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First, detection of loci using BIC-based model selection results in a high proportion of model misspecification in low-power situations (small sample size, low allele frequencies) but yields good results (low proportion of false discoveries and one or both of the specified loci correctly identified) with reasonably large sample sizes and similar allele frequencies.
For the affected loci, the conventional mapping methods propose a consensus that has no real biological meaning and they fail to map these loci correctly.
Overall, the eight outlier loci correctly self-assigned 92.0% of all individuals to ecotype based on the leave-one-out test implemented in oncor (Kalinowski et al. 2007), while the neutral eight and neutral 44 loci data sets correctly assigned 59.1% and 71.8%, respectively (data not shown).
In this case, the panel of eight outlier loci correctly assigned 92.9% of 2010 individuals to ecotype and outperformed other marker types in MC analyses (Table 4), levels on par to those revealed by simulation approaches based on the 2007 baseline alone (Table 3).
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The true-positive rate of calling a CN = 1 locus correctly (among CN = 2 loci) as a function of false-positive rate is depicted in Figure 1 for each of the three methods.
32 of 37 homozygous loci are correctly called.
In both cases the relative proportions of the corresponding loci were correctly assessed whatever the region and motif considered.
This feature was verified using a VNTR analysis program [ 75], and most of identified loci were correctly predicted as VNTR, except for locus 3 in B. pertussis and B. bronchiseptica, and for locus 4 in B. bronchiseptica (data not shown).
This approach also served to identify loci with correctly and incorrectly annotated Ensembl gene model predictions, as well as novel loci not predicted by the current Genebuild (release 70) in zebra finches.
A recent simulation-based study suggested that sampling of a moderate number (up to ten) of loci could correctly delimit recently diverged biological species with a coalescent theory-based approach, even without relying on their reciprocal monophyly [ 53].
One consequence of such transfers is that parasites may appear closely related to their hosts, thereby obscuring their true phylogenies; however, if such occurrences are relatively uncommon, the majority of loci should correctly predict the phylogenetic positions of most parasites.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com