A UNIQUE IDENTIFIER
A Preliminary Key to Common Shop Fasteners
1a. Shaft threaded…………………………………………………. Screws and their allies 2 1b. Shaft not
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
head
slot
shaft
head
shape
slot
cost
Will the real DNA barcode please stand up?
No Tree
Characters
Distances
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
2
3
4
5
6
7
8
9
10
11
12
A
A
A
A
A
A
G
G
G
G
G
G
A
A
G
A
A
G
A
G
A
A
G
A
A
G
A
G
A
G
A
A
A
A
A
A
G
G
G
G
G
G
G
G
G
G
G
G
A
A
A
A
A
A
A
G
A
G
A
G
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
G
G
A
G
A
G
A
A
G
A
A
G
A
G
A
A
G
A
A
A
A
A
A
A
A
A
G
A
G
A
G
G
A
G
G
A
G
A
G
G
A
G
A
A
A
G
A
G
G
G
G
G
A
G
G
A
G
A
G
G
G
A
A
G
A
G
A
G
A
G
A
G
A
A
A
A
A
A
G
G
A
G
A
G
A
G
A
A
G
A
G
A
A
A
A
A
G
G
A
G
G
G
A
G
G
A
G
G
G
G
A
G
G
A
A
A
A
A
A
A
A
A
G
A
G
A
A
A
G
A
A
G
A
G
A
A
G
A
A
G
G
A
G
G
C
C
T
T
C
T
Simple Pure Diagnostic
S, pu (A)
1
2
3
4
5
6
7
8
9
10
11
12
A
A
A
A
A
A
G
G
G
G
G
G
A
A
G
A
A
G
A
G
A
A
G
A
S, pu (G)
A
G
A
G
A
G
A
A
A
A
A
A
G
G
G
G
G
G
G
G
G
G
G
G
A
A
A
A
A
A
A
G
A
G
A
G
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
G
G
A
G
A
G
A
A
G
A
A
G
A
G
A
A
G
A
A
A
A
A
A
A
A
A
G
A
G
A
G
G
A
G
G
A
G
A
G
G
A
G
A
A
A
G
A
G
G
G
G
G
A
G
G
A
G
A
G
G
G
A
A
G
A
G
A
G
A
G
A
G
A
A
A
A
A
A
G
G
A
G
A
G
A
G
A
A
G
A
G
A
A
A
A
A
G
G
A
G
G
G
A
G
G
A
G
G
G
G
A
G
G
A
A
A
A
A
A
A
A
A
G
A
G
A
A
A
G
A
A
G
A
G
A
A
G
A
A
G
G
A
G
G
C
C
T
T
C
T
Simple Pure Diagnostic
1
2
3
4
5
6
7
8
9
10
11
12
A
A
A
A
A
A
G
G
G
G
G
G
A
A
G
A
A
G
A
G
A
A
G
A
A
G
A
G
A
G
A
A
A
A
A
A
G
G
G
G
G
G
G
G
G
G
G
G
A
A
A
A
A
A
A
G
A
G
A
G
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
G
G
A
G
A
G
A
A
G
A
A
G
A
G
A
A
G
A
A
A
A
A
A
A
A
A
G
A
G
A
G
G
A
G
G
A
G
A
G
G
A
G
A
A
A
G
A
G
G
G
G
G
A
G
G
A
G
A
G
G
G
A
A
G
A
G
A
G
A
G
A
G
A
A
A
A
A
A
S, pu (A,G)
G
G
A
G
A
G
A
G
A
A
G
A
G
A
A
A
A
A
G
G
A
G
G
G
A
G
G
A
G
G
G
G
A
G
G
A
A
A
A
A
A
A
A
A
G
A
G
A
A
A
G
A
A
G
A
G
A
A
G
A
A
G
G
A
G
G
C
C
T
T
C
T
S, pu (C,T)
Some Sleight of Hand: Private Attributes Payoff
S pr (G)
1
2
3
4
5
6
7
8
9
10
11
12
A
A
A
A
A
A
G
G
G
G
G
G
A
A
G
A
A
G
A
G
A
A
G
A
A
G
A
G
A
G
A
A
A
A
A
A
G
G
G
G
G
G
G
G
G
G
G
G
A
A
A
A
A
A
A
G
A
G
A
G
Private Attributes
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
G
G
G
A
G
