A UNIQUE IDENTIFIER

A Preliminary Key to Common Shop Fasteners1a. Shaft threaded…………………………………………………. Screws and their allies 2 1b. Shaft not threaded……………………………………………… Nails and their allies 9

2a. Head without a slot ………………………………………………………….threaded nail

2b. Head with a slot …………………………………………………….....screws and bolts 3

3a. Shaft cylindrical, not tapered, tip truncate ………………………..….……………bolts 4

3b. Shaft tapered, at least at tip, tip pointed ………………………………..…true screws 5

4a. Head flat ……………………………………………………..……………..flat-head bolt

4b. Head rounded ……………………………………………….………….round-head bolt

5a. Slot "X"-shaped …………………………………………………...Phillips head screws 6

5b. Slot linear, a single straight channel …………………………………standard screws 8

6a. Head flat ……………………………………………………………………………………7

6b. Head rounded…………………………………………………………….machine screw

7a. Shaft black …………………………………………………………….…..drywall screw

7b. Shaft silver ………………………………………………….…common Phillips screw

8a. Head rounded ………………………………………….. round-head standard screw

8b. Head flat……………………………………………………...flat-head standard screw

9a. Head diameter much greater than shaft diameter, H/S ratio = 0.3 - 2.0…….tacks 10

9b. Head diameter not much greater than shaft diameter, ratio <0.2 ……….true nails 11

10a. Shaft angled, with flat surfaces; H/S 0.5 ………………………………..carpet tack

10b. Shaft circular in cross section, H/S 1.7 ………………………….…….. thumb tack

11a. Head diameter slightly greater than shaft, H/S < 0.1 ……………….finishing nails 12

11b. Head diameter about twice that of shaft, H/S 0.1 …………….….common nails 13

12a. Total length 50-60 mm……………………………………………..…6d finishing nail

12b. Total length 35-45 mm…………………………………………….….4d finishing nail

13a. Total length 40-50 mm ………………………………………...…..…4d common nail

13b. Total length 60-70 mm…………………………………………….….8d common nail

headslot

shaft headshape

slot

cost

Will the real DNA barcode please stand up?

CharactersDistances

No Tree

Tree

Tree

No Tree

BLAST

How much? Information content??

Is there enough information in a single marker??

YES!!

Do we necessarily want to use a single marker??

NO!!!

Some Numbers

“The survey of just 15 of these nucleotide positions creates the possibility of 415 (1 billion) codes, 100 times the number that would be required to discriminate life if each taxon was uniquely branded.”

Hebert et al., 2002

Population Aggregation Analysis

Pure Diagnostics

1 A A A G A A A A A G A G A G G A A A A2 A A G G A A A A A G A A G G A G A A G3 A G A G A A A G A A A G A A A G A G G4 A A G G A A A A A G G A G G A A A A A5 A A A G A A A A A G A G A A A G A A G6 A G G G A A A G A A G G G G A G A G G7 G A A G A A G A A G G G A A G G A A C8 G G A G G A G G A A G A A G G G A G C9 G A A G A A A A G G G A A A A A G A T10 G A A G G A G A A G G G A A G G A A T11 G G A G A A A G G A A A A G G G G G C12 G A A G G A G A A G G G A A G A A A T

1 A A A G A A A A A G A G A G G A A A A2 A A G G A A A A A G A A G G A G A A G3 A G A G A A A G A A A G A A A G A G G4 A A G G A A A A A G G A G G A A A A A5 A A A G A A A A A G A G A A A G A A G6 A G G G A A A G A A G G G G A G A G G7 G A A G A A G A A G G G A A G G A A C8 G G A G G A G G A A G A A G G G A G C9 G A A G A A A A G G G A A A A A G A T10 G A A G G A G A A G G G A A G G A A T11 G G A G A A A G G A A A A G G G G G C12 G A A G G A G A A G G G A A G A A A T

