Peeling Back the Layers: First Phylogenomic Insights into the Ledebouriinae (Scilloideae, Asparagaceae)

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. An understanding of the phylogenetic relationships within the group have been historically difficult to reconstruct, however. Here, we provide the first phylogenomic perspective into the Ledebouriinae. We use this renewed phylogenetic framework to hypothesize historical factors that have resulted in the topology recovered. 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 also suggest that the Ledebouriinae underwent a rapid radiation leading to rampant incomplete lineage sorting.

A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

“…More than a dozen studies utilising Angiosperms353 probes are already published (e.g. Larridon et al 2019; Howard et al 2020; Murphy et al 2020; Pérez-Escobar et al 2020; Shee et al 2020; Slimp et al 2020; McLay et al in press), and two journal special issues focused on the probe set are in preparation arising from a recent symposium (Lagomarsino and Jabaily 2020). The probe set has also been adopted by the Genomics for Australian Plants consortium (https://www.genomicsforaustralianplants.com/), which aims to sequence all Australian angiosperm genera, coordinating with the PAFTOL project to optimise collective taxonomic coverage.…”

Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants

“…Much deeper analyses are underway to fully assess the signal and conflict in these data. However, an increasing body of evidence—including 10 studies across monocots, rosids, and asterids presented in this issue—shows that Angiosperms353 data are indeed highly informative for resolving relationships among families within orders (in this special issue: Antonelli et al, 2021; Lee et al, 2021; Maurin et al, 2021; Thomas et al, 2021b; Zuntini et al, 2021), and among genera within families (Gaynor et al, 2020; Howard et al, 2020 [Preprint]; Larridon et al, 2021a, b; Starr et al, 2021; and in this special issue: Buerki et al, 2021; Clarkson et al, 2021; Pérez‐Escobar et al, 2021; Pillon et al, 2021; Shah et al, 2021). Within each of the groups covered here, Angiosperms353 is resetting the phylogenetic baseline with far larger data quantities than have previously been utilized, including the sampling of many genera for which no DNA sequence data are currently available in public repositories (e.g., Buerki et al, 2021; Clarkson et al, 2021).…”

“…There is mounting evidence that the sequence data recovered by the Angiosperms353 probe set are sufficiently variable to reconstruct relationships at the species level, especially when noncoding sequences serendipitously captured from regions flanking the target genes (the so‐called “splash zone”) are also taken into account. A number of studies exploring the suitability of Angiosperms353 for species‐level phylogenetic inference have already been published (e.g., Gaynor et al, 2020; Howard et al, 2020 [Preprint]; Larridon et al, 2020, 2021a, 2021b; Murphy et al, 2020; Shee et al, 2020; Starr et al, 2021). In this issue, A. Thomas et al (2021a) specifically investigated species‐level relationships among recently radiated lineages in Veronica sect.…”

“…In addition, early evidence suggests that Angiosperms353 genes, if analyzed appropriately, can be phylogenetically informative across multiple taxonomic scales (including at the population level; Beck et al, 2021 [Preprint]; Slimp et al, 2021; Wenzell et al, 2021). Broad uptake of Angiosperms353 is now being reported at conferences (e.g., Lagomarsino and Jabaily, 2020), but to date, published empirical studies in which applications of Angiosperms353 have been fully explored remain relatively few in number (Brewer et al, 2019; Van Andel et al, 2019; Gaynor et al, 2020; Howard et al, 2020 [Preprint]; Larridon et al, 2020, 2021a, 2021b; Murphy et al, 2020; Shee et al, 2020; Baker et al, 2021; Beck et al, 2021 [Preprint]; Starr et al, 2021). This special issue, and its companion in Applications in Plant Sciences , aims to address this gap, and to thoroughly explore the potential and pitfalls of this exciting new toolkit.…”

From southern Africa and beyond: historical biogeography of a monocotyledonous bulbous geophyte

“…In sub-Saharan Africa, the Ledebouriinae are predominantly found within more seasonal landscapes, with highest diversity in the Limpopo, Mpumalanga, and KwaZulu-Natal regions of South Africa (Venter, 1993), yet some occurrences are documented from more wet, tropical regions (Figure 1). Much diversity within the Ledebouriinae, however, remains undescribed to science (Howard, 2014; Howard et al, 2022). Additionally, an expanded phylogenomic analysis of the group suggests that a complex biogeographical history awaits to be thoroughly examined (Howard et al, 2022).…”