Herbarium Genomics: Plant Archival DNA Explored

The sweet tabaiba or there and back again: phylogeographical history of the Macaronesian Euphorbia balsamifera

BACKGROUND AND AIMS

Biogeographical relationships between the Canary Islands and north-west Africa are often explained by oceanic dispersal and geographical proximity. Sister-group relationships between Canarian and eastern African/Arabian taxa, the 'Rand Flora' pattern, are rare among plants and have been attributed to the extinction of north-western African populations. Euphorbia balsamifera is the only representative species of this pattern that is distributed in the Canary Islands and north-west Africa; it is also one of few species present in all seven islands. Previous studies placed African populations of E. balsamifera as sister to the Canarian populations, but this relationship was based on herbarium samples with highly degraded DNA. Here, we test the extinction hypothesis by sampling new continental populations; we also expand the Canarian sampling to examine the dynamics of island colonization and diversification.

METHODS

Using target enrichment with genome skimming, we reconstructed phylogenetic relationships within E. balsamifera and between this species and its disjunct relatives. A single nucleotide polymorphism dataset obtained from the target sequences was used to infer population genetic diversity patterns. We used convolutional neural networks to discriminate among alternative Canary Islands colonization scenarios.

KEY RESULTS

The results confirmed the Rand Flora sister-group relationship between western E. balsamifera and Euphorbia adenensis in the Eritreo-Arabian region and recovered an eastern-western geographical structure among E. balsamifera Canarian populations. Convolutional neural networks supported a scenario of east-to-west island colonization, followed by population extinctions in Lanzarote and Fuerteventura and recolonization from Tenerife and Gran Canaria; a signal of admixture between the eastern island and north-west African populations was recovered.

CONCLUSIONS

Our findings support the Surfing Syngameon Hypothesis for the colonization of the Canary Islands by E. balsamifera, but also a recent back-colonization to the continent. Populations of E. balsamifera from northwest Africa are not the remnants of an ancestral continental stock, but originated from migration events from Lanzarote and Fuerteventura. This is further evidence that oceanic archipelagos are not a sink for biodiversity, but may be a source of new genetic variability.

Phylogenomic inference of the African tribe Monodoreae (Annonaceae) and taxonomic revision of Dennettia, Uvariodendron and Uvariopsis

Monodoreae (Annonaceae) is a tribe composed of 11 genera and 90 species restricted to the tropical African rain forests. All the genera are taxonomically well circumscribed except the species rich genera Uvariodendron and Uvariopsis which lack a recent taxonomic revision. Here, we used a robust phylogenomic approach, including all the 90 currently accepted species, with several specimens per species, and based on more than 300 Annonaceae-specific nuclear genes, to infer the phylogenetic tree of the Monodoreae and test the limits between the genera and species. We recover all the genera as monophyletic, except the genus Uvariopsis for which the species Uvariopsistripetala falls outside this clade. We thus reinstate the monotypic genus Dennettia for its single species Dennettiatripetala. We also erect a new tribe, Ophrypetaleae trib. nov., to accommodate the genera Ophrypetalum and Sanrafaelia, as we recover them excluded from the Monodoreae tribe with good support. Below the genus level, the genera Isolona, Monodora, Uvariastrum, Uvariodendron and Uvariopsis show weakly supported nodes and phylogenetic conflicts, suggesting that population level processes of evolution might occur in these clades. Our results also support, at the molecular level, the description of several new species of Uvariodendron and Uvariopsis, as well as several new synonymies. Finally, we present a taxonomic revision of the genera Dennettia, Uvariodendron and Uvariopsis, which contain one, 18 and 17 species respectively. We provide a key to the 11 genera of the Monodoraeae and describe four new species to science: Uvariodendronkimbozaense Dagallier & Couvreur, sp. nov., Uvariodendronmossambicense Robson ex Dagallier & Couvreur, sp. nov., Uvariodendronpilosicarpum Dagallier & Couvreur, sp. nov. and Uvariopsisoligocarpa Dagallier & Couvreur, sp. nov., and provide provisional descriptions of three putatively new species. We also present lectotypifications and nomenclatural changes implying synonymies and new combinations (Uvariodendroncitriodorum (Le Thomas) Dagallier & Couvreur, comb. et stat. nov., Uvariodendronfuscumvar.magnificum (Verdc.) Dagallier & Couvreur, comb. et stat. nov., Uvariopsiscongensisvar.angustifolia Dagallier & Couvreur, var. nov., Uvariopsisguineensisvar.globiflora (Keay) Dagallier & Couvreur, comb. et stat. nov., and Uvariopsissolheidiivar.letestui (Pellegr.) Dagallier & Couvreur, comb. et stat. nov.).

