Genomic data inform conservation of rare tree species: clonality, diversity and hybridity in Eucalyptus series in a global biodiversity hotspot

Abstract

Rare species are key targets of biodiversity conservation worldwide, but assessments of genetic diversity and conservation priority can be impeded by limited sample size. Reduced-representation genome sequencing improves resolution of analysis in this context, enabling applications in conservation genomics. The tree genus Eucalyptus contains many rare taxa, but clarity on conservation actions can be confounded in this group due to taxonomic complexity, unrecognised clonality and hybridisation. Using SNPs, we address key questions surrounding taxonomy, clonality and genetic diversity in two rare species, Eucalyptus virginea and a putative hybrid E. × phylacis, to inform conservation. We confirm that a highly disjunct population belongs to E. virginea despite sharing a multi-stemmed short-statured (‘mallee’) growth form and geographic proximity with a closely-related species, indicating that growth form was unrelated to phylogenetic distance. Clonality was confirmed in the disjunct population but the number of discrete clumps vs unique genets was not equal, reflecting the importance of genetic assessments of population size. The small, clonal, disjunct population had the lowest allelic richness and highest differentiation, as expected. However, heterozygosity excess suggested that clonality may prevent the loss of heterozygosity in mallee eucalypts by facilitating long-term persistence, contrary to expectations that small, isolated populations face increased conservation genetic threat. Analyses also confirmed that the Critically Endangered E. × phylacis is an F1 hybrid of E. decipiens and E. virginea, therefore its conservation listing should be revised. Our data highlight the usefulness of genomic analysis in applied conservation of non-model taxa.

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Data availability

Data accompanying this study are available from Mendeley Data; 10.17632/zd3g8skn69.1.

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Acknowledgements

We thank Andrew Webb and Janine Liddelow for information on the species and populations, and Stephen Hopper for discussion on the species relationships. Andrew Webb, Janine Liddelow and David Coates assisted with field collections, Bronwyn Macdonald undertook DNA extraction and preparation of samples for DArTseq analysis.

Funding

The study was funded by the Department of Biodiversity, Conservation and Attractions.

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MB conceived the study and conducted the sampling. RMB and DB designed and conducted analyses. All authors interpreted the data. DB wrote the first draft of the manuscript. All authors reviewed, edited and approved the final version of the manuscript.

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Correspondence to Donna Bradbury.

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Communicated by Daniel Sanchez Mata.

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Bradbury, D., Binks, R.M. & Byrne, M. Genomic data inform conservation of rare tree species: clonality, diversity and hybridity in Eucalyptus series in a global biodiversity hotspot. Biodivers Conserv (2021). https://doi.org/10.1007/s10531-020-02106-2

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Keywords

  • Eucalyptus virginea
  • Eucalyptus × phylacis
  • SNP
  • Mallee
  • Conservation genomics
  • DArTseq