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Museomics for reconstructing historical floristic exchanges: Divergence of Stone Oaks across Wallacea

Cite this dataset

Strijk, Joeri et al. (2020). Museomics for reconstructing historical floristic exchanges: Divergence of Stone Oaks across Wallacea [Dataset]. Dryad.


Natural history collections and tropical tree diversity are treasure troves of biological and evolutionary information, but its accessibility is impeded by several properties. DNA in historical specimens generally occurs in a highly fragmented state, complicating the recovery of high-grade genetic material for scientific studies. Our understanding of hyperdiverse, wide-spread tree assemblages suffers from patchy information on distributions, phenology and paucity of diagnostic characters. This prohibits rapid identification and the strengthening of taxonomic frameworks and in turn, delay the application of downstream conservation actions. Congruently, a sizeable component of botanical collections are sterile, eluding identification and slowing down progress in systematic treatments. With rapid advances in genomics and bioinformatic approaches to biodiversity research, museomics is emerging as a new field breathing life into natural collections built up over centuries. 

Using MIGseq (multiplexed ISSR genotyping by sequencing), we generated 10,000s of short loci for both freshly collected and museum specimens (aged >100 years) of Lithocarpus, a widespread tropical tree genus endemic to the Asian tropics. Loci recovery from museum and recent samples was unaffected by age and preservation history of the study material, underscoring the reliability and flexibility of the MIGseq approach.

Phylogenomic inference and biogeographic reconstruction across insular Asia highlights repeated divergence, migration and diversification patterns between continental Lithocarpus and islands species. Results indicate that co-occurring insular species at the extremity of the distribution range are not monophyletic, raising the possibility of multiple independent dispersals along the outer edge of Wallacea. This suggests that dispersal of large seeded tree genera throughout Malesia and across Wallacea may have been less affected by large geographic distances and the presence of marine barriers than generally assumed. 

We demonstrate the utility of MIGseq in museomic studies using non-model taxa and present the first range-wide genomic assessment of Lithocarpus and tropical Fagaceae as a proof-of-concept. Our study shows the potential for developing innovative genomic approaches to improve the capture of novel evolutionary signals using valuable natural history collections of hyperdiverse taxa.