A UNIQUE IDENTIFIER

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A UNIQUE IDENTIFIER
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A Preliminary Key to Common Shop Fasteners 1a.
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 ...Ph
illips 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 lt0.2 .true
nails 11 10a. Shaft angled, with flat surfaces
H/S _at_ 0.5 ..carpet tack 10b. Shaft
circular in cross section, H/S _at_ 1.7
... thumb tack 11a. Head diameter
slightly greater than shaft, H/S lt 0.1
.finishing nails 12 11b. Head diameter
about twice that of shaft, H/S _at_ 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
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head slot
head shape
shaft
slot
cost
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Will the real DNA barcode please stand up?
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How much? Information content??

• Is there enough information in a single marker??
• YES!!
• Do we necessarily want to use a single marker??
• NO!!!

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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
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Population Aggregation Analysis
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Pure Diagnostics
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1 A A A G A A A A A G A G A G G A A A A 2 A A G
G A A A A A G A A G G A G A A G 3 A G A G A A A
G A A A G A A A G A G G 4 A A G G A A A A A G G
A G G A A A A A 5 A A A G A A A A A G A G A A A
G A A G 6 A G G G A A A G A A G G G G A G A G
G 7 G A A G A A G A A G G G A A G G A A C 8 G G
A G G A G G A A G A A G G G A G C 9 G A A G A A
A A G G G A A A A A G A T 10 G A A G G A G A A G
G G A A G G A A T 11 G G A G A A A G G A A A A G
G G G G C 12 G A A G G A G A A G G G A A G A A A T
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Simple Pure Diagnostic
S, pu (A)
1 A A A G A A A A A G A G A G G A A A A 2 A A G
G A A A A A G A A G G A G A A G 3 A G A G A A A
G A A A G A A A G A G G 4 A A G G A A A A A G G
A G G A A A A A 5 A A A G A A A A A G A G A A A
G A A G 6 A G G G A A A G A A G G G G A G A G
G 7 G A A G A A G A A G G G A A G G A A C 8 G G
A G G A G G A A G A A G G G A G C 9 G A A G A A
A A G G G A A A A A G A T 10 G A A G G A G A A G
G G A A G G A A T 11 G G A G A A A G G A A A A G
G G G G C 12 G A A G G A G A A G G G A A G A A A T
S, pu (G)
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Simple Pure Diagnostic
S, pu (A,G)
1 A A A G A A A A A G A G A G G A A A A 2 A A G
G A A A A A G A A G G A G A A G 3 A G A G A A A
G A A A G A A A G A G G 4 A A G G A A A A A G G
A G G A A A A A 5 A A A G A A A A A G A G A A A
G A A G 6 A G G G A A A G A A G G G G A G A G
G 7 G A A G A A G A A G G G A A G G A A C 8 G G
A G G A G G A A G A A G G G A G C 9 G A A G A A
A A G G G A A A A A G A T 10 G A A G G A G A A G
G G A A G G A A T 11 G G A G A A A G G A A A A G
G G G G C 12 G A A G G A G A A G G G A A G A A A T
S, pu (C,T)
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Some Sleight of Hand Private Attributes Payoff
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Private Attributes
S pr (G)
1 A A A G A A A A A G A G A G G A A A A 2 A A G
G A A A A A G A A G G A G A A G 3 A G A G A A A
G A A A G A A A G A G G 4 A A G G A A A A A G G
A G G A A A A A 5 A A A G A A A A A G A G A A A
G A A G 6 A G G G A A A G A A G G G G A G A G
G 7 G A A G A A G A A G G G A A G G A A C 8 G G
A G G A G G A A G A A G G G A G C 9 G A A G A A
G A G G G A A A A A G A T 10 G A A G G A A A A G
G G A A G G A A T 11 G G A G A A G G G A A A A G
G G G G C 12 G A A G G A G A A G G G A A G A A A T
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C, pu (AA)
1 A A A G A A A A A G A G A G G A A A A 2 A A G
G A A A A A G A A G G A G A A G 3 A G A G A A A
G A A A G A A A G A G G 4 A A G G A A A A A G G
A G G A A A A A 5 A A A G A A A A A G A G A A A
G A A G 6 A G G G A A A G A A G G G G A G A G
G 7 G A A G A A G A A G G G A A G G A A C 8 G G
A G G A A G A A G A A G G G A G C 9 G A A G A A
G A G G G A A A A A G A T 10 G A A G G A A A A G
G G A A G G A A T 11 G G A G A A G G G A A A A G
