This course will cover methods for documenting and describing species-level diversity of invertebrate animals and applications of these methods in ecology, evolution, resource management, etc. Emphasis will be placed on small and often overlooked taxa (e.g., meiofauna), but the content of the course will be broadly applicable to the study of diverse invertebrates. Typical marine ecosystems hold thousands of multicellular species; metazoan diversity around FHL is likely between 3-5,000 species. A large proportion of marine species are complexes of previously undifferentiated taxa. Many species are identified incorrectly in regional checklists (e.g., Kozloff) because of a history of fitting local species into named taxa from other regions, ubiquity of cryptic species complexes, and limitations of past approaches. Thus, the taxonomy of most major marine taxa needs to be reevaluated and often redone.

Integrative taxonomy, which combines study of live and preserved animals and DNA sequence data, can rapidly and effectively delineate species, although does not in itself lead to proper identification. Online and traditional taxonomic resources greatly facilitate identification, as can specialist taxonomists who are increasingly networked and connected globally.

DNA can be extracted and sequenced from individual organisms (i.e., DNA barcoding) as well as environmental samples, including sediment, plankton, water, gut contents, etc. Metabarcoding – the amplification of one or more genetic markers from environmental samples, followed by sequencing of hundreds of thousands to millions of copies on high-throughput sequencing platforms allows effective documentation of the diversity present in the sample. DNA barcoding and metabarcoding provide valuable information on biodiversity and can be used to infer evolutionary relationships, although genome-scale data (e.g., transcriptomes) are increasingly being used to in phylogenetics.

The objectives of this course are to train students broadly in morphological and molecular approaches in invertebrate biodiversity and taxonomy. This course will help train the next generation of researchers who will use integrative taxonomic approaches to document and improve understanding of invertebrate biodiversity. Students will learn the crucial considerations of study design in the field, lab, and bioinformatic stages of this fast-emerging field.

The first objective will teach students how to sample, recognize, document, describe, and name species-level taxa using morphology. This portion of the course will focus on practical skill development in small and large-scale field sampling, and morphological characterization leveraging traditional tools such as photography, light and electron microscopy, and histology as well as cutting-edge approaches such as micro-computed tomography and extended focal imaging (i.e., photo stacking). For this portion of the course, students will work closely with specialist taxonomists who will join the course as guest mentors to develop expertise in the identification of species in a taxon of their choice.

The second objective will cover molecular approaches for large-scale and rapid species delineation, characterization, and identification as well as phylogeny reconstruction. Students will genetically document species in the area by sequencing the DNA barcoding marker COI and test species limits and infer evolutionary relationships with integrated morphological-molecular methods. This effort will generate subst

antial DNA barcode libraries for the biota around FHL, which together with other data available in online databases will be the basis for interpreting environmental DNA samples.

The third objective will be to analyze diversity in environmental samples through metabarcoding. Students will collect environmental samples and extract and amplify the same DNA barcoding marker (COI) from these samples. These products will be pooled and sequenced on an Illumina sequencing platform, and students will become familiar with the computational challenges and bioinformatic tools associated with massively parallel sequence data.  Students will become comfortable with the core skills necessary to process and analyze metabarcoding datasets.

Students in the course will be graded based on laboratory exercises and a final student project of their design that combines both traditional taxonomic and modern molecular approaches.

Gustav Paulay is Curator of Invertebrates at the Florida Museum of Natural History.  His lab focuses on documenting marine biodiversity through large-scale field work, integrative taxonomy, and digitization.  See more at: https://www.floridamuseum.ufl.edu/museum-voices/gustav-paulay/

Kevin Kocot is an Associate Professor at the University of Alabama and Curator of Invertebrate Zoology at the Alabama Museum of Natural History. The Kocot lab studies the biodiversity, evolution, and genomics of marine invertebrates with an emphasis on things that are weird. Learn more at: www.kocotlab.com

Photos credit: Gustav Paulay