Taxonomic Research

DRAFT

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The cycle that includes character discernment and further inductive reasoning certainly needs further work.

It is particular to discipline and methodology.

Background

Steps, Methods, & Process

There is no one path in Taxanomic Research. Generally research involves a number of goals conflated into a single programme (e.g. classification and phylogeny).

α-Taxonomy

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Pinch Points in Alpha taxonomy

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From Edit, the main bottlenecks identified (in alpha taxonomy) were:
1) Gathering type specimens
2) Gathering literature
3) Entering label data
4) Preparing illustrations
5) Preparing plates

Alpha taxonomy quickstart

making comparisons with a type
  • gather specimens
    • from other collections (means for remote examination?)
      • loan material where required or
      • travel to view material that cannot be leant

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  • "Sorting" (tools?)
    • Examination
      • first order examination

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Goal


alpha.gif

* sort
      • examine again in detail
      • measure and record
    • re-sort and examine
    • repeat until there is a taxonomic concept
  • test concept
    • further analysis

  • repeat Research_linear_process._alpha_taxonom_inductive_1.31.gif

Research process.

  • Data collection
  • Data management
  • Data visualisation
  • Data analysis
  • Hypothesis development/conclusion
  • Special cases
    • Morphological data
    • Molecular data
    • Spatial data
    • Taxon Profile data

Below is Bernard Pfeil's view on the elements inside the black box that is taxonomic research. It typifies the idiosyncratic nature of all research. As an entirety (with current tools), there is little prospect of massive productivity gains through the streamlining of these processes except where they are trivial. They critically rely on the judgement and cumulative experience of the researcher (alpha-taxonomists).

However, this diagram is a very good basis on which we might proceed. I think its a very good start towards filling in the hard bits of the taxonomic assessment

Of course there will be many different "pipelines". I think I can do pipelines for other parts of the process...

If (for sake of argument) we captured these pipelines for different researchers:-
  • by interview (as we are currently doing in an informal way) or
  • by survey

Research by Goal

Tools
  • Nomenclature?

we could align common elements in the process and maybe identify places where we can best put our efforts. It is highly likely that we can identify tools which augment taxonomic research removing some of the hard grist.

DNA barcoding can be added to this diagram.

Provisionally:-

Collect material-> Extract DNA-> Barcode-> Signal as to liklihood of new species-> feed into alpha-taxonomic assessment.

Analysis methods

Analysis:- (many opportunities for informatics)
  • DNA
  • phylogenetic
  • chemical
  • anatomical
    • microscopy
    • morphometrics
    • SEM
    • TEM
  • others....

Tools

  • Nomenclature, taxon databases
  • Specimen databases / sample (LIMS)
  • Analytic, molecular, phylogenetic, tools
  • Interactive identification tools
  • Descriptive data management
  • Multimedia management

Software

  • Examination
    • Maclade
    • MESQUITE
  • Specimen access
    • Collections Databases
    • image banks
    • online
  • Communication
  • Image processing
  • Descriptive,
    • keys
      • DELTA
      • intkey
      • LUCID

  • Phylogenetic,
    • Henning86
    • PAUP
    • WinClada?
  • Geographical
    • ESRI
      • Arc Explorer
      • Arc View

  • Audio
    • Some quick (fragmentary) notes

      http://linguistlist.org/emeld/school/classroom/audio/howto.html

      http://linguistlist.org/emeld/school/classroom/audio/index.html


      Format for long term storage
      * mp3. sampling loss.
      * wav. best format? (no loss, open, transparent, multivendor).

      Metadata & Best Practices document....

      http://www.dlib.indiana.edu/projects/sounddirections/papersPresent/sd_bp_07.pdf

  • Analysis
    • Statistics
      • SPSS
      • R
      • Systat
      • Matlab
      • BUGS
      • Systat

  • Literature Searches
    • Endnote / bibtex / refer
    • online databases

Add your Comments here

 

Consultations

Bernard Pfeil's research path.

taxonomy_pipeline.gif Tools.

Research ANWC style

Tissue samples

Researchers want tissue samples for genetic analysis. This involves using the database to locate the specimens (regnos) of the species of interest which actually have samples of the appropriate tissues - we are analysing this process at the moment with the aim of putting an administrative system together to streamline the process for the Director and Collection Manager.

