6 pages of multiple choice
Which of these tree topologies in Newick format represents a 2-domain tree of life? Taxon names indicate clades containing species from only one of the three domains (Bacteria, Archaea, and Eukaryotes) as indicated. Do not consider alternative rootings for rooted trees. Select all that apply. a) (Archaea, bacteria, (arachea, eukaryotes)); b) (eukaryotes, archaea, (bacteria, bacteria)); c) (bacteria, archaea, (bacteria, eukaryotes)); d) ((bacteria, eukaryotes), (archaea, archaea); e) ((bacteria, archaea), (archaea,eukaryotes); f) ((archaea, archaea), bacteria, eukaryotes); g) ((archaea, eukaryotes), bacteria, archaea); h) (bacteria, (archaea, (eukaryotes, eukaryotes)); i) (bacteria, archaea, (archara, eukaryotes)); j) ((archaea, (eukaryotes, archaea)), bacteria); k) ((eukaryotes, archaea), bacteria, bacteria); l) (archaea, (eukaryotes, bacteria), bacteria); What is bootstrapping ? Select one. a. Calculating a tree based on a random selection of half the sites in an alignment. b. Calculating a tree based on a non-random selection of half the sites in an alignment. c. Calculating a tree based on a non-random selection of sites from an alignment equivalent to the total number of sites present; a site can be sampled multiple times. d. Calculating a tree based on a random selection of sites from an alignment equivalent to the total number of sites present; a site can be sampled multiple times. Which of the following does not bias a phylogenetic analysis? Select one. a. Vertical inheritance of nucleotide substitutions b. Recombination between homologous genes c. Homoplasy between analogous genes d. Horizontal gene transfer between homologous genes e. Long branch attraction between distant relatives For building a phylogenetic tree for taxonomic classification, which of the following genes would be considered? Select one. a. Antibiotic resistance, ribosomal proteins, recA protein b. Antibiotic resistance, ribosomal proteins c. Ribosomal proteins, recA protein d. All of the above e. None of the above Match these traits of microbial cells with a relevant genetic factor discussed in class. · Hyperthermophily, translation of the genetic code common among extant terrestrial life, methanogenesis, oxygenic photosynthesis, phagocytosis · Genes that do not code for proteins, a gene encoding a protein that forms polymers, genes encoding integral membrane proteins that form complexes, gene encoding subunits of reductase enzyme, a gene encoding an enzyme that supercoils chromosomes This trait is unique to archaea. Select one: a) Ester-linked fatty acid bilayer cell membrane b) Ether-linked isoprenoid monolayer cell membrane c) S-layer protein in cell wall d) Peptidoglycan layer in cell wall e) None of the above Consider the following scenario: An archaeal genome contains a genome with 2,237 genes. Another archaeal genome contains 3,663 genes. There are 564 single-copy genes in the first archaeal genome that are orthologues of 564 single-copy orthologous genes in the second genome. If the first genome is a reference genome, and the second is your query genome, what is the percentage of shared genes between these two genomes? Enter as a percentage (decimal number between 0.00 and 100.00) with two significant digits and without units. Two homologous genes have an identical nucleotide at the same position in a multiple sequence alignment. These have not been inherited from a common ancestor but have arisen through independent evolutionary events. This is: a) Homology b) Homoplasy c) Single nucleotide polymorphism d) Paralogy e) Orthology Select all that apply: a) A topoisomerase III homologue may have been lost in the evolution of Yersinia pestis. b) The genome of LUCA must have contained reverse gyrase. c) The last common ancestor of Homo sapiens and Bacillus cereus is not the last common ancestor of Aeropyrum pemix and Escherichia coli. d) Type 1A-like DNA topoisomerases were present in the last bacterial common ancestor, but not the last archaeal common ancestor. e) Aquifex topoisomerase I homologues are polyphyletic. f) The relationships among reverse gyrase orthologues as depicted in this tree are compatible with the currently accepted 2-domain tree of life topology. g) This tree is consistent with a 3-domain topology of the tree of life. h) An important prior assumption of this phylogenetic analysis is that reverse gyrases are paralogous to archaeal topoisomerase III. i) An important prior assumption of this phylogenetic analysis is that reverse gyrases are homologous to eukaryotic topoisomerase III. j) More sequence changes occurred in the evolution of Homo sapiens topoisomerase III alpha than in the evolution of Bacillus cereus topoisomerase III, since their divergence from their common ancestral gene. k) The last common ancestor of Archaea must have possessed a reverse gyrase orthologue. l) The evolutionary relationships among topoisomerase III orthologues are consistent with monophyly of the TACK archaea. m) Reverse gyrase may have originated in bacteria, archaea, or could have already been present in their common ancestor. n) The last universal common ancestor may have possessed fewer topoisomerase III paralogues than are found in the genome of Entamoeba histolytica. o) Bacterial reverse gyrase orthologues are polyphyletic. p) Bacterial reverse gyrase orthologues are polyphyletic. The image shown below is a screenshot of a clade in a real phylogenetic tree of amino acid sequences of sulfur carrier proteins. How many bacterial orders are represented by the sequences in this clade? In the clade shown, taxon names start with a 10-character code followed by the species name, which is then followed by information about the specific sequence. Use the species names and the NCBI taxonomy database to answer the question. Do not disregard candidate taxonomic groups present in the NCBI taxonomy, but do disregard species that have not been assigned to a group of the relevant taxonomic rank. Enter your answer as a whole number without sign or units. Consider the following scenario: The image below represents an SSU rRNA gene phylogeny of novel archaea recently isolated from a remote location. To extract genetic information from these isolates including both SSU rRNA sequences and sequences of other genes, you subjected these isolates to single-cell genome sequencing. To understand the evolution of specific archaeal traits in this novel environment, you looked a key gene of interest, "gene x". In particular you are interested in detecting any HGT of this gene among these isolates. Assuming that the SSU rRNA phylogeny below matches the true phylogeny of these organisms, which of these gene trees suggests some possibility of HGT? Select all that apply. a) None of these trees b) c) d) e)