Appendix S1 Expanded Discussion
The window of detecting outliers
Outlier genes become more detectable when the comparison is made between slightly differentiated
sister species, e.g., Quercus rober/Q. petraea (FST = 0.0176, outliers 12.1%) and Howea belmoreana/H.
forsteriana (FST = 0.31, outliers only 1.5%) (Strasburg et al., 2011). It also seems likely that the
discovery of “divergent genes” between long split species might not be possible; the evolutionary
footprints may be wiped out by the elevating divergent background. This hypothesis remains to be
tested; so far, only a very few studies have used multiple genes to explore genomic divergence between
species (cf. Andrew and Riesberg, 2013).
Genome with only few genes displaying high differentiation is consistent with the island model of
genomic divergence (Michel et al., 2010), in a metaphor of which the sea level represents the averaged
FST value of background genes, while islands emerging the sea level denote genes with high genetic
differentiation. In reviewing papers dealing with the intraspecific outliers, mostly based on
microsatellite fingerprinting, low proportions of genome were identified as high-diverged outliers, e.g.,
3.4% in Cryptomeria japonica (Tsumura et al., 2007), 5.5% in Picea glauca (Namroud et al., 2008),
0.2% in Pinus taeda (Eckert et al., 2010), and 2.4% in Viola cazorlensis (Herrera and Bazaga, 2008),
while with exceptions in Populus tremula (17.1%) (Lexer et al., 2010), and seagrass Zostera marina
(12.0%) (Oetjen and Reusch, 2007). The existence of low-frequency outliers in genome suggests that
the possibilities of detecting adaptive divergence at population level may not be high (cf. Gossmann et
al., 2010).
At species level, the number of outliers decreases as the divergence time prolongs, as revealed by the
dramatic reduction from 13 genes (18.1%) between most closely related southern M. sinensis and M.
floridulus down to 7 (9.7% between southern and northern M. sinensis) and 3 genes (4.2% between M.
floridulus and northern M. sinensis). The striking reduction of outlier loci co-occurred with elevating
genetic differentiation at background genes, here from FST of 0.08 (between southern M. sinensis and M.
floridulus) to 0.15 (between southern and northern M. sinensis), and 0.18 (M. floridulus and northern M.
sinensis), implying a scenario of genome hitchhiking, which is known as a global reduction in average
genome-wide gene flow due to natural selection and/or hybrid incompatibility (Feder et al., 2012).
Elevating differentiation across the genome inevitably makes many genomic islands of divergence
“submerged”. Accordingly, the optimal time window for screening outliers in Miscanthus lies with a
small range between 1.47 and 1.59 MYA.
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