G G G G C 12 G A A G G A A A A G G G A A G A A A T
C, pu (GA or AG)
Compound Pure Diagnostic
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Something Really Interesting PolymorphicAttribut
es Do To
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Polymorphic Single Attributes
1 A A A G A A A A A G A G A G G A A A A 2 A A G
G A A A A A G A A G G A G A A G 3 A G A G A A A
G A A G G A A A G A G G 4 A A G G A A A A A G A
A G G A A A A A 5 A A A G A A A A A G A G A A A
G A A G 6 A G G G A A A G A A G G A G A G A G
G 7 G A A G A A G A A G G A A A G G A A C 8 G G
A G G A A G A A A G G G G G A G C 9 G A A G A A
G A G G G A A A A A G A T 10 G A A G G A A A A G
G G G A G G A A T 11 G G A G A A G G G A A A A G
G G G G C 12 G A A G G A A A A G G G G A G A A A T
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C, pu (AG / GA)
1 A A A G A A A A A G A G A G G A A A A 2 A A G
G A A A A A G A A G G A G A A G 3 A G A G A A A
G A A G G A A A G A G G 4 A A G G A A A A A G A
A G G A A A A A 5 A A A G A A A A A G A G A A A
G A A G 6 A G G G A A A G A A G G A G A G A G
G 7 G A A G A A G A A G G A A A G G A A C 8 G G
A G G A A G A A A G G G G G A G C 9 G A A G A A
G A G G G A A A A A G A T 10 G A A G G A A A A G
G G G A G G A A T 11 G G A G A A G G G A A A A G
G G G G C 12 G A A G G A A A A G G G G A G A A A T
C, pu (AA/GG)
Compound Pure Diagnostic
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This Matrix Has Four Pure Diagnostics
1 A A A G A A A A A G A G A G G A A A A 2 A A G
G A A A A A G A A G G A G A A G 3 A G A G A A A
G A A G G A A A G A G G 4 A A G G A A A A A G A
A G G A A A A A 5 A A A G A A A A A G A G A A A
G A A G 6 A G G G A A A G A A G G A G A G A G
G 7 G A A G A A G A A G G A A A G G A A C 8 G G
A G G A A G A A A G G G G G A G C 9 G A A G A A
G A G G G A A A A A G A T 10 G A A G G A A A A G
G G G A G G A A T 11 G G A G A A G G G A A A A G
G G G G C 12 G A A G G A A A A G G G G A G A A A 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.
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Caveats Overdiagnose Underdiagnose
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CAOS

• Character
• Character States
• Attribute
• Characters
• Organization System

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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
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• A Barcorder
• How might it work ?

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Old School PCR DROPOFF

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Old School PCR DROPOFF
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Old School PCR DROPOFF
Anchor Primer
No match on 3 end


No Product
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Old School PCR DROPOFF
Anchor Primer


Anchor Primer
Match on 3 end


Product!!
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READ LENGTH 10 TO 26 BP
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• Is it not extraordinary that young taxonomists
  are trained
• like performing monkeys, almost wholly by
  initiation
• 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

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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
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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. Lipscom
b et al., TREE 2003
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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.
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Doyen, J. T. and Slobodchikoff, C. N. (1974) An
operational approach to species classification.
Syst. Zool. 23239-247.
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Type Specimens
Muntiacus rooseveltorum Osgood 1932
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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?
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DNA Barcoding of Leeches
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Will the real DNA barcode please stand up?
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Will the real DNA barcode please stand up?