So how do you know what characters are synapomorphies and "good" characters to use in a phylogenetic analysis? First, a good character shows greater variation among the taxa you are interested in (called operational taxonomic units or OTUs) than within each taxon. Second, this variation must be heritable and independent of other characters. For example, the character "has secondary xylem" and the character "has a vascular cambium" are NOT independent because secondary xylem is produced by a vascular cambium. Third, you must make sure that the characters and character states that you are examining are truly comparable, that is, homologous. The term homology was first introduced by Sir Richard Owen in 1843. The word is derived from "homologia" in Greek which means "agreement". Homology (see also discussion in Lab 1) denotes structures and organs that have evolutionary correspondence, regardless of their current function. It can be recognized based on three criteria of homology:
Correspondence in structure between sister groups is referred to as taxic homolgy (Figure 2.4; C). The wings of birds, forelimbs of a lizard and human arms are (taxic) homologies, because they are all derived from the same primitive structure in the common ancestor of these groups. Similarly, the fronds of ferns and leaves of dicots are also taxic homologies. Synapomorphies must always be taxic homologies.
The term homoplasy was coined by Lankester in 1870. It refers to analogous structures, i.e. structures that show similarity and may perform the same function, but that are not derived from a structure found in a common ancestor. The wings of bats and insects are analogous (homoplastic) because they both function for flight, but evolved from different primitive structures. Homoplasy is due to convergent evolution, parallell evolution or character reversal. It is a fundamental characteristic of many structures in land plants, which may be one of the reasons why phylogenetic studies were unpopular among paleobotanists in the early 19th century. Can you think of examples of homoplasy in living land plants? Why is this such a common occurrence in plants?
Deciding whether features are homologous or analogous is key when interpreting evolutionary relationships. However, making this interpretation is seldom straightforward. For example, Johann Wolfgang von Goethe noted in Metamorphosis in Plants (1790), that plant organs such as cotyledons, foliage leaves, bracts, and some flower parts are variously modified leaves (serial homology). A phylogenetic analysis therefore starts out with a careful character analysis, where each character is treated as a "hypothesis of putative homology" and examined according to the three criteria of homology listed above.
A character is any recognizable attribute of an organism, such as "eye color" or "presence of tracheids". A character state is the value of the character, for example "blue" and "yes", respectively. Note that characters that are related to some function are more likely to be homoplastic or convergent, e.g., size and shape of leaf.
The character states are entered into a matrix as for example "1" for "present" and "0" for "absent", or "1" for "green", "2" for "blue" and "3" for "red". For many characters it is possible to establish an evolutionary order -- which character state must follow on another in a character transformation series. However, it is more difficult to decide on the polarity; the actual direction of evolutionary change. IF one is able to do this, it becomes much easier to decide what organisms are basal (that is, near the root of the cladogram), which of course helps resolve the phylogeny. The polarity can be deduced by looking at a variety of lines of evidence: ontogenetic precedence (a character state present early in development but subsequently lost), stratigraphic character precedence (a character state present in organisms of the same lineage earlier in Earth's history), and outgroup comparison (comparison with hypothesized sister taxa).
A phylogenetic analysis starts by defining the taxa for which you want to reconstruct evolutionary relationships. These are OTUs and will each occupy a ROW in your data matrix. After you have decided which characters will be useful for an evolutionary reconstruction, each character is given a COLUMN in your data matrix. The character state for each character and for each OTU is then scored to fill up your data matrix. The data matrix can then be analyzed by any of several computer programs that use an algorithm that joins OTUs based on the greatest number of shared derived characters. The algorithm that is most appropriate for morphological data and that you are going to experiment with uses as a grouping principle maximum parsimony. Parsimony ("Okkham's razor") is based on three assumptions about evolution:
1. Organisms reproduce (replication) 2. Character states and character state changes are inherited; that is, variation is correlated between parent and offspring (heritability), giving rise to transformational homology 3. Evolution occurs with splitting or divergence as a predominant pattern, i.e. branching happens at a relatively high rate as compared to the rate of changes in character states in a single lineage. This gives rise to taxic homology or homology between sister groups.
The consequence of this is that a similarity in a derived character state is more likely to be due to a common ancestry (homology) than through random or non-random assimilation of the same feature in two different lineages (homoplasy). The algorithm Maximum Parsimony chooses the "true" phylogeny, i.e. the phylogeny that gives the minimum amount of "steps" (character state changes). In addition, it is possible in the algorithm to "weight" or emphasize a character according to how important you think it is. For example, you might want to down-weight the character "shape of seed" in relation to "presence of endosperm", since the former character is more likely to display homoplasy. Similarly, certain changes between character states within one character can be weighted differentially. For example, it is more probable for some structures to disappear than to originate, or the other way around. Can you think of an example of this?
As you are no doubt realizing, the cladistic method is not entirely objective. The systematist still has to make interpretations about homology and about how to weight and order characters for analysis. However, the cladistic paradigm does force the systematist to state explicitly why she believes characters are homologous or should be ordered in a certain way. This provides bases for falsifying hypotheses and promotes testing of alternatives. This makes the subjectivity science.
The result of a cladistic analysis is a cladogram (Figure 2.3), a diagram of nested synapomorphies that defines relationships in a relative way. These synapomorphies are used to recognize monophyletic clades (monophyletic groups of organisms of any taxonomic rank), arranged in a hierarchical manner. Note that a cladogram does not have a time axis, and does not make any statements as to the theory of evolution (tempo or mode). It is merely a hypothesis of character evolution and possible relationships. As such it can be carefully compared-character by character-to competing hypotheses, and tested and refuted with additional data. Many systematists want to replace the existing Linnean taxonomy with a phylogenetic one, which would better reflect the hierarchical pattern of clades. However, the potential instability of such a system is a major problem.