Observations from molecular marker studies on recently diverged species ind
icate that substitution patterns in DNA sequences can often be complex and
poorly described by tree-like bifurcating evolutionary models. These observ
ations might result from processes of-species diversification and/or proces
ses of sequence evolution that are not tree-like. In these Cases, bifurcati
ng tree representations provide poor visualization of phylogenetic signals
in sequence data. In this paper, we use median networks to study DNA sequen
ce substitution patterns in plant nuclear and chloroplast markers. We descr
ibe how to prune median networks to obtain so called pruned median networks
. These simpler networks may help to provide a useful framework for investi
gating the phylogenetic complexity of recently diverged taxa with hybrid or
igins.: (C) 2001 Academic Press.