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    08 Numerical Phenetic

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    josua n
    Numerical phenetics is a methodology used in taxonomy to classify organisms based on overall similarity rather than evolutionary relationships. It uses numerical measures of similarity across multiple characteristics to cluster organisms into taxa. While it introduced objective, computerized analysis, phenetics is limited because similarity does not always indicate evolutionary relationship and different algorithms can produce different trees. It is still used for lower taxonomic levels but has not proven useful for higher-level classification.

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    08 Numerical Phenetic

    Uploaded by

    josua n
    54 views15 pages
    Numerical phenetics is a methodology used in taxonomy to classify organisms based on overall similarity rather than evolutionary relationships. It uses numerical measures of similarity across multiple characteristics to cluster organisms into taxa. While it introduced objective, computerized analysis, phenetics is limited because similarity does not always indicate evolutionary relationship and different algorithms can produce different trees. It is still used for lower taxonomic levels but has not proven useful for higher-level classification.

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    teori fenetik numerik

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    Numerical phenetics is a methodology used in taxonomy to classify organisms based on overall similarity rather than evolutionary relationships. It uses numerical measures of similarity across multiple characteristics to cluster organisms into taxa. While it introduced objective, computerized analysis, phenetics is limited because similarity does not always indicate evolutionary relationship and different algorithms can produce different trees. It is still used for lower taxonomic levels but has not proven useful for higher-level classification.

    Copyright:

    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    54 views15 pages

    08 Numerical Phenetic

    Uploaded by

    josua n
    Numerical phenetics is a methodology used in taxonomy to classify organisms based on overall similarity rather than evolutionary relationships. It uses numerical measures of similarity across multiple characteristics to cluster organisms into taxa. While it introduced objective, computerized analysis, phenetics is limited because similarity does not always indicate evolutionary relationship and different algorithms can produce different trees. It is still used for lower taxonomic levels but has not proven useful for higher-level classification.

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    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    of 15

    Numerical Phenetic

    Approach
    Numerical Phenetics
    • similarity only, not evolution, not phylogeny (1950-1960)
    – computerized, reproducible, “objective,” modern
    – goal to remove all subjectivity, measure everything, use
    matrix of distances
    – sometimes called “Numerical Taxonomy” after book by
    Sokal & Sneath (1963)
    – cluster based on overall similarity
    – the end product of clustering process is a phenogram 
    not a classification or evolutionary trees

     Numerical phenetics is the methodology of assembling


    individuals into taxa on the basis of an estimate of
    unweighted overall similarity
    BIOSIST2010-07
    Phenogram of phenetic classification

    BIOSIST2010-07
    OTU and phenetic criteria
    • OTU (Operational Taxonomic Unit) refers to a very
    heterogeneous class of entities. Some OTUs are
    individuals, some are populations, some are historical
    entities.
    • Phenetic employ four criteria to determine whether or
    not a given classification satisfactorily represents the
    probable relationship of the included taxa :
    1. Closeness to the original similarity matrix
    2. Maximal similarity within the taxa
    3. Maximal predictive value
    4. Stability of classification
    BIOSIST2010-07
    Phenetics - the good
    1. Phenetics deserves credit for having introduced the
    computer into taxonomy
    2. Quite useful in classifying large genera with numerous
    closely related species, all with similar evolutionary
    propensities and hence abundant homoplasy
    3. Sometimes useful when a determination of the
    degree of similarity is the objective
    4. Demanded explicit character analysis & laid
    groundwork for numerical phylogenetics
    5. Still used for lower-level problems (e.g.
    morphometrics, species demarcations) and some
    higher-level problems
    BIOSIST2010-07
    Phenetic Problems and Weakness
    1. Discrepancy between the endeavor to study overall
    similarity and the actual use of a very limited number
    of characters
    2. Reproducible but no agreement on which clustering
    algorithm or statistic to use…
    - different algorithms = different trees
    e.g. UPGMA, PCA… etc.
    - although there is only one true evolutionary
    tree, there are many alternative ‘similarity’
    trees depending on the data & algorithm used
    3. Similarity doesn’t always = evolutionary relationship!
    BIOSIST2010-07
    Weak Points of Phenetic Methods
    1. Practical difficulties
    a. The method is rather laborious and data assembly of a
    complete character matrix for a large number of characters
    and species is forbiddingly time consuming compared with
    some other method
    b. The success of the method in traditional taxonomy depends
    on the availability of a large assortment of variable
    morphological characters
    c. Phenetic classification cannot be improved gradually, because
    any addition of new characters requires a new analysis
    d. Numerical phenetic has failed to make a substantial
    contribution to the classification of any mature group or to
    the classification of haigher taxa

