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Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae, yet the backbone of the subfamily phylogeny remains unresolved. In this study, we sequenced and assembled 39 new plastomes that are covering key genera representing the morphological diversity in the subfamily. From 244 total taxa, we produced eight datasets for maximum likelihood (ML) analyses based on entire plastomes and/or concatenated sequences of 77 protein-coding sequences (CDS) and two datasets for multispecies coalescent (MSC) analyses based on individual gene trees. We additionally produced a combined nucleotide dataset comprising CDS plus matK gene sequences only, in which most papilionoid genera were sampled. A ML tree based on the entire plastome maximally supported all of the deep and most recent divergences of papilionoids (223 out of 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, and Amburaneae), Cladrastis, Andira, and Exostyleae clades formed a grade to the remainder of the Papilionoideae, concordant with nine ML and two MSC trees. Phylogenetic relationships among the remaining five papilionoid lineages (Vataireoid, Dermatophyllum , Genistoid s.l., Dalbergioid s.l., and Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because of insufficient support and/or conflicting relationships among trees. Our study fully resolved most of the deep nodes of Papilionoideae, however, some relationships require further exploration. More genome-scale data and rigorous analyses are needed to disentangle phylogenetic relationships among the five remaining lineages.
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Target‐enrichment sequencing reveals for the first time a well‐resolved phylogeny of the core Bromelioideae (family Bromeliaceae)
Abstract A phylogenomic analysis of the so far phylogenetically unresolved subfamily Bromelioideae (Bromeliaceae) was performed to infer species relationships as the basis for future taxonomic treatment, stabilization of generic concept, and further analyses of evolution and biogeography of the subfamily. A target‐enrichment approach was chosen, using the Angiosperms353 v.4 kit RNA‐baits and including 86 Bromelioideae species representing previously identified major evolutionary lineages. Phylogenetic analyses were based on 125 target nuclear loci, assembled off‐target plastome as well as mitogenome reads. A Bromelioideae phylogeny with a mostly well‐resolved backbone is provided based on nuclear (194 kbp), plastome (109 kbp), and mitogenome data (34 kbp). For the nuclear markers, a coalescent‐based analysis of single‐locus gene trees was performed as well as a supermatrix analysis of concatenated gene alignments. Nuclear and plastome datasets provide well‐resolved trees, which showed only minor topological incongruences. The mitogenome tree is not sufficiently resolved. A total of 26 well‐supported clades were identified. The generaAechmea,Canistrum,Hohenbergia,Neoregelia, andQuesneliawere revealed polyphyletic. In core Bromelioideae,Acanthostachysis sister to the remainder. Among the 26 recognized clades, 12 correspond with currently employed taxonomic concepts. Hence, the presented phylogenetic framework will serve as an important basis for future taxonomic revisions as well as to better understand the evolutionary drivers and processes in this exciting subfamily.
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- Award ID(s):
- 2110875
- PAR ID:
- 10496620
- Publisher / Repository:
- John Wiley & Sons
- Date Published:
- Journal Name:
- TAXON
- Volume:
- 72
- Issue:
- 1
- ISSN:
- 0040-0262
- Page Range / eLocation ID:
- 47 to 63
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript
- Journal Article:
- https://doi.org/10.1002/tax.12831
