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Phylogeny of the ingoid clade (Caesalpinioideae, Fabaceae), based on nuclear and plastid data

Citation

Ferm, Julia; Ståhl, Bertil; Wikström, Niklas; Rydin, Catarina (2021), Phylogeny of the ingoid clade (Caesalpinioideae, Fabaceae), based on nuclear and plastid data, Dryad, Dataset, https://doi.org/10.5061/dryad.b2rbnzscn

Abstract

We investigated generic relationships in the ingoid clade (Fabaceae) (sensu Koenen & al. 2020a), with main focus on genera with a taxonomic history in Calliandra s.l. of the tribe Ingeae (i.e. AfrocalliandraCalliandra s.s., Sanjappa,Thailentadopsis, Viguieranthus, Zapoteca), and three genera of the tribe Acacieae (i.e., AcaciaAcaciella, Senegalia). The nuclear ribosomal ETS and ITS, and the plastid matKtrnL-trnF and ycf1 DNA-regions were analysed for 246 representatives from 36 genera using maximum likelihood as implemented in IQ-tree. The results show an Ingeae–Acacia clade within the ingoid clade, resolved in three major clades. Clade 1 (Calliandra s.s. and Afrocalliandra) is sister to clades 2 and 3. Clade 2 comprises FaidherbiaSanjappaThailentadopsisViguieranthus and Zapoteca. Clade 3 comprises the remaining genera of the Ingeae, plus Acacia. The ingoid genus Senegalia is excluded from the Ingeae–Acacia clade. Acaciella is sister to the remaining ingoid clade when nuclear ribosomal data is included in the analyses, but included in the Ingeae–Acacia clade based on plastid data. Acacia and perhaps also Acaciella are thus nested within Ingeae. Species traditionally referred to Calliandra (Calliandra s.l.) are resolved in two clades, and the “Calliandra-pod” has apparently evolved independently several times.

Methods

Alignment files of the DNA sequences ETS, ITS, trnL-trnF, matK and ycf1. Sequences amplified using sanger sequencing and DNA extracted from herbarium material or silica dried leaf material. Additional sequences downloaded from Genbank, information in appendix 1. The consensus trees from the separate analyses of the nuclear (Suppl. Fig. 1) and plastid datasets (Suppl. Fig. 2) are also provided, as well as the results from the combined (nuclear and plastid) analysis excluding nuclear sequences for Acaciella (Suppl. Fig. 3). All phylogenetic trees are provided with support values, approximate Bayes support values (aBS) and maximum likelihood Bootstrap support values (BS), on nodes, presented aBS/BS.

Usage Notes

Nuclear dataset: ETS 1-844; ITS 845-2049

Plastid dataset: trnL-trnF 1-1562; matK 1563-5000; ycf1 5001-12107

Datasets with excluded bases shown, as used for analysis.

Funding

Stiftelsen Lars Hiertas Minne

Helge Ax:son Johnsons Stiftelse

Regnell foundation, Uppsala University

Royal Swedish Academy of Sciences