Box Cladistic analysis

There are three steps in drawing a cladogram: character analysis, outgroup comparison and tree calculation. The character analysis is the process of listing characters that vary among the organisms of interest, and identifying those that are possible apomorphies. Characters are often coded as presence/absence or 0/1. So, for example, in a character analysis of the apes, a possible apomorphy might be "possession of an opposable thumb, used for gripping". This would be coded as present (or 1) in humans, and as absent (or 0) in chimpanzees and gorillas.

The outgroup comparison is the phase when characters and their codings are tested for validity. If the group under study, the ingroup, consists of the apes, then the outgroup might be monkeys. The outgroup could really be oak trees and worms, but they are so distantly related to the apes that comparisons would be largely meaningless (oak trees and worms do not even have thumbs). Com-

parison with the outgroup of monkeys shows that monkeys, chimpanzees and gorillas have non-opposable thumbs. So this is coded "0", and the opposable thumb of humans appears to be unique, an apomorphy, and so is coded "1".

The final step is the tree calculation. All the characters and their codings are listed in a data matrix, a tabulation of the data, listing all the species and all the characters and their codings. The tree calculation is usually run by computer, and a search is carried out, using different methods, to find the single tree, or group of trees, that best explain the data.

We give a simple worked example here, to determine the relationships of six vertebrates: shark, salmon, frog, lizard, chicken and mouse. These are distant relatives, of course, representing cartilaginous fishes, bony fishes, amphibians, reptiles, birds and mammals, respectively, but if we can sort out their relationships, we have a broad outline of the phylogenetic tree of all vertebrates.

Ten (out of many) characters are listed in the data matrix below, and their codings are shown (0 = absent; 1 = present) for each of the six animals. Next, outgroup comparison will help to sort out the phylogenetically informative characters from the plesiomorphies. We will choose two examples: the shark and the salmon have fins (character 1) while the others have legs (character 2), and the chicken and mouse are warm-blooded and the others are cold-blooded (character 3). Out-group comparison of these two sets of characters suggests that warm-bloodedness is probably an apomorphy (because most members of the outgroup, such as clams, oak trees and bugs, are coldblooded), but it is harder to tell whether fins or legs are apomorphies or not, so these two are retained.

Character

Shark

Salmon

Frog

Lizard

Chicken

Mouse

1 Fins

0 0

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