Tackling Rapid Radiations With Targeted Sequencing

Larridon, Isabel; Villaverde, Tamara; Zuntini, Alexandre R.; Pokorny, Lisa; Brewer, Grace E.; Epitawalage, Niroshini; Fairlie, Isabel; Hahn, Marlene; Kim, Jan; Maguilla, Enrique; Maurin, Olivier; Xanthos, Martin; Hipp, Andrew L.; Forest, Félix; Baker, William J.

doi:10.3389/fpls.2019.01655

Cited by 107 publications

(137 citation statements)

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“…Whereas Kadlec et al (2017) argued that high sequence variability across angiosperm orders precluded the usefulness of universal probes in resolving species-level relationships, Chau et al (2018) found that general purpose probes can be as effective as taxon-specific ones. While we do not compare these alternative probes, the results from our study, Larridon et al (2020) and Murphy et al (2020) suggest that an appropriately designed universal probe set can capture adequate phylogenomic information to resolve relationships at the species-level and even at the population-level (Van Andel et al, 2019). Liu et al (2019) showed experimentally that when probes are <30% divergent from regions targeted, enrichment worked adequately (see Figure 6 and Supplementary Figure S6 in Liu et al, 2019).…”

Section: Efficacy Of Universal Probesmentioning

confidence: 80%

“…To date, other than in Schefflera, the Angiosperms-353 enrichment panel (Johnson et al, 2018) has only been tested at the species level in sedges (Cyperus; Larridon et al, 2020) and Old World pitcher plants (Nepenthes; Murphy et al, 2020) and at the population level (SNPs) in rice (Oryza; Van Andel et al, 2019). When comparing data matrices containing on-target loci only, both Larridon et al (2020) and Murphy et al (2020) had a higher capture success (Table 3); an expected result since they worked with a greater proportion of silica-dried tissue (Brewer et al, 2019). However, their mean P PIC was lower than ours (Table 3), probably as a result of our filtering approach, which combined two custom scripts -max_overlap (representativeness x completeness x evenness) and optrimAl (per locus gap threshold optimization) -to increase signal while reducing missing data in our data matrixes.…”

Section: Efficacy Of Universal Probesmentioning

confidence: 99%

“…To overcome this design and optimization hurdle, the Angiosperms-353 probe set was developed from available transcriptome and genome data (One Thousand Plant Transcriptomes Initiative, 2019)including twelve Apiales representatives, three of them (Hedera, Hydrocotyle, and Polyscias) in Araliaceae -with universal probes that capture 353 nuclear single-copy loci shared across all angiosperms (Johnson et al, 2018). By using the Angiosperms-353 sequence capture probes, our study is among the first to test the efficacy of this probe set to resolve species-level relationships from either historical herbarium specimens (Brewer et al, 2019;Larridon et al, 2020;Murphy et al, 2020) or fresh tissue (Van Andel et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

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Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics

et al. 2020

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With its large proportion of endemic taxa, complex geological past, and location at the confluence of the highly diverse Malesian and Australian floristic regions, Papuasia-the floristic region comprising the Bismarck Archipelago, New Guinea, and the Solomon Islands-represents an ideal natural experiment in plant biogeography. However, scattered knowledge of its flora and limited representation in herbaria have hindered our understanding of the drivers of its diversity. Focusing on the woody angiosperm genus Schefflera (Araliaceae), we ask whether its morphologically defined infrageneric groupings are monophyletic, when these lineages diverged, and where (within Papuasia or elsewhere) they diversified. To address these questions, we use a high-throughput sequencing approach (Hyb-Seq) which combines target capture (with an angiosperm-wide bait kit targeting 353 single-copy nuclear loci) and genome shotgun sequencing (which allows retrieval of regions in high-copy number, e.g., organellar DNA) of historical herbarium collections. To reconstruct the evolutionary history of the genus we reconstruct molecular phylogenies with Bayesian inference, maximum likelihood, and pseudo-coalescent approaches, and co-estimate divergence times and ancestral areas in a Bayesian framework. We find strong support for most infrageneric morphological groupings, as currently circumscribed, and we show the efficacy of the Angiosperms-353 probe kit in resolving both deep and shallow phylogenetic relationships. We infer a sequence of colonization to explain the present-day distribution of Schefflera in Papuasia: from the Sunda Shelf, Schefflera arrived to the Woodlark plate (presentday eastern New Guinea) in the late Oligocene (when most of New Guinea was submerged) and, subsequently (throughout the Miocene), it migrated westwards (to the Maoke and Bird's Head Plates and thereon) and further diversified, in agreement with previous reconstructions.

