Phylogeny and Systematics
Assessment Statement
D.5.1
D.5.2
D.5.3
D.5.4
D.5.5
D.5.6
D.5.7
D.5.8
D.5.9
D.5.10
Outline the value of classifying organisms
Explain the biochemical evidence provided by the universality of DNA
and protein structures for the common ancestry of living organisms
Explain how variations in specific molecules can indicate phylogeny
Discuss how biochemical variations can be used as an evolutionary clock
Define clade and cladistics
Distinguish, with examples, between analogous and homologous
characteristics
Outline the methods used to construct cladograms and the conclusions
that can be drawn from them
Construct a simple cladogram
Analyse cladograms in terms of phylogenetic relationships
Discuss the relationship between cladograms and the classification of
living organisms
One of the objectives of classification is to represent how living and extinct organisms
are connected, which means natural classification. Phylogeny is the study of the
evolutionary past of a species. Species which are the most similar are most likely to be
closely related, whereas those which show a higher degree of difference are considered
less likely to be closely related.
There are several values to classifying this way.
1. We can identify unknown organisms, as other similar organisms are grouped
together using a key.
2. We can see how organisms are related in and evolutionary way. By looking at
organisms, which have similar anatomical features, it is possible to see
relationships on their phylogenetic tree. DNA evidence confirms the anatomical
evidence for placing organisms in the same group.
3. It allows for the prediction of characteristics shared by members of a group.
Biochemical Evidence for common ancestry
Biochemical evidence, including DNA and other protein structures, has brought new
validity and confirmation to the ideas of a common ancestor.
The fact that every known living organism on Earth uses DNA as its main source of
genetic information is compelling evidence that all life came from a common ancestor.
All the proteins found in living organisms use the same 20 amino acids to forms their
polypeptide chains. Genetic engineering has provided some evidence of this.
Amino acids can have two possible orientations: left-handed and right-handed,
depending on how the atoms are attached. All the living organisms on Earth have lefthanded amino acids and none are right-handed, leading to the belief that there is a
common ancestor.
Traditionally, looking for similarities has been done using morphology. More attention
recently to molecular differences is now the area of study.
Although the same components are used to make DNA and protein in all organisms, the
sequence of these components may be different. If we compare the amino acid sequences
of haemoglobin in humans, cats and earthworms, we see that cats and humans have
greater similarities that humans and earthworms.
This shows two trends:
1. The more similar the biochemical evidence, the more interrelated the species are
2. The more similar the evidence, there is less time since the two species had a
common ancestor (ie. The ancestor of earthworms lived a longer time ago than
the ancestor of cats and human.
3. Changes in the DNA sequences of genes from one generation to another are
partly due to mutations and the more differences there are between two species,
the les closely related they are.
Here is an imaginary example of DNA sequence from four different species.
1.
2.
3.
4.
AAAATTTTCCCCGGGG
AAAATTTACCCCGGGG
AAAATTTACCCGCGGG
AACATCTTCCACGCTG
It is clear that species 1 and 2 have the fewest differences between them and we can
conclude that they are more closely related.
Since this evidence is not conclusive on its own, it is often used together with other data,
such as palaeontological data.
The evolutionary clock
The principle is you study similar molecules in different species and determine how
much difference there is between the molecules. The more difference there is, the longer
the time span since the two species had a common ancestor. Differences in polypeptide
sequences accumulate steadily and gradually over time, as mutations occur from
generation to generation in a species. The changes can be used as a kind of clock to
estimate how far back in time two related species split from a common ancestor. This is
called the evolutionary clock.
Commonly used proteins are haemoglobin, cytochrome c (a respiratory protein which is
part of the electron transport chain) and nucleic acids. We count up the number of base
pairs, which do not match.
Using haemoglobin show that humans are more closely related to chimps rather than
gorillas or gibbons. Using cytochrome c, we see that humans have identical molecules,
while rhesus monkeys only differ by one amino acid. Humans and rhodospirillium
(bacteria) or yeast (fungi) have identical amino acid sequences in part of the cytochrome
c molecule!!!
Number of differences in the Beta Haemoglobin Chain compared to Human
Haemoglobin.
Imagine comparing certain DNA sequences form three species A, B and C. Between the
DNA samples from A and C there are 83 differences. Between A and B, there are only
26 differences. We can conclude that A is more closely related to B than C. There has
been more time for DNA mutations to occur since the split between A and C than since
the split of A and B.
One technique, which has been successful in measuring differences in biochemical
studies, is DNA hybridization. We take one strand of DNA from species A and a
homologous strand from B and fuse them together. Where the base pairs connect, there
is a match; where they are repelled and do not connect, there is a difference in the DNA
sequence.
This can be taken further. If we see that 83 differences is approximately three times more
than 26 differences, we can conclude that the split between species A and C happened
about three times further in the past that the split between species A and B. We can
express this in a cladogram. There are two forms, which we will look at in a little bit.
Percentage difference in DNA
A
B
C
C
B
A
Time in mya
Keep in mind this clock is not a consistent “tick-tock” like the clock on the wall.
Mutations happen at varying rates. The above is an estimation of the events. Again this
is all compared to morphological data and radioisotope dating.