A complete digitization of German herbaria is possible, sensible and should be started now

Plants, fungi and algae are important components of global biodiversity and are fundamental to all ecosystems. They are the basis for human well-being, providing food, materials and medicines. Specimens of all three groups of organisms are accommodated in herbaria, where they are commonly referred to as botanical specimens.

The large number of specimens in herbaria provides an ample, permanent and continuously improving knowledge base on these organisms and an indispensable source for the analysis of the distribution of species in space and time critical for current and future research relating to global biodiversity. In order to make full use of this resource, a research infrastructure has to be built that grants comprehensive and free access to the information in herbaria and botanical collections in general. This can be achieved through digitization of the botanical objects and associated data.

The botanical research community can count on a long-standing tradition of collaboration among institutions and individuals. It agreed on data standards and standard services even before the advent of computerization and information networking, an example being the Index Herbariorum as a global registry of herbaria helping towards the unique identification of specimens cited in the literature.

In the spirit of this collaborative history, 51 representatives from 30 institutions advocate to start the digitization of botanical collections with the overall wall-to-wall digitization of the flat objects stored in German herbaria. Germany has 70 herbaria holding almost 23 million specimens according to a national survey carried out in 2019. 87% of these specimens are not yet digitized. Experiences from other countries like France, the Netherlands, Finland, the US and Australia show that herbaria can be comprehensively and cost-efficiently digitized in a relatively short time due to established workflows and protocols for the high-throughput digitization of flat objects.

Most of the herbaria are part of a university (34), fewer belong to municipal museums (10) or state museums (8), six herbaria belong to institutions also supported by federal funds such as Leibniz institutes, and four belong to non-governmental organizations. A common data infrastructure must therefore integrate different kinds of institutions.

Making full use of the data gained by digitization requires the set-up of a digital infrastructure for storage, archiving, content indexing and networking as well as standardized access for the scientific use of digital objects. A standards-based portfolio of technical components has already been developed and successfully tested by the Biodiversity Informatics Community over the last two decades, comprising among others access protocols, collection databases, portals, tools for semantic enrichment and annotation, international networking, storage and archiving in accordance with international standards. This was achieved through the funding by national and international programs and initiatives, which also paved the road for the German contribution to the Global Biodiversity Information Facility (GBIF).

Herbaria constitute a large part of the German botanical collections that also comprise living collections in botanical gardens and seed banks, DNA- and tissue samples, specimens preserved in fluids or on microscope slides and more. Once the herbaria are digitized, these resources can be integrated, adding to the value of the overall research infrastructure. The community has agreed on tasks that are shared between the herbaria, as the German GBIF model already successfully demonstrates.

We have compiled nine scientific use cases of immediate societal relevance for an integrated infrastructure of botanical collections. They address accelerated biodiversity discovery and research, biomonitoring and conservation planning, biodiversity modelling, the generation of trait information, automated image recognition by artificial intelligence, automated pathogen detection, contextualization by interlinking objects, enabling provenance research, as well as education, outreach and citizen science.

We propose to start this initiative now in order to valorize German botanical collections as a vital part of a worldwide biodiversity data pool.