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Consequently, the recombining histories of multiple nuclear loci are being used increasingly in empirical estimates of population genetic parameters [7] [9].
Theoretical work suggests that data from multiple nuclear loci provide better estimates of population genetic parameters than do single loci, but just how many loci are needed and how much sequence is required from each has been little explored.
An unequivocal resolution of this species will likely require the inclusion of multiple nuclear loci [ 30].
The 11 tissue samples were used for sequencing multiple nuclear loci.
Likewise, inspection of the post-palatal bridge, presumably controlled by multiple nuclear loci, revealed no intermediate morphs.
Such cases might explain some strongly supported conflicts between our results and those based on multiple nuclear loci.
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Therefore, incongruence caused by hybridization and lineage sorting could be differentiated when comparing phylogenies based on multiple unlinked nuclear loci.
Excluding the possibility of paralogs, incongruence caused by hybridization and lineage sorting could be differentiated by comparing phylogenies of multiple unlinked nuclear loci.
In future studies, sampling multiple, unlinked nuclear loci will be necessary to tease apart the relative contributions of these two opposing forces within H. formosa using coalescent-based models.
Although mitochondrial genes are frequently used for detecting genetic patterns in recently diverged populations [ 1], multiple independent nuclear loci are generally thought to provide more reliable estimates of the evolutionary history of populations [ 2].
However, we recognize that mtDNA is limited in that all sites belong to a single 'super-locus', and so a significant reduction of uncertainty (e.g. the slope in Figure 6) will ultimately require the supplement of multiple independent nuclear loci.
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