Abstract
We aimed to test the extent to which plastid DNA gives incongruent phylogeographic patterns to nuclear DNA in a species of eucalypt, Eucalyptus behriana, a taxonomic group where chloroplast capture is a well-established phenomenon. Furthermore, we aimed to test the degree of influence chloroplast capture has on the observed patterns by broadly sampling co-occurring, related species. A genome skimming approach was used to sequence and assemble chloroplast genomes from population-level sampling of E. behriana, as well as samples of twenty-one other Eucalyptus section Adnataria species which co-occur with it. Phylogenetic analyses were first undertaken on just E. behriana to allow direct comparison to previously reported phylogeographic patterns based upon nuclear markers. A subsequent analysis including the related taxa was undertaken to investigate the degree of chloroplast capture and how this may be influencing the observed phylogeographic patterns. We found strong geographic structuring of plastid DNA relationships across the geographic range of E. behriana, with a basal divergence between the most northerly isolated population at West Wyalong and all other populations which does not match phylogeographic patterns based on nuclear markers. When outgroups were included, we found that E. behriana is highly polyphyletic with respect to all other species, starkly contrasting with the species well-supported monophylly based upon nuclear markers, and that chloroplast capture is so widespread that geographic patterns of the plastid genomes are consistent across species boundaries.
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Data availability
All data generated during this study are publicly available on the NCBI GenBank database and datasets used in analyses are included in the electronic supplementary material attached to this article.
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Acknowledgements
We thank Stephen Wilcox of the Walter and Eliza Hall Institute for assistance with DNA sequencing. Patrick Fahey is supported by the Jim Ross PhD Studentship from the Cybec Foundation and the Royal Botanic Gardens Victoria and is grateful for additional support from The University of Melbourne Botany Foundation. Collections for this study were completed under permits granted by the Department of Environment, Land, Water and Planning in Victoria (10008557), NSW National Parks & Wildlife Service (SL102100) and Department for Environment and Water in South Australia (Q26766).
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Research costs were supported by a grant from Eucalypt Australia (grant number 2016–42).
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Patrick Fahey, Frank Udovicic, David Cantrill and Michael Bayly conceived the ideas; Patrick Fahey, Frank Udovicic, David Cantrill, Rachael Fowler and Michael Bayly conducted the fieldwork; Patrick Fahey and Rachael Fowler generated and analysed the data and Patrick Fahey led the writing with assistance from Frank Udovicic, David Cantrill, Rachael Fowler and Michael Bayly.
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Fahey, P.S., Fowler, R.M., Udovicic, F. et al. Use of plastid genome sequences in phylogeographic studies of tree species can be misleading without comprehensive sampling of co-occurring, related species. Tree Genetics & Genomes 17, 43 (2021). https://doi.org/10.1007/s11295-021-01524-9
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DOI: https://doi.org/10.1007/s11295-021-01524-9