PHENETIC CLASSIFICATION SYSTEMS

I. Some preliminaries

A. Definition of classification
    Process or result (product) of arranging taxa into groups in accordance with a plan and in conformity with a naming system

B. Function/Purpose

• information storage & retrieval
• reflect nature
• easy to use
• stable
• predictive
• concise

C. General Considerations
    Since there are about 250,000 angiosperms, humans have needed to classify and arrange these species in some sort of pigeonholes to be able to store and retrieve information about these species. In order to refer to the groups, they must be named according an accepted system of nomenclature. Thus, there is information content inherent in a name since the name refers to a specific category(s) in the classification system. The Linnean hierarchy of categories include: Kingdom, Division (phylum in zoological circles), Class, Order, Family, Genus species. The mnemonic, 'King David cried "Oh, for goodness sake"' is a good way to remember these categories. Remember that a group at any level is called a taxon (plural - taxa) and that each category has a standard ending (Division - ophyta; Class - opsida; SuperOrder - iflorae; Order - ales; Family - aceae; Subfamily - oideae; genus and species have no standard endings). Theoretically, the classification system is built from the bottom up. In other words, the species is the basic unit of classification and it these are placed in progressively larger and more inclusive pigeonholes.

D. What is a species?
    This is the basic unit of taxonomy and it has been defined in various ways by different botanists. Historically, a species was considered to be an "actual or potentially interbreeding populations reproductively isolated from other such groups". This definition highlights the notion of the "biological species concepts" which is based on reproductive isolation. Although it may be appropriate for animal systems, there are many problems when applying it to plants because plants have a diversity of breeding systems. For example, hybridization and uni-parental reproduction (i.e., selfing) are common and make the biological species concepts less useful for plants. Plant biologists primarily define species as individuals that share morphological, ecological, geographic and other characteristics and are separate evolutionary lineages. This latter notion represents a phylogenetic approach to species.

E. OTU's
    Operational taxonomic units; this is a fancy way of indicating the groups (taxa) being classified. An OTU can refer to any level of the taxonomic hierarchy including individuals of a species, or different species, or different genera, and so on.

F. Philosophy of classification
    Taxa are grouped based on the relationships the taxonomist perceives to exist between the individuals. There are two major types of relationships that exist between individuals:

1. Phenetic relationships - relationship of similarity. In other words, taxa are grouped on the basis of their overall similarity (or dissimilarity) to other individuals. The more features two taxa share, the more likely they will be put in the same group. Taxonomists base their groupings on many characters plants including chemical, morphological, anatomical, physiological, and ecological ones. In other words, any feature, not just morphological ones, can provide information for a classification. Artificial and phenetic (also called 'natural') classifications (see below) are based on phenetic relationships.  
    
2. Phylogenetic (ancestral or evolutionary) relationships - relationship of descent; or in other words, the degree of relatedness to a common ancestor. Evolutionary and cladistic classification systems attempt to reflect phylogenetic relationships.
   
3. Example:  Consider a campus post office with a set of 100 postal boxes in 10 columns of 10 each.  We could set up this system to reflect a variety of relationships between the individuals who obtain their mail.  For example, each column could represent a dorm with each row the room number or floor.  This would be a phenetic type classification.  Alternately, we could set up the system to reflect relationships between the students.  We could perhaps have the columns represent the region of the world the family is from (i.e., Europe, North American, South America, Asia) and each row represent a separate country.  This latter classification would obviously be less useful for delivering mail, but it would tell us about the history of the individuals. 

G.  Conflicts
    Users want functionality vs. different idea of creator

II. Artificial & Mechanical Classification Systems - ancient phenetic systems
    Based on one or a limited number of characters. The characters are selected first, then the OTU's are analyzed and grouped based on the criteria selected. This is referred to as an a priori classification because the criteria are first established, and then the OTU's placed into the system.

    Theophrastus, Greek philosopher (370-285 BC), was one of the first to classify plants. He used habit (i.e., tree, shrub) as the main character and then further subdivided them into cultivated and wild kinds. He was a student of Aristotle and is sometimes called the Founder (politically correct version of "father") of Botany. He was a good botanist - he distinguished between annual, perennial and biennial life cycles; recognized superior vs. inferior ovaries; determinate vs. indeterminate; and distinct vs. connate petals.

    The Herbalists, who came later, classified plants primarily on the basis of their medicinal use. They believed in the Doctrine of Signatures (God gave us an indication of what a plant was good for in its general appearance. Therefore, bloodroot was considered good for disorders of the blood).

    Thus, early classification systems were artificial and based primarily on habit and/or characteristics important to humans (i.e., medicines, food).

    Linnaeus, our friend, also used an artificial system. His system was based on stamen number with secondary groups based on style number.

Artificial & Mechanical classification systems have advantages and disadvantages:

Advantages - artificial classifications are easy to use and reproducible.

Disadvantages - these systems lack any predictive value since they are not concerned about real (biological) relationships between units. Let's use an example from Keil and Walters – assume for that we decide to classify objects based on whether or not they have legs. Using this criteria we would group such unrelated objects as a table, human, ladder, and spider. Botanically speaking, if habit is used as a character, that means we would we separate such obviously similar plants as Red-osier dogwood (Cornus stolonifera) which is a shrub, and bunchberry (Cornus canadensis) which is an herb. Similarly, we would group obviously dissimilar plants such as Magnolia and Rosa if we used stamen number as a character since both have numerous stamens.

    The de Jussieu's (French; published Genera Plantarum) grouped plants on overall similarity. So did the de Candolle's (Swiss; published Prodromous Systematis Naturalis Regni Vegetabilis). Hooker and Bentham (British, Kew Gardens; Genera Plantarum) also prepared a well-respected natural system.

    Remember, these classifications were essentially "Pre-Darwinian". The prevailing paradigm of the time was that species were fixed. Hence, biologists assumed that these phenetic classification systems would be a perfect way to organize and catalog biological diversity. However, once evolutionary ideas arrived, natural and phenetic classifications were largely abandoned for phylogenetic (phyletic) ones. That is, until phenetics was resurrected by the computer.

IV. Numerical Taxonomy - computerized phenetic systems

A. General.
    The advent of computers allowed numerical taxonomists to study large data sets and determine the similarity of the OTU's in a critical, unbiased manner. Sokal and Sneath helped to popularize numerical taxonomy. In essence, the computer calculates the similarity for every pair of OTU's and then plots a dendrogram (based on a cluster analysis) that shows the similarity between the OTU's. Three important assumptions/principles underlying this classification system are:

1. the greater the amount of information for a taxon, the greater the strength of the classification
2. Every character gets equal weighting
3. classification is based on overall similarities in the OTU's.

B.  Method.  In a numerical study:

1. select taxa
2. select characters 
3. estimate similarity.  In performing the analysis:  don't weight characters, throw out meaningless ones (i.e., number of leaves on a tree), throw out invariant ones (i.e., all members have)
4. create dendrogram (groups constructed).  Computer programs such as NTSYS and other clustering programs (e.g., Clustering Calculator by John Brzustowski, University of Alberta) are used for these analyses
5. interpret results (i.e., does it represent evolution?)

C. Advantages

1. reproducible
2. greater predictive value than other phenetic classifications
3. objective and free from bias
4. integrate data from many sources
5. can handle large amounts of data

D. Disadvantages

1. doesn't readily account for evolutionary change (vertical change);
2. convergent evolution - two species exposed to same selection pressures share similar features. For example, "cacti-like" plants live in deserts. These "cacti" belong to various families including Asclepiadaceae, Euphorbiaceae, Asteraceae and Cactaceae, to name just a few. For example, true Cactaceae only occur in the western hemisphere. In other words, not all species that look alike are necessarily members of the same group.

E. End  Product
    A numerical classification produces a dendrogram that reflects the similarity of the OTU's. Remember that when reading a dendrogram, it is not supposed to indicate phylogeny (ancestry), just similarity. Some taxonomists believe, often with good reason, that species that are more similar are more likely to be closely related than those that look different.  For a nice overview of

V. Sham Plants
    We will illustrate artificial and phenetic classification using "sham" plants created by Dr. W. Wagner, Michigan.  Also, check out the "Cookophyte" example by J. McNeill.

VI.  A brief timeline of classification systems