Leptospermum scoparium J. R. Forst et G. Forst, known as mānuka
by Māori, the indigenous people of Aotearoa (New Zealand), is a
culturally and economically significant shrub species, native to New
Zealand and Australia. Chemical, morphological and phylogenetic studies
have indicated geographical variation of mānuka across its range in New
Zealand, and genetic differentiation between New Zealand and Australia.
We used pooled whole genome re-sequencing of 76 L. scoparium and
outgroup populations from New Zealand and Australia to compile a dataset
totalling ~2.5 million SNPs. We explored the genetic
structure and relatedness of L. scoparium across New Zealand, and
between populations in New Zealand and Australia, as well as the complex
demographic history of this species. Our population genomic
investigation suggests there are five geographically distinct mānuka
gene pools within New Zealand, with evidence of gene flow occurring
between these pools. Demographic modelling suggests three of these gene
pools have undergone expansion events, whilst the evolutionary histories
of the remaining two have been subjected to contractions. Furthermore,
mānuka populations in New Zealand are genetically distinct from
populations in Australia, with coalescent modelling suggesting these two
clades diverged ~9 –12 million years ago. We discuss
the evolutionary history of this species and the benefits of using
pool-seq for such studies. Our research will support the management and
conservation of mānuka by landowners, particularly Māori, and the
development of a provenance story for the branding of mānuka based
products.