Utility of targeted sequence capture for phylogenomics in rapid, recent angiosperm radiations: Neotropical Burmeistera bellflowers as a case study

Bagley, Justin C.; Uribe‐Convers, Simon; Carlsen, Mónica M.; Muchhala, Nathan

doi:10.1016/j.ympev.2020.106769

Cited by 40 publications

(57 citation statements)

References 106 publications

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“…Similar findings of the inability to resolve relationships in the backbone of phylogenetic trees, particularly in plant groups with early radiations, are well known (Léveillé‐Bourret et al, 2017). Furthermore, despite the substantial increases in the number of loci via sequence capture, deep backbone phylogenetic relationships with short branches continue to remain unresolved in plant groups such as the Cyperaceae (Léveillé‐Bourret et al, 2017) and Campanulaceae (Bagley et al, 2020), but see both these studies for discussion on possible methodological and phylogenetic analysis solutions towards solving this problem. In common with our observations in orchids, these problematic backbone nodes are characterized by short branches, low bootstrap support, and high levels of gene tree discordance.…”

Section: Discussionmentioning

confidence: 99%

A multitiered sequence capture strategy spanning broad evolutionary scales: Application for phylogenetic and phylogeographic studies of orchids

Peakall

Wong

Phillips

et al. 2021

Molecular Ecology Resources

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With over 25,000 species, the drivers of diversity in the Orchidaceae remain to be fully understood. Here, we outline a multitiered sequence capture strategy aimed at capturing hundreds of loci to enable phylogenetic resolution from subtribe to subspecific levels in orchids of the tribe Diurideae. For the probe design, we mined subsets of 18 transcriptomes, to give five target sequence sets aimed at the tribe (Sets 1 & 2), subtribe (Set 3), and within subtribe levels (Sets 4 & 5). Analysis included alternative de novo and reference‐guided assembly, before target sequence extraction, annotation and alignment, and application of a homology‐aware k‐mer block phylogenomic approach, prior to maximum likelihood and coalescence‐based phylogenetic inference. Our evaluation considered 87 taxa in two test data sets: 67 samples spanning the tribe, and 72 samples involving 24 closely related Caladenia species. The tiered design achieved high target loci recovery (>89%), with the median number of recovered loci in Sets 1–5 as follows: 212, 219, 816, 1024, and 1009, respectively. Interestingly, as a first test of the homologous k‐mer approach for targeted sequence capture data, our study revealed its potential for enabling robust phylogenetic species tree inferences. Specifically, we found matching, and in one case improved phylogenetic resolution within species complexes, compared to conventional phylogenetic analysis involving target gene extraction. Our findings indicate that a customized multitiered sequence capture strategy, in combination with promising yet underutilized phylogenomic approaches, will be effective for groups where interspecific divergence is recent, but information on deeper phylogenetic relationships is also required.

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Section: Discussionmentioning

confidence: 99%

A multitiered sequence capture strategy spanning broad evolutionary scales: Application for phylogenetic and phylogeographic studies of orchids

Peakall

Wong

Phillips

et al. 2021

Molecular Ecology Resources

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“…Commonly used target enrichment assembly pipelines (e.g., Faircloth 2016;Johnson et al 2016;Andermann et al 2018) use different criteria to flag assembled loci with putative paralogs that are later filtered or processed prior to phylogenetic analysis. The most used common approach for dealing with paralogous loci in target enrichment datasets is removing the entire locus that show any signal of potential paralogy (e.g., Crowl et al 2017;Montes et al 2019;Bagley et al 2020). The removal of paralogous loci can significantly reduce the size of target enrichment datasets and most often do not take in consideration the reason why a locus was flagged for putative paralogy (i.e., allelic variation or gene duplication).…”

Section: Processing Paralogs In Target Enrichment Datasetsmentioning

confidence: 99%

“…Commonly used target enrichment assembly pipelines (e.g.,Faircloth 2016;Andermann et al 2018) use different criteria to flag assembled loci with putative paralogs that are later filtered or sorted prior to phylogenetic analysis. The most common approach for processing paralogs in target enrichment datasets is removing the entire loci that show any signal of potential paralogy (e.g.,Crowl et al 2017;Montes et al 2019;Bagley et al 2020). Other approaches either retain or remove contigs based on the distinction between putative allelic variation (flagged sequences form monophyletic groups) or putative paralogs (non-monophyletic) in combination with study-specific threshold or random selection (e.g.,Villaverde et al;Liu et al 2019; Stubbs et al 2019), or manual processing (e.g.,Garcia et al.…”

