Supplemental Material for Lillie et al., 2019

Experimental populations of model organisms provide valuable
opportunities to unravel the genomic impact of selection in a controlled
system. The Virginia body weight chicken lines represent a unique resource to
investigate signatures of selection in a system where long-term, single-trait,
bidirectional selection has been carried out for more than 60 generations. At 55 generations
of divergent selection, earlier analyses of pooled genome resequencing data
from these lines revealed that 14.2% of the genome showed extreme
differentiation between the selected lines, contained within 395 genomic
regions. Here, we report more detailed analyses of these data exploring the regions
displaying within- and between-line genomic signatures of the bidirectional selection
applied in these lines. Despite
the strict selection regime for opposite extremes in body weight, this did not
result in opposite genomic signatures between the lines. The lines often
displayed a duality of the sweep signatures, where an extended region of
homozygosity in one line, in contrast to mosaic pattern of heterozygosity
in the other line. These haplotype mosaics consisted of short, distinct
haploblocks of variable between-line divergence, likely the results of a
complex demographic history involving bottlenecks, introgressions and moderate inbreeding.
We demonstrate this using
the example of complex haplotype mosaicism in the growth1 QTL[ÖC1] [ÖC2] .[ÖC3] These mosaics represent the standing genetic
variation available at the onset of selection in the founder population. Selection
on standing genetic variation can thus result in different signatures depending
on the intensity and direction of selection.