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


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Visualizing amino acid variation in a large BARCODE dataset

In PLoS ONE 2012 e:43992 Kevin Kerr and I reported that most of what appeared to be rare nucleotide and amino acid variants in avian BARCODEs were in fact sequencing errors, based on finding these were strongly concentrated at the ends of the amplified barcode segment. Here I look at the nature of common and rare amino acid substitutions in this same dataset of 11,333 avian BARCODEs from 2,709 species. Do these support our inference that rare variants are mostly errors?  I believe the large figure below says yes.

The more common variants (present in >0.1% sequences) are shown at top and the rare variants (present in <0.1% sequences) at bottom. The left shows variants at each of the 216 amino acid positions, sorted according to the mode amino acid (shown in gray) and grouped by codon 2nd position nucleotide. At right, the proportion of substitutions for each amino acid is shown, weighted according to the modal amino acid frequency.

The main observation is that common variants are relatively few in number (69) and type (mostly isoleucine (I) <–> valine(V)), suggesting strong biological constraints on allowable variation.  On the other hand, rare variants are many (377) and diverse, which is what one would expect if these are largely sequencing errors.

A larger version of the figure is here, and the Excel file used to generate the figure is here.

I think there is potentially more of interest here in terms of allowable substitutions. For example, Breen et al Nature 2012 490:535 recently demonstrated that molecular evolution is highly constrained by epistasis, such that most mutations are not allowed in a given context, which is presumably what underlies the restricted variation in avian COI. (Breen and colleagues calculations were based on alignments of 2 nuclear and 14 organellar genes, the latter including COI.) In a general way this makes sense–birds can have different kinds of feathers but none have scales like fish. It might be of interest to compare COI amino acid variation in birds to other barcode datasets such as fish or lepidoptera.

Happy Thanksgiving!

This entry was posted on Wednesday, November 21st, 2012 at 10:55 pm and is filed under General. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site.

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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.