A UNIQUE IDENTIFIER A Preliminary Key to Common Shop Fasteners 1a. Shaft...
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Transcript of A UNIQUE IDENTIFIER A Preliminary Key to Common Shop Fasteners 1a. Shaft...
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
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
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
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
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
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
“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
Geography
Morphology
DNA
Classical Morphological Taxonomy
Crypticism DNA Taxonomy
Geography
Morphology
DNA
No diagnosisOne taxon
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?