BARCODE Quality Assessment: Frequency Matrix Approach Mark Y Stoeckle, Rockefeller University Kevin C R Kerr, Royal Ontario Museum PLoS ONE August 2012.

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Presentation transcript:

BARCODE Quality Assessment: Frequency Matrix Approach Mark Y Stoeckle, Rockefeller University Kevin C R Kerr, Royal Ontario Museum PLoS ONE August 2012 e43992

Potential BARCODE errors Taxonomic mislabeling Pseudogenes Sequencing Error

Hypothesis: Sequencing Errors Sequencing Errors = Rare Variants Rare Variants

Avian BARCODEs: large, representative dataset 11K records/2.7K species (27% known)

Most 1 st, 2 nd positions >99.9% conserved

Most aa positions >99.9% conserved

Working definitions for rare variants: VERY LOW FREQUENCY VARIANT (VLF): nt, aa in <0.1% seqs at a given position SINGLETON VLF: in 1 indiv/species SHARED VLF: in ≥2 indiv/species VERY LOW FREQUENCY VARIANT (VLF): nt, aa in <0.1% seqs at a given position SINGLETON VLF: in 1 indiv/species SHARED VLF: in ≥2 indiv/species

Singleton VLFs: (mostly) seq error Shared VLFs: (mostly) biological Concentrated at ends of segment Relatively evenly distributed Spatial distribution of VLFs

Sliding window analysis nVLFs

Calculating Error Rate Most (94%) 2 nd positions >99.9% conserved (Nearly) all 2 nd position seq errors are VLFs nd pos si-nVLFs (probable errors) nd pos/BC x 10,760 BC = 8 x errors/base pair >

Limitations, Observations First seq error assessment for BARCODEs Some singleton nVLFs likely biological—calc rate is upper limit ~3% BARCODEs ≥ 1 error (av 1.7/BARCODE) Seq errors unlikely to affect species ID Increased apparent intraspecific variation

Applications: 1. Compare database quality Error bars =95% CI

2. Highlight BARCODEs w probable errors--annotate? Annotated Homer Simpson Portrait

3. BONUS: cryptic pseudogenes flagged by multiple SHARED VLFs Alder flycatcher (Empidonax alnorum)

Fuscous flycatcher (Cnemotriccus fuscatus) Canada goose (Branta canadensis) Cryptic pseudogenes uncommon: 0.1% BARCODEs

Conclusions Avian BARCODE sequence quality high and improving Frequency matrix potential utility for sequence database QA Caution on studies involving rare variants

Acknowledgments Natural Sciences and Engineering Research Council of Canada Jesse Ausubel Alan BakerJan Lifjeld Arild JohnsenPer Ericson Carla DoveGary Graves Pablo TubaroDario Litjmaer