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Phylogenetic Trees
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Phylogenetic Trees

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Questions and Answers

What are the two types of phylogenetic trees?

  • Biological and Statistical
  • Rooted and Unrooted (correct)
  • Simple and Complex
  • Horizontal and Vertical

    • Which method can be used to automatically root a phylogenetic tree?

  • Statistical rooting
  • Mid-point rooting (correct)
  • Biological rooting
  • Manual rooting

    • What is the purpose of including an outgroup in a sequence data set?

  • To complicate the analysis
  • To increase the computational time
  • To normalize the branches of the unrooted tree (correct)
  • To reduce the accuracy

    • What is the formula to calculate the number of rooted trees (NR) for n sequences?

    <p>(2n-3)!/2n-2(n-2)!</p> Signup and view all the answers

    What is the formula to calculate the number of unrooted trees (NU) for n sequences?

    <p>(2n-5)!/2n-3(n-3)!</p> Signup and view all the answers

    Why is it necessary to be cautious when choosing an outgroup?

    <p>Because it involves assumptions that may not be correct</p> Signup and view all the answers

    What is the purpose of rooting a phylogenetic tree?

    <p>To infer evolutionary relationships</p> Signup and view all the answers

    How many types of phylogenetic methods are there?

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

    What is a key assumption of character-based methods in phylogenetic tree construction?

    <p>Each character substitution is independent of its neighbors</p> Signup and view all the answers

    What is the primary goal of the maximum likelihood method in phylogenetic reconstruction?

    <p>To determine the most likely sequence of evolutionary events</p> Signup and view all the answers

    How does the maximum likelihood method differ from the maximum parsimony method?

    <p>Maximum likelihood uses a model of evolution with different rates of transition-transversion ratios</p> Signup and view all the answers

    What is the purpose of bootstrapping in phylogenetic tree reconstruction?

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

    What is the primary advantage of the maximum likelihood method over other phylogenetic reconstruction methods?

    <p>It is a more realistic tree estimation method</p> Signup and view all the answers

    What is a key feature of the maximum likelihood method in phylogenetic reconstruction?

    <p>It uses a model of evolution with different rates of transition-transversion ratios</p> Signup and view all the answers

    How does the maximum likelihood method calculate the probability of each tree?

    <p>By calculating the probability of each nucleotide substitution</p> Signup and view all the answers

    What is the general pattern observed in transitions and transversions?

    <p>Transitions occur roughly 3 times as often as transversions</p> Signup and view all the answers

    What is the primary step in constructing a guide tree in distance-based clustering methods?

    <p>Multiple alignments based on all against all pairwise comparisons</p> Signup and view all the answers

    What is the purpose of constructing a guide tree in distance-based clustering methods?

    <p>To cluster the distances and construct a guide tree</p> Signup and view all the answers

    What is the characteristic of the Unweighted Pair Group Method with Arithmatic Mean (UPGMA) method?

    <p>It produces a rooted tree</p> Signup and view all the answers

    What type of tree does the Neighbor-Joining method produce?

    <p>Unrooted tree</p> Signup and view all the answers

    What is the main difference between distance-based clustering methods and other phylogenetic reconstruction methods?

    <p>Distance-based clustering methods do not guarantee the one true tree</p> Signup and view all the answers

    What is the main challenge in evaluating different phylogenetic reconstruction methods?

    <p>Comparing the relative consistency of the existing methods</p> Signup and view all the answers

    Which of the following programs is not a phylogenetic package?

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

    What is the purpose of the distances matrix in phylogenetic reconstruction?

    <p>To cluster the distances</p> Signup and view all the answers

    What is the main limitation of phylogenetic reconstruction methods?

    <p>They do not guarantee the one true tree</p> Signup and view all the answers

    What is the purpose of multiple alignments in phylogenetic reconstruction?

    <p>To compare all the sequences</p> Signup and view all the answers

    What is the primary goal of Maximum Parsimony in phylogenetic tree construction?

    <p>To find a tree that explains the data with as few evolutionary changes as possible</p> Signup and view all the answers

    What is the consequence of making errors in indel placement during multiple alignment?

    <p>The reconstructed phylogenetic tree is unlikely to be correct</p> Signup and view all the answers

    What is a characteristic of a phylogenetic tree?

    <p>It is characterized by its topology and length</p> Signup and view all the answers

    What is the main difference between Maximum Parsimony and Maximum Likelihood methods?

    <p>One aims to find a tree with as few evolutionary changes as possible, while the other aims to find a tree that maximizes the probability of the genetic data</p> Signup and view all the answers

    What is the purpose of bootstrapping in phylogenetic tree construction?

