Abstract
Compared to traditionally used plastid or ribosomal markers, nuclear gene markers provide many advantages for molecular systematics of plants, and high-throughput sequencing technologies are making large nuclear datasets available at an unprecedented rate. We used targeted amplicon sequencing of 44 nuclear genes to construct a time-calibrated phylogeny of genus Metrosideros (Myrtaceae), evaluate recent systematic revisions, and assess whether phylogenetic signal within the Hawaiian Archipelago is correlated with island biogeography or morphological diversification. We generated a final dataset of 40 nuclear genes for 187 specimens, used multiple search heuristics and species-tree analysis to estimate a phylogeny, and incorporated new fossils for the genus to estimate divergence times across the dataset. All analyses supported the monophyly of Metrosideros, including Carpolepis and Tepualia. Hawaiian Metrosideros were monophyletic and dated to 3.1 MYA using new fossils for the genus, which is intermediate to previous estimates based on nuclear ribosomal/chloroplast loci and calibrated with island ages. Within the Hawaiian Metrosideros clade, we observed short branch lengths and unresolved relationships, and phylogenetic patterns were not concordant with biogeographic hypotheses of island progression, or the delineation of taxa or morphotypes. Average nucleotide diversity was relatively consistent across the Hawaiian Islands with the exception of slightly lower diversity on Kauaʻi. These results provide a data-rich estimate of the timing of a single introduction of Metrosideros to Hawai‘i and highlight the need for molecular markers with higher evolutionary rates for resolution of relationships within this recent radiation.
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Acknowledgements
The authors thank J. Johansen and A. Williams for assistance with sample collection and the Hawaiʻi Division of Forestry and Wildlife for permission to collect from state forests. They also thank Laure Barrabé, Abby Cuttriss, Gildas Gâteblé, Melissa Johnson, Jean-Yves Meyer, Greg Plunkett (“Plant and People of Vanuatu” Project), Laurence Ramon, Ravahere Taputuarai, the staff of the national Park of American Samoa, the herbarium NOU, Eve Lucas and the Kew DNA bank for providing DNA samples, and Mark Simmons, for comments on an earlier draft of this manuscript. Fluidigm Access Array amplification and MiSeq sequencing were conducted at the Institute for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho. Data processing and analysis were conducted on the moana HPC cluster at the United States Department of Agriculture, Agricultural Research Service, Daniel K. Inouye Pacific Basin Agricultural Research Center. USDA is an equal opportunity employer. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. Funding was provided by NSF DEB 0954274 and NSF HRD 0833211. Figures were prepared using FigTree v1.4.4 (Rambaut and Drummond 2010) and Inkscape v0.91 (The Inkscape Team 2017).
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Raw reads are provided as a NCBI Sequence Reads Archive (BioProject PRJNA526920, SRA accessions: SRR8737094-SRR8737280), and data input and parameter files are available in the Electronic Supplementary Material.
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Note, specimen identifiers might differ between supplementary files, but DNA numbers are consistent. For detailed specimen information, see Online Resource 1.
Online Resource 1. Detailed specimen information, and summarized gene information in final dataset.
Online Resource 2. Main DNA alignment.
Online Resource 3. Partitions for main DNA alignment.
Online Resource 4. Maximum likelihood consensus tree with SH-aLRT/ufBS values for node support, maximum parsimony consensus tree with ufBS values for node support, and ASTRAL-III species tree with locPP values for node support.
Online Resource 5. Input tree file for ASTRAL-III analysis.
Online Resource 6. Gene trees in newick format.
Online Resource 7. Gene trees in pdf format, rooted with best available outgroup or else rooted mid-tree.
Online Resource 8. Input XML file for BEAST analysis.
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Dupuis, J.R., Pillon, Y., Sakishima, T. et al. Targeted amplicon sequencing of 40 nuclear genes supports a single introduction and rapid radiation of Hawaiian Metrosideros (Myrtaceae). Plant Syst Evol 305, 961–974 (2019). https://doi.org/10.1007/s00606-019-01615-0
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DOI: https://doi.org/10.1007/s00606-019-01615-0