AIM: Construction of cladograms based on morphological characters.

Theory: Phylogenies are inferred from morphological characters using cladistic techniques
Phylogenetic inference using morphological characters proceeds in the same way with both
living and fossil species. For fossil species, we usually have evidence only from hard parts, such
as bones in vertebrates or shells in mollusks. For living species, we have further evidence from
the soft parts. We also have evidence from characters that are not morphological in a narrow
sense, but can be included with morphological characters in phylogenetic research. For instance,
mammals are viviparous (produce live young) and lactate, whereas birds are oviparous (lay
eggs). Reproductive and physiological characters of this kind are all good evidence for
phylogenetic inference. In this note, “morphological” evidence refers to all observable characters
in the whole organism, as distinct from molecular characters.
The techniques used with morphological characters are called cladistic techniques. (The word
cladistics comes from the Greek word for a branch.) For cladistic analysis, the evidence consists
of a number of characters, each with a number of discrete character states. For example, one
character might be “mode of reproduction” and it might have the states “viviparity” or
“oviparity.” Another character might be “structure of forelimb,” and its states might be “wing”
and “arm.” The particular characters and character states will depend on the species that are
being studied. Phylogenetic inference is not simple, mainly because not all the characters for
which we have evidence will point to the same phylogeny. However, in an easy case, all the
characters will agree and point to the same phylogeny.
But suppose now that we are studying the phylogeny of humans, a bat, and a bird. Some
character states are similar in birds and bats: both have wings and other skeletal adaptations for
flight. Other character states are similar in humans and bats: both are viviparous and lactate.
Now which evidence should we rely on?
Another famously problematic example, from the relations of birds and reptiles. Suppose we are
studying the phylogeny of a crocodile, a bird, and a lizard. The crocodile and lizard share
many similarities: they have scales and walk on four legs, whereas birds have feathers and walk
with two of their appendages and fly with the other two. But a detailed study of the skull shows
that birds and crocociles have important similarities there, whereas lizards have a different skull
anatomy. Which evidence should we rely on now? These two examples illustrate a general
problem with cladistics technique of phylogenetic trees.
The techniques of cladistics work by distinguishing between reliable and unreliable characters.
The unreliable characters, once identified, can be discarded. The analysis of characters, to
distinguish reliable from unreliable characters, proceeds in two stages: we first distinguish
homologies from homplasies, and then distinguish derived homologies from ancestral
homologies.
Homologies provide reliable evidence for phylogenetic inference, and homoplasies provide
unreliable evidence
The first stage of cladistic analysis is to distinguish homologies from homoplasies. The
difference between homologies (or a homologous character) and homoplasies (or a homoplasious
character) is as follows. A homology is a character shared between two or more species that was
present in their common ancestor. A homoplasy is a character shared between two or more
species that was not present in their common ancestor. Thus we start with a character that is
similar in two species. We then trace all the way back to their most recent common ancestor. If
the common ancestor had that same character, then the character in the two descendant species is
similar by common evolutionary descent and is a homology. If the common ancestor had some
different character state, then the character in the two descendant species evolved independently
(through convergent evolution) and is a homoplasy. The distinction matters because homologies
may reveal phylogenetic relationships, whereas homoplasies do not.
Derived homologies are more reliable indicators of phylogenetic relations than are
ancestral homologies
The next stage is to divide the homologies into ancestral and derived homologies. Consider the
Ancestral homologies are characters that were present in the common ancestor of the group of
species under study. Derived homologies are homologies that evolved after the common
ancestor, within the group of species under study.
Example: number of digits on the feet of a frog, a dog, and a horse. The frog and dog have
standard tetrapod feet, with five digits. This is the ancestral state for all tetrapods. Horses have
reduced the number of their digits, and have only one of the five digits left. The similarity of the
dog and frog is not evidence that they share a more recent common ancestor with each other than
either does with a horse. Indeed, both the dog and the horse are mammals, and share a more
recent common ancestor than either does with a frog. However, if we are studying instead the
relations of a frog, a dog, and a fish, the five digit foot is no longer the ancestral state. It was not
present in the common ancestor of the three species. For these three species, the five-digit foot is
a derived homology. It evolved within the group of species that we are studying and tells us
something about the phylogeny. It tells us that the frog and dog share a more recent common
ancestor with each other than either does with the fish.
Example: In cases such as a bird, a crocodile, and a lizard.
Birds have evolved wings and other skeletal and physiological adaptations for flight. Crocodiles
and lizards have both retained ancestral reptilian characters such as scales and walking on four
legs. The crocodile and lizard therefore look relatively similar compared to birds. But the
similarity between crocodiles and lizards is ancestral similarity. It is a characters that were
present in the common ancestor of all three groups. This similarity is thus not evidence that
crocociles and lizards share a more recent common ancestor with each other than either does
with birds.
Source book: Evolution by Mark Ridley