Biology 356 - Major Features of Vertebrate Evolution
Dr. Robert Reisz, University of Toronto
Introduction: Classification and Phyologeny
Linnean classification:
From the beginning of systematics in the 18th century until just a few decades
ago, the Linnean classification was the only form of classification. It is a
hierarchical system based on the Roman army.
In this system, each organism is classified in a series of taxa from the most
inclusive (Kingdom) down to the species. Each species is identified by the
Linnean binomial name including the genus and species (for instance, humans
belong to the species Homo sapiens). You can never give only the specific
name. Sapiens means nothing in the Linnean system.
The Linnean system used the following main categories, from the most inclusive
to the lease inclusive. I will also give the taxa corresponding to these main
categories for man.
Table 3.1. The categories of the Linnean classification.
Category
Kingdom
Phylum
Class
Order
Family
Genus
Species
Corresponding taxon for man
Animalia
Chordata
Mammalia
Primates
Hominidae
Homo
sapiens
Early Linnean classifications and even many of the recent ones did not reflect
phylogeny, either because it wasn’t known, or because systematists chose to
classify together animals that looked similar rather than animals that were closely
related.
Early classifications were often horizontal classifications. By horizontal, I mean
that they included animals that looked similar to each other, but not all closely
related animals were grouped together. We will look at amniotes to illustrate the
concept of horizontal classification.
Figure 3.1. Illustration of horizontal and vertical classifications. The traditional
Reptilia, the paraphyletic group, and its members are in blue.
The class Reptilia (fig. 2.1) included all the earliest amniotes, squamates,
crocodiles, and the early relatives of mammals and birds, but it excluded
mammals and birds. The Reptilia included ectothermic tetrapods that were
covered by epidermal scales. The reason for excluding mammals and birds from
the Reptilia is that they looked different: for example, they are endotherms and
they were covered with hair or feathers instead of scales.
Cladistics
We will now discuss a second type of classification called phylogenetic
systematics or cladistics (the first one was the Linnean classification). This
second method of classification is necessary because systematists now want to
avoid horizontal classifications. We want classifications that directly reflect
phylogeny. This means that we must use only taxa including an ancestor and all
its descendants. Such a taxon is called a clade. For instance, the Amniota is a
clade, but the Reptilia as I defined it previously is not a clade. A clade is a
monophyletic taxon. These two expressions are synonyms.
A lot of old taxa are not clades. We call these paraphyletic taxa. Paraphyletic
means that the taxon does not include all the descendants of the last common
ancestor of the group. Such taxa includes the Reptilia, Pisces (fishes),
Osteichthyes (bony fishes), the Dinosauria (in the old sense; excluding birds).
In the literature, you will also read about polyphyletic taxa. These are even
worse. They include species or groups of species coming from more than one
ancestral lineage. Of course, we don’t recognize polyphyletic or paraphyletic taxa
in cladistics.
Let me now introduce a few more technical words that we will use often:
•
Homology: The relationship between the structures found in different
species having been derived from a common ancestor. The structures
must all be derived from the same structure found in the ancestral
species. For example, the wing of a bird and the arm of a crocodile are
homologous because they are both derived from the arm of an ancestral
archosaur.
•
Analogy: The relationship between similar structures that have been
derived independently. For example, the wing of a bird and the wing of a
bee are not derived from a wing in a distant common ancestor of birds and
bees. Therefore, they are analogous structures.
•
Character: Any feature having at least two states and visible in at least a
few taxa.
•
Synapomorphy: A shared derived character. By shared, I mean that at
least two taxa must possess this character. Derived indicates that it must
be a character that appeared not long before the taxa that possess it. For
example, horses, and zebras have a single functional digit (or finger) in
each hand and foot. This is a recent character and other mammals don’t
have this character. Therefore, the presence of a single functional digit in
horses and zebras is a synapomorphy.
•
Symplesiomorphy: A shared primitive character. By primitive, I mean that
it is an old character that is present in other animals than those that you
compare. For instance, horses and zebras have hair, but so do tigers,
bears, kangaroos, and most other mammals. Therefore, the presence of
hair in horses and zebras is a symplesiomorphy.
