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A link to answers for the nomenclature assignment will be posted on the lecture syllabus. Corrected assignments will be returned in lab.
Textbook by Judd et al.,Plant Systematics: A Phylogenetic Approach, 3rd edition
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Approaches to Classification
The characters which naturalists consider as showing true affinity between any two or more species, are those which have been inherited from a common parent, all true classification being genealogical.
Charles Darwin 1859: 391
Classification: the theory and practice of grouping and ranking organisms.
There are many ways to do this -- and you will learn about these in our lecture on historical systematics -- but the approach we and your textbooks take is phylogenetic. There are two major steps in producing a phylogenetic classification:
What is a Phylogeny?
A phylogeny is a diagram (a phylogenetic tree or cladogram) that depicts the evolutionary relationships among organisms. Comparative morphological, anatomical, embryological, molecular, behavioral, physiological, chemical, geographical, and fossil data can all be used, together or separately, to construct the phylogeny.
A phylogeny provides the historical perspective from which to interpret the evolution of characters, patterns and processes of diversification, rates of evolution, historical biogeography, and co-evolutionary phenomena, such as the relationships between hosts and parasites or plants and herbivores.
A phylogeny is used to classify organisms on the basis of their inferred evolutionary relationships (the phylogenetic approach to classification).
A phylogeny is a hypothesis based on the best interpretation of the data at hand and subject to further evaluation (and possibly change) as new data become available.
Introduction to the Concept of Phylogeny
Levels of detail in genetic history: from individuals to the phylogenetic tree.
A lineage or clade is an ancestor-descendant sequence of populations (these are the lines of a cladogram)
How Do New Species Arise?
Speciation depends upon many interacting factors, such as nonrandom mating, migration, genetic drift (founder effects, population bottlenecks], mutations, and natural selection.
The Divergence of Populations
Stages in the formation of a new species (from Grant, 1963 and 1981, and the University of Alabama). This is basically the same illustration as provided below, with more detail.
Here is an illustrative example of geographic speciation from the University of Alabama. This poor quality figure shows the separation of two populations by some geographic barrier.
If a population should become divided into two by a geographic barrier (or if some individuals are transported to a new area outside the parent's range), evolution of each new population continues independently due to the forces of natural selection, genetic drift, migration, nonrandom mating, and mutation. Differences between the two, including differences in reproductive processes, gradually accumulate such that reproductive isolating mechanisms become more and more effective over prolonged periods of time.
New species arise when genetic differences accumulate to the point when the two groups can no longer successfully mate and reproduce (if and when they come back into contact). Species can be defined as groups of actually or potentially interbreeding populations that are reproductively isolated from other such groups.
Speciation events lead to the multiplication and diversification of species into higher taxa (e.g., genera, families, orders, classes, phyla, etc.). All species (animals, plants, fungi, and all major groups of microorganisms) can be traced back to a single origin of life on earth. Evolution is a continuing process that explains the history of life on earth, as well as the diversity of life today.
Speciation can occur within the range of the parent population (and sometimes quite rapidly). Gene flow can be disrupted by:
These polyploids can self-fertilize or breed among themselves. In humans and other animals, polyploidy is lethal. In plants, polyploidy is quite common and has given rise to many new species. It is estimated that as many as 50% of extant flowering plant species have evolved via polyploidy.
The illustration below shows the splitting of populations into separate lineages (each circle represents a plant). Members of the new populations have new gene characteristics and, possibly, changes in their overall form.
Below, in a very simple example, white-flowered ancestors give rise to descendants having either red or blue flowers. Each of these new lineages then acquire further distinctive characteristics. These new (or derived) features (relative to those found in the ancestors) tell us that a new lineage has been established.
Summarization
The diagram above can be summarized as branching trees. Only those features that have changed (the derived characteristics) are indicated on the bottom tree.
The phylogenetic approach to classification
Dissatisfied with both the phyletic or natural approach (because of its intuitive nature) and with phenetics (because it reflects total similarity and not evolutionary history), taxonomists have sought an explicit approach to classification that directly reflects evolutionary relationships. Phylogeneticists work under the principle that there is a single and historically unique genealogic history relating all organisms.
