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differentiation to the genomic regions affecting key divergently selected QTL is what makes it possible to use outlier analysis during stage 1 to distinguish genomic regions harboring these branch-defining loci.

At the end of stage 1, the gene trees for loci unaffected by divergent selection will still resemble a discordant collection of “tangled twigs” (Avise, 2000, p. 307), which reflects a combination of unresolved ancestral polymorphism, recent gene flow, and stochastic effects of the coalescent process (Maddison, 1997). At this point, any phylogeographic or phylogenetic analysis based on a set of randomly chosen neutral markers is likely to yield discordant results (Beltran et al., 2002; Machado and Hey, 2003; Mallarino et al., 2004; Dopman et al., 2005; Pollard et al., 2006). If Fst outliers can be identified in such analyses, their gene trees will reflect a clear branching pattern consistent with the phenotypic divergence, but most randomly chosen markers will produce noisy and uninformative phylogenetic patterns [examples in Wilding et al. (2001), Campbell and Bernatchez (2004), Emelianov et al. (2004), Dopman et al. (2005), and Via and West (2008)].

An important prediction of this model of speciation is that phylogenetic discordance will persist through speciation and possibly well beyond. Therefore, to detect the evolutionary story of lineage branching that will be reflected in the future species tree, it is necessary to focus on analyses of Fst outliers that are in linkage disequilibrium with QTL under divergent selection [see examples in Wilding et al. (2001), Emelianov et al. (2004), Dopman et al. (2005), and Via and West (2008)]. Early in speciation, these outliers will reveal the history of adaptive divergence. The truly neutral markers in other genomic regions will still be useful, however, for analyses of demographic events such as bottlenecks or range expansion.

Preferentially using markers affected by divergent selection for phylogeographic or phylogenetic analysis of populations conflicts with the clear preference for neutral markers in species-level phylogenetics. This apparent contradiction results from the gene tree-species tree mismatch, which persists until phylogenetic concordance is reached. Until that time, variability among gene trees leads will inevitably produce highly variable “cloudograms,” instead of the simple species-level cladograms that will eventually be visible (Maddison, 1997).

In sum, there are 2 key ideas in this model: first, the branching pattern of the QTL and their linked outliers reveals the branching pattern with which all of the discordant gene trees will eventually fall in line, and second, this pattern can be seen even during the period of rampant gene tree discordance if one analyzes Fst outliers rather than a random sample of markers.

As the portions of the genome affected by divergent selection become increasingly resistant to interrace gene exchange during stage 1, genes and



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