Evolution and Molecular Phylogeny
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Questions and Answers

What does the Molecular Clock Hypothesis state about molecular evolution?

  • It varies significantly among all genes.
  • Molecular evolution occurs at random intervals.
  • The rate of molecular evolution is approximately constant for a given gene. (correct)
  • The rate of molecular evolution is the same across all organisms.

    • Which factor does not influence the rate of molecular evolution according to the caveat mentioned?

  • Different organisms
  • Functional retention of the gene
  • Different genes/proteins
  • Environmental conditions (correct)

    • What is the primary focus of Molecular Phylogeny?

  • Understanding genetic mutations over time
  • Classifying organisms based on physical traits
  • Evaluating environmental impacts on species
  • Studying evolutionary relationships using molecular biology techniques (correct)

    • In the context of a phylogenetic tree, what does 'topology' refer to?

    <p>The relationships among proteins or objects depicted in the tree</p> Signup and view all the answers

    Which statement accurately reflects a limitation of the Molecular Clock Hypothesis?

    <p>It is only applicable when a gene retains its function over time.</p> Signup and view all the answers

    Which of the following is true about the 'clock' referenced in the Molecular Clock Hypothesis?

    <p>It varies among different genes and proteins.</p> Signup and view all the answers

    What does the term 'external node' refer to in a phylogenetic tree?

    <p>The terminal points representing actual species or sequences</p> Signup and view all the answers

    What is one potential drawback of using molecular data for phylogenetic analysis?

    <p>The accuracy can vary based on gene function retention.</p> Signup and view all the answers

    What is the first step in the TREE-PUZZLE Program?

    <p>Quartet puzzling for support estimation</p> Signup and view all the answers

    What does Bayesian Methods primarily model?

    <p>Uncertainty in complex models</p> Signup and view all the answers

    What is a common method used to assess the accuracy of phylogenetic trees?

    <p>Bootstrap analysis</p> Signup and view all the answers

    Which of the following describes the process of generating a consensus tree in the TREE-PUZZLE Program?

    <p>Estimating support from quartet puzzling</p> Signup and view all the answers

    What threshold is sometimes used to consider bootstrap values as supportive of clade designations?

    <p>70%</p> Signup and view all the answers

    What is the main output of Bayesian inference in tree-building methods?

    <p>The most probable tree</p> Signup and view all the answers

    Which step follows the creation of an artificial dataset from random MSA columns in bootstrap analysis?

    <p>Generating initial phylogenetic trees</p> Signup and view all the answers

    In the context of evaluating phylogenetic trees, which of the following is NOT a parameter to assess accuracy?

    <p>Determinacy</p> Signup and view all the answers

    What does Hamming Distance measure in regards to molecular sequences?

    <p>The degree of divergence between sequences</p> Signup and view all the answers

    Which model corrects Hamming Distance by adjusting the probability of mutation rates?

    <p>Jukes-Cantor One-Parameter Model</p> Signup and view all the answers

    What is a key feature of the Kimura Two-Parameter Model?

    <p>Adjusts probabilities for transition and transversion mutations</p> Signup and view all the answers

    Which tree-building method is computationally fast for a large number of sequences?

    <p>Unweighted-Pair Group Method with Arithmetic Mean (UPGMA)</p> Signup and view all the answers

    What assumption does the Unweighted-Pair Group Method with Arithmetic Mean (UPGMA) make?

    <p>Constant molecular clock</p> Signup and view all the answers

    Which model adjusts for GC content during analysis?

    <p>Tamura's Model</p> Signup and view all the answers

    What is the main drawback of the Neighbor Joining (NJ) method compared to UPGMA?

    <p>It does not make constant clock assumptions</p> Signup and view all the answers

    Which model accounts for unequal substitution rates across variable sites?

    <p>Gamma (Γ) model</p> Signup and view all the answers

    What is the first stage of phylogenetic analysis?

    <p>Sequence Acquisition</p> Signup and view all the answers

    Which stage involves aligning sequences that are homologous?

    <p>Multiple Sequence Alignments</p> Signup and view all the answers

    In the context of multiple sequence alignments, what is a key consideration?

    <p>Using only partial sequences</p> Signup and view all the answers

    What should be inspected according to sequence metadata during multiple sequence alignments?

    <p>The alignment quality</p> Signup and view all the answers

    What is the purpose of evaluating trees in phylogenetic analysis?

    <p>To validate the phylogenetic relationships proposed</p> Signup and view all the answers

    Which method is NOT part of the five stages of phylogenetic analysis?

    <p>Data Cleaning Methods</p> Signup and view all the answers

    What is crucial when handling gaps in multiple sequence alignments?

    <p>Their implications should be understood and addressed</p> Signup and view all the answers

    Which of the following is a method used in phylogenetic analysis?

    <p>Tree-Building Methods</p> Signup and view all the answers

    What does a branch in a phylogenetic tree connect?

    <p>Two nodes</p> Signup and view all the answers

    What does branch length in a phylogenetic tree represent?

    <p>The number of molecular changes that occurred</p> Signup and view all the answers

    Which type of node represents an ancestral taxon in a phylogenetic tree?

    <p>Internal node</p> Signup and view all the answers

    What does the root of a phylogenetic tree indicate?

    <p>The most recent common ancestor of all sequences</p> Signup and view all the answers

    What is the term for a group that includes all taxa derived from a common ancestor plus the ancestor itself?

    <p>Clade</p> Signup and view all the answers

    In a phylogenetic tree, what does an external node represent?

    <p>An extant taxon or operational taxonomic unit</p> Signup and view all the answers

    What do distance-based methods primarily rely on to begin the construction of a tree?

