Data from: Insights into the ecology and evolution of polyploid plants through network analysis

Polyploidy is a widespread phenomenon throughout eukaryotes, with
important ecological and evolutionary consequences. Although genes operate
as components of complex pathways and networks, polyploid changes in genes
and gene expression have typically been evaluated as either individual
genes or as a part of broad-scale analyses. Network analysis has been
fruitful in associating genomic and other 'omic'-based changes
with phenotype for many systems. In polyploid species, network analysis
has the potential not only to facilitate a better understanding of the
complex 'omic' underpinnings of phenotypic and ecological traits
common to polyploidy, but also to provide novel insight into the
interaction among duplicated genes and genomes. This adds perspective to
the global patterns of expression (and other 'omic') change that
accompany polyploidy and to the patterns of recruitment and/or loss of
genes following polyploidization. While network analysis in polyploid
species faces challenges common to other analyses of duplicated genomes,
present technologies combined with thoughtful experimental design provide
a powerful system to explore polyploid evolution. Here, we demonstrate the
utility and potential of network analysis to questions pertaining to
polyploidy with an example involving evolution of the transgressively
superior cotton fibres found in polyploid Gossypium hirsutum. By combining
network analysis with prior knowledge, we provide further insights into
the role of profilins in fibre domestication and exemplify the potential
for network analysis in polyploid species.