The limit of divergence is achieved if the sex-specific sex chromosome is lost altogether, as occurred in the Ryukyu spiny rat (Kuroiwa et al. 2010).
According to proposed molecular typing criteria (1), the limits of intraserotypic divergence should be <25% nucleotide sequence differences or <12% amino acid sequence differences.
Pairwise nucleotide divergence between the three HRV species was 0.7 64.3%, and a limit of <9% divergence between genotype pairs was chosen for similar genotype assignment in one species [15].
Using a neutral nucleotide substitution rate of 0.2%/mya [16], a limit of 5% divergence would contain integrations that occurred around 12.5 mya whereas an integration with a 10% divergence would have occurred around 25 mya.
Sequence identity at CO sites was as low as 82%, due to indels of up to 18 bp, which might not even comprise the lower limit of sequence divergence at CO sites.
Because most of the specific elements insert posterior to the divergence of two subspecies and most shared ones insert prior to that, so the distributions of d intra of specific and shared elements give the upper and lower limit of the divergence date, respectively.
Chloroplast sequences should also limit the impact of "divergence hitchhiking", where linked neutral loci go to fixation through being linked to a locus under selection [ 61].
Within that time span, periodic disturbances and geographic constraints have interacted with salmon life history to limit the strength of divergence we see in contemporary populations.
Over longer periods of time, changes in sea levels during cycles of glaciation will radically alter the available intertidal habitat and limit the degree of divergence among outcrops within a region.
The specificity limit in terms of divergence from the tiled L segment sequence (531 nucleotides) was estimated at about 13 14%, a value exceeded by the undetected Iranian samples, and approached by the poorly detected China strain (13.7%), which lacked significant match by BLASTN analysis.
