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

Natural history collections are storehouses of evolutionary and biological information, constituting exceptional investments of time, money and human endeavor spanning centuries. The world’s ~3400 herbaria hold an estimated 350 million samples, collected over the last 400 years. With the rapid development of museomic and novel bioinformatic approaches to process large genomic datasets from a wide range of sources, the use of historical specimens for taxa that could not be field collected nowadays for various reasons can address evolutionary questions, resolve taxonomic placement of extinct taxa, or aid in constructing a biodiversity catalog for entire floras.

Similarly, complex tropical tree communities represent a treasure trove of biological and evolutionary information. Unfortunately, studies of exceptionally rich species assemblages are inherently time-consuming, costly and logistically challenging due to the need of meeting adequate taxonomic coverage and confidently verifying specimen identification. Tropical tree communities in particular consist of a complex mix of evolutionary histories resulting in patterns of disparity in phenology, distribution and ecological strategies, offering significant obstacles for scientific inquiry.

Rapid advances in genomics and bioinformatic approaches to biodiversity research are shaping museomics as an emerging field, breathing life into natural history collections that have been built up over centuries, although many challenges remain, especially in botany where herbarium DNA decays up to six times faster than in bones.

In the study, a novel approach was applied for the harvesting of DNA loci from historical collections, which contain highly fragmented genomic material owing to their age, exposure to a wide range of preservation treatments and storage methods.

Using MIGseq (multiplexed ISSR genotyping by sequencing), 10,000s of short loci were generated, for both fresh materials and museum specimens (aged >100 years) of Lithocarpus – a widespread tropical tree genus endemic to the Asian tropics.

Phylogenomic inference and biogeographic reconstruction across insular Asia, highlights repeated migration and diversification patterns between continental regions and islands. 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. 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.

The study shows the potential for developing innovative genomic approaches to improve capture of novel biological and evolutionary signals using valuable natural history collections of hyperdiverse tree communities, at low cost and with a high success-rate, allowing for rapid assessments in phylogenomics, evolutionary diversity, taxonomy and historical biogeography.

The UBD co-authors, Assoc. Professors Dr Rahayu Sukmaria Hj Sukri and Dr Ferry Slik are both in collaboration with Dr Joeri Strijk.