S, pu (A)

S, pu (G)

Simple Pure Diagnostic

S, pu (A,G)

S, pu (C,T)

1 A A A G A A A A A G A G A G G A A A A2 A A G G A A A A A G A A G G A G A A G3 A G A G A A A G A A A G A A A G A G G4 A A G G A A A A A G G A G G A A A A A5 A A A G A A A A A G A G A A A G A A G6 A G G G A A A G A A G G G G A G A G G7 G A A G A A G A A G G G A A G G A A C8 G G A G G A G G A A G A A G G G A G C9 G A A G A A A A G G G A A A A A G A T10 G A A G G A G A A G G G A A G G A A T11 G G A G A A A G G A A A A G G G G G C12 G A A G G A G A A G G G A A G A A A T

Simple Pure Diagnostic

Some Sleight of Hand: Private Attributes Payoff

S pr (G)Private Attributes

1 A A A G A A A A A G A G A G G A A A A2 A A G G A A A A A G A A G G A G A A G3 A G A G A A A G A A A G A A A G A G G4 A A G G A A A A A G G A G G A A A A A5 A A A G A A A A A G A G A A A G A A G6 A G G G A A A G A A G G G G A G A G G7 G A A G A A G A A G G G A A G G A A C8 G G A G G A G G A A G A A G G G A G C9 G A A G A A G A G G G A A A A A G A T10 G A A G G A A A A G G G A A G G A A T11 G G A G A A G G G A A A A G G G G G C12 G A A G G A G A A G G G A A G A A A T

C, pu (AA)

C, pu (GA or AG)

Compound Pure Diagnostic

1 A A A G A A A A A G A G A G G A A A A2 A A G G A A A A A G A A G G A G A A G3 A G A G A A A G A A A G A A A G A G G4 A A G G A A A A A G G A G G A A A A A5 A A A G A A A A A G A G A A A G A A G6 A G G G A A A G A A G G G G A G A G G7 G A A G A A G A A G G G A A G G A A C8 G G A G G A A G A A G A A G G G A G C9 G A A G A A G A G G G A A A A A G A T10 G A A G G A A A A G G G A A G G A A T11 G G A G A A G G G A A A A G G G G G C12 G A A G G A A A A G G G A A G A A A T

Something Really Interesting: PolymorphicAttributes Do To

Polymorphic Single Attributes

1 A A A G A A A A A G A G A G G A A A A2 A A G G A A A A A G A A G G A G A A G3 A G A G A A A G A A G G A A A G A G G4 A A G G A A A A A G A A G G A A A A A5 A A A G A A A A A G A G A A A G A A G6 A G G G A A A G A A G G A G A G A G G7 G A A G A A G A A G G A A A G G A A C8 G G A G G A A G A A A G G G G G A G C9 G A A G A A G A G G G A A A A A G A T10 G A A G G A A A A G G G G A G G A A T11 G G A G A A G G G A A A A G G G G G C12 G A A G G A A A A G G G G A G A A A T

C, pu (AG / GA)

C, pu (AA/GG)

Compound Pure Diagnostic

1 A A A G A A A A A G A G A G G A A A A2 A A G G A A A A A G A A G G A G A A G3 A G A G A A A G A A G G A A A G A G G4 A A G G A A A A A G A A G G A A A A A5 A A A G A A A A A G A G A A A G A A G6 A G G G A A A G A A G G A G A G A G G7 G A A G A A G A A G G A A A G G A A C8 G G A G G A A G A A A G G G G G A G C9 G A A G A A G A G G G A A A A A G A T10 G A A G G A A A A G G G G A G G A A T11 G G A G A A G G G A A A A G G G G G C12 G A A G G A A A A G G G G A G A A A T

This Matrix Has Four “Pure Diagnostics”

When the matrix is randomized by shuffling individualsand then making a population subdivision in the middle of thematrix 100 times, only 3 times pure diagnostics are found.

