Indeed, that is the observation, especially between primates and carnivores, when we used more stringent thresholds (coding divergence minus 1 SD or half of coding divergence; see supplementary fig. S2, Supplementary Material online).
Second, the genome-wide significance threshold of the present study is quite stringent, requiring high divergence in allele frequency between populations.
A genomic species definition for protists based on proteome divergence is stringent, because genomic rearrangements, the acquisition of new genes via duplication or even a few mutations within a subset of genes may be sufficient to delineate two species [17], [18].
Even with more stringent thresholds (e.g., coding divergence minus 1 SD or half of coding divergence) between the reference genomes and the most diverged species, although the differences become smaller, the patterns remain essentially the same (see supplementary fig. S2, Supplementary Material online).
Isolates H3977 and H2199 exhibited greater than 78% relatedness (RBR) under both the optimum and stringent reassociation criteria and had divergence (D) of less than 5 to the labeled DNA from the B. rhizoxinica type strain.
However, mean dS/dN values for members of the PSMR subclass are much lower (1.8 2.0), indicating that the selective pressures exerted on these sequences are less stringent and reflect ongoing sequence divergence from either SUG and SMP subclasses similar to observations made from our phylogram (Additional file 1; Figure 1).
Where this occurs, the constraints on RCL sequence divergence will be less stringent than for strictly non-redundant serpin functions.
While this cut-off for absent is highly stringent, the stringent hybridisations conditions equate to divergence of greater than approximately 5% which may result in an 'absent' call to a coding sequence that is present hence 'absent/highly divergent'.
In other words, ungapped alignments can be considered if the reference was generated from the same haploid sample as the assembly, and less stringent alignments can be considered if greater divergence is expected between the assembly and reference.
Less stringent masking (i.e. without a divergence threshold) not only reduces the genomic sequence available for read matches, but also increases the effective size of 5 kub (kilo of unmasked bases) windows, which comprise 5 kb of unmasked nucleotides plus the interposed masked ones.
