And with the web as big as it is, the long tail of incompatible sites remains massive.
The majority of these sites also use browser detection and often serve up incompatible sites to IE9 and 10 because they don't recognize that these new versions of IE aren't exactly legacy browsers anymore.
To detect recombination in the single-copy ortholog gene families and into the rice lineage, we used a simple and robust statistical test: The Pairwise Homoplasy Index (PHI) test (Bruen et al. 2006) based on detection of phylogenetically incompatible site-pairs.
However, incompatible sites can arise through recurrent mutations as well as recombination.
Significance, including incompatible sites and recombination blocks, was evaluated by performing 1000 permutations using SNAP Map.
Incompatible sites were located within as well as between the three sequenced loci.
The mean distance between incompatible sites is 1,191 bases indicating that each genome is a mosaic of intraspecies recombination.
The recombination analysis revealed an anomalous region of the genome that lacked incompatible sites over a span of 20,134 bp.
In particular, we obtain more stable trees due to the exclusion of phylogenetically incompatible sites that most likely represent strongly randomized characters.
No evidence for recombination blocks among the three sequenced loci were found, although incompatible sites were regularly observed (data not shown).
Sequences were collapsed into unique haplotypes using SNAP map [ 57] and SITES version 1.1 [ 58] by removing indels and incompatible sites.
