DOI: 10.5061/dryad.qr2vv
title: Data from: Phylogeny of Salix subgenus Salix s.l. (Salicaceae): delimitation biogeography and reticulate evolution

description: 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.
description: sequences alignments
 used in this studyThe alignments/matrixes
 include two nrDNA sequences (ITS and ETS) and four plastid sequences
 (rbcL, atpB-rbcL, matK and trnDT) and the combined data matrix of the four
 plastid sequenced just mentioned. The sequences were assembled using
 Geneious v5.4 and aligned with Muscle. The combined plastid matrix and
 nrDNA ITS and ETS were used for: (1) phylogenetic analysis, include
 maximum parsimony method implemented in PAUP* v4.0b10 and maximum
 likelihood method implemented in raxML v7.2.8;and (2) phylogenetic network
 analysis implemented in Dendroscope v3.2.8. The combined plastid matrix
 was also used for divergence time estimation implemented in BEAST v1.5.4
 and character evolutionary analysis implemented in Mesquite
 v2.75.sequences
 alignments.zip