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These different 4DTv values might be caused by different evolutionary rates of nucleotide substitution in these two lineages.
The performance of the loss-only history appears to be steady and not much affected by different evolutionary rates.
However, individual gene trees can be affected by different evolutionary rates of genes between species, pseudogenization and individual gene duplication and loss.
Lineages characterized by different evolutionary rates than the seahorses, as well as lineages that were not tested either because different positions of a particular molecular marker were used or because they were used as outgroup for the relative rate test were also plotted for comparison, but were not considered in the analyses.
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However, this analysis is complicated by the possibility of different evolutionary rates in different sequences.
This tree was multiplied by different factors to obtain sequences of different evolutionary rates.
Thus, the different evolutionary rates in Diplodus fishes might reflect differences in satellite copy number.
This hypothesis is reinforced by sequential removal of rapidly evolving lineages and by the exploration of phylogenetic signal using partitions of sites with different evolutionary rates.
Second, different species may have different evolutionary rates for homologous ERV loci.
Different evolutionary rates of the mitochondrial segments, especially the faster evolution of the D-loop, may explain the discrepancies in divergence observed by restriction digestion analysis of mtDNA in previous studies.
First, 3' LTR and 5' LTR have different evolutionary rates that depend on selective pressures on each end of the locus.
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