class: center, middle, inverse, title-slide # How does plankton inform what we know about marine biodiversity? ### François Michonneau ### February 27th, 2017 --- # We don't know enough about biodiversity ### How many species? -- <!-- --> --- # We don't know enough about biodiversity ### How many species? ### Where do species live? -- ### Questions: - What is the impact of pollution, perturbations? - Which species are invasive? - How does global change affect communities? --- class: inverse, center, middle # What can we do? --- # What can we do? ## Traditional Biodiversity Surveys --- # What can we do? ## DNA barcoding <img src="images/barcoding.png" height="400px"/> --- # What can we do? ## Metabarcoding <img src="images/metabarcoding.png" height="400px" /> --- # What can we do? ## Barcoding .pull-left[ ### What can it tell us? * Species delineation, speeds up taxonomy * Works on all stages of the life cycle * Associated with museum specimens and photographs ] .pull-right[<img src="images/barcoding.png" height="200px" />] --- # What can we do? ## Metabarcoding .pull-left[ ### What can it tell us? * Number of species * Where are the species distributed? * Applicable to many types of environmental samples * **Well-suited for monitoring** ### Pre-requisites * Comprehensive and accurate databases * Need to ground truth the results ] .pull-right[<img src="images/metabarcoding.png" height="200px" />] --- # Questions ## Which species live in the area? -- ## How well do we know the fauna? --- # Project design ## Plankton sampling - Capture in a single habitat a diversity of species - Bi-monthly sampling for a year - Document larval stages of local species -- ## DNA barcoding on individual larvae -- ## Metabarcoding on full plankton tows --- # How many species? .pull-left[ Sampling effort <!-- --> ] .pull-right[ - Number of larvae sequenced: 433 - Number of species sequenced: 253 <!-- --> ] --- # Known diversity - Number of known species found in the plankton: 62 (out of 253) - Breakdown by phylum (0 match for Platyhelminthes, Phoronida, Acoelomorpha): <!-- --> --- # Known diversity .pull-left[ <!-- --> ] -- .pull-right[ <!-- --> ] --- class: inverse, center, middle # How to interpret these numbers? --- # How to interpret these numbers? ### If only we knew the total number of species... ### Instead we have: * Expert faunistic lists - most comprehensive, limited in geographic scope -- * Museum specimens - can be validated, not everything digitized -- * Described species - almost complete, only captures described species -- * Species occurences - good for species ranges, difficult to validate --- # How to interpert these numbers? ### Instead we have: * Expert faunistic lists * Museum specimens ⟶ **iDigBio** * Described species ⟶ **WoRMS** * Species occurences ⟶ **GBIF, OBIS** -- ### **First synthesis of knowledge for marine invertebrates** * How much of what we know is captured in these databases? * How much do we know? * What should we do next? --- # Expert lists * Kozloff's "Marine Invertebrates of the Pacific Northwest" - 2705 species * Felder and Camp's "Gulf of Mexico Origin, Waters, and Biota" - 8570 species --- # Expert lists ‒ Pacific Northwest <!-- --> --- # Expert lists ‒ Gulf of Mexico <!-- --> --- # Museum Records <!-- --> --- # Museum Records <!-- --> --- # Museum Records <!-- --> --- # Museum Records <!-- --> --- # Museum Records <!-- --> --- # Proportion barcoded <!-- --> --- # Recommendations * More sampling - Proportion of species known from a single specimen: 27.2% - Proportion of species known from less than 5 specimens: 59.5% - Proprotion of species not collected since 1980: 41.2% - Number of species added: + between 1960 and 1970: 1163 + since 2000: 498 - Need more information about small phyla -- * Use metabarcoding and existing data to inform future sampling effort -- * Improve bioinformatics tools to get better species assignment of not barcoded taxa