Rockefeller University

Program for the Human Environment

The Barcode Blog

A mostly scientific blog about short DNA sequences for species identification and discovery. I encourage your commentary. -- Mark Stoeckle

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Sponge barcoding on the web

The Sponge Barcoding Project https://www.spongebarcoding.org/ aims to barcode all described sponges, about 8,000 species in the phylum Porifera. The initial phase of 3 years will focus on 2,000 species covering all genera.

Sponges are thought to be the earliest living branch on the multicellular animal tree and are difficult even for experts to identify. In addition to their ecological importance, sponges are sources for novel pharmaceuticals and biomaterials (eg Sipkema et al 2005 Biotech Bioengineer 90:201).

Like some corals, some sponges show very few differences in mitochondrial DNA with the standard COI barcode (corals, Shearer et al 2002 Mol Ecol 11: 2475; sponges, Erpenbeck et al 2006 Mol Ecol Notes 6: 550). The latter study suggests that the 3′ end of COI may provide greater resolution for Porifera and Cnidaria. An important goal of the initial phase of the project is to determine the best strategy for obtaining species-level identifications, one that provides sufficient resolution to separate most of the closely-related species and still takes advantage as much as possible of the benefits of standardization on 5′ COI.

I note that in animals closely related sister species are often largely or completely allopatric. In such cases, combining genetic barcode data with GIS coordinates may improve the certainty of some identifications.

For fun, I close with a sponge video:

 

 

 

This entry was posted on Thursday, October 26th, 2006 at 12:05 am and is filed under General. You can follow any responses to this entry through the RSS 2.0 feed. Both comments and pings are currently closed.

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Contact: mark.stoeckle@rockefeller.edu

About this site

This web site is an outgrowth of the Taxonomy, DNA, and Barcode of Life meeting held at Banbury Center, Cold Spring Harbor Laboratory, September 9-12, 2003. It is designed and managed by Mark Stoeckle, Perrin Meyer, and Jason Yung at the Program for the Human Environment (PHE) at The Rockefeller University.

About the Program for the Human Environment

The involvement of the Program for the Human Environment in DNA barcoding dates to Jesse Ausubel's attendance in February 2002 at a conference in Nova Scotia organized by the Canadian Center for Marine Biodiversity. At the conference, Paul Hebert presented for the first time his concept of large-scale DNA barcoding for species identification. Impressed by the potential for this technology to address difficult challenges in the Census of Marine Life, Jesse agreed with Paul on encouraging a conference to explore the contribution taxonomy and DNA could make to the Census as well as other large-scale terrestrial efforts. In his capacity as a Program Director of the Sloan Foundation, Jesse turned to the Banbury Conference Center of Cold Spring Harbor Laboratory, whose leader Jan Witkowski prepared a strong proposal to explore both the scientific reliability of barcoding and the processes that might bring it to broad application. Concurrently, PHE researcher Mark Stoeckle began to work with the Hebert lab on analytic studies of barcoding in birds. Our involvement in barcoding now takes 3 forms: assisting the organizational development of the Consortium for the Barcode of Life and the Barcode of Life Initiative; contributing to the scientific development of the field, especially by studies in birds, and contributing to public understanding of the science and technology of barcoding and its applications through improved visualization techniques and preparation of brochures and other broadly accessible means, including this website. While the Sloan Foundation continues to support CBOL through a grant to the Smithsonian Institution, it does not provide financial support for barcoding research itself or support to the PHE for its research in this field.