[Coral-List] diversity of (oyster) reefs

[Nancy Knowlton]

This is the link to our new paper in PNAS (open access) using
next-generation sequencing methods to understand the diversity of reefs.
We are quite happy about it as it was literally almost a decade in the
making.  this first example is for oyster reefs (so you might miss it with
a search) but the methods are equivalent for coral reefs and an analysis of
coral reefs will be published in a bit.
http://www.pnas.org/content/early/2015/01/27/1424997112.full.pdf+html

*cheers, nancy knowlton*


*Abstract*
Documenting the diversity of marine life is challenging because many
species are cryptic, small, rare, and belong to poorly known groups. New
sequencing technologies, especially when combined with standardized
sampling, promise to make comprehensive biodiversity assessments and
monitoring feasible on a large scale. We used this approach to characterize
patterns of diversity on oyster reefs across a range of geographic scales
comprising a temperate (Virginia) and subtropical (Florida) location.
Eukaryotic organisms that colonized multi-layered settlement surfaces
(Autonomous Reef Monitoring Structures, or ARMS) over a six-month period
were identified by Cytochrome c oxidase subunit I barcoding (>2mm mobile
organisms) and metabarcoding (sessile and smaller mobile organisms). In a
total area of ~15.64 m2 and volume of ~0.09 m3, 2179 operational taxonomic
units (OTUs) were recorded from 983,056 sequences. However, only 10.9%
could be matched to reference barcodes in public databases, with only 8.2%
matching barcodes with both genus and species names. Taxonomic coverage was
broad, particularly for animals (22 phyla recorded), but 35.6% of OTUs
detected via metabarcoding could not be confidently assigned to a taxonomic
group. The smallest size fraction (500-106µm) was the most diverse (more
than two thirds of OTUs). There was little taxonomic overlap between
Virginia and Florida, and samples separated by ~2 m were significantly more
similar than samples separated by ~100 m. Ground-truthing with independent
assessments of taxonomic composition indicated that both presence-absence
and relative abundance information are captured by metabarcoding data,
suggesting considerable potential for ecological studies and environmental
monitoring.