A phylogenetic tree is the only figure in On the Origin of Species. This shows the immense central importance of such trees to evolutionary biology. It is a graph used to show the evolutionary history of a group of homologous sequences or organisms from which information about the evolutionary history of genes and inheritance patterns may be deduced. The trees shown above are Phylograms and organisms with high degrees of molecular similarity are expected to be more closely related than those that are dissimilar. The first tree above represents beta-globin sequences. It illustrates the relationship between globin sequences of different species and illustrates the patterns of beta-globin evolution. The second phylogenetic tree represents human globin sequences. These two trees enable us to determine information about the history of the gene cluster. Globin gene clusters in animals are paralogous genes, meaning they are related by duplication of a common ancestral locus. Paralogous genes within an organism are duplicated to occupy different positions in the same genome. An example of a pair of paralogous genes is the haemoglobin gene in humans and the myoglobin gene in chimpanzees.
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Terminal nodes indicate the taxa for which molecular information has been obtained, and internal nodes represent common ancestors before branching occurs, producing two separate groups of organisms. Branch lengths are scaled to show the amount of divergence between the taxa they connect. At each node of the phylogenetic tree, gene clustering is performed, using the evolutionary relationships of the organisms and pair-wise protein distances as input. This process means that at each node of the tree, the genes of the descending taxa are more closely related to each other than they are from the taxa in the outgroup.
A hierarchical approach is often used, staring at the base of the most understood evolutionary tree and proceeding up the tree. At each node, taxa are grouped so that those organisms on one branch are clade A and on the other branch clade B. This means that genes from organisms within clade A are more similar to each other than they are to clade B and genes from clade A and clade B are more closely related to each other than to any genes in other groups on the phylogenetic tree.
Why do you think the paper has been so useful? Briefly list its main achievements and how it led to the new technology of DNA barcoding and how this is being applied. [25 marks]
This paper explores animal evolution based on mitochondrial DNA (mtDNA). DNA barcoding is a taxonomic method, using a short genetic marker in the DNA of an organism to identify it as belonging to a particular species. The goal of DNA barcoding is to identify an unknown sample through a known classification.
The construction and screening of clone libraries is tedious and a high level of expertise is required, making it unviable for routine use. Restriction analysis produced limited understanding of the dynamics of DNA sequence evolution. This means that it is difficult to determine whether a high rate of evolution and a transition bias are characteristic of all animal mtDNAs. There was a need for a simple method of sequencing mtDNA. This is where the polymerase chain reaction (PCR) was introduced. Wilsonâ€™s group was a pioneer of the polymerase chain reaction and the success of this paper can be attributed to the use of the polymerase chain reaction. PCR enables the user to clone sequence in vitro in just a few hours. PCR can be easily automated and hundreds of samples can be amplified each day. The number of copies of the target segment grows exponentially as each copy can be used as a template for the production of further copies. Wilsonâ€™s group took advantage of the stability of rRNA, the anticodon loops of tRNAs and the active site of enzymes in using the polymerase chain reaction. PCR is so effective because it requires absolute matching of the primer to the template only in the last few bases of the 3â€™ end, meaning primers with several mismatches can be used. DNA was sequenced using a commercially and widely available DNA sequencing kit (Sequenase), enabling the method stated in this paper to be used by anyone wanting to carry out PCR.
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When carrying out the polymerase chain reaction, it is also not necessary to purify mtDNA prior to amplification, total cellular DNA can be used for amplification. Also, the amount of tissue needed to produce a sequence is only a few nanograms, and if the specimen is older, a few milligrams. This means PCR is much quicker than other methods, as it is simple to access the tissue needed.
Another advantage of PCR is that if errors are generated, they are distributed at random in terms of position within codons and to codons within the cytochrome b gene. As universal primers can be designed for parts of genomes, the necessity for cloning is bypassed and sequences can be obtained directly from the polymerase chain reaction. From this method, it will be possible to follow gene frequency changes through time using many possible specimens. PCR will make it possible to organise the knowledge of minute single celled natural populations that cannot easily be grown in the laboratory, as they have enough mtDNA to allow PCR to take place. Homologous sequences can be gathered simply and easily, allowing insights into genetic structure and function based on phylogenetic history produced by the polymerase chain reaction.
Neighbour-joining tree of the 15 sequences, presented as a Phylogram.
Neighbour-joining tree of the 15 sequences, presented as a Cladogram. (The most basic type of tree, which just show the branching order)
Neighbour-joining tree presented using Jalview.
How is your tree similar or different from the three trees presented by Kocher et al. (1989)?
If they differ at all, why might this be? (Check the legend to Figure 3.) [20 marks]
The three trees presented by Kocher et al. are shown below.
The first tree, that of the neighbour-joining tree of the 15 sequences as a Phylogram shows that Rodents and Fish are more closely related than Rodents and Birds as shown in the trees presented by Kocher et al. The second tree, that of the 15 sequences presented as a Cladogram shows the same relationship, that Rodents and Fishes are more closely related than Rodents and Birds. The neighbour-joining tree presented using Jalview is the tree closest to that shown by Kocher et al. The Jalview tree shows that Birds and Rodents are closely related, with Birds and Fishes less so. When comparing the groups, it is clear that in the trees by Kocher et al., Rodents are the oldest group, then birds and finally the fish, due to the amount of transversion. In my phylogenetic graph, Rodents are shown to be the oldest, corresponding to the trees shown by Kocher et al., then Fish then Birds. The lines on the phylogram represent evolutionary changes. Rodents have the longest lines are they have evolved more than the birds and fish.