    BIOSIST2010-07
    2. Inability to meet the claims of objectivity and repeatability
    a. Subjectivity
    b. Lack of theoretical justification of choice among clustering methods
    c. Repeatability and choice of computational method
    d. Repeatability and selection characters

    3. Other unsubtantiated assumptions


    a. Possible differences in the importance (weight) of different characters
    must be ignored in the absence of reliable methods for weighting
    b. The amount of unweighted phenetic similarity reflects an equal amount
    of underlying similarity of the genotype and can be safely used for
    ranking
    c. The use of a sufficiently large number of characters makes it
    unnecessary to partition them into similarities due to descent and
    those due to homoplasy
    d. Taxa can be satisfactorily ranked by drawing arbitrary “phenon” lines
    horizontally across a phenogram
    BIOSIST2010-07
    4. Weakness in the theoretical foundation of phenetics
    a. strict empiricism
    b. failure to take mosaic evolution into account
    c. conflict between a desire for complete objectivity and
    awareness of evolution
    d. inability to serve as a heuristic device

    BIOSIST2010-07
    Phenetic Method
    • Similarity coefficients and distances
    – Imagine we are studying two animals A and B , by
    identifying three characters a, b, c. which can be
    given a numerical value
    (For instance leg length; legs may be absent (=0) 0-
    1cm long (=1) 1-2cm long (=2) etc.):
    Character a Character b Character c
    Organism A 1 2 3
    Organism B 2 2 3

    This table is called a character matrix

    BIOSIST2010-07
    • Similarity coefficient S

    for the above matrix

    • Distance coefficient E
    * May be measured, for example by the Euclidean
    distance
    * Where n is the number of characters

    for the above matrix

    BIOSIST2010-07
    • Examples
    Below are reproduced two character matrices based upon fruit
    and toys. The fruit character matrix is worked to show a table of
    distances and a phenogram indicating the pattern of similarities
    between fruits. A phenogram is a table of similarities.
    • Classification of fruit

    BIOSIST2010-07
    BIOSIST2010-07
    Numerical Phenetic Today and in the
    Future
    • Modern applications of phenetics are common in botany,
    and some examples can be found in most issues of the
    journal Systematic Botany. Indeed, due to the effects of
    horizontal gene transfer, polyploid complexes and other
    peculiarities of plant genomics, phenetic techniques in
    botany - though less informative altogether - are also less
    prone to errors compared cladistic analysis of DNA
    sequences.
    • In addition, many of the techniques developed by
    phenetic taxonomists have been adopted and extended
    by community ecologists, due to a similar need to deal
    with large amounts of data.
    BIOSIST2010-07
    Reading sources
    • Jones, S.B. and A.E. Luchsinger. 1987. Plant
    Systematics. 2nd edition. McGraw Hill Book Co.
    Singapore.
    • Mayr, E. and Ashlock. 1991. Principles of
    Systematic Zoology. McGraw Hill, Inc. United
    States. pp 195-205.
    • Ross, H. 1974. Biological Systematic. Addison-
    Wesley Publ. Co., Inc. Philippines.
    • http://homepage.mac.com/wis/Personal/lectur
    es/human-evol/2.html
    BIOSIST2010-07

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