automated barcoding using the characteristic attribute organization system indra neil sarkar, phd...

Automated Barcoding Using theCharacteristic Attribute Organization System

Indra Neil Sarkar, PhDDivisions of Invertebrate Zoology & Library Services

American Museum of Natural History

Consortium for the Barcoding of LifeData Analysis Working Group

Muséum National d’Histoire NaturelleJuly 06, 2006

© 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006

Ambition&

Being BOLD

http://www.jaestudio.com/


Barcoding

• Identify Species– Recall– Precision

• Speed– Simplicity– Consistency


Similarity Based Methods

• BLAST– Database Retrieval

• Clustering Algorithms– Phenetics


Phenetic vs Cladistic

• Tree Topologies Are Often Different!– Which Is Right?– Does it Matter?

• Similarity Methods (Phenetic)– Evolution of Complete Sequences– FAST

• Character Methods (Cladistic)– Evolution of Individual Characters – SLOW


A Character Mindset

MLAT

MLBT

MRBT

MLCTMRCTMRCA

MLATMLBTMRBTMLCTMRCTMRCA


A Character Mindset

MLAT

MLBT

MRBT

MLCTMRCTMRCA

Characters


A Character Mindset

MLAT

MLBT

MRBT

MLCTMRCTMRCA

CharacterStates


CAOS

• Characteristic– Character States

• Attribute– Characters

• Organization System

• Originally Designed as a Character-Based Heuristic for Phylogenetic Classification


CAOS

A

B

C

D


CAOS

Pure (Pu)Private (Pr)

Simple (s)Compound (c)

ALL Members of One Group HaveThe SameCharacter State

SOME Members of One Group HaveThe SameCharacter State

CA’s with single positionCA’s with multiple positions


CAOS Classification

Rule Set

UnclassifiedSequence


Characters vs Vectors

• Characters = Diagnostic– Apomorphies

• Vectors ≠ Diagnostic– Similarity Score

Which approach provides a consistent phylogenetic representation of data?


Mopalia Test Case

• 569bp COI

• 19 In-Group Species

• 116 Individuals (~6/Species)

• What Happens to Classification Accuracy with Limited Sampling (e.g., 50%)?


Entire Dataset

Phenetic 100%

CAOS 100%

AB

Phenetic 59%

CAOS 96%

A B

BA

Phenetic 69%

CAOS 100%


Proceeding BOLDly


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------------------------T------------------------------------------------T------------------------------------------------T------------------------------------------------T------------------------------------------------T------------------------------------------------T------------------------------------------------T------------------------------------------------T------------------------------------------------T------------------------

------------------------A------------------------ ------------------------A------------------------------------------------A------------------------------------------------A------------------------------------------------A------------------------------------------------A------------------------------------------------A------------------------------------------------A------------------------------------------------A------------------------

1 2

------------------------T------------------------------------------------T------------------------------------------------T------------------------------------------------T------------------------------------------------T------------------------------------------------T------------------------------------------------T------------------------------------------------T------------------------------------------------T------------------------

1

------------------------A------------------------------------------------A------------------------------------------------A------------------------------------------------A------------------------------------------------A------------------------------------------------A------------------------------------------------A------------------------------------------------A------------------------------------------------A------------------------

2

T

A


On Being Ambitious...

• Inter- vs. Intra- Species Classification

• Limited Sampling Strategies

• Accuracy at the Cost of Speed


On Being BOLD...

• Diagnostics

• Primers– Drop-Off– PCR– TAQ Assay

• Single Molecular Sequencing Oligos• Diagnostic-Based Query Interface

(In Addition to NJ Interface)


Will the Real DNA Barcode Please Stand Up?Will the Real DNA Barcode Please Stand Up?


Acknowledgments

Rob DeSalleRyan P KellyPaul J PlanetMark Siddall

Al Phillips

MLA Donald A.B. Lindberg Research FellowshipNational Science Foundation (IIS-0241229)

Lewis B. & Dorothy Program for Molecular Systematics


Indra Neil Sarkar, [email protected]

automated barcoding using the characteristic attribute organization system indra neil sarkar, phd...

Documents

phdcbol dawg

characterbased heuristic

phylogenetic classification

automated barcoding

classification accuracy

barcoding of lifedata

mopalia test case569bp

species116 individuals