BLGY2201: Multiple alignments and phylogeny-Biology Assignment

Internal Code: MAS154

Biology Assignment Assignment:

Question: Re-examining Globin Gene Phylogeny 1.Print out your molecular phylogeny of ?-globin sequences as a phylogram and produce a similar one for the human globin genes, for which the file can also be found in the VLE Resources. 2.Explain in less than 500 words what the phylogenies tell us about the history of the gene cluster. 3.Use Clustal to estimate a neighbour-joining (NJ) tree of the 15 sequences. Check the topology (that is, the branching structure) of the tree as a Cladogram then as a Phylogram. 4.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 ? Gene Phylogeny Analysis of Tyrosine Hydroxylase 1.Tyrosine hydroxylase is the key enzyme for synthesis of dopamine and norepinephrine in neurones. Hence it is found in all animals with some form of brain. We will examine its phylogeny and investigate its orgins. Using NCBI, search the protein database for eukaryotic tyrosine hydroxylases. Make a list of 25 different species with a known tyrosine hydroxylase by reading through entries. Select a set of ten from your search with as wide an evolutionary spectrum as possible based on the phylogeny shown next to the sequences (hint: right side of page). The spectrum should include mammals, mollusca, Arthropoda, and chordates. 2.Build a CLUSTAL alignment, find the optimal phylogenetic gene tree (which clustering method?) and print the dendogram. How does your tyrosine hydroxylase gene tree compare with published evolutionary trees for the included organisms found in the literature/textbooks? 3.Tyrosine hydroxylase is a member of a family of related proteins. Describe the family and it's characteristics. Download the protein sequences of members of this family from human and rat. Based on multiple alignments and phylogenetic analysis, describe the evolution of tyrosine hydroxylase. For example, you will need to determine whether there is stronger conservation between members of this family within an organism or within tyrosine hydroxylases. A few paragraphs are expected to explain and justify your results and their comparison to published literature. References should be cited. Further credit will be given for other appropriate choices of organisms to support your argument.