•
Homoplasy or convergence: A shared character that was independently
developed in at least two lineages. For instance, the wing of birds was
developed independently from the wing of bats. Therefore, the presence
of a wing in these two taxa is a homoplasy.
•
Autapomorphy: A unique character. It indicates that the animal is different
from the others. It gives no clues about phylogeny.
In cladistics, we are interested only in synapomorphies, because only
synapomorphies allow us to study phylogeny.
Most speciation events occur in a dichotomous fashion; one species splits into
two. This phenomenon is critical for phylogenetic analysis, because we want to
show the history of animals as a series of branching events.
Let me explain how we study phylogeny.
First, we choose the taxa that we want to study. Let’s take sharks,
actinopterygians, salamanders, and a lizards.
We then have to choose an outgroup. An outgroup is a taxon that is not part of
the group that you study, but that should be close to this group. In this case, we
study jawed vertebrates, also called gnathostomes, so we will choose a jawless
vertebrate, the lamprey, as the outgroup.
The next step is to find characters that allow you to differentiate and group the
animals.
1) Sharks and actinopterygians have internal gills, whereas salamanders and
lizards don’t.
2) Actinopterygians, salamanders and lizards have a bony internal skeleton,
whereas sharks have a cartilaginous internal skeleton.
We now have to polarize the characters, to know which condition is primitive and
which is derived. The condition present in the outgroup, here the lamprey, is
usually the primitive one.
1) Lampreys have gills. Therefore, the gills of sharks and actinopterygians
are primitive, and the absence of gills in salamanders and lizards is
derived and indicate relationship.
2) Lampreys have a cartilaginous endoskeleton. Therefore, the cartilaginous
skeleton of sharks is primitive, whereas the bony skeleton of
actinopterygians, salamanders and lizards is derived and indicates
relationship.
We build a data matrix, in which we code the states of all the characters in all the
taxa. We score a 0 for a primitive state, and a 1 for a derived state.
Table 3.2 A simple data matrix.
Taxon
Sharks
Actinopterygians
Salamanders
Lizards
Character
1
0
0
1
1
2
0
1
1
1
We then count the number of synapomorphies between every pair of taxa. There
are none between the shark and actinopterygians, none between sharks and
salamanders, none between sharks and lizards, one between actinopterygians
and the salamanders, one between the actinopterygians and lizards, and two
between the salamanders and the lizards. These results are best put into a table.
Table 3.3. Number of synapomorphies between taxa.
Shark
Salmon
Salamander
Lizard
Shark
--0
0
0
Salmon
0
--1
1
Salamander
0
1
--2
Lizard
0
1
2
---
Note: the table is symmetrical, so only half is needed (either the half above or
below the dashed line).
Therefore, we put salamanders and lizards together in a clade. Of the two taxa
left over, actinopterygians shares one derived character with salamanders and
lizards. Therefore, actinopterygians are the sister-group of the clade including
salamanders and lizards. The resulting tree
is: (shark(actinopterygians(salamanders, lizards))).
Figure 3.2. Phylogeny reconstructed. Apomorphies are indicated by bold and
color. Notice that the treelength is 2.
This is the shortest possible tree given our data. Any other tree will require more
steps (see fig. 3.3).
Figure 3.3. Other randomly chosen tree. Notice that it requires 3
steps. Therefore, it is not as parsimonious as the tree reconstructed in fig. 3.2.
This is a simplified example. The reality is usually more complex, and there are
often incompatibilities between characters. This happens when a character
evolves convergently in two species. When there is convergence, we simply
choose the tree that requires the least amount of convergence. The method that
we used to find the tree does not guarantee to find the most parsimonious
tree. To do that, we would have to look at all the trees. This is possible when you
study just a few taxa, but the number of trees increases very fast with the number
of taxa. Therefore, you can not look at all the trees when you study several
taxa. Even with a few taxa (5 or 6), a rigorous analysis would be very timeconsuming if it were done by hand.
Modern phylogenetic studies often include more than ten taxa and at least fifty
characters. With data sets this large, the analysis has to be done by
computer. There are now several phylogenetic analysis programs for
microcomputers, especially for the Macintosh and the IBM compatibles.