Phylogeny and Systematics

Assessment Statement

D.5.1Outline the value of classifying organisms

D.5.2Explain the biochemical evidence provided by the universality of DNA and protein structures for the common ancestry of living organisms

D.5.3Explain how variations in specific molecules can indicate phylogeny

D.5.4Discuss how biochemical variations can be used as an evolutionary clock

D.5.5Define clade and cladistics

D.5.6Distinguish, with examples, between analogous and homologous characteristics

D.5.7Outline the methods used to construct cladograms and the conclusions that can be drawn from them

D.5.8Construct a simple cladogram

D.5.9Analyse cladograms in terms of phylogenetic relationships

D.5.10Discuss 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 left-handed 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. AAAATTTTCCCCGGGG
  2. AAAATTTACCCCGGGG
  3. AAAATTTACCCGCGGG
  4. 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
  4. Examples are:
  5. Eukaryotic
  6. Backbone
  7. Amniote egg
  8. Limbs
  9. Hair
  10. Opposable thumbs
  11. Multicellular
  12. Segmented body
  13. Jaws
  14. Placenta
  15. Mammary glands
  16. 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.
  17. You make a table like below, showing the derived characteristics.
  18. 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.