ArticleSystematic biology2020
Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).
Article in Systematic biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed.
- Using Nuclear Genomic Data to Address Intractable Relationships and Gene Tree Discordance in an Ancient Group of Gymnosperms (Ecology and evolution · 2026Article
- Phylogenomic conflict in Moraceae: Evidence for pervasive introgression and incomplete lineage sorting.Plant diversity · 2026Article
- The complete chloroplast genome ofMitochondrial DNA. Part B, Resources · 2026Article
- First record of the complete chloroplast genome of the Sri Lankan endemic species,Mitochondrial DNA. Part B, Resources · 2026Article
- Comparative Plastome Analysis ofEcology and evolution · 2026Article
- Characterization and phylogenetic analysis of the first complete mitochondrial genome sequence of threeFrontiers in plant science · 2025Article
- Article
- Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora.Systematic biology · 2024Article
- The sweet tabaiba or there and back again: phylogeographical history of the Macaronesian Euphorbia balsamifera.Annals of botany · 2024Article
- Echoes of ancient introgression punctuate stable genomic lineages in the evolution of figs.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- The genetic structure and demographic history revealed by whole-genome resequencing provide insights into conservation of critically endangeredFrontiers in plant science · 2023Article
- Jack of all trades: Genome assembly of Wild Jack and comparative genomics ofFrontiers 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
- Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae).Frontiers in plant science · 2022Article
- Plastome sequences fail to resolve shallow level relationships within the rapidly radiated genusFrontiers in plant science · 2022Article
- Article
- Multilocus sequence typing of diverse phytoplasmas using hybridization probe-based sequence capture provides high resolution strain differentiation.Frontiers in microbiology · 2022Article
- Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae).Systematic biology · 2021Article
- Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics.Applications in plant sciences · 2021Article
- On the potential of Angiosperms353 for population genomic studies.Applications in plant sciences · 2021Article
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7 authors.
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Abstract
We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. While codon partitioning did not result in any substantial topological differences, the inclusion of flanking non-coding sequence in analyses significantly increased the resolution of gene trees. We also found that increasing the size of datasets increased convergence between analysis methods but did not reduce gene tree conflict. We optimized the HybPiper targeted-enrichment sequence assembly pipeline for short sequences derived from degraded DNA extracted from museum specimens. While the subgenera of Artocarpus were monophyletic, revision is required at finer scales, particularly with respect to widespread species. We expect our results to provide a basis for further studies in Artocarpus and provide guidelines for future analyses of datasets based on target enrichment data, particularly those using sequences from both fresh and museum material, counseling careful attention to the potential of off-target sequences to improve resolution.
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