Data from: From gene trees to a dated allopolyploid network: insights from the angiosperm genus Viola (Violaceae)

Allopolyploidisation acounts for a significant fraction of speciation
events in many eukaryotic lineages. However, existing phylogenetic and
dating methods require tree-like topologies and are unable to handle the
network-like phylogenetic relationships of lineages containing
allopolyploids. No explicit framework has so far been established for
evaluating competing network topologies, and few attempts have been made
to date phylogenetic networks. We used a four-step approach to generate a
dated polyploid species network for the cosmopolitan angiosperm genus
Viola L. (Violaceae Batch.). The genus contains ca 600 species and both
recent (neo-) and more ancient (meso-) polyploid lineages distributed over
16 sections. First, we obtained DNA sequences of three low-copy nuclear
genes and one chloroplast region, from 42 species representing all 16
sections. Second, we obtained fossil-calibrated chronograms for each
nuclear gene marker. Third, we determined the most parsimonious
multilabelled genome tree and its corresponding network, resolved at the
section (not the species) level. Reconstructing the ‘correct’ network for
a set of polyploids depends on recovering all homoeologs, i.e. all
subgenomes, in these polyploids. Assuming the presence of Viola subgenome
lineages that were not detected by the nuclear gene phylogenies (‘ghost
subgenome lineages’), significantly reduced the number of inferred
polyploidisation events. We identified the most parsimonious network
topology from a set of five competing scenarios differing in the
interpretation of homoeolog extinctions and lineage sorting, based on (1)
fewest possible ghost subgenome lineages, (2) fewest possible
polyploidisation events, and (3) least possible deviation from expected
ploidy as inferred from available chromosome counts of the involved
polyploid taxa. Finally, we estimated the homoploid and polyploid
speciation times of the most parsimonious network. Homoploid speciation
times were estimated by coalescent analysis of gene tree node ages.
Polyploid speciation times were estimated by comparing branch lengths and
speciation rates of lineages with and without ploidy shifts. Our analyses
recognise Viola as an old genus (crown age 31 Ma) whose evolutionary
history has been profoundly affected by allopolyploidy. Between 16 and 21
allopolyploidisations are necessary to explain the diversification of the
16 major lineages (sections) of Viola, suggesting that allopolyploidy has
accounted for a high percentage – between 67% and 88% – of the speciation
events at this level. The theoretical and methodological approaches
presented here for (1) constructing networks and (2) dating speciation
events within a network, have general applicability for phylogenetic
studies of groups where allopolyploidisation has occurred. They make
explicit use of a hitherto underexplored source of ploidy information from
chromosome counts to help resolve phylogenetic cases where incomplete
sequence data hampers network inference. Importantly, the coalescent-based
method used herein circumvents the assumption of tree-like evolution
required by most techniques for dating speciation events.