A vexatious issue for the ANWC is the organisation of samples in the freezer; until recently, they were stored chronologically and not by species. Of course, when people want to look at tissues, they want to do it by species. This creates a headache for the Collection Manager who has to go all over the place to get the samples. Location in the freezer is a crucial data item in the database. Moving everything around would take ages, require scrupulous changes in the database - which would inevitably entail data entry error and therefore "loss" of some samples, and may not solve the problem anyway, because how do you know how much space to leave for each species? Some solution for this would be nice, but I'm not sure how relevant this is. Brilliant ideas gratefully accepted.

Molecular data

The results of molecular analysis do not go into the ANWC database. Sequences go to GENBANK, presumably, but the recording of accession number is not mandatory. However, there is no tracking of who has done what and with which and to whom, or what works and what doesn't. I am not sure of the relevance of this to the ANWC database, and would like to sort this out so I know how to cater (or not to cater) for the information in the database.

We do have a loans system (also in process of analysis to put together one more convenient for the Collection Director and Manager), so we know to whom we have given tissue samples, as well as tracking specimen loans and exchanges.

Taxonomic character data

Researchers spend hours measuring birds from beak to tail and everything in between, peering at jawbones, fur/feather colours, counting numbers of scales etc. They write these measurements down on bits of paper, publish a summary of their findings and throw the bits of paper - the raw taxonomic character data - away, so the next time someone wants to do the same thing they have to come in and measure all over again. This is daft in terms of wear and tear on the specimens and reinvention of wheels.

We need protocols which state something like: yes, you can come in and measure our specimens, HOWEVER, in return, we want an electronic record of the character states by registration number. I can see a simple IT solution in the form of a PDA, with something as uncomplicated as Pocket Excel, which we can make available to researchers to record the data at the bench top. They could leave with their data already in electronic form and we would have a copy immediately, ready to be loaded into the database.

-- MargaretC - 06 Jul 2008
 
-- GarryJolleyRogers - 22 Jul 2008

Things which take time

  • gathering specimens (type and non type) for comparison

Research Tools

Resource lists Main.HubRISLinks#Research

More Resources

Species/ Taxa - delimitation

Bond, J. E. & Stockman A. K. (2008) "An Integrative Method for Delimiting Cohesion Species: Finding the Population-Species Interface in a Group of Californian Trapdoor Spiders with Extreme Genetic Divergence and Geographic Structuring" Systematic Biology, Volume 57, Issue 4 August 2008 , pages 628 - 646

Doyen, J.T. and Slobodchikoff, C.N. 1974. An operational approach to species classification. Systematic Zoology 23: 239-247.

Sites, J. W. and Marshall, J. C. (2004) Empirical criteria for delimiting species. Ann. Rev. Ecol. Evol. Syst. 35 , pp. 199-227.

Maddison, W. P. and Maddison, D. R. (2007) Mesquite: A modular system for evolutionary analysis. — Version 2.0. http://mesquiteproject.org.

Rambaut, A. and Drummond, A. (2005) Tracer, A program for analyzing results from Bayesian MCMC programs such as BEAST & MrBayes?. — Version 1.3. Oxford, UK. Available at http://evolve.zoo.ox.ac.uk/software.html?id=tracer (last accessed 12 February 2006).

Zwickl, D. J. (2006) — Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum-likelihood criterion. PhD? dissertation, the University of Texas at Austin.

Swofford, D. L. (2002) — PAUP*: Phylogenetic analysis using parsimony (*and other methods). Version 4.0b8a. Sinauer Associates, Sunderland, Massachusetts.

Sites, J. W. Jr & Marshall J. C. (2003) "Delimiting species: a Renaissance issue in systematic biology" Trends in Ecology & Evolution Volume 18, Issue 9, September 2003, Pages 462-470 Sites, J. W. Jr & Marshall J. C. (2003) "Delimiting species: a Renaissance issue in systematic biology" Trends in Ecology & Evolution Volume 18, Issue 9, September 2003, Pages 462-470

Winston, J.E. 1999. Describing species: parctical taxonomic procedure for biologists. New York: Columbia University Press, 518 pp. ISBN 0 231 06824 7.

Bibliography

Wu D, Hartman A, Ward N, Eisen JA (2008) An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP). PLoS? ONE 3(7): e2566. doi:10.1371/journal.pone.0002566 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0002566#s4

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