Data from: Phylogeny of Salix subgenus Salix s.l. (Salicaceae): delimitation biogeography and reticulate evolution

Background The taxonomy and systematics of Salix subgenus Salix s.l. is
difficult. The reliability and evolutionary implications of two important
morphological characters (number of stamens, and morphology of bud scales)
used in subgeneric classification within Salix remain untested, and a
disjunct Old–New World distribution pattern of a main clade of subgenus
Salix s.l., revealed by a previous study, lacks a reasonable explanation.
To study these questions, we conducted phylogenetic analyses based on
4,688 bp of sequence data from four plastid (rbcL, trnD–T, matK, and
atpB–rbcL) and two nuclear markers (ETS and ITS) covering all subgenera of
Salix, and all sections of subgenus Salix s.l. Results Subgenus Salix came
out as para- or polyphyletic in both nrDNA and plastid trees. The plastid
phylogeny successfully resolved relationships among the major clades of
Salix, but resolution within subgenus Salix s.l. remained low.
Nevertheless, three monophyletic groups were identifiable in subgenus
Salix s.l.: the ‘main clade’ of subgenus Salix s.l., with New and Old
World species being reciprocally monophyletic; the section Triandroides
clade; and the subgenus Pleuradenia clade. While nrDNA regions showed
higher resolution within subgenus Salix s.l., they failed to resolve
subgeneric relationships. Extensive, statistically significant gene-tree
incongruence was detected across nrDNA–plastid as well as nrDNA ETS–ITS
phylogenies, suggesting reticulate evolution or hybridization within the
group. The results were supported by network analyses. Ancestral-state
reconstructions indicated that multiple stamens and free bud scales
represent the plesiomorphic states within Salix, and that several
significant shifts in stamen number and bud scale morphology have
occurred. Conclusions Subgenus Salix s.l. is not monophyletic, and the
evolutionary history of the subgenus has involved multiple reticulation
events that may mainly be due to hybridization. The delimitation of
subgenus Salix s.l. should be redefined by excluding section Triandrae and
subgenus Pleuradenia from it. The evolutionary lability of bud-scale
morphology and stamen number means that these characters are unreliable
bases for classification. The disjunct Old–New World distribution of
subgenus Salix s.l. appears to be linked to the profound climatic cooling
during the Tertiary, which cut off gene exchange between New and Old World
lineages.