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Peeling back the layers: First phylogenomic insights into the Ledebouriinae (Scilloideae, Asparagaceae)

Citation

Howard, Cody; Crowl, Andrew; Harvey, Timothy; Cellinese, Nico (2022), Peeling back the layers: First phylogenomic insights into the Ledebouriinae (Scilloideae, Asparagaceae), Dryad, Dataset, https://doi.org/10.5061/dryad.nzs7h44q6

Abstract

The Ledebouriinae (Scilloideae, Asparagaceae) are a widespread group of bulbous geophytes found predominantly throughout seasonal climates in sub-Saharan Africa, with a handful of taxa in Madagascar, the Middle East, India, and Sri Lanka. Phylogenetic relationships within the groups have been historically difficult to elucidate. Here, we provide the first phylogenomic perspective into the Ledebouriinae. Using the Angiosperms353 targeted enrichment probe set, we consistently recovered four major clades (i.e., two Ledebouria clades, Drimiopsis, and Resnova). The two Ledebouria clades closely align with geography, either consisting almost entirely of sub-Saharan African taxa (Ledebouria Clade A), or East African and non-African taxa (Ledebouria Clade B). Our results suggest that the Ledebouriinae likely underwent a rapid radiation leading to rampant incomplete lineage sorting. We additionally find evidence for potential historical hybridization between Drimiopsis and a subclade within Ledebouria Clade A.

Methods

DNA extraction of samples includes both field collected and herbarium specimen leaf tissue. The alignment files are the result of targeted enrichment using the Angiosperm 353 probe set. Phylogenetic analyses were performed using IQ-Tree v2.0-rc1. Species tree estimation was performed using ASTRAL III and SVDQuartets. We also performed Quartet Sampling, SNaq analyses for testing for hybridization, and visualized discordance using DiscoVista.

Usage Notes

See README.txt for information on the alignment and tree files.