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At lower levels of divergence (≥ 97% identity), only 13% of genes were identified as diverged.
Hybrids between species with lower levels of divergence developed to metamorphosis, while hybrids with higher levels of divergence stopped developing in gastrula and larval stages.
As expected, the nuclear fragment showed much lower levels of divergence due to the lower evolutionary rate of nuclear coding regions relative to mtDNA.
The lowest FST values are generally between Lake Masaya and Lake Nicaragua, while Lake Xiloa also shows lower levels of divergence from Lake Masaya and Lake Nicaragua.
However, shared polymorphisms in populations with lower levels of divergence have a stronger clustering of S sites than models with migration.
Another approach to identify functional regions in the genome is to compare sequences from species showing lower levels of divergence that are far from saturation [ 12].
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It is somewhat surprising that the impact of damage on SNP call accuracy was more pronounced at a lower level of divergence.
We also noted that there was a lower level of divergence among nucleotide sequences compared with that among amino acid chains.
Although different species usually show more than 2% interspecific divergence, lower levels of sequence divergence should occur in young species, and they have been detected in many groups [ 87, 88].
Recent molecular phylogenetic studies [21], [22], [23] revealed a well supported clade with on average twice the level of sequence divergence (the so-called long branch clade, LBC) when compared to a second major clade with lower levels of sequence divergence (the so-called short-branch clade).
However, prior reports demonstrate that both rbcL [30] and trnH-psbA [28] show significantly lower levels of genetic divergence within species than between species.
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