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Although recombinants were often found in tissue sequence populations with high divergence, they were also found in sequence populations with a comparatively low sequence divergence (this is especially apparent in the two lymphoma cases).
For the latter, this genus was split between a benthic-living species group, Prorocentrum lima (0.27% similarity to P. levis), Prorocentrum levis, and a planktonic species group, Prorocentrum minimum, Prorocentrum micans and Prorocentrum triestinum with high divergence rates between these two groups.
Hence, fragile target genes with high divergence of TFs should show high trans divergence, whereas robust target genes with high divergence of TFs unnecessarily show high trans divergence.
Comparative analysis of the I2 locus in tomato and potato showed that the I2 locus contains a large number of homologues with high divergence.
We conclude that this approach is rather conservative at the SNP level and identifies only genes with high divergence and is likely to miss single SNPs.
We detected 5,245 SNPs with high divergence (Fst > 0.7) and significant differences in allele frequency (Fisher's exact test, FDR < 0.05).
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This approach will overestimate the number of true species in genera with higher divergence rates and underestimate those with lower rates of divergence, but on average it should give a reasonable estimate of species diversity.
To map reads with higher divergence we additionally performed alignment with BFAST [ 51].
This allowed mapping of reads to regions of reference sequence with higher divergence.
In a pattern corroborating the previous findings in yeast [ 25] and rodents [ 9] higher sequence divergence between paralogs correlates with higher divergence of tissue-specific expression.
These genes are highly similar to those found in 5632 with ca. 85% and 78% similarity, respectively, with higher divergence in the N-terminal of 5632 sau96I-like gene.
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