ated with genes causing the most obvious differences between ecotypes is premature.
Using a linkage map that shows locations of the QTL affecting phenotypic traits known to be under divergent selection, the hypothesis that outliers are linked to key phenotypic traits under divergent selection can be tested: Are Fst outliers scattered randomly on the map, or are they clustered near divergently selected QTL? This approach requires a system in which the phenotypic traits involved in divergence and reproductive isolation are well known, the strength of selection on these traits has been measured, and QTL affecting the key traits have been localized on a linkage map, so that mapped markers can be used in an Fst analysis of field-collected samples. The pea aphid host races on alfalfa and red clover [A. pisum pisum (Harris)] are such a system.
The pea aphid complex is a worldwide group of phloem-feeding insects, found primarily on legumes (Eastop, 1971). Although the pea aphid host races on alfalfa and red clover are in the same subspecies, A. pisum pisum, sympatric pea aphid populations on alfalfa, red clover, and other legumes are highly genetically divergent and ecologically specialized in the eastern United States (Via, 1991b), Europe (Sandstrom, 1996; Simon et al., 2003; Ferrari et al., 2007, 2008), and South America (Peccoud et al., 2008).
Experimental studies in both the field and laboratory have documented extensive ecologically based reproductive isolation between the pea aphid host races in eastern North America because of strong selection against migrants to the alternate host (Via, 1989, 1991a,b, 1999), environmentally mediated selection against hybrids (Via et al., 2000), and habitat choice (Via et al., 2000). It is unknown whether divergence between the pea aphid host races began in sympatry [e.g., Coyne and Orr (2004, pp. 163 and 164)]. However, conditions of the initial split are far less relevant to the study of speciation than is the fact that divergent selection currently maintains genetically based phenotypic differentiation and significant ecologically based reproductive isolation between sympatric populations.
Via and West (2008) estimated Fst between the pea aphid host races for 45 markers with known locations on a QTL map of genomic regions affecting early fecundity and behavioral acceptance of each plant. They then estimated the map distance from each marker to the nearest QTL for one of the key host use traits and found that Fst outliers were significantly clustered around the QTL involved in reproductive isolation (P < 0.05; Fig. 1.4).