Addressing major gaps in our knowledge of Colombia fern diversity

In order to improve understanding of Colombian fern diversity, we are conducting field expeditions to understudied, species-rich areas across Colombia in order to document the fern diversity present there. These expeditions involve extensive planning and coordination with many colleagues and partners in Colombia. Specimens collected during these trips will be deposited at herbaria in Colombia and internationally, and will be publicly available through online data portals to facilitate study by as many users as possible.

Tens of thousands of important collections of ferns are already housed in herbaria around the world, but many of these remain poorly curated. To improve the usefulness of these specimens and learn more about the Colombian fern flora, we are studying thousands of specimens at numerous herbarium collections in Colombia and the USA, updating identifications and organizing specimen-associated data as we go.

Generating unified taxonomic resources for the ferns of Colombia

A principal limitation to progress in the study of Colombian fern diversity is a lack of unified and up-to-date taxonomic resources. To overcome this, we are developing Ferns of Colombia Online, a comprehensive, specimen-driven taxonomic resource for Colombian ferns that we have initiated within the existing framework of the Pteridoportal web portal. The data aggregated on Ferns of Colombia Online will be derived directly from expert-identified herbarium specimen records from Colombia hosted on Pteridoportal, including all collections made during this project and specimen data from herbaria of partner institutions in Colombia. When complete, this taxonomic resource will leverage Symbiota’s flexible interface and Pteridoportal’s >40,000 Colombian fern specimens to present a user-friendly, data-rich, and dynamic resource. This approach will seamlessly and automatically integrate new collections added to Pteridoportal and incorporate taxonomic changes. Because of this, Ferns of Colombia Online can be continuously updated over time, unlike traditional taxonomic treatments.

Producing genomic resources for the ferns of Colombia

DNA sequence data are critical for resolving taxonomic problems and placing Colombian fern diversity in an evolutionary context, but these data are lacking for most Colombian fern species. As part of this project, we are developing a bank of silica-dried tissue and generating target-capture sequence data for all species of Colombian ferns. These data will provide us with a powerful toolkit to aid in the discovery of cryptic species, provide insights into genetic diversity among Colombian ferns, and advance the study of tropical fern evolution. Both our silica-dried tissue and all DNA sequence data will be made publicly available.

Accelerate lineage discovery and taxonomic research on Colombian ferns

A major component of this project is to generate data and develop capacity necessary to document and describe unknown fern diversity in Colombia. Because of the high predicted number of undescribed ferns in Colombia, innovative and efficient approaches are needed to achieve this goal. As part of this project, we are developing a “next-generation” approach to lineage discovery and description that leverages the resources and data that we are producing through our other research activities.

In order to evaluate the effectiveness of this approach, we are focusing on four genera as test cases: Elaphoglossum (Dryopteridaceae; focusing on a clade of approximately 15 species), Pityrogramma (Pteridaceae), Pleopeltis (Polypodiaceae), and Polystichum (Dryopteridaceae). In short, our approach consists of the following steps: These activities are summarized in the following steps: 1) resolve the placement of unidentified specimens in our comprehensive phylogeny and assess monophyly whenever possible; 2) use SNP-based ploidy inference to distinguish diploid and polyploid accessions; 3) resolve hybrid species complexes with reticulation network analyses; 4) identify putative undescribed taxa based on criteria evaluated in steps 1–3 (i.e., cryptic polyploids/diploids, non-monophyletic taxa); 5) compare putative undescribed taxa to similar species from resources on Ferns of Colombia Online, herbarium specimens (including types), and species descriptions; and 6) formally describe new taxa in taxonomic publications.

We are also piloting an approach to generate taxonomic treatments semi-automatically from spreadsheets containing specimen data and morphological measurements using custom R scripts. Using this automated workflow presents several advantages over traditional approaches to writing taxonomic treatments: it allows for large sections of text to be generated rapidly, treatments can be easily updated to incorporate new records or taxonomic changes, and errors can be reduced. Treatments will be made available in both English and Spanish and will include genus and species descriptions, identification keys, lists of specimens examined, specimen images, distribution maps, and indices to collectors.