[Laboratory II -- Phylogenetics -- The Science of Who's Related to Who]

One of the most important aspects of paleobotany is establishing relationships between the organisms that we encounter in the fossil record. Interpreting ecological or biological diversity patterns of groups depends on incorporating information about relationships. For example, botanists have noticed a striking similarity between the flowering plants of Chile and those in California. In fact, pairs of species have been identified (one species in Chile and one in California) that botanists hypothesize are descendants of an ancestral species whose range spanned distance. Alternatively, the ancestral species might have been dispersed between these disjunct ranges by migrating animals, such as birds. These hypotheses hang on whether the Chile-California species pairs are actually closely related. If they are not, both hypotheses are falsified, and we need to consider new ones.

Systematics is the science of describing the relationships between organisms and the processes behind these relationships. Systematics also encompasses questions of diversity and disparity today and through time. Systematics includes (but is sometimes incorrectly equated to) taxonomy; the rules for description, naming and formal classification of groups of organisms.

Since the ancient Greeks founded systematics, overall or phenetic similarity has been the main basis for systems of classification and relationships among living things. Carl Linnaeus' hierarchical system and binomial nomenclature for flowering plants was meant to reflect the natural order of God's creation, as manifested in overall morphological similarity. Like most people of his time, Linneaus believed that the species had been constant since their creation. He recognized that the grouping criteria he used (for flowers-number and arrangement of stamens and carpels) united many taxa that clearly did not belong together as well as split up morphologically coherent groups of plants. Nonetheless, Linnaeus, and generations of botanists since, have accepted the system because it satisfies a practical, descriptive need.

After the acceptance of evolution through the work of natural scientists such as Jean-Baptiste de Lamarck, Charles Darwin and Alfred Wallace, systematists realized that they needed to incorporate knowledge of the evolutionary relationships among organisms into schemes of classification. For example, each distinguishable group of organisms should have a single common origin (compare monophyly). Under this scheme, the classification scheme doesn't simply reflect overall similarity, but evolutionary history. Under such a classification system, we can use evolutionary groups to ask evolutionary questions-a central theme in Integrative Biology and this course in particular.

Integrative Biology faculty member and Director of the U.C. Herbarium, Brent Mishler has pioneered the application of cladistic methods to big questions in plant evolution (Mishler and Churchill, 1985, for example). This work illustrates that the phylogenetic approach can be a powerful tool for falsifying hypotheses and thus indispensable for plant evolution. Prof. Mishler is now coordinating a world-wide effort to develop a phylogeny for all the green plants. When completed, this phylogeny will push plants light years ahead of animals as subjects of macroevolutionary study. Prof. Mishler, along with U.C. Museum of Paleontology Director, David Lindberg, teaches a hands-on course in phylogenetic reconstruction in Integrative Biology.

Evolutionary Systematics

Evolutionary systematics in the tradition of Ernst Mayr (1904) and George G. Simpson (1961) was practiced by most taxonomists of this era. In this school of thought, classification reflected relatedness as well as morphological disparity (overall similarity). The introduction to a lineage of a major new trait (apomorphy, e.g., flowers in the angiosperm lineage) therefore results in the formation of a new so called "natural group" (Figure 2.1; "flowering plants") of the same rank as the "natural" group from which it arose (Figure 2.1; "gymnosperms"); in this example, the group "gymnosperms" contains the ancestors of "flowering plants". In another example, the class "Reptilia" was thought to have evolved from the class "Amphibia" by the invention of the amniote egg. Unfortunately, this classification lead to the creation of paraphyletic taxa (taxa that do not encompass all the descendants of their common ancestor), or evolutionary grades instead of truly monophyletic taxa. Consider the "Pteridophyta" (vascular plants that reproduce by spores)-are they a monophyletic group or a grade? Why? If you are unsure of their relationships, consult the Virtual Paleobotany Laboratory.

Figure 2.1: Evolutionary systematics interpretation of land plant evolution. Paraphyletic groups give rise to other groups of the same rank. For example: "Trimerophytes", "gymnosperms", and "bryophytes".

This early version of evolutionary systematics was based on a very imprecise, subjective, and complicated set of rules that only scientists with lots of experience working with their organisms were able to use. The resulting phylogenies became impossible to reproduce other than by the specialists themselves. This practice of systematics was more art than science, and led to a call for more repeatable and objective methods.


A more rigorous and objective way of generating and choosing among phylogenies was numerical taxonomy or phenetic systematics. This method was made possible by the advent of computers in the 1960's because phenetics relies on extensive mathematical calculations. Organisms are grouped by a mathematical analysis of a large set of characters (preferably all possible characters!) according to overall similarity. The results are certainly reproducible, but fail to create groups that reflect evolutionary relationships (Figure 2.2). Phenetics failed to create truly evolutionary groups because organisms can be similar because they live in similar environments or because they make their living in similar ways, not just because they are descended from a common ancestor. The main advocates of phenetic systematics are James Rohlf, Robert Sokal, and Peter Sneath.

Phenetics broke the log-jam of systematic methodology, opening biologists to the idea of considering characters in an objective and reproducible way. However, the overall-similarity methods failed to reconstruct evolutionary groups and so additional new methods were sought.

Despite the failure of phenetics to reconstruct evolutionary relationships, the numerical methods themselves have applications to a variety of other problems, such as delimiting variation within and between populations of individuals. This approach can be particularly useful to paleobotanists as we try to circumscribe species with their associated ranges of variation from collections of individual specimens. Often observation alone leads the paleobotanist to focus on just one or two characters. The numerical or morphometric methods use the power of the computer to consider all characters together in recognizing groups within a collection or a gradation between dissimilar end members.

[Phenetic diagram]
Figure 2.2: Classification of some animal groups according to numerical taxonomy. A and B represent different characters; the states are noted on the figure. These characters are then used to group the organisms. Are these characters homologous? Are they homoplastic? Plesiomorphic?

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