Abstract
Premise: Phylogenetic relationships within major angiosperm clades are increasingly well resolved, but largely informed by plastid data. Areas of poor resolution persist within the Dipsacales, including placement of Heptacodium and Zabelia, and relationships within the Caprifolieae and Linnaeeae, hindering our interpretation of morphological evolution. Here, we sampled a significant number of nuclear loci using a Hyb-Seq approach and used these data to infer the Dipsacales phylogeny and estimate divergence times. Methods: Sampling all major clades within the Dipsacales, we applied the Angiosperms353 probe set to 96 species. Data were filtered based on locus completeness and taxon recovery per locus, and trees were inferred using RAxML and ASTRAL. Plastid loci were assembled from off-target reads, and 10 fossils were used to calibrate dated trees. Results: Varying numbers of targeted loci and off-target plastomes were recovered from most taxa. Nuclear and plastid data confidently place Heptacodium with Caprifolieae, implying homoplasy in calyx morphology, ovary development, and fruit type. Placement of Zabelia, and relationships within the Caprifolieae and Linnaeeae, remain uncertain. Dipsacales diversification began earlier than suggested by previous angiosperm-wide dating analyses, but many major splitting events date to the Eocene. Conclusions: The Angiosperms353 probe set facilitated the assembly of a large, single-copy nuclear dataset for the Dipsacales. Nevertheless, many relationships remain unresolved, and resolution was poor for woody clades with low rates of molecular evolution. We favor expanding the Angiosperms353 probe set to include more variable loci and loci of special interest, such as developmental genes, within particular clades.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 1122-1142 |
| Number of pages | 21 |
| Journal | American journal of botany |
| Volume | 108 |
| Issue number | 7 |
| DOIs | |
| State | Published - Jul 2021 |
Bibliographical note
Funding Information:The authors thank the many people who collected and processed the specimens that made this work possible including Chuck Bell, Dave Boufford, Sara Carlson, Nancy Pyck, Stephen Smith, and Patrick Sweeney. We also thank Michael Dossman and Kathryn Richardson and the Arnold Arboretum for permission to work in the living collections, and Ned Friedman and Xu Bo for the use of their photographs. Our gratitude to Santiago Cardenas for assistance with plastid assemblies and Michael Landis for advice regarding divergence time analysis. Norm Wickett, Matt Johnson, and Lindsey Bechen greatly facilitated this work by providing us with early access to the Angiosperms353 probe set and providing space to carry out the initial stages of benchwork in his laboratory at the Chicago Botanic Garden. We thank Lisa Pokorny and two anonymous reviewers for providing insightful comments on the manuscript. The authors acknowledge using the ELSA high performance computing cluster at The College of New Jersey for the research reported in this paper. This cluster is funded by the National Science Foundation under grant number OAC‐1828163. This work was funded by National Science Foundation grants to W.L.C. (DEB‐1929670) and M.J.D. (DEB‐1929533).
Funding Information:
The authors thank the many people who collected and processed the specimens that made this work possible including Chuck Bell, Dave Boufford, Sara Carlson, Nancy Pyck, Stephen Smith, and Patrick Sweeney. We also thank Michael Dossman and Kathryn Richardson and the Arnold Arboretum for permission to work in the living collections, and Ned Friedman and Xu Bo for the use of their photographs. Our gratitude to Santiago Cardenas for assistance with plastid assemblies and Michael Landis for advice regarding divergence time analysis. Norm Wickett, Matt Johnson, and Lindsey Bechen greatly facilitated this work by providing us with early access to the Angiosperms353 probe set and providing space to carry out the initial stages of benchwork in his laboratory at the Chicago Botanic Garden. We thank Lisa Pokorny and two anonymous reviewers for providing insightful comments on the manuscript. The authors acknowledge using the ELSA high performance computing cluster at The College of New Jersey for the research reported in this paper. This cluster is funded by the National Science Foundation under grant number OAC-1828163. This work was funded by National Science Foundation grants to W.L.C. (DEB-1929670) and M.J.D. (DEB-1929533).
Publisher Copyright:
© 2021 The Authors. American Journal of Botany published by Wiley Periodicals LLC on behalf of Botanical Society of America.
Keywords
- Adoxaceae
- Caprifoliaceae
- divergence times
- fossils
- Heptacodium
- Hyb-Seq
- Morinoideae
- phylogenomics
- target enrichment
- Zabelia
PubMed: MeSH publication types
- Journal Article
- Research Support, U.S. Gov't, Non-P.H.S.