1 A A A G A A A A A G A G A G G A A A A2 A A G G A A A A A G A A G G A G A A G3 A G A G A A A G A A G G A A A G A G G4 A A G G A A A A A G A A G G A A A A A5 A A A G A A A A A G A G A A A G A A G6 A G G G A A A G A A G G A G A G A G G7 G A A G A A G A A G G A A A G G A A C8 G G A G G A A G A A A G G G G G A G C9 G A A G A A G A G G G A A A A A G A T10 G A A G G A A A A G G G G A G G A A T11 G G A G A A G G G A A A A G G G G G C12 G A A G G A A A A G G G G A G A A A T

CaveatsOverdiagnoseUnderdiagnose

CAOS

• Character– Character States

• Attribute– Characters

• Organization System

DOES THIS WORK ON REAL DATA???

In an analysis of two potential sturgeonentities using cytB

700 bp sequenced for over 150 individualsfrom geographically diverse locations

Between these two entities there were 36 variablesites

These variable sites resulted in

exactly 3 simple pure sitesexactly 15 simple private sitesexactly 7 compound pure “sites” compound pure diagnostics from polymorphics not assessed

A Barcorder

How might it work ?

Old SchoolPCR DROPOFF

*

Old SchoolPCR DROPOFF

**

Anchor Primer

Old SchoolPCR DROPOFF

**

Anchor Primer

No Product

No match on 3’ end

Old SchoolPCR DROPOFF

**

Anchor Primer

**

Anchor Primer

Product!!

Match on 3’ end

READ LENGTH 10 TO 26 BP

“Is it not extraordinary that young taxonomists are trainedlike performing monkeys, almost wholly by initiation…” A. J. Cain

“There are authorities who maintain that one should not think too much about taxonomy but just do it. I have been doing it for many years, but like the would bephilosopher who was thwarted by having cheerfulness break in, I have found thought breaking in.”

G. G. Simpson

Maintaining Credibility Amongst Taxonomic Community

Recognizing the intellectual content of taxonomy

Demonstrating the utility of DNA barcoding in classical taxonomy problems

Integrating DNA barcoding approaches withclassical taxonomy and taxonomic methods

Recognizing the intellectual content of taxonomy

“We feel that a DNA-based taxonomy along the suggested lines would catastrophically retard taxonomic activity.”Seberg et al., TREE 2003

“The first priority must be to know the organisms, to understand their features and to be able to identify a taxon visually using keys.”Dunn, TREE 2003

“DNA taxonomy seems not to understand the peerless intellectual content based on available informationor the hypothesis driven nature of modern revisionarywork.”Lipscomb et al., TREE 2003

There is an intellectual content in taxonomy and this must be recognized by DNA barcoding.

What is it?

It is a highly hypothetico-deductive process

Corroboration

Hypotheses of species units are made and then tested with available data; most preferably characters.

Diagnosis is most often used as the yardstick of taxonomyie. Taxonomic keys.

Doyen, J. T. and Slobodchikoff, C. N. (1974) An operational approach to species classification. Syst. Zool. 23:239-247.

Geography Morphology

DNA

Reproduction

Ecology

Geography

Morphology

DNA

Geography

Morphology

DNA

Classical Morphological Taxonomy

Crypticism DNA Taxonomy

Geography

Morphology

DNA

No diagnosisOne taxon

Type specimen sequence

Muntiacus rooseveltorum Osgood 1932

Type Specimens

Will the real European Medicinal Leech please stand up?!

Hirudo medicinalis-used for ~2 centuries in bloodletting-approved in 2004 by US FDA as medical device-20 yr record in post-operative haematoma treatment-EST library development in France and CA-whole genome already under way

But what if all of this is being done with the wrong species?

DNA Barcoding of Leeches

traditional collectionmethod

Will the real DNA barcode please stand up?

Will the real DNA barcode please stand up?