Clades and Cladistics
Cladistics – a system of classification, which groups taxa together according to the
characteristics, which have most recently evolved. It is the concept of
common descent that decides into which group an organism belongs. It is
therefore an example of natural classification, where primitive and derived
traits are looked at as to how many are shared.
Clade – a monophyletic group. This means it is a group composed of the most recent
common ancestor of the group and all its descendents. It could be made up of
several species. Comes from the Greek work ‘klados’ meaning ‘branch’.
To decide how close a common ancestor is, researchers look at how many primitive and
derived characteristics the organisms share. Primitive traits (plesiomorphic traits) are
characteristics which have the same structure and function and which evolved early on in
the organism’s development. Derived traits (apomorphic traits) are characteristics which
have the same structure and function, but which evolved more recently as modifications
of a previous trait. A primitive trait would be plants with vascular tissue in leaves but a
derived trait are the flowers, which developed after the leaves in angiosperms.
Analogous and homologous characteristics
To put organisms in the appropriate clades, two types of characteristics considered are
analogous and homologous characteristics.
Homologous – are characteristics from the same part of the common ancestor.
Pentyldactal limbs are examples. Eyes are another example.
Analogous – are characteristics which may have the same function but do not have the
same structure. All animals with wings fly, but they are not in the same
clade due to the structural differences between a fly wing, and a bird’s
wing.
How cladograms are made
To represent the findings of cladistics in a visual way, a cladogram is used. It is a
diagram, in which nodes are used to separate species and organisms, which have diverged
from the common ancestor and form a clade. The cladogram below takes into account
skeletal structures and that bats and dolphins are placental mammals.
The way to construct a cladogram is to look at biochemical differences or morphological
differences.
1. Make a list of the organisms involved
2. Make a list of as many possible characteristics, which each organism possesses.
3. From the list many traits will clearly be derived characteristics
a. Examples are:
i. Eukaryotic
ii. Backbone
iii. Amniote egg
iv. Limbs
v. Hair
vi. Opposable thumbs
vii. Multicellular
viii. Segmented body
ix. Jaws
x. Placenta
xi. Mammary glands
4. Once the list has been established, there will be one, which is common to all the
organisms being studied. The ancestral trait is considered the primitive
characteristic. Morphologically, would be eukaryotic or multicellular. In
biochemical data, it might be a certain sequence to base pairs.
5. You make a table like below, showing the derived characteristics.
6. You make the cladogram with the first branch form the bottom belonging to the
organism with the fewest derived traits. The organism with the most derived
characteristics goes to the top of the last branch.
Why are cladograms constructed?
To show the evolutionary relationships between organisms. It can be concluded that
organisms whose branches start at the bottom of the cladogram are the earliest ones to
have evolved and the ones at the top are the ones, which have evolved most recently
among the organisms considered in the cladogram.
Each time there is a point where the branch forks into two, a split occurred between
species to develop into two lineages. This splitting point is called a node and it shows
where a new species and a new clade, was founded. This makes the assumption that only
one branching off can happen at any one time, generating two species where there was
previously one.
One of the basic ideas behind cladistics is the concept of parsimony. This refers to the
preference for the least complicated explanation for a phenomenon. It would be unlikely
that a species would take two steps to evolve, if one step is possible.
To confirm the common ancestry from a cladogram, which is based on morphological
evidence, another should be made using biochemical data for the same organisms. The
two cladograms should be identical.
Construct a Cladogram
The organisms are paramecium, flatworm, shark, hawk, koala, camel, human
Characteristics are eukaryotic, multicellular, have a vertebral column, produce an
amniote egg, have hair, have a placenta, have one opposable thumb on each forelimb.
Construct your cladogram
Analyze
What was the primitive characteristic?
For each node, list the characteristic to put the organism in each clade.
Cladograms and classification
Cladistics attempts to find the most logical and most natural connections between
organisms to reveal their evolutionary past. Every cladogram drawn is a working
hypothesis. It is open for testing and falsification. This makes cladistics scientific but
changes are new evidence arises.
Each time a derived characteristic is added to the list shared by organisms in a clade, the
effect is similar to going up one level in the traditional hierarchy of the Linnaean
classification scheme. Hair is what defines a mammal, so any species with hair is a
mammal.
What about feathers? If an organism has feathers, is it automatically a bird? In
traditional classification, birds occupy a class of their own, but this is where cladistics
comes up with a surprise. When preparing a cladogram, it becomes clear that birds share
a significant number of derived characteristics with a group of dinosaurs called the
theropods. This suggests that birds are an offshoot of dinosaurs rather than a separate
class of their own.
Since birds are one of the most well documented classes of organisms on Earth, this idea
was controversial. Some derived characteristics are:
 Fused clavicle (wishbone)
 Flexible wrists
 Hollow bones
 Characteristic egg shell
 Hip and leg structure, notably with backward pointed knees
Following parsimony, it would be more likely that birds evolved from dinosaurs that they
evolved from another common ancestor. This is where cladistics is clearer than the
Linnaean system. In cladistics, the rules are always the same concerning shared derived
characteristics and parsimony. In the Linnaean system, apart from the definition of
species, which we have already seen can be challenged, the other hierarchical groupings
are not always clearly defined: what makes a class a class and a phylum a phylum?
Biologists now increasingly adopt cladistics as a useful tool for determining natural
classification and evolutionary connections.