The Barcode Blog

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

Subscribe to this blog

Sign up for email notifications

Taxonomy disentanglement

Veneridae, commonly known as venus clams, are the largest family of heterodont bivalves (clams and cockles), with about 500 named species, all marine, distributed in mostly shallow water areas around the globe.  In June 2011 Plos ONE, researchers from Fisheries College, Ocean University of China apply DNA barcodes to perform what they call “taxonomy distentanglement” on 315 venerid specimens representing about 60 species collected along the coast of mainland China. This qualifies as the largest analysis of DNA barcodes for marine bivalves to date. Chen and colleagues note “species boundaries of these clams are difficult or even impossible to define accurately based solely on morphologic features,” so there is a potentially a big role for DNA characters.

The clams were collected over a 6 year period from 2004-2010, stored in 95% ethanol (marine specimens are traditionally stored in formalin, which is an effective preservative but makes it difficult to recover DNA), and deposited as voucher specimens in Fisheries College. DNA was extracted from adductor muscle (some bivalves inherit mitochondrial DNA from both male and female parents, but the male type is restricted to gonadal tissue). Given that not many bivalves have been barcoded, it is of interest to learn what primer pairs were effective (BOLD taxonomy browser lists barcodes for 966 of the approximately 10,000 bivalve species).  Starting with Folmer primers, two additional published sets and 4 sets developed for this study were used if needed, with recovery of COI from all specimens.

I note that genetic differences within Family Veneridae are remarkably large–average pairwise COI K2P distance within the family (not counting conspecific and congeneric comparisons) is around 35% and maximum is over 50%. For comparison, in birds, average and maximum distances within families are about half as large, and even within birds as a whole (Class Aves, i.e., two hierarchical levels above family), average and maximum distances are only 20% and 33%, respectively (I generated bird stats by merging public projects in BOLD and running “Distance Summary.”) I wonder if what we call Families in vertebrates and invertebrates reflect different levels on the evolutionary tree.

Back to the paper. Chen and colleagues used neighbor-joining, maximum-likelihood, and MOTU analysis to examine their data with and without 310 additional venerid sequences downloaded from BOLD/GenBank. All individuals that could be morphologically identified to species possessed distinct (reciprocally monophyletic) COI sequences, with the exception of one species pair. 11/23 sequences from specimens that could not be identified morphologically formed five monophyletic clusters, likely representing species new to science or unreported in China. The remaining 12 sequences from morphologically-puzzling specimens clustered within named species, suggesting these represent morphologically variant specimens. Sorting puzzling specimens into genetic clusters led the authors to recognize previously overlooked diagnostic morphologic characters.  A number of existing records in BOLD/GenBank prior to this study clustered with different species, suggesting these specimens were misidentified by submitters or reflected outdated taxonomy.

Chen and colleagues conclude that DNA barcoding has a third purpose in addition to species identification (assigning unknown specimens to known species) and species discovery (flagging divergent clusters), namely what they call “taxonomy disentanglement,” which other authors have called iterative or integrative use of barcoding (for example Smith et al,  Extreme diversity of tropical parasitoid wasps exposed by iterative integration of natural history, DNA barcoding, morphology, and collections, 2008 PNAS). I like the term “disentanglement”–it brings to mind the many confusions in existing classifications and specimen labels, many of which can be unknotted with DNA barcodes.

This entry was posted on Wednesday, July 13th, 2011 at 5:46 pm 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.

One Response to “Taxonomy disentanglement”

  1. saedul Says:

    I am doing M.phil research work on Bivalve Taxonomy not in that family but my work is on Arcidae family i have identified few specimen for their morphological characters like No.of Ribs, sculpture, Adductor muscle scar, Hinge teeth, Color pattern, periostracum Length, Height etc bt i faced a lot of problem in that family for conformation bc live specimens are very diffult to collect ..Thanks …..


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.