Anchored Phylogenomics of Angiosperms I: Assessing the Robustness of Phylogenetic Estimates

Abstract

An important goal of the angiosperm systematics community has been to develop a shared approach to molecular data collection, such that phylogenomic data sets from different focal clades can be combined for meta-studies across the entire group. Although significant progress has been made through efforts such as DNA barcoding, transcriptome sequencing, and whole-plastid sequencing, the community current lacks a cost efficient methodology for collecting nuclear phylogenomic data across all angiosperms. Here, we leverage genomic resources from 43 angiosperm species to develop enrichment probes useful for collecting ~500 loci from non-model taxa across the diversity of angiosperms. By taking an anchored phylogenomics approach, in which probes are designed to represent sequence diversity across the group, we are able to efficiently target loci with sufficient phylogenetic signal to resolve deep, intermediate, and shallow angiosperm relationships. After demonstrating the utility of this resource, we present a method that generates a heat map for each node on a phylogeny that reveals the sensitivity of support for the node across analysis conditions, as well as different locus, site, and taxon schemes. Focusing on the effect of locus and site sampling, we use this approach to statistically evaluate relative support for the alternative relationships among eudicots, monocots, and magnoliids. Although the results from supermatrix and coalescent analyses are largely consistent across the tree, we find support for this deep relationship to be more sensitive to the particular choice of sites and loci when a supermatrix approach as employed. Averaged across analysis approaches and data subsampling schemes, our data support a eudicot-monocot sister relationship, which is supported by a number of recent angiosperm studies.

A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae)

“…() using their Angiosperm‐353 kit, which in comparison recovered sequences from 76% (269) of the target genes for this species and >50% of the target length for 43% (152) of these genes (Johnson et al., ). No Dioscoreales taxa were enriched using the Angiosperm v.1 kit (Buddenhagen et al., ), precluding comparison. Of the 260 loci targeted by our Dioscorea ‐specific kit, 23 genes overlap with the Angiosperm‐353 probe set (Johnson et al., ) and 21 with the Angiosperm v.1 kit (Buddenhagen et al., ); six loci overlap across all three kits (see the two comparison files in the Dryad Digital Repository for lists of overlapping genes among the three kits; Soto Gomez et al., ).…”

“…No Dioscoreales taxa were enriched using the Angiosperm v.1 kit (Buddenhagen et al., ), precluding comparison. Of the 260 loci targeted by our Dioscorea ‐specific kit, 23 genes overlap with the Angiosperm‐353 probe set (Johnson et al., ) and 21 with the Angiosperm v.1 kit (Buddenhagen et al., ); six loci overlap across all three kits (see the two comparison files in the Dryad Digital Repository for lists of overlapping genes among the three kits; Soto Gomez et al., ). Our kit on average recovered 95% (70–100%) of the target sequence length from D. calcicola for the 23 genes that overlap with the Angiosperm‐353 probe set; it retrieved most (16) genes in full, 90–93% the length of four genes and 70–86% the length of three genes.…”

“…This is particularly important for groups such as Dioscorea that are large and geographically widespread (Wilkin et al., ), with few species in wide cultivation. Genomic targets of hybridization‐based enrichment approaches can be recovered using “universal” baits optimized across broad taxon sets (e.g., the Angiosperm v.1 kit of Buddenhagen et al., ; the Angiosperms‐353 probe set of Johnson et al., ; the fern bait kit of Wolf et al., ) and using “taxon‐specific” baits designed for a focus group, ranging in taxonomic scale from populations (e.g., Euphorbia balsamifera Aiton; Villaverde et al., ) to a variety of higher‐level taxa (e.g., Inga Mill., Nicholls et al., ; Asclepiadoideae, Weitemier et al., ; Asteraceae, Mandel et al., ). The increasing availability of public transcriptome data and pipelines for LSCN gene discovery and bait development that require relatively few genomic resources can enable clade‐specific bait design, making phylogenomic research in groups of interest more attainable (see McKain et al., for details).…”

Increasing phylogenetic support for explosively radiating taxa: The promise of high‐throughput sequencing for Oxytropis (Fabaceae)

“…Libraries were prepared and indexed on a liquid‐handling robot (Beckman‐Coulter Biomek FXp, Brea, California) using the protocol of Meyer & Kircher (). After indexing, samples were pooled in equal quantities, and one solution‐based enrichment reaction was carried out using the Angiosperm v. 1 kit (Agilent Technologies Custom SureSelect XT kit—probe sequences available from Buddenhagen et al, ). Enrichment pools were run in equal quantities for sequencing on replicate PE150 Illumina HiSeq2500 lanes.…”

Maple phylogeny and biogeography inferred from phylogenomic data

“…A well‐resolved phylogeny is essential for understanding the evolution and biogeography of maples in the world and has been made possible by the development of anchored phylogenomics (Lemmon et al, ) that enabled orthologous data to be collected efficiently across broad taxonomic groups. The DNA sequence data from multiple nuclear loci have been used successfully in constructing solid phylogenetic frameworks for large plant genera (Buddenhagen et al, ; Mitchell et al, ; Wanke et al, ). Therefore, the main objectives of the study were to generate a robust phylogeny of Acer for the first time using the anchored phylogenomics data and to explore implications of the well‐resolved phylogeny for the previous biogeographic hypotheses.…”