see attached
Untitled document Types of homology case study material Following questions will refer to the phylogenetic tree described below. The image below is a phylogenetic tree of EF-Tu (EF-1α) and EF-G (EF-2) protein-coding genes. Branch supports are bootstrap percentages (bootstrap percentages from multiple methods are shown on some branches in bold font). The tip labels indicate the genus (or in some cases the genus and species) of the organism from which the gene sequences were derived. The brackets on the right side of the tree indicate the domain of life into which the genera/species are classified: Euk = Eukaryotes, Arc = Archaea, Eub = Eubacteria (Bacteria). This image is also available in PDF format here: link to PDF. https://drive.google.com/file/d/1dTTN-NutMPkiOpKwF0cYO0po70MvV7e0/view?usp=sharing 1. Rank these gene sequences (as named in the phylogenetic tree) by predicted similarity to Entamoeba EF-G. Assume that the topology of the tree is correct and that degree of sequence similarity between any two sequences is inversely proportional to time since divergence from the common ancestor. Also, ignore the possibility of variable rates of substitution among lineages. The sequence you predict to be most similar should be ranked first (as 1), and the sequence you predict to be least similar should be ranked last. If you predict that two or more sequences would have equivalent rank, then assign them equivalent rank. StaphylothermusEF-Tu Deinonema EF-Tu Anacystis EF-Tu Escherichia EF-Tu Candida EF-Tu Giardia EF-G Halobacterium EF-G Micrococcus EF-G Interpretation of phylogenetic tree topologies case study material Questions in the following section may refer to the example phylogenetic trees of microbial species shown below. Example trees The trees below are labelled/named A, B, and C, and questions will refer to specific trees by these names. These images are also available in PDF form here: link to PDF. In these trees, the microbial species (taxon names) have each been assigned numbers. Questions may include trees with these taxon numbers instead of the full taxon names for convenience. https://drive.google.com/file/d/1yu-skvgxSm3q67e1G-S7gams-adCU2Re/view?usp=sharing 2. In comparison to example tree C, which of the trees here is topologically consistent with the example tree? In other words, which of these tree topologies could be obtained through modifying the original topology by removing original taxa, adding new taxa, or re-rooting the example tree, or a combination of these three manipulations? Select all that apply. Select all that apply: a. b. 3. Define the appropriate order steps in phylogenetic analysis of genetic sequences. Set the first step as "1", the second step as "2", and so on. Mask any sites in an alignment of homologous sequences that do not show clear homology based on aligned characters at the site or in adjacent sites. Select likely homologues from among similar sequences, by inference from their similarity to your sequence of interest. Identify nucleotide sequences with similarity to the nucleotide sequence of a gene of interest for your study. Choose a branch on which to root the maximum likelihood tree based on prior knowledge or assumptions regarding identity of an appropriate outgroup taxon. Use a likelihood-based method to identify an unrooted tree with relatively high likelihood of generating the input sequence alignment (observed data) given a model of sequence substitution. Align homologous sequences in a multiple sequence alignment. 4. Regarding example tree A, which of the trees here would support all internal branches of the example tree topology if they were inferred from bootstrapped alignments? Select all that apply. a. (12,(10,11),(13,(14,(((((1,2),3),((4,5),6)),((7,8),9)),((15,16),(18,17)))))); b. None of these trees. https://eclass.srv.ualberta.ca/mod/quiz/attempt.php?attempt=8543333&cmid=5575939&page=8# c. (17,16,((((((1,2),3),((4,5),6)),((7,8),9)),((((10,11),12),13),14)),(18,15))); d. (2,7,(9,((((1,8),3),((4,5),6)),(((((10,11),12),13),14),((15,16),(18,17)))))); e. (13,((10,11),12),(14,(((((1,2),3),((4,5),6)),((7,8),9)),((15,16),(18,17))))); f. (14,(((10,11),12),13),(((((1,2),3),((4,5),6)),((7,8),9)),((15,16),(18,17)))); https://eclass.srv.ualberta.ca/mod/quiz/attempt.php?attempt=8543333&cmid=5575939&page=8# https://eclass.srv.ualberta.ca/mod/quiz/attempt.php?attempt=8543333&cmid=5575939&page=8#