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TaxonEvolutionary BiologyPeer-reviewed journal article

A new phylogeny and phylogenetic classification for Solanaceae

Rocío DeannaiD, Gloria E. BarbozaiD, Lynn BohsiD, Steven DodsworthiD, Edeline GagnoniD, Leandro Lacerda GiacominiD, Sandra KnappiD, Andrés OrejuelaiD, Péter PoczaiiD, Tiina SärkineniD, Stacey D. SmithiD, Richard G. OlmsteadiD

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Abstract

Solanaceae are a globally distributed family of considerable economic importance. Recent phylogenetic work on various clades in the family has resulted in a plethora of names at various taxonomic levels. This results in a confusing set of names applied to clades at different ranks, and to the use of informal names that are often not accepted in online resources. To solve this problem, we present here a phylogenetic classification following the PhyloCode for the Solanaceae. Traditional taxon names previously recognized at the ranks of tribe, genus, and section were maintained when associated with clades. We base our clade definitions on a newly constructed phylogeny of the family using 10 plastid and nuclear markers with a broad sampling of 1,474 species, roughly half of the diversity of the family. We complement this marker-based analysis with a phylogenomic analysis of 110 taxa (including 97 of the 102 genera in the family) using the Angiosperms353 probe set. This pair of analyses produced highly concordant phylogenies and provides strong support for the clades included in the classification. In total, we propose and define rank-free names for 38 major clades, including 16 infrageneric taxa within the mega-diverse Solanum. This rank-free system intends to promote name stability as new data become available, avoiding name changes to well-known groups.

In-depth summary

Claude Opus 5.5 · xhigh effort · 5 Nov 2026 · from the full text of version 1 (12 Jul 2025) · CC BY-NC-ND 4.0

A 1,474-species 10-marker phylogeny and a 110-taxon Angiosperms353 phylogenomic dataset support a rank-free PhyloCode classification defining 38 clades across Solanaceae, including 16 infrageneric clades in Solanum.

Recent phylogenetic work in Solanaceae has produced conflicting taxon names across ranks and informal names that online databases often reject, while traditional rank-based revisions cannot stably accommodate every clade. Tying 38 clade definitions directly to reference phylogenies under the PhyloCode establishes rank-free nomenclature that remains stable as phylogenetic hypotheses evolve.

Key results

  1. ShownA 10-marker maximum likelihood phylogeny of 1,474 Solanaceae species recovers major family-level clades with high bootstrap support, though the family root remains weakly supported.

    Across 10,914 bp of aligned plastid and nuclear data (1,475 taxa including outgroup), the X=12 clade has 88% bootstrap support, former subfamilies (/Cestroideae, /Goetzeoideae, /Nicotianoideae, /Solanoideae) have 93-100% support, /Petunieae reaches 93%, and /Leptostemonum has 96%, whereas /Goetzeoideae as sister to remaining Solanaceae has 35% bootstrap support. · Marker-based phylogenetic inference; Marker-based family tree; Figure legends

  2. ShownTarget enrichment sequencing of 110 Solanaceae species with the Angiosperms353 probe set yields a core set of 227 nuclear genes across 97 of 102 recognized genera.

    On average, over 300 genes were mapped per taxon with an on-target rate of 1-8% (several taxa recovering >250 genes at >=50% length and >100 genes at >=75% target length), leaving 227 genes after paralog filtering and 30% missing-data trimming. · Abstract; Taxon sampling, DNA extraction, and a353…; Phylogenomic analyses; A353 Gene Recovery

  3. ShownConcatenated maximum likelihood and coalescent species trees from the 227 Angiosperms353 genes recover all 38 PhyloCode clades from the 10-marker tree, despite widespread gene tree discordance.

    All 38 defined clades are congruent between the 10-marker and 227-gene trees, yet PhyParts and concordance factor (gCF and sCF) analyses show that at many nodes with >95% bootstrap support, a majority of individual gene trees conflict with the species tree topology (bootstrap >=50%) or are uninformative (<50%). · Phylogenomic analyses; Phylogenomic analyses using A353 data; Figure legends

  4. ShownFormal PhyloCode definitions establish 38 rank-free clade names across Solanaceae, encompassing suprageneric groups, the genus Solanum, and major infrageneric Solanum lineages.

    The classification defines 25 minimum clades and 13 maximum clades across 21 suprageneric taxa, one genus (/Solanum, 1,239 species), and 16 infrageneric clades in Solanum; 30 converted clade names come from validly published names under the traditional Code, 3 come from informal clade names, and 5 are newly proposed. · Abstract; Clade names in Solanaceae; Appendix 1. Solanaceae clade names and…

Methods, data and reproducibility

Sequences from 10 nuclear and plastid loci across 1,474 Solanaceae species (10,914 bp after pruning 100 rogue taxa) were aligned with MUSCLE and analyzed by partitioned maximum likelihood in RAxML. For 110 ingroup species (97 genera), Angiosperms353 target capture reads were assembled with HybPiper and SPAdes into 227 nuclear genes and analyzed with IQ-TREE, ASTRAL, and PhyParts.

  • 10-marker nuclear and plastid sequence dataset (ITS, LEAFY, matK, ndhF, ndhF-rpl32, psbA, rbcL, trnLF, trnSG, waxy; 10,914 bp aligned) · Solanaceae and outgroup Ipomoea purpurea · n = 1,474 Solanaceae species plus outgroup (1,475 taxa; 100 pruned from 1575) · https://osf.io/zem8b/?view_only=91df995fc9e54beeae90f24bbea7dfe1
  • Angiosperms353 target enrichment sequencing dataset (227 nuclear genes retained) · Solanaceae (97 of 102 genera) and outgroup Ipomoea purpurea · n = 110 ingroup species plus 1 outgroup (111 taxa)
Methods & tools
PyPHLAWD, MUSCLE, Mega v. 12, RogueNaRok, RAxML-VI-HPC v.8, FastQ Screen, Bowtie2, BBDuk, HybPiper v.2.3.2, IQ-TREE v2.3.6, ASTRAL v5.7.8, PhyParts
Reagents & environment
Mega v. 12, RAxML-VI-HPC v.8, HybPiper v.2.3.2, BWA v.0.7.17, SAMtools v.1.17, SPAdes v.3.15.5, Exonerate v.2.4.0, MAFFT v7.49, IQ-TREE v2.3.6, ASTRAL v5.7.8
Experimental conditions
RAxML trees were run on the CIPRES Science Gateway, and target-capture read processing and assembly ran on the Puhti supercomputer (CSC, Finland).
Reproducibility gaps
GenBank and NCBI SRA accessions for individual taxa are listed in supplementary tables (Tables S1 and S3) rather than in the main text.
Limitations (3)
  • The position of the Solanaceae root node remains unstable across datasets and analyses, with /Goetzeoideae recovered as sister to the rest of the family with only 35% bootstrap support in the 10-marker tree. · stated by the authors
  • Taxon sampling of extant species is uneven across clades (e.g., 19% in Cestreae vs. 80% in Datureae), and 5 of 102 genera (Darcyanthus, Mellissia, Combera, Calliphysalis, Melananthus) were unsampled in the Angiosperms353 dataset. · stated by the authors
  • Internal relationships within /Leptostemonum, /Physalideae, and Capsiceae remain insufficiently resolved to formally define all subclades. · stated by the authors

Read this if you study Solanaceae systematics, comparative genomics, or trait evolution and need a PhyloCode clade classification backed by family-wide marker and Angiosperms353 phylogenies.

Citations
13
FWCI
83.06
Field percentile
top 1%

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