Week 1. September 8 - Introduction

Knowledge of life’s diversity exists both intensively (knowing all there is to know about a single living entity) as well as extensively (knowing all of living entities there are to know and the relationships among them). Prime examples of the former include genome projects that aim to document every aspect of the genetic make-up of a single species. Molecular biology and genetics are the scientific fields that endeavor to accomplish this task.

An example of extensive knowledge is the reconstruction of the evolutionary history of life. Systematics and phylogenetics are the branches of biology that are concerned with this charge. Other branches of biology that broadly approach life’s patterns and processes include community ecology, demography, and population genetics.

Traversing the organizational hierarchy of living systems from biological molecules through cells, tissues, organs, individuals, populations, species, communities, ecosystems, and higher taxa, several important distinctions can be made. Collections of interbreeding individuals form populations and are the objects of study for demographers and population geneticists. Genetically and genealogically unrelated populations that coexist in space and time form the basis of community ecology and ecosystem studies. Communities and ecosystems taken over time are in the province of paleoecology.

Collections of genetically related populations constitute species and they, plus higher taxa, are the focus of study for systematists. The distinctions to be made are whether or not the interactions occur over time and whether or not the entities connected over time are genetically and genealogically related. Systematics is concerned with the evolution of genetically related entities, particularly from the population/species level on up.

Evolutionary biology focuses on changes in related populations through time (i.e., the populations and higher taxa have evolved). When enough change has taken place and the populations have undergone speciation, the course of evolution can be plotted as a tree-like, nested hierarchy. Since we generally assume that there is but one history of biological diversification on earth, it is the goal of systematics to reconstruct the Tree of Life.

Goals of systematics

Systematic biology is the comparative study of living and fossil species including taxonomy, the science of classifying organisms. In short, it tries to put all information about all organisms into a system, one that inherently conveys information and tries to illustrate the evolutionary relationships among organisms. In this course, we are specifically concerned with phylogenetic (= genealogical evolutionary) relationships as opposed to ecological, spatial, physical, or other types of relationships. A taxonomy of organisms, using the various rules of nomenclature, allows us to order this information and is best based on knowledge of phylogenetic relationships.

In day to day practice, systematics is concerned with:

Discovering and describing biological diversity.

Applying an unequivocal system of scientific nomenclature.

Elucidating evolutionary relationships between organisms.

Constructing hierarchical classifications that reflect these relationships.

Systematic biology therefore provides the fundamental framework for all biological study, allowing researchers to compare results from one study to the next. It also provides the knowledge and skills needed to discover and utilize new natural resources and to conserve the Earth's biological diversity. This science is of paramount importance in an era when biodiversity is being lost at an unprecedented rate. Knowledge of the variety and interrelationships of organisms also has important applications in medicine, agriculture and industry.

(modified from R. Page’s web site)

Origin and representation of diversity

A nested-hierarchical approach to organizing information on the diversity of life is entirely consistent with our understanding of biodiversity’s origin and evolution.

  1. Biological diversity is the result of evolution (i.e., descent with genetically determined character modification). The historical course of evolution is both a continuum and a discontinuum.
  2. Discontinua and the nested-hierarchical pattern of descent are a result of speciation. There are many modes of speciation and character evolution may accompany, cause, or proceed independently of speciation.
  3. The patterns of speciation may be recovered when speciation is coupled with character modification. A phylogenetic tree is a representation of the course of speciation. A phylogenetic reconstruction is a hypothesis.
  4. Monophyly is phylogenetic relationship. Characters supporting this are synapomorphies (homologies). Determining synapomorphy and monophyly are the essences of cladistic analyses. Other forms of argument (e.g., probabilistic, intuitive, etc.) may be used to estimate phylogenies or construct phylogenetic hypotheses but they defer to other forms of logic or scientific method.