Phylogenetics or cladistics is a philosophical and methodological approach to classification that attempts to recover genealogical relationships among groups of organisms by producing branching trees (called phylogenies or cladograms) that reflect these relationships. Its core concept is the use of shared derived character states to reconstruct common ancestry. This concept was first formalized by Willi Hennig, a German entomologist, in a landmark book published by the University of Illinois Press. Hennig argued that the best classification of organisms is one that exactly reflects the genealogical relationships among these organisms.
Some definitions:
Determining Evolutionary History
More definitions:
Methodology
Make evolutionary assumptions. This includes selecting the taxa to be examined and determining whether they are monophyletic or not. (Often, this isn't confirmed until the study is complete.)
Select characters of evolutionary interest. In practice, the number of characters much be one less than the number of taxa for all branches of the tree to be resolved. The characters used can be diverse, representing those obtained from both morphology and molecular studies. In phenetic approaches to classification, many more characters are used.
Describe and/or measure the character states. It is essential to ensure that the same kinds of characters are being compared from one species to another. (One state of a character is derived directly from another state of that same character.)
Constructing a data matrix
Once the characters have been selected, an appropriate coding (using letters or numbers) must be assigned to the states so that they can be placed conveniently into a data matrix. In the matrix below, the number "1" is assigned to those character states that represent the derived condition and the number "0" is assigned to those character states representing the ancestral condition. (This isn't always so, however. Often, the "polarity" of a character state isn't known until after the analysis is done.)
The most commonly used method for constructing cladograms is the method of parsimony. This method attempts to minimize the number of character state changes among the taxa (the simplest evolutionary hypothesis). Using shared derived character states, the trees are constructed. (There are other methods of tree construction that can also be used, such as minimum distances.)
Interpretation:
Phylogenetic Classifications
Integrating the results of a phylogenetic analysis into a classification is an extremely contentious issue in systematics. Basically, taxa are recognized on the basis of monophyly. Then the groups are ranked and placed in a hierarchy. In the cladogram above, for example, species A, B, C & D may all be recognized as comprising the same genus (with two subgroups, possibly) and species E & F as comprising another genus. Or, species A-D may comprise one family (with two subfamilies, possibly) and species E & F another family.
BUT
species E, F & D should not be recognized as a taxon (upon the exclusion of species A, B & C) nor should species A, B & C be recognized as a taxon (upon the exclusion of species D). Each of these two taxa are not monophyletic because they each do not contain all the descendants of their common ancestors.
There are some systematists who want to abandon the traditional way of naming and ranking plants. Indeed, the concept of ranks (that is, the taxonomic hierarchy) may be abandoned altogether.
It's important to realize that many current classifications do NOT represent phylogenies. They were developed many years ago, before anyone had any idea about evolution.
Monophyly, Polyphyly, and Paraphyly
This information comes from W. Zomlefer, Guide to Flowering Plant Families, p. 15.
"Dicotyledons" and Monocotyledons: an example of paraphyly
The "dicots" do not form a monophyletic group (they do not contain all the descendants of their common ancestor). They are rejected as a formal group. Basically, it's difficult to circumscribe the "dicots" without including the monocots. Some "dicots" are more similar to monocots than they are to other "dicots." The "dicots" are paraphyletic, whereas the monocots can be defined by several synapomorphies.
Within angiosperms, three main lineages are apparent: a Magnolia-like group (e.g., Magnoliaceae), a tricolpate-pollen group (e.g., the typical "dicots"), and a paleoherb group (which contains the monocots). This cladogram may more accurately reflect angiosperm relationships than the conventional monocot-dicot split.
Cladogram of angiosperm groups showing relationship between monocots and "dicots", as modified from Zomlefer (1994).
Angiosperm Phylogeny
The relationships among the major angiosperm groups are modeled after the system of the Angiosperm Phylogeny Group 2003 (referred to as APG II, 2003; Botanical Journal of the Linnean Society, 2003, 141: 399-436). This system is based on published cladistic analyses primarily using molecular data. Only those families that are monophyletic are recognized. The APG II system classifies families into orders, where strong evidence suggests that the order is monophyletic. Some monophyletic groups containing several orders are given informal names, such as "magnoliids," "monocots," "eudicots," "rosids," "eurosids I and II," "asterids," etc. As much as we are able, we will follow this classification in IB 335. The APG II phylogeny below is similar, but not identical, to that one used in the Judd et al., Third Edition (2007).
Lecture Assignment Two
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