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Phylogeny trees are also known as dendrograms. Phylogeny trees are used as evolutionary models using branch lengths. The nodes on the tree represent different organisms and edges are used to show lines of descent. The lengths of some branches may be used to indicate the actual evolutionary distances between taxa. The phylogram suggests that a group of organisms are descended from a particular common ancestor. The groups of organisms included within are defined as arbitrarily (French, Hodgman and Westhead, 2009).
The unrooted tree has no sense of time. The evolutionary distances on the tree suggest the similarity between two sequences by the number of changes observed in the nucleotide bases. There are several algorithms to generate phylogeny trees.
UPGMA algorithm is a popular way of generating phylogeny trees because of the simplicity assuming that evolution occurs at the same time on all tree branches i.e. molecular clock and the distances in the tree are additive. As a result, incorrect trees can be made. For example, two sequences might be similar as they have evolved very similarly but not because of a common ancestor compared to the other sequences being analysed. It produces a tree that has direct common ancestor (French, Hodgman and Westhead, 2009).
The neighbouring joining (NJ) doesn't assume fixed evolutionary rate i.e. molecular clock. It is a clustering method which is related to UPGMA that finds the nearest evolutionary distance (Nei and Saitou, 1987). The algorithm tries to find those elements that will generate smallest distances. It uses Clustral W/X programs to estimate trees from multiple sequence alignment.
There is another method of constructing the phylogeny tree which is known as Maximum Parsimony Likelihood. It uses the idea of minimum number of mutations required from one to another protein by the identification and analysis of corresponding positions in each sequence. This method is expensive in computer time so NJ is preferred. The other limitations are it can generate incorrect sequence alignment and fail to account for variation of evolution rates at different sites within the sequence (French, Hodgman and Westhead, 2009). Therefore, caution should be taken.
The softwares that can be used to generate phylogeny trees are PAUP and PHYLIP they carry out phylogenetic analysis using parsimony and interference package respectively. These softwares are updated regularly with latest phylogenetic algorithms (French, Hodgman and Westhead, 2009).
The instructions were followed as described in the protocol. The 'NCBI taxonomy browser' was accessed at the following URL: http://www.ncbi.nlm.nih.gov/Taxonomy/ to work out position of each of the animals on the tree. Then 'Taxonomy common tree' was selected in which one at the time the common/Latin name of the animals were typed in. This produced the taxonomy tree which was compared with the one constructed by hand using the genetic distances given and following this the positions of the animals were induced on the tree as shown in figure 1.
Figure 1 shows the phylogeny tree constructed using UPGMA algorithm1.
Assuming that the vertebrate evolution started 450 million years ago (MYA), the split between marsupials and the rest of the mammals has been estimated to occur 123 MYA2. Retrotransposons have been used to identify the origin of kangaroos. The idea was to look at the same region of different individuals within the species to identify if they share anything common. If they do, this will suggest that they have originated from the same ancestor. Recently, two genomes of marsupials have been sequenced and were found that there were retrotransposon elements that were specific to the kangaroo or opossum or both. There is no clear evidence which marsupials split first but it's evident that the Australian kangaroos have split off later than South American kangaroos (Churakov et al., 2010)
According to the tree constructed as shown in figure 1, dogs are more closely related than kangaroos to the humans. It is evident that the human genome is more similar to dogs than mice by analysing the genetic footprint. Moreover, the genetics of the dog is being used to gain some knowledge of human diseases. Around 5% of the dog genome is highly conserved and this region has an important function for gene regulation (Lender, 2005).
The two sequences that appear to be most closely related by viewing the tree are HV1H3 and HV1B1, the genetic distances are 0.01098 and 0.00538. These sequences had the smallest differences between the two sequences compared to the others.
A general pattern regarding the phylogeny of gp120 is seen where monkeys are much diverged from chimpanzees i.e. there are two distinct groups seen on the unrooted phylogeny tree3 probably diverged from a common ancestor.
The gp120 sequences isolated from chimpanzee Simian Immunodeficiency Viruse (SIV) is ENV_SIVCZ and from rhesus monkey SIV are ENV_SIVML, ENV_SIVMK and ENV_SIVM1. HIV has originated from SIVs which is closely related to HIV-1 and HIV-2. SIVs are originated from monkeys and it's thought that two different forms of SIVs have been transmitted to chimpanzees. It has caused the depletion of "CD4+ T-cell" which increases the chances of death of normal chimpanzees. This suggests that the AIDS originated before HIV-1 (Hahn and Sharp, 2010). HIV-1 is the propagator of AIDS and has been originated from chimpanzee whereas HIV-2 has been originated from monkeys. The fact that is found in humans is thought be by consuming chimpanzee meat which might have been infected by SIVs (commonly HIV-1 from M group) (Wolfe et al., 2004).
Multiple substitutions is a problem that requires correction because the sequences will be underestimated of the real numbers of changes that has occurred in the evolution. For example, if a base has changed from Adenine to Thymine to Thymine and then back to Adenine. This will be referred to zero changes.
The effect of the correction is hits are more clustered together4 suggesting that there were multiple substitutions in the sequences. The tree is less diverged as the sequences from similar origin are clustered together.
The main difference in the shape of the rooted tree5 and the UPGMA tree of the alpha-globins is the UPGMA tree suggests that all the organisms evolved at the same time/rate. On the other hand, the tree constructed by PHYLIP suggests that it has been evolved at different times due to selection pressures. Therefore, the difference reflects that evolution rate is not the same and is under pressure. PHYLIP produces a better and realistic tree.
All the methods to construct phylogeny trees have their own limitations. Therefore, the trees should be tested for their reliability. This can be done by using different methods to generate the tree and if the tree produced is similar with two of the methods. This suggests that the tree constructed is reliable. Moreover, the raw data could be re-sampled to test for statistical significance. This can be done by a technique called boostrapping in which the data are sampled randomly from any position within the multiple sequence alignment generating an artificial tree. This tree should match with the original one and if any branch on the tree gives bootstrapping of more than 70%. This indicates that the branch is almost correct (French, Hodgman and Westhead, 2009).
Churakov G, Nilsson MA, Sommer M, Tran NV, Zemann A, et al. (2010) Tracking Marsupial Evolution Using Archaic Genomic Retroposon Insertions. doi:10.1371/journal.pbio.1000436
French, Hodgman and Westhead (2009) Instant Notes in Bioinformatics 2nd Edition. Taylor and Francis Group.
Lender Eric (7th dec, 2005). Issue 8 of Nature. [Online]. Available at http://www.broadinstitute.org/news/253. Broad Institute Communications [accessed on 9th January, 2011].
Nei M. And Saitou N. ( July, 2004). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4(4):406-25
Hahn Beatrice H. and Paul M. Sharp (27 August 2010). The evolution of HIV-1 and the origin of AIDS doi: 10.1098/rstb.2010.0031 Phil. Trans. R. Soc. B vol. 365 no. 1552 2487-2494
Wolfe, ND et al. (20th March, 2004). Naturally acquired simian retrovirus infections in Central African Hunters The Lancet, 363(9413)
NCBI, Taxonomy Browser [Online]. Available at http://www.ncbi.nlm.nih.gov/Taxonomy/. [Accessed on 17th December, 2010].