    <p>To evaluate the statistical significance of the obtained phylogenetic tree</p> Signup and view all the answers

    What type of phylogenetic method is Neighbour Joining (NJ)?

    <p>A method indirectly based on sequences</p> Signup and view all the answers

    What is the first step in tree construction?

    <p>Consider the set of sequences to analyse</p> Signup and view all the answers

    Why is alignment essential in phylogenetic tree construction?

    <p>It is a preliminary step to ensure accurate tree construction</p> Signup and view all the answers

    What is the purpose of applying phylogenetic tree methods?

    <p>To infer evolutionary relationships among organisms</p> Signup and view all the answers

    What type of data can be used with PHYLIP?

    <p>Molecular sequences, gene frequencies, restriction sites and fragments, distance matrices, and discrete characters</p> Signup and view all the answers

    What is the advantage of using a consensus tree?

    <p>It provides a summary of the major patterns in the data</p> Signup and view all the answers

    What is the purpose of bootstrapping?

    <p>To assess the confidence of the phylogenetic tree</p> Signup and view all the answers

    What is the difference between maximum parsimony and distance methods?

    <p>One is based on minimum evolutionary steps, the other on genetic distances</p> Signup and view all the answers

    What is the purpose of obtaining multiple alignments of sequences?

    <p>To align sequences properly for phylogenetic analysis</p> Signup and view all the answers

    What is the advantage of using maximum likelihood methods?

    <p>They are more realistic models of evolution</p> Signup and view all the answers

    What is the purpose of checking the validity of the result?

    <p>To ensure the phylogenetic tree is accurate and reliable</p> Signup and view all the answers

    Study Notes

    Phylogenetic Trees

    • Phylogenetic trees can be unrooted or rooted, and rooted trees can be constructed using statistical tools, such as mid-point rooting.
    • Rooting involves assumptions, and the choice of the outgroup is crucial in normalizing the branches of the unrooted tree.

    Rooting Trees

    • Mid-point rooting involves finding the midpoint of the sum of the distances between two sequences.
    • Example: if the distance between sequences A and D is 18, the midpoint would be 9.

    Number of Possible Trees

    • The number of rooted trees (NR) and unrooted trees (NU) for n sequences can be calculated using formulas:
      • NR = (2n-3)!/2n-2(n-2)!
      • NU = (2n-5)!/2n-3(n-3)!

    Tree Construction Methodology

    • The steps involved in constructing a phylogenetic tree are:
      1. Consider the set of sequences to analyze.
      2. Align the sequences properly.
      3. Apply phylogenetic tree construction methods.
      4. Evaluate the obtained phylogenetic tree statistically.

    Alignment

    • Alignment is a crucial step in constructing a phylogenetic tree.
    • Errors in indel placement can lead to incorrect tree reconstruction.

    Phylogenetic Tree Construction Methods

    • There are three main classes of phylogenetic methods:
      1. Methods directly based on sequences:
        • Maximum Parsimony: find a tree that explains the data with as few evolutionary changes as possible.
        • Maximum Likelihood: find a tree that maximizes the probability of the genetic data given the tree.
      2. Methods indirectly based on sequences:
        • Distance-based methods (Neighbour Joining): find a tree such that branch lengths of paths between sequences fit a matrix of pairwise distances.
    • Character-based methods assume that each character substitution is independent of its neighbors.
    • Validation methods include bootstrapping and jackknifing.

    Reconstructing Phylogenies

    • The rules for reconstructing a phylogeny include:
      1. Maximum likelihood states that when considering multiple phylogenetic hypotheses, one should take into account the one that reflects the most likely sequence of evolutionary events given certain rules about how DNA changes over time.

    Maximum Likelihood

    • Maximum likelihood is a statistically-based method that creates all possible trees and calculates the probability of each tree reflecting the sequence data.
    • The tree with the best probability is shown as the maximum likelihood tree.

    Phylogenetic Software

    • PHYLIP (Phylogeny Inference Package) is a software package that offers parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees.
    • Other software packages include MEGA, PAML, and Clustalw.

    Choosing a Phylogenetic Method

    • The choice of phylogenetic method depends on the strength of similarity between sequences:
      • Strong similarity: Maximum Parsimony.
      • Distant similarity: Distance-based methods.
      • Very weak similarity: Maximum Likelihood.

    Distance-Based Clustering Methods

    • Examples include:
      • Neighbor-Joining (unrooted tree