For the most divergent data set, deeper internal nodes of the concatenated tree have almost no congruence with the nodes in single gene trees, except the branch separating archaebacteria and eubacteria.
If LGT is the cause of incongruence between concatenation and individual trees, we would have expected to see greater degrees of incongruence for more divergent prokaryotic data sets, which was not observed, although estimated rates of LGT suggest that LGT is responsible for at least some of the observed incongruence.
To reduce false negatives that can be caused by sequence variability, a new universal primer pair was designed against a divergent sequence data set, targeting the open reading frame 4 (heat shock protein 70 homologue gene), and optimised for conventional one-step RT-PCR and one-step SYBR Green real-time RT-PCR assays.
Subsequently, we apply our method to human data sets from divergent populations [17] and bovine data sets from several breeds.
Using 129 SNP that have highly divergent FST values in both data sets, we identified 12 regions that had additive effects on the traits residual feed intake, beef yield or intramuscular fatness measured in the Australian sample.
In summary, in addition to expressing highly divergent sets of miRNAs, both testes and ovaries express very different sets of miRNAs compared to other tissues: their respective miRNA profiles appear as the most divergent of our data set.
Furthermore, by integrating these two data sets we assessed divergent gene-expression profiles between the myocardial and Epi lineages and found a central role for Wnt signaling to be associated with the "epicardial lock".
For large data sets containing very divergent sequences this is almost always the best fit model of sequence evolution [ 47].
Such models can also be used to classify large sets of highly divergent data quickly and accurately.
In contrast to BAT-enriched genes, the data sets are remarkably divergent for genes that are more highly expressed in WAT compared with BAT.
