Genetic states that differ by only one mutation are always reversible if one state is more fit in one environment and the other is more fit in the other.
The majority of the remaining haplotypes differ by only one mutation from either haplotype 0 or haplotype 1.
We can disentangle these two hard sweeps by assigning the rare haplotypes to either of the two founding haplotypes if they differ from the latter by only one mutation.
Only four different haplotypes were detected among the 74 samples analyzed: the most common haplotype, found in 52 coral colonies, was separated by only one mutation from the two less common ones (respectively found in 2 and 3 individuals), whereas the fourth haplotype, present in 17 individuals, was 16 mutations away.
These two haplotypes were present in eight (Ht1: YAKa15, 21, 29, 31, 34, 39, 40, 41) and seven individuals (Ht2: YAKa66, 67, 68, 69, 69, 70, 78), and differed from each other by only one mutation step at the loci DYS389II and DYS392.
Due to the low amount of variation detected with the Y-chromosome loci, haplotypes often differ by only one mutation and five mutations at most (Figure S2).
It is possible that this mutation has occurred frequently by chance, and with only one mutation shared between elements it is harder to distinguish between source gene activity and parallel mutation.
In a family in which two affected individuals had only one mutation identified by sequencing exonic regions, we directly sequenced cDNA representing the entire DYSF mRNA in the patients' myogenic cells, identifying an intronic sequence that was inserted within the cDNA.
In addition, testing for exonic deletions/duplications is useful in autosomal recessive conditions in which only one mutation is identified by sequence analysis.
Similar results were recently reported by Markowski et al (2012), who found only one mutation in a single endometrial polyp and no mutations in the lipomas.
The most frequent region of mutation was exon 5 (6/16), followed by exon 8 (5/16), exon 4 and exon 2 (2/16); only one mutation was found in exon 6 (Table 7).