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confidence: 99%

Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events inAlchemillas.l. (Rosaceae)

Morales‐Briones

Gehrke

Huang

et al. 2020

Preprint

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Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci. Common approaches for processing paralogs in target enrichment datasets include removal, random selection, and manual pruning of loci that show evidence of paralogy. These approaches can introduce errors in orthology inference, and sometimes significantly reduce the number of loci, especially in groups experiencing whole-genome duplication (WGD) events. Here we used an automated approach for paralog processing in a target enrichment dataset of 68 species of Alchemilla s.l. (Rosaceae), a widely distributed clade of plants primarily from temperate climate regions. Previous molecular phylogenetic studies and chromosome numbers both suggested the polyploid origin of the group. However, putative parental lineages remain unknown. By taking paralogs into consideration, we identified four nodes in the backbone of Alchemilla s.l. with an elevated proportion of gene duplication. Furthermore, using a gene-tree reconciliation approach we established the autopolyploidy origin of the entire Alchemilla s.l. and the nested allopolyploidy origin of four clades within the group. Here we showed the utility of automated orthology methods, commonly used in genomic or transcriptomic datasets, to study complex scenarios of polyploidy and reticulate evolution from target enrichment datasets.

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“…Next-generation sequencing data has reinvigorated phylogenetic analyses of traditionally challenging groups characterized by recent or rapid diversification (Wagner et al, 2013;Bagley et al, 2020;Léveillé-Bourret et al, 2020) as well as hybridization (Eaton & Ree, 2013;Carter et al, 2019;Hipp et al, 2020). Reduced representation DNA sequencing approaches [e.g., RADseq; genotyping-by-sequencing (GBS)] have been increasingly utilized in phylogenetic studies due to their ability to effectively sample large numbers of orthologous loci throughout the genomes of non-model organisms without the need for prior genomic resources (Leaché & Oaks, 2017;Parchman et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Evidence for both phylogenetic conservatism and lability in the evolution of secondary chemistry in a tropical angiosperm radiation

Uckele

Jahner

Tepe

et al. 2020

Preprint

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Over evolutionary timescales, shifts in plant secondary chemistry may be associated with patterns of diversification in associated arthropods. Although foundational hypotheses of plant-insect codiversification and plant defense theory posit closely related plants should have similar chemical profiles, numerous studies have documented variation in the degree of phylogenetic signal, suggesting phytochemical evolution is more nuanced than initially assumed. We utilize proton nuclear magnetic resonance (1H NMR) data, chemical classification, and genotyping-by-sequencing to resolve evolutionary relationships and characterize the evolution of secondary chemistry in the Neotropical plant clade Radula (Piper; Piperaceae). Sequencing data substantially improved phylogenetic resolution relative to past studies, and spectroscopic characterization revealed the presence of 35 metabolite classes. Broad metabolite classes displayed strong phylogenetic signal, whereas the crude 1H NMR spectra featured evolutionary lability in chemical resonances. Evolutionary correlations were detected in two pairs of compound classes (flavonoids with chalcones; p-alkenyl phenols with kavalactones), where the gain or loss of a class was dependent on the other's state. Overall, the evolution of secondary chemistry in Radula is characterized by strong phylogenetic signal of broad compound classes and concomitant evolutionary lability of specialized chemical motifs, consistent with both classic evolutionary hypotheses and recent examinations of phytochemical evolution in young lineages.

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Utility of targeted sequence capture for phylogenomics in rapid, recent angiosperm radiations: Neotropical Burmeistera bellflowers as a case study

Cited by 40 publications

References 106 publications

A multitiered sequence capture strategy spanning broad evolutionary scales: Application for phylogenetic and phylogeographic studies of orchids

A multitiered sequence capture strategy spanning broad evolutionary scales: Application for phylogenetic and phylogeographic studies of orchids

Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events inAlchemillas.l. (Rosaceae)

Evidence for both phylogenetic conservatism and lability in the evolution of secondary chemistry in a tropical angiosperm radiation

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