Data from: Ancestral gene flow and parallel organellar genome capture result in extreme phylogenomic discord in a lineage of angiosperms

While hybridization has recently received a resurgence of attention from
systematists and evolutionary biologists, there remains a dearth of case
studies on ancient, diversified hybrid lineages-clades of organisms that
originated through reticulation. Studies on these groups are valuable in
that they would speak to the long-term phylogenetic success of lineages
following gene flow between species. We present a phylogenomic view of
Heuchera, long known for frequent hybridization, incorporating all three
independent genomes: targeted nuclear (~400,000 bp), plastid (~160,000
bp), and mitochondrial (~470,000 bp) data. We analyze these data using
multiple concatenation and coalescence strategies. The nuclear phylogeny
is consistent with previous work and with morphology, confidently
suggesting a monophyletic Heuchera. By contrast, analyses of both
organellar genomes recover a grossly polyphyletic Heuchera,consisting of
three primary clades with relationships extensively rearranged within
these as well. A minority of nuclear loci also exhibit phylogenetic
discord; yet these topologies remarkably never resemble the pattern of
organellar loci and largely present low levels of discord inter alia. Two
independent estimates of the coalescent branch length of the ancestor of
Heuchera using nuclear data suggest rare or nonexistent incomplete lineage
sorting with related clades, inconsistent with the observed gross
polyphyly of organellar genomes (confirmed by simulation of gene trees
under the coalescent). These observations, in combination with previous
work, strongly suggest hybridization as the cause of this phylogenetic
discord.