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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.
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.
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 paper could lead to advancements in ecological genetics, especially that of marine ecosystems
This paper will make it possible to follow gene frequency changes through time using old museum specimens and modern representatives of a population.
This paper will make it possible to organize knowledge of genetic diversity in natural populations of minute organisms that are not easily grown in the laboratory.
Homologous gene sequences can be gathered easily, this could lead to synergy between molecular and evolutionary biology.
The ability to compare individuals in this way could have a profound effect on ecological genetics, especially in the marine biosphere.
The construction and screening of clone libraries is tedious and a high level of expertise is required, making it unviable for routine use. Using restriction analysis produces a smaller understanding of DNA sequences evolution than the polymerase chain reaction produces. This means that it is difficult for an individual to determine if a high rate of evolution and a transition bias is characteristic of all animal Mitochondrial DNA Transition bias refers to the degree by which the transition to transversion ratio deviates from the expected 1/2. There was a need for a simple method of sequencing mtDNA. This is where the polymerase chain reaction (PCR) was introduced. Wilson'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 many samples can be amplified and produced with relative ease each day. The beauty of PCR is that the number of copies of the specified target segment is able to grow exponentially, as each copy can be used as a template for the production of further copies. Wilson's group were able to take advantage of the active site of enzymes, the anticidon loops of tRNAs and the stability of ribosomal ribonucleic acid in using the polymerase chain reaction. PCR is so effective because it only requires absolute matching of the primer to the template in the last few bases of the 3 prime end of the protein, 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.
When carrying out the polymerase chain reaction, it is not necessary to purify mtDNA before 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 become much easier to record gene frequency changes using many different species. Tracking them through time will also become possible, meaning it will become possible to follow gene frequency changes through time. 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 valuable insights into genetic structure and function based on phylogenetic history produced Kocher et al.'s method of PCR.
DNA barcoding uses short sequences of DNA from the genome of a species that is unique to that particular species. A sample of an organism can be taken and sequenced to find the region of its genome that acts as its barcode. This eliminates the need to sequence the entire genome, which can be immensely time consuming and expensive. The site of the genome that is commonly used to act as the site of the barcode is the 648bp region in the mitochondrial cytochrome c oxidase 1 gene (the CO1 gene). This region cannot be used in plants due to the slow evolutionary development of this particular region. This paper has successfully contributed to DNA barcoding because of the method of PCR that Kocher et al produced, as mentioned above. Their PCR method made it possible for DNA sequences to be identified from only a few nanograms of tissue, although the older the specimen, the more tissue that would be needed. This helps to identify DNA sequences because it allows the identification of sequences of a species from known taxa. It would enable you to analyse, for example, which larvae belong to which species. As the mass of larvae is small, it is not feasible to use ordinary PCR methods. This method causes less damage to the larvae and it much quicker and more cost effective that ordinary PCR methods.
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.
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. Kocher et al.'s sequences show the number of transversion differences among pairs of species above the diagonal, and the number of transitions below the diagonal. The most parsimonious trees are deduced by a character-state analysis of the data. The branch lengths of the trees are drawn proportional to the number of transversions on each lineage, with each transition being considered equivalent to 0.1 transversion. Notably, our tree is rooted. This means it is a directed tree, with a unique 'node' corresponding to the most recent common ancestor of all the entities at the leaves of the tree. Most commonly, trees are rooted using an outgroup. An outgroup is a taxon which we know diverged before the most recent common ancestor of the group in consideration. Our outgroup was the River Lamprey, Lampetra similis. This species was chosen because, as seen on the jalview sequence, it is close enough to allow interferences from sequence data, but far enough out to be seen clearly as an outgroup.
The trees by Kocher et al. are unrooted. This means it shows the relatedness of the leaf nodes without making assumptions about ancestry. A root cannot be inferred from an unrooted tree without identifying ancestry, done again by including an outgroup in the data.