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Exploring Angiosperms353: an open, community toolkit for collaborative phylogenomic research on flowering plantsThe unveiling of the angiosperm (flowering plant) tree of life over the past three decades has been one of the great success stories of modern plant biology. Flowering plants underpin most terrestrial biomes: they fix vast amounts of terrestrial carbon, in turn producing a substantial fraction of planetary oxygen, and drive major biogeochemical cycles. The bulk of human calories are derived either directly (crops) or indirectly (fodder) from angiosperms, as are many medicines, fuel, dyes, beverages, timber, fibers, and other materials. Countless indispensable and mundane items that impact human existence find their origins in flowering plants, and without them, life would be decidedly drearier—imagine a world without herbs, spices, or garden flowers, for example. In this context, the importance of a comprehensive understanding of the angiosperm tree of life cannot be overstated. The tree of life is the fundamental, biological roadmap to the evolution and properties of plants (e.g., Wong et al., 2020). For evolutionary biologists, phylogenies allow us to better understand the spectacular rise of the flowering plants to dominance over the past 140 million or so years (e.g., Lutzoni et al., 2018; Ramírez-Barahona et al., 2020). Information about angiosperm phylogenetic relationships also underpins modern angiosperm classification (e.g., APG IV, 2016), and helps us to better understand species origins and boundaries (e.g., Fazekas et al., 2009). Today, tree of life research is undergoing a renaissance due to the development of powerful, new phylogenomic methods (Dodsworth et al., 2019). In this special issue of the American Journal of Botany, together with a companion issue of Applications in Plant Sciences, we gather a set of papers that focus on a new, common phylogenomic toolkit, the Angiosperms353 probe set (Johnson et al., 2019), and illustrate its potential for evolutionary synthesis by promoting open collaboration across our community.
Exploring Angiosperms353: developing and applying a universal toolkit for flowering plant phylogenomicsSpecial Issue Introduction. Target enrichment represents a useful, cost-effective method for researchers working on the phylogenomics of non-model organisms (e.g., Cronn et al., 2012; Hale et al., 2020). The ability to sequence a customizable predefined genomic subset for several dozens or even hundreds of taxa allows in-depth analyses and the testing of phylogenetic hypotheses in ways that were not previously possible (reviewed in McKain et al., 2018). The most popular methods for targeted sequencing of genomic loci in phylogenomics include (long-)amplicon sequencing (Rothfels et al., 2017) and hybridization capture (Mandel et al., 2014; Weitemier et al., 2014). Targeted amplicon sequencing is based on single-fragment PCR amplification or by using multiplexing methods such as a microfluidic PCR-based amplification of multiple pre-selected genomic regions (e.g., Zhang and Ozdemir, 2009; Ho et al., 2014), which can then be pooled and sequenced. Massively parallel amplicon sequencing was first used in medical diagnostics (Turner et al., 2009) and was later applied to metazoan phylogenetics (Bybee et al., 2011; O’Neill et al., 2013). Microfluidic PCR and long-amplicon sequencing were subsequently applied in plant systematics (Uribe-Convers et al., 2014, 2016; Gostel et al., 2015). Amplicon-based methods can be time consuming as they require careful optimization and validation of primers. These methods are also susceptible to many of the common problems in PCR (such as nonspecific products, inability to amplify large loci in their entirety, or simply no products). Recently, amplicon approaches have been largely supplanted by hybridization-based targeted enrichment, which allows for relatively rapid probe design with reference to a few related transcriptomes or genomes, and allows simultaneous and efficient recovery of many hundreds of genes.
A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe setTo further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit. We combined high-throughput sequencing and target enrichment with the Angiosperms353 probe kit to evaluate a sample of 485 species across 305 genera (76% of all genera in the order). Results provide the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks, such as the relationship of the early-diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. Technical considerations for processing HTS data are also discussed. High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events.
Resolving species boundaries in a recent radiation with the Angiosperms353 probe set: the Lomatium packardiae/L. anomalum clade of the L. triternatum (Apiaceae) complexSpeciation not associated with morphological shifts is challenging to detect unless molecular data are employed. Using Sanger-sequencing approaches, the Lomatium packardiae/L. anomalum subcomplex within the larger Lomatium triternatum complex could not be resolved. Therefore, we attempt to resolve these boundaries here. The Angiosperms353 probe set was employed to resolve the ambiguity within Lomatium triternatum species complex using 48 accessions assigned to L. packardiae, L. anomalum, or L. triternatum. In addition to exon data, 54 nuclear introns were extracted and were complete for all samples. Three approaches were used to estimate evolutionary relationships and define species boundaries: STACEY, a Bayesian coalescent-based species tree analysis that takes incomplete lineage sorting into account; ASTRAL-III, another coalescent-based species tree analysis; and a concatenated approach using MrBayes. Climatic factors, morphological characters, and soil variables were measured and analyzed to provide additional support for recovered groups. The STACEY analysis recovered three major clades and seven subclades, all of which are geographically structured, and some correspond to previously named taxa. No other analysis had full agreement between recovered clades and other parameters. Climatic niche and leaflet width and length provide some predictive ability for the major clades. The results suggest that these groups are in the process of incipient speciation and incomplete lineage sorting has been a major barrier to resolving boundaries within this lineage previously. These results are hypothesized through sequencing of multiple loci and analyzing data using coalescent-based processes.