G
A
A
G
A
A
G
A
G
A
A
G
A
A
A
A
A
A
A
A
A
G
A
G
A
G
G
A
G
G
A
G
A
G
G
A
G
A
A
A
G
A
G
G
G
G
G
A
G
G
A
G
A
G
G
G
A
A
G
A
G
A
G
A
G
A
G
A
A
A
A
A
A
G
G
A
G
A
G
A
G
A
A
G
A
G
A
A
A
A
A
G
G
A
G
G
G
A
G
G
A
G
G
G
G
A
G
G
A
A
A
A
A
A
A
A
A
G
A
G
A
A
A
G
A
A
G
A
G
A
A
G
A
A
G
G
A
G
G
C
C
T
T
C
T
C, pu (AA)
1
2
3
4
5
6
7
8
9
10
11
12
A
A
A
A
A
A
G
G
G
G
G
G
A
A
G
A
A
G
A
G
A
A
G
A
A
G
A
G
A
G
A
A
A
A
A
A
G
G
G
G
G
G
G
G
G
G
G
G
A
A
A
A
A
A
A
G
A
G
A
G
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
G
A
G
A
G
A
A
A
G
A
A
G
A
G
A
A
G
A
A
A
A
A
A
A
A
A
G
A
G
A
G
G
A
G
G
A
G
A
G
G
A
G
A
A
A
G
A
G
G
G
G
G
A
G
G
A
G
A
G
G
G
A
A
G
A
G
A
G
A
G
A
G
A
A
A
A
A
A
G
G
A
G
A
G
A
G
A
A
G
A
G
A
A
A
A
A
G
G
A
G
G
G
C, pu (GA or AG)
Compound Pure Diagnostic
A
G
G
A
G
G
G
G
A
G
G
A
A
A
A
A
A
A
A
A
G
A
G
A
A
A
G
A
A
G
A
G
A
A
G
A
A
G
G
A
G
G
C
C
T
T
C
T
Something Really Interesting: PolymorphicAttributes Do To
Polymorphic Single Attributes
1
2
3
4
5
6
7
8
9
10
11
12
A
A
A
A
A
A
G
G
G
G
G
G
A
A
G
A
A
G
A
G
A
A
G
A
A
G
A
G
A
G
A
A
A
A
A
A
G
G
G
G
G
G
G
G
G
G
G
G
A
A
A
A
A
A
A
G
A
G
A
G
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
G
A
G
A
G
A
A
A
G
A
A
G
A
G
A
A
G
A
A
A
A
A
A
A
A
A
G
A
G
A
G
G
A
G
G
A
G
A
G
G
A
G
A
A
G
A
A
G
G
A
G
G
A
G
G
A
G
A
G
G
A
G
A
G
A
G
A
G
A
G
A
A
A
G
A
G
A
G
G
G
A
G
A
G
A
G
A
A
G
A
G
A
A
A
A
A
G
G
A
G
G
G
A
G
G
A
G
G
G
G
A
G
G
A
A
A
A
A
A
A
A
A
G
A
G
A
A
A
G
A
A
G
A
G
A
A
G
A
A
G
G
A
G
G
C
C
T
T
C
T
C, pu (AG / GA)
1
2
3
4
5
6
7
8
9
10
11
12
A
A
A
A
A
A
G
G
G
G
G
G
A
A
G
A
A
G
A
G
A
A
G
A
A
G
A
G
A
G
A
A
A
A
A
A
G
G
G
G
G
G
G
G
G
G
G
G
A
A
A
A
A
A
A
G
A
G
A
G
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
G
A
G
A
G
A
A
A
G
A
A
G
A
G
A
A
G
A
A
A
A
A
A
A
A
A
G
A
G
A
G
G
A
G
G
A
G
A
G
G
A
G
A
A
G
A
A
G
G
A
G
G
A
G
G
A
G
A
G
G
A
G
A
G
A
G
A
G
A
G
A
A
A
G
A
G
A
G
G
G
A
G
A
G
A
G
A
A
G
A
G
A
A
A
A
A
G
G
A
G
G
G
A
G
G
A
G
G
G
G
A
G
G
A
C, pu (AA/GG)
Compound Pure Diagnostic
A
A
A
A
A
A
A
A
G
A
G
A
A
A
G
A
A
G
A
G
A
A
G
A
A
G
G
A
G
G
C
C
T
T
C
T
This Matrix Has Four “Pure Diagnostics”
1
2
3
4
5
6
7
8
9
10
11
12
A
A
A
A
A
A
G
G
G
G
G
G
A
A
G
A
A
G
A
G
A
A
G
A
A
G
A
G
A
G
A
A
A
A
A
A
G
G
G
G
G
G
G
G
G
G
G
G
A
A
A
A
A
A
A
G
A
G
A
G
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
G
A
G
A