    <p>Pairwise distances between molecular sequences</p> Signup and view all the answers

    What distinguishes a phylogram from a cladogram?

    <p>Cladograms do not indicate evolutionary change</p> Signup and view all the answers

    Which of the following represents the concept of an operational taxonomic unit (OTU)?

    <p>A defined taxon that can be studied</p> Signup and view all the answers

    Which tree-building method assumes a constant molecular clock?

    <p>Unweighted-Pair Group Method with Arithmetic Mean (UPGMA)</p> Signup and view all the answers

    What does maximum parsimony aim to achieve when constructing a tree?

    <p>Fewer evolutionary changes</p> Signup and view all the answers

    What is a key limitation of the Maximum Parsimony method?

    <p>It is prone to long-branch attraction artifacts.</p> Signup and view all the answers

    What is the primary focus of the Maximum Likelihood method in tree-building?

    <p>Determining the most likely tree topology</p> Signup and view all the answers

    Which method is known for being computationally fast for a large number of sequences?

    <p>Unweighted-Pair Group Method with Arithmetic Mean (UPGMA)</p> Signup and view all the answers

    Which of the following statements about distance-based methods is true?

    <p>They can be overly simplistic in their assumptions.</p> Signup and view all the answers

    What is an advantage of using the Neighbor-Joining (NJ) method over UPGMA?

    <p>NJ can handle unequal evolutionary rates.</p> Signup and view all the answers

    Study Notes

    Evolution

    • Evolution is the theory that groups of organisms change over time, with descendants differing structurally and functionally from their ancestors.
    • It's the biological process by which organisms inherit morphological and physiological traits defining a species.
    • Heredity is usually consistent, yet structures and functions of organisms change over generations.
    • Darwinian Evolution explains this in several ways:
      • Perpetual Change: the world is not constant
      • Common Descent: every organism has a common ancestor
      • Multiplication of Species: geographic isolation causing species diversification
      • Gradualism – change occurs slowly
      • Natural Selection: favoured traits leading to survival and reproduction.

    Molecular Phylogeny

    • Goal: determine the evolutionary relationships between all species.
    • True vs. Inferred Trees: True trees represent the actual evolutionary history. Inferred trees are our best hypothesis based on the available data.
    • Molecular Clock Hypothesis: States that for a given gene (or protein), the rate of molecular evolution is approximately constant.
    • Caveat:
      • Rates of molecular evolution vary significantly between organisms and different genes.
      • The molecular clock is only reliable when the gene under consideration maintains its function throughout the evolutionary timeline.

    Molecular Phylogeny: Detailed

    • Study of evolutionary relationships among organisms/molecules.
    • Topology: defines the relationships of objects (e.g., the common ancestor's location).
    • Branches: reflect the degree of relatedness.
    • Phylogenetic Tree: a graph of branches (edges) and nodes representing the objects (genes, organisms) under study.
    • Branch Lengths: represent the number of changes that have occurred.
    • Nodes: intersection/terminating point of two or more branches.
      • External Node: extant taxon.
      • Internal Node: ancestral taxon.
    • Clade: group of all taxa (incl. the common ancestor).
    • Root: represents the most recent common ancestor of all sequences included.
    • Outgroup vs. Midpoint Root: different starting points for the tree, one comparison with an outgroup (related but not part of the group), or midpoint rooting (calculated based on the total length between branch splits).

    Types of Trees

    • Species Trees: depict the evolutionary relationships of species. Internal nodes represent speciation events (the creation of a new species from an existing one). Use of molecular clocks and concatenated genes/proteins.
    • Gene/Protein Trees: depict the relationships between genes and proteins. Internal nodes represent divergence events (a lineage arising from another). Divergence may occur before speciation. Branch length may overestimate if speciation occurs before the genetic change, or if there's different topologies.

    Five Stages of Phylogenetic Analysis

    • 1. Sequence Acquisition: Gathering DNA sequences from various organisms using readily available libraries (e.g., GenBank, Ensembl, WormBase, UniProt, FlyBase, PDB).

    • 2. Multiple Sequence Alignments (MSA): Aligning the collected sequences to identify homologous regions.

    • 3. Models of DNA and Amino Acid Substitution: Selecting the most appropriate model to account for evolutionary changes in the sequences, considering variable substitution rates among sites and considering different types of mutations (e.g., transitions and transversions).

    • 4. Tree-Building Methods: Constructing phylogenetic trees using different methods:

      • Distance-Based: computing pairwise distances between sequences and assembling the tree. Calculates the rate of change between sequences. Includes UPGMA (assumes constant molecular change) and Neighbor-Joining (doesn't assume constant molecular change).
      • Maximum Parsimony: seeks the tree with the fewest evolutionary events. Identifies informative sites and builds a tree aiming for the fewest overall substitutions.
      • Maximum Likelihood: identifying the tree with the highest likelihood of producing the dataset observed. Employs a statistical model of molecular evolution to evaluate the probability of the tree given the data.
      • Bayesian Methods: employing a statistical approach to model uncertainty in complex phylogenetic models. Incorporates prior information and estimate the posterior probability distribution of the tree.

    • 5. Evaluating Trees: assessing consistency, efficiency, and robustness (e.g., bootstrap analysis, maximum likelihood, Bayesian Inference). Bootstrap analysis assesses the probability that the topology of the generated tree is correct, while Bayesian Inference identifies the most probable tree given a complex set of prior assumptions and data.

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    LO8 Molecular Phylogeny and Evolution PDF

    Description

    This quiz explores the theory of evolution, covering key concepts such as Darwinian Evolution and its principles, including natural selection and common descent. Additionally, it delves into molecular phylogeny, focusing on the determination of evolutionary relationships among species. Test your understanding of these foundational biological concepts!

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