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Section: Efficacy Of Universal Probesmentioning

confidence: 80%

Section: Efficacy Of Universal Probesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics

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“…The CTAB protocol can be easily modified to suit different tissue types and ages, regardless of preservation strategies, and upscaled to process 96–192 samples at a time (see Dryad repository associated with Beck et al., , b; and supplementary materials for Larridon et al., ) with a Geno/Grinder. For dried and old herbarium materials, higher concentrations of β‐mercaptoethanol (i.e., 0.4%) are recommended in the CTAB step, a fast vortex and clean‐up with chloroform : isoamyl alcohol, and long incubations in isopropanol at −20°C (e.g., 48 h, or even up to a week for precious and difficult materials; Larridon et al., ). Phenol cleaning is highly recommended in plant DNA isolation protocols (Drábková et al., ), but high DNA concentrations can be achieved without it.…”

Section: Dna Extractionmentioning

confidence: 99%

Strategies for reducing per‐sample costs in target capture sequencing for phylogenomics and population genomics in plants

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Citation: Hale, H., E. M. Gardner, J. Viruel, L. Pokorny, and M. G. Johnson. 2020. Strategies for reducing per-sample costs in target capture sequencing for phylogenomics and population genomics in plants. Applications in Plant Sciences 8(4): e11337.The reduced cost of high-throughput sequencing and the development of gene sets with wide phylogenetic applicability has led to the rise of sequence capture methods as a plausible platform for both phylogenomics and population genomics in plants. An important consideration in large targeted sequencing projects is the per-sample cost, which can be inflated when using off-the-shelf kits or reagents not purchased in bulk. Here, we discuss methods to reduce per-sample costs in high-throughput targeted sequencing projects. We review the minimal equipment and consumable requirements for targeted sequencing while comparing several alternatives to reduce bulk costs in DNA extraction, library preparation, target enrichment, and sequencing. We consider how each of the workflow alterations may be affected by DNA quality (e.g., fresh vs. herbarium tissue), genome size, and the phylogenetic scale of the project. We provide a cost calculator for researchers considering targeted sequencing to use when designing projects, and identify challenges for future development of low-cost sequencing in non-model plant systems. KEY WORDS enzymatic fragmentation; herbariomics; high-throughput workflow implementation; Hyb-Seq; low-cost sequence capture; pooling and multiplexing strategies. Applications in Plant Sciences 2020 8(4): e11337 Hale et al.-Low-cost Hyb-Seq • 2 of 10

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“…The accessions available for phylogenetic studies in natural history collections are essential to survey the diversity of species-rich groups, to include narrow endemics difficult to collect in the field and to account for variation in widespread and polymorphic species (Särkinen et al, 2012;Buerki and Baker, 2016;Bieker and Martin, 2018;Valderrama et al, 2018). The use of target enrichment strategies to gather low or single copy nuclear loci for phylogenomics of plant lineages at different scales (Nicholls et al, 2015;Sass et al, 2016) is becoming a standard technique, and the establishment of universal probe sets could reduce costs and time while enabling the merging of datasets from different studies and across plant lineages (Johnson et al, 2019;Larridon et al, 2020). However, divergence between the target sequences and the baits does affect capture efficiency (Larridon et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Unraveling the Spiraling Radiation: A Phylogenomic Analysis of Neotropical Costus L

et al. 2020

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The family of pantropical spiral gingers (Costaceae Nakai; c. 125 spp.) can be used as a model to enhance our understanding of the mechanisms underlying Neotropical diversity. Costaceae has higher taxonomic diversity in South and Central America (c. 72 Neotropical species, c. 30 African, c. 23 Southeast Asian), particularly due to a radiation of Neotropical species of the genus Costus L. (c. 57 spp.). However, a well-supported phylogeny of the Neotropical spiral gingers including thorough sampling of proposed species encompassing their full morphologic and geographic variation is lacking, partly due to poor resolution recovered in previous analyses using a small sampling of loci. Here we use a phylogenomic approach to estimate the phylogeny of a sample of Neotropical Costus species using a targeted enrichment approach. Baits were designed to capture conserved elements' variable at the species level using available genomic sequences of Costus species and relatives. We obtained 832 loci (generating 791,954 aligned base pairs and 31,142 parsimony informative sites) for samples that encompassed the geographical and/or morphological diversity of some recognized species. Higher support values that improve the results of previous studies were obtained when including all the available loci, even those producing unresolved gene trees and having a low proportion of variable sites. Concatenation and coalescent-based species trees methods converge in almost the same topology suggesting a robust estimation of the relationships, even under the high levels of gene tree conflict presented here. The bait set design here presented made inferring a robust phylogeny to test taxonomic hypotheses possible and will improve our understanding of the origins of the charismatic diversity of the Neotropical spiral gingers.

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Tackling Rapid Radiations With Targeted Sequencing

Abstract: be merged for downstream analyses. Moreover, our study contributes to the growing consensus that targeted sequencing data are a powerful tool in resolving rapid radiations.

Cited by 107 publications

References 86 publications

Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics

Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics

Strategies for reducing per‐sample costs in target capture sequencing for phylogenomics and population genomics in plants

Unraveling the Spiraling Radiation: A Phylogenomic Analysis of Neotropical Costus L

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