ArticleApplications in plant sciences2019
An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae.
Article in Applications in plant sciences, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
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- Historical introgression as a driver of diversification of diploid Picris (Compositae) in the Mediterranean Basin.The Plant journal : for cell and molecular biology · 2025Article
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- Retrieval of long DNA reads from herbarium specimens.AoB PLANTS · 2023Review
- Nano-Strainer: A workflow for the identification of single-copy nuclear loci for plant systematic studies, using target capture kits and Oxford Nanopore long reads.Ecology and evolution · 2023Article
- Nested singletons in molecular trees: Utility of adding morphological and geographical data from digitized herbarium specimens to test taxon concepts at species level in the case ofEcology and evolution · 2023Article
- Phylogenomic analyses of Sapindales support new family relationships, rapid Mid-Cretaceous Hothouse diversification, and heterogeneous histories of gene duplication.Frontiers in plant science · 2023Article
- Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae).Frontiers in plant science · 2022Article
- New Insights Into the Relationships Within Subtribe Scorzonerinae (Cichorieae, Asteraceae) Using Hybrid Capture Phylogenomics (Hyb-Seq).Frontiers in plant science · 2022Article
- Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae).Systematic biology · 2021Article
- Lineage-specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family.Applications in plant sciences · 2021Article
- How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow UsingFrontiers in plant science · 2021Article
- Phylogenomics ofFrontiers in plant science · 2021Article
- Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb-Seq.Applications in plant sciences · 2020Article
- An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae.Applications in plant sciences · 2019Article
- LoCoLotive: In silico mining for low-copy nuclear loci based on target capture probe sets and arbitrary reference genomes.Applications in plant sciencesArticle
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14 authors.
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No grant is acknowledged in the PubMed record.
Abstract
premiseHybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq probe set and the outcomes of different phylogenetic analyses are investigated here.
methodsHyb-Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non-paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae.
resultsAlignments of the Asteraceae family-wide Hyb-Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches. DISCUSSION: The approach used to build a Hyb-Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb-Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage-specific.
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