescences' topology, indicating substantial incomplete lineage sorting.
A gsi of 1 (= monophyly) was only estimated for several taxa for the cytb locus and for E. mongoz for the eno and vwf loci and for E. rubriventer and E. coronatus for the vwf locus, indicating substantial incomplete lineage sorting for our genetic loci.
All trees implied substantial ghost lineages as indicated by the fairly low MSM* scores (0.11-0.12); however, GER scores, which are standardized by the maximum possible sum of all ghost lineages, are much higher (0.83-0.84).
Although consideration of additional genes with substantial sampled lineages may support a convergence in robustness between the two method classes, the computational performance advantage of tree-ignorant methods establishes them as the metric of choice for comprehensive surveys of molecular coevolution.
However, a substantial number of lineage- or species-specific miRNA genes do exist (Fahlgren et al., 2007; Kasschau et al., 2007; Lindow and Krogh, 2005; Molnar et al., 2007; Rajagopalan et al., 2006; Zhang et al., 2006), which escape the detection of a conservation-based approach.
The concatenated phylogenetic analysis identifies three to four major lineages, with substantial phylogeographic structure within these lineages.
As discussed above for mutation there are more events in the O157 H7 lineages, but still a substantial number in the O55 lineage.
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