G
A
A
A
G
A
A
G
A
G
A
A
G
A
A
A
A
A
A
A
A
A
G
A
G
A
G
G
A
G
G
A
G
A
G
G
A
G
A
A
G
A
A
G
G
A
G
G
A
G
G
A
G
A
G
G
A
G
A
G
A
G
A
G
A
G
A
A
A
G
A
G
A
G
G
G
A
G
A
G
A
G
A
A
G
A
G
A
A
A
A
A
G
G
A
G
G
G
A
G
G
A
G
G
G
G
A
G
G
A
A
A
A
A
A
A
A
A
G
A
G
A
A
A
G
A
A
G
A
G
A
A
G
A
A
G
G
A
G
G
C
C
T
T
C
T
When the matrix is randomized by shuffling individuals
and then making a population subdivision in the middle of the
matrix 100 times, only 3 times pure diagnostics are found.
Caveats
Overdiagnose
Underdiagnose
CAOS
• Character
– Character States
• Attribute
– Characters
• Organization System
DOES THIS WORK ON REAL DATA???
In an analysis of two potential sturgeon
entities using cytB
700 bp sequenced for over 150 individuals
from geographically diverse locations
Between these two entities there were 36 variable
sites
These variable sites resulted in
exactly 3 simple pure sites
exactly 15 simple private sites
exactly 7 compound pure “sites”
compound pure diagnostics from polymorphics not assessed
A Barcorder
How might it work ?
Old School
PCR DROPOFF
*
Old School
PCR DROPOFF
Anchor Primer
*
*
Old School
PCR DROPOFF
No match
on 3’ end
*
*
Anchor Primer
No Product
Old School
PCR DROPOFF
Anchor Primer
*
*
Match on
3’ end
Anchor Primer
*
*
Product!!
READ LENGTH 10 TO 26 BP
“Is it not extraordinary that young taxonomists are trained
like 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 be
philosopher 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 with
classical 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 information
or the hypothesis driven nature of modern revisionary
work.”
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 taxonomy
ie. Taxonomic keys.
Doyen, J. T. and Slobodchikoff, C. N. (1974) An operational
approach to species classification. Syst. Zool. 23:239-247.
DNA
Geography
Morphology
Reproduction
Ecology
DNA
Geography
DNA
Geography
Morphology
Classical Morphological
Taxonomy
DNA
Geography
Morphology
Crypticism
DNA Taxonomy
Morphology
No diagnosis
One taxon
Type Specimens
Muntiacus rooseveltorum Osgood 1932
Type
specimen
sequence
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 collection
method
Will the real DNA barcode please stand up?
Will the real DNA barcode please stand up?