Minimum of 350 words please.
Untitled document Read the email below. Upload the provided Newick format phylogenetic tree to iTOL for visualization as demonstrated in class. You may find it useful to select "At tips" in the "label options". Also, you will want to display bootstraps in "Text" form in the "Advanced" options tab. Note that the taxon names begin with real NCBI accession numbers (in case you want to look up these sequences in NCBI databases). Also note that carefully choosing a branch on which to root the tree may be very important for interpreting the tree. Interpret and analyze the the phylogenetic tree using concepts discussed in class as well as information from the email. Write a response in the space provided. This is worth 10 marks in as follows: Format your response as a coherent email in your own words [1 mark]. Your response should address each of the sequences from Enterococcus species, and for each provide an explanation of the topology of the phylogenetic tree (i.e., why it contrasts with the rRNA trees shown in Bergey's Manual) [3 marks] as well as a recommendation for how to proceed with the phylogenomics project described in the email [3 marks]. Each of these points should be justified using concepts learned in class. Suggest a potential improvement to the phylogenetic analysis that could help test whether the explanations you provided are correct (i.e., what would make you more confident in your conclusions?) [1 mark]. Cite any sources you refer to by including the author, year, and Digital Object Identifier (DOI) number [1 mark]. In-text citations are sufficient if they include these elements. At least one scientific article (which supports at least one of your points) must be cited. Limit your response length to a minimum of 350 words and a maximum of 550 words [1 mark]. Bibliographies are not necessary, but if included they will not be included in the word count. (Hint: Compose first in a google document, count words with the word count tool, then paste into the response box). Please do not sign your response with your real name. You may use a pseudonym instead if you wish. https://itol.embl.de/upload.cgi Email: __________________________________________________________________________________________________ ___ From: linda@somebiguniversity.edu Date: October 28, 2021 Dear Colleague, I am writing to ask for your expert advice on a project of mine. I am trying to perform a phylogenomic analysis of Firmicutes, using some Actinobacteria as an outgroup. For this, I've curated a concatenated gene alignment of hundreds of core genes. The problem I've encountered is that in my results, there is surprisingly low support for the monophyly of species in the genus Enterococcus. I was expecting to see support for this, and a topology similar to the ribosomal RNA phylogenies in the Bergey's Manual article on Enterococcus. What I've started doing is looking through the individual gene alignments in my dataset to look for issues. One potentially problematic alignment seems to be the alignment of elongation factor proteins. I ran a quick approximate maximum-likelihood phylogenetic analysis (substitution model: LG) on a few representative sequences from this alignment, and the results are confusing to me (see tree in Newick format below). The branch support values of 0.85 (out of 1) or higher indicate strong support from the method I used. A mutual friend of ours mentioned that you have some experience with phylogenetics of elongation factor proteins, so I was hoping you would be able to provide some insight. Is there anything I can improve to get better support in my phylogeny of Firmicutes? Here's the tree in Newick format: (WP_031510638.1_elongation_factor_Tu_Streptomyces_megasporus:0.258042247, (WP_027825487.1_elongation_factor_Tu_Lactobacillus_psittaci:0.163509994, (AAG39235.1_elongation_factor_Tu_partial_Enterococcus_hirae:0.082290248, (WP_031366687.1_elongation_factor_Tu_Lactococcus_chungangensis:0.062952248, WP_135782561.1_elongation_factor_Tu_Streptococcus_rubneri:0.035143364)0.977: 0.061474746)0.956:0.065854297)0.979:0.084683263, ((AAG39230.1_elongation_factor_Tu_partial_Enterococcus_durans:0.016889282, WP_127978067.1_elongation_factor_Enterococcus_avium:1.877692333)0.625:0.045553103, (WP_126434594.1_elongation_factor_Tu_Bacillus_freudenreichii:0.084154502, ATV00233.1_elongation_factor_Tu_Bacillus_velezensis:0.058240580)0.918:0.033585222)0.946:0.05 5771479); Thank you in advance, Sincerely, Dr. Linda Margulis -- Assistant Professor Department of Microbiology and Protistology Some Big University __________________________________________________________________________________________________ ___