A UNIQUE IDENTIFIER

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 …………………………………………………...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 = …….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 mm……………………………………………..…6d finishing nail 12b. Total length mm…………………………………………….….4d finishing nail 13a. Total length mm ………………………………………...…..…4d common nail 13b. Total length mm…………………………………………….….8d common nail

head slot shaft head shape slot cost

Will the real DNA barcode please stand up?

Characters Distances No 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 4 15 (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 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

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 (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 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 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 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

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 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

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 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 (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 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

This Matrix Has Four “Pure Diagnostics” 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. 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

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 * * Anchor Primer No Product No match on 3’ end

Old School PCR DROPOFF * * Anchor Primer * * Product!! Match on 3’ end

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:

Geography Morphology DNA Reproduction Ecology

Geography Morphology DNA Geography Morphology DNA Classical Morphological Taxonomy Crypticism DNA Taxonomy Geography Morphology DNA No diagnosis One 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 collection method

Will the real DNA barcode please stand up?