(modified from Wiley, 1981; see Panchen, 1992 for commentary)

Historical perspective on methods of taxonomic organization

Several qualities are desirable in biological classification and the development of biological systematics has seen increases in each of these:

1) Consistency in the ordering of diversity

2) High information content

3) Based on evolutionary criteria

4) Objectivity, repeatability, testability

1) Artificial systems — a priori, monothetic

Among the first verifiable taxonomies are the very early works of the Greeks, (e.g., Theophrastus, Aristotle, etc.) who classified organisms by their overall form, function, or utility using pre-determined criteria (tree vs. herb; swims in water vs. walks on land; poisonous vs. non-poisonous, etc.). This tradition, based on a need for practical taxonomies and a desire to put order to the world, continued for centuries in the form of herbals and other works. Indigenous or folk taxonomies still maintain this perspective as the utilitarian aspects of a classification are most important to people that are highly dependent upon biological diversity for their livelihood. The beginnings of modern, Western science produced a great influx of new material and better ways of observing nature (e.g., the microscope) opening up parts of the organism not seen before. Furthermore, theoretical and philosophical innovations arose from changes in global political and economic developments.

Workers such as Linnaeus proceeded to introduce more complete surveys that were based on simple, a priori (before the fact), monothetic (single character) criteria. The overall information content (predictability) of this approach was quite low. In general, Divine creation was thought to be the genesis of organic diversity and the task of biologists was to ascertain the underlying order to this diversity. Fundamentally, a fixed or typological concept of species is maintained. This is consistent as both the immutability is assumed for both the units (species or other taxa) and the structure of relationships among them.

2) Natural systems — a posteriori, polythetic

The ever increasing amount of new material (a result of European colonial expansion), new ways of looking at material (such as the microscope) required extensive reorganization of existing classifications. Furthermore, major revolutions in science overall (consider the French and American Revolutions as parallel) introduced much critical evaluation of the procedures that gave rise to systems of classification. The basic question of "Why do organisms resemble each other?" entered into the process of classification. Additionally, the greater amounts of material and new tools for studying specimens offered much more detailed descriptions of organismal diversity. Older monothetic and a priori methods were superseded by approaches that focused on polythetic (multi-character) criteria applied in an a posteriori fashion. Because of the attention to these details, the information content of classifications increased. Nonetheless, these methods were often subjective and not always consistent — two different workers looking at the same specimens could emphasize different characters and end up with different groupings.

Appeals to a specific form of genesis for biological diversity were not necessary since the process of organizing diversity was an "after the fact" exercise. One can use similar lines of reasoning to group and classify almost any set of objects — animate or otherwise. Nonetheless, workers such as Adanson were able to put diversity into meaningful systems of classification that form the basis of most modern taxonomies.

3) Phylogenetic systems - evolution-based

By the mid-19th century, some form of organic evolution was considered to be behind the origin of living diversity but the specific mechanism was still unclear Among the types of evidence Darwin used to develop his ideas was the tree-like pattern of relationship among organisms. In particular, his definition of evolution (descent with modification) is entirely consistent with an evolutionary, phylogenetic system of classification.

Phylogenetic methods adopt a clear evolutionary basis to explain the current patterns of biological diversity. The pattern of development among these approaches shows increasing information content, more objective criteria for choosing among alternate phylogenies, closer scrutiny of underlying philosophical considerations, and greater attention to patterns of character evolution.

Phyletics (often called evolutionary taxonomy) is based on relatively intuitive evolutionary assumptions and interpretations. Directionality, adaptive significance, and homology (sensu Owen) are inferred from common principles or inductive reasoning and lead to evolutionary scenario building to describe the resultant patterns of diversity. Differences in rates of evolution, convergence, and overemphasis of certain characters due to subjective bias have often led to inaccurate evolutionary scenarios. Phyletic approaches are direct outgrowths of the natural (pre-evolutionary) systems.

Phenetics (also called numerical taxonomy) followed up on the principles of the natural system and employs the concept of evolutionary "distance". The main assumption is that overall similarity is directly proportional to evolutionary relatedness. (Sneath, 1956; Sokal & Sneath, 1963). Problems with this approach include the lack of an evolutionary explanatory basis, difficulty in handling varying rates of change, a frequent lack of directionality in assessing change or the course of evolution, and frequent lack of repeatability. Addtionally, character information is lost in the transformation of raw character data to summary distance information. Although the approach has had limited success for most morphological data (except at the species and intraspecific level), many distance approaches are quite good at recovering phylogenetic histories with molecular data.

Cladistics focuses on the branching patterns of relationship among organisms; a direct logical consequence of the assumption that life has evolved in a tree-like fashion following descent with modification. It is a more objective offshoot of phyletics in that it usually assumes evolution (although see transformed cladistics) but invokes a more objective approach to character change polarity assessment. A major assumption is that the primary process of evolution is cladogenesis in which an ancestor species gives rise to a distinct descendent species via a split in lineages. After speciation, the two taxa are referred to as sister-taxa or sister-groups. Anagenetic change (change in lineage without speciation) is sometimes difficult to accommodate and is often at the root of differences between cladistic and phyletic taxonomies. The principal difference with phenetic approaches is the focus on a "special" form of similarity between organisms: that of derived characters (apomorphies). Shared derived character states are called synapomorphies. Ancestral character states are called plesiomorphies. In cladistic phylogenetics, the definition of homology is equal to synapomorphy as opposed to the structural or functional-based definitions of earlier authors (particularly the evolutionary taxonomists). Synapomorphies are evidence of monophyletic groups or clades (an ancestor plus all of its descendents) which are the only groups allowed in cladistics. Non-monopyletic groups are paraphyletic (an ancestor without all of its descendents) or polyphyletic (several descendents without the common ancestor). Synapomorphies (homologies) and monophyly are nonetheless hypotheses that can be refuted by the weight of counter-evidence. The principal of parsimony is usually used to decide between conflicting characters or character states. Related approaches include character compatibility and clique methods.

Note that cladistic methods can be used to organize almost any type of information that has developed through an "evolutionary" process (that is, descent with modification). Thus, the "evolution" of machine parts, automobiles, languages, paper clips, and even pasta shapes can be classified using cladistic principles. Additionally, it should be noted that the principle of parsimony is not unique to cladistics as it is a general approach in science to explaining data. More on these issues later.

Explicit model-based methods such as maximum-likelihood employ probability-based approaches to model the evolution of a sample of characters from a group of organisms. The goal is to establish or estimate the set of parameters (probabilities of changing from one character state given certain conditions) including the tree (both its topology and branch lengths) that best describe a given data set. In practice, this method is limited to molecular sequence data although in theory it can be applied to any data set for which the parameters are known or can be estimated. Note that maximum likelihood methods are not restricted to phylogenetic studies — they are routinely used in many fields where one wants to model the process and conditions that produced a set of observations (data). The likelihood is only one of several optimality criteria (parsimony being one of simplest; some distance methods such as minimum evolution being other examples) where we try to find the best explanation (for phylogenetics, a tree plus other descriptors or parameters) for a set of observations (character data).

Readings: Page Ch 1 & 2, Kitching, Ch 1; see also: Maddison, Ch 1-2; Wiley, Ch 1-2.

Computer lab: Introduction to Systematics Internet resources; specimen and taxonomy-based on-line resources. MacClade (time permitting).

Some useful links:


Tree of Life




American Museum of Natural History

Natural History Museum (UK)

Smithsonian Institution - National Museum of Natural History


UC Berkeley


Society of Systematic Biologists

Willi Hennig Society

Additional references:

Hall, BK (ed.) 1994. Homology. The Hierarchical basis of Comparative Biology. Academic Press. San Diego, CA.

Lipscomb, D. 1998. Basics of Cladistic Analysis. Unpublished manuscript. (see: Cladistics.pdf).

Maddison, WP & DR Maddison. 1992. MacClade. Analysis of Phylogeny and Character Evolution. (User's manual). Sinauer Assoc. Sunderland, MA. (see: http://ag.arizona.edu/macclade/macclade.html)

Panchen, AL. 1992. Classification, Evolution, and the Nature of Biology. Cambridge Univ. Press. Cambridge, UK.

Sanderson, M & L Hufford. 1995. Homoplasy. The Recurrence of Similarity in Evolution. Academic Press. New York.

Swofford, D. L. 1998. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, MA. (see paup 4b1.pdf)

Wiley, EO.1981. Phylogenetics. The Theory and Practice of Phylogenetic Systematics. Wiley Interscience. New York.

Wiley, EO, D Siegel-Causey, DR Brooks, & VA Funk. 1991. The Compleat Cladist. A Primer of Phylogenetic Procedures. Univ. Kansas Museum of Natural History Special Publ. 19. Lawrence, KS. (see CompleatCladist.pdf)

Bibliography: (see: bibliography.pdf)


Cladistics in practice (modified from UC-Berkeley Museum of Paleontology)

1. Choose the taxa or terminal units whose evolutionary relationships interest you. These taxa must be clades if you hope to come up with plausible results. If species are the terminals, then appropriate species concepts must be utilized. If the terminals are higher level taxa of concern, appropriate sampling and representation of diversity must be employed. The use of exemplar taxa to represent large groups (e.g., a single species to represent all protista in an analysis of life) may be necessary but is not without pitfalls.

2. Determine the characters (features or attributes of an organism) and their alternate states (character coding). Examine each taxon to determine the character states present in that taxon. Character coding is probably the single most important part of the whole exercise. Although a cladistic analysis will help check for support of the homology of characters and character states, some previous knowledge or hypothesis of character evolution usually guides character coding.

3. Determine the polarity of characters (whether each character state is original or derived in each taxon). Note that this step is not absolutely necessary in some computer algorithms. Examining the character states in outgroups to the taxa you are considering helps you determine the polarity.

4. Group taxa by synapomorphies* (shared derived characteristics) not plesiomorphies (original, or "primitive" characteristics).

5. Work out conflicts that arise by some clearly stated method, usually parsimony (minimizing the number of conflicts).

6. Build your cladogram, which is NOT an evolutionary tree but a character tree that serves as an estimate of the true evolutionary tree or phylogeny.


To accomplish the task of creating a good cladogram, you must use your judgment. Ask yourself the following questions and answer them carefully.

-- Could a supposed synapomorphy be the result of independent evolutionary development?

-- Are your characters and character states appropriate?

-- Should you consider other characters?

-- Should you consider additional taxa?

Phylogenetic Terms (modified from: UC-Berkeley; Wiley, 1981; and other references)

adaptation -- Change in a organism resulting from natural selection; a structure which is the result of such selection.

anagenesis -- Evolutionary change along an unbranching lineage; change without speciation.

ancestor -- Any organism, population, or species from which some other organism, population, or species is descended by reproduction.

basal group -- The smaller of two sister groups; often used as the outgroup for a study of the larger clade.

character -- Heritable trait possessed by an organism; characters are usually described in terms of their states, for example: "hair present" vs. "hair absent," where "hair" is the character, and "present" and "absent" are its states.

clade -- A monophyletic taxon; a group of organisms which includes the most recent common ancestor of all of its members and all of the descendants of that most recent common ancestor. From the Greek word "klados", meaning branch or twig.

cladogenesis -- The development of a new clade; the splitting of a single lineage into two distinct lineages; speciation.

cladogram -- A diagram, resulting from a cladistic analysis, which depicts a hypothetical branching sequence of lineages leading to the taxa under consideration. The points of branching within a cladogram are called nodes. All taxa occur at the endpoints of the cladogram.

convergence -- Similarities which have arisen independently in two or more organisms that are not closely related. Contrast with homology.

crown group -- All the taxa descended from a major cladogenesis event, recognized by possessing the clade's synapomorphy. See: stem group.

derived -- Describes a character state that is present in one or more subclades, but not all, of a clade under consideration. A derived character state is inferred to be a modified version of the primitive condition of that character, and to have arisen later in the evolution of the clade. For example, "presence of hair" is a primitive character state for all mammals, whereas the "hairlessness" of whales is a derived state for one subclade within the Mammalia.

diversity -- Term used to describe numbers of taxa, or variation in morphology.

endosymbiosis -- When one organism takes up permanent residence within another, such that the two become a single functional organism. Mitochondria and plastids are believed to have resulted from endosymbiosis.

evolution -- Darwin's definition: descent with modification. The term has been variously used and abused since Darwin to include everything from the origin of man to the origin of life.

evolutionary tree -- A diagram which depicts the hypothetical phylogeny of the taxa under consideration. The points at which lineages split represent ancestor taxa to the descendant taxa appearing at the terminal points of the cladogram.

extinction -- When all the members of a clade or taxon die, the group is said to be extinct.

gradualism -- A model of evolution that assumes slow, steady rates of change. Charles Darwin's original concept of evolution by natural selection assumed gradualism. Contrast with punctuated equilibrium.

homology -- Two structures are considered homologous when they are inherited from a common ancestor which possessed the structure. This may be difficult to determine when the structure has been modified through descent. The term holds both for characters as well as character states.

hypothesis -- A concept or idea that can be falsified by various scientific methods.

ingroup -- In a cladistic analysis, the set of taxa which are hypothesized to be more closely related to each other than any are to the outgroup.

lineage -- Any continuous line of descent; any series of organisms connected by reproduction by parent of offspring.

monophyletic -- Term applied to a group of organisms which includes the most recent common ancestor of all of its members and all of the descendants of that most recent common ancestor. A monophyletic group is called a clade.

nomenclature -- The naming of groups of organisms; a process that interacts with classification.

outgroup -- In a cladistic analysis, any taxon used to help resolve the polarity of characters, and which is hypothesized to be less closely related to each of the taxa under consideration than any are to each other.

paraphyletic -- Term applied to a group of organisms which includes the most recent common ancestor of all of its members, but not all of the descendants of that most recent common ancestor.

parsimony -- Refers to a rule used to choose among possible cladograms, which states that the cladogram implying the least number of changes in character states is the best.

phenetic -- Based on overall similarity without regard to polarity.

phyletic (evolutionary) taxonomy - Based on intuitive, subjective criteria.

phylogenetics -- Genealogical relationships and representation (classification) of that order, branching order / cladism in strict sense; evolutionary history of a group in broad sense.

phylogeny -- The evolutionary relationships among organisms; the patterns of lineage branching produced by the true evolutionary history of the organisms being considered.

plesiomorphy -- A primitive character state for the taxa under consideration.

polarity of characters states -- The states of characters used in a cladistic analysis, either original or derived. Original characters are those acquired by an ancestor deeper in the phylogeny than the most recent common ancestor of the taxa under consideration. Derived characters are those acquired by the most recent common ancestor of the taxa under consideration.

polyphyletic -- Term applied to a group of organisms which does not include the most recent common ancestor of those organisms; the ancestor does not possess the character shared by members of the group.

primitive -- Describes a character state that is present in the common ancestor of a clade. A primitive character state is inferred to be the original condition of that character within the clade under consideration. For example, "presence of hair" is a primitive character state for all mammals, whereas the "hairlessness" of whales is a derived state for one subclade within the Mammalia.

pseudoextinction -- The apparent disappearance of a taxon. In cases of pseudoextinction, this disappearance is not due to the death of all members, but the evolution of novel features in one or more lineages, so that the new clades are not recognized as belonging to the paraphyletic ancestral group, whose members have ceased to exist. The Dinosauria, if defined so as to exclude the birds, is an example of a group that has undergone pseudoextinction.

punctuated equilibrium -- A model of evolution in which change occurs in relatively rapid bursts, followed by longer periods of stasis.

radiation -- Event of rapid cladogenesis, believed to occur under conditions where a new feature permits a lineage to move into a new niche or new habitat, and is then called an adaptive radiation.

rank -- In traditional taxonomy, taxa are ranked according to their level of inclusiveness. Thus a genus contains one or more species, a family includes one or more genera, and so on.

relatedness -- Two clades are more closely related when they share a more recent common ancestor between them than they do with any other clade.

reticulation -- Joining of separate lineages on a phylogenetic tree, generally through hybridization or through lateral gene transfer. Although probably fairly common in certain land plant clades, reticulation is thought to be rare among metazoans.

selection -- Process which favors one feature of organisms in a population over another feature found in the population. This occurs through differential reproduction -- those with the favored feature produce more offspring than those with the alternate feature, such that they occupy a greater percentage of the population in the next generation.

sister group -- The two clades resulting from the splitting of a single lineage.

stasis -- A period of little or no discernible change in a lineage.

stem group -- All the taxa in a clade preceding a major cladogenesis event. They are often difficult to recognize because they may not possess synapomorphies found in the

crown group.

synapomorphy -- A character state that is derived, and because it is shared by the taxa under consideration, is used to infer common ancestry.

systematics -- Field of biology that deals with the evolution and historical genealogical relations of organisms.

taxon -- Any named group of organisms with a proper name, not necessarily a clade.

taxonomy - Description and order; theory of organismal classification.

vicariance -- Speciation which occurs as a result of the separation and subsequent isolation of portions of an original population.