The two large and comprehensive SLE studies of the 6q23 region have yielded multiple independent association signals, including polymorphisms in the TNFAIP3 gene [ 6, 7].
The most parsimonious interpretation is that such replacements represent ancestral polymorphisms rather than multiple independent substitutions in different lineages, and this likely affects the reliability of ω estimates.
In our analysis of the emm59 GAS epidemic in Canada, we rapidly identified several polymorphisms that arose multiple, independent times in the strains studied.
These species are recently diverged (0.5% genomic divergence per site; 0.4% genomic divergence following polymorphism masking) and form multiple independent hybrid zones in river systems in the Sierra Madre Oriental of Mexico (Culumber et al., 2011).
Recently, sea urchin ARCs were cloned via a different approach [9], and our slightly different sequences are probably attributable to polymorphisms [7] identified in multiple independent RT-PCR clones.
4 More recent high-density single nucleotide polymorphism (SNP) genotyping studies have demonstrated multiple independent signals across the MHC in northern European cohorts.
In humans, FoxO1 and FoxO3 polymorphisms are associated with extreme longevity in multiple independent cohorts of centenarians (Lunetta et al. 2007; Willcox et al. 2008; Anselmi et al. 2009; Flachsbart et al. 2009; Li et al. 2009; Pawlikowska et al. 2009).
The non-HLA genetic polymorphism that has been most strongly replicated across multiple independent studies is PTPN22 [ 9, 11- 16, 16, 21- 24].
Some evidence of multiple independent effects within the MHC locus had been suggested by association analysis using single-nucleotide polymorphisms (SNPs) or classic two- or four-digit alleles of human leukocyte antigen (HLA) genes [ 1– 4].
Here, we took an iterative integrative-taxonomy approach – comparing multiple, independent data sets of the same sample – and used traditional morphometrics, Wolbachia symbionts, mitochondrial DNA, amplified fragment length polymorphism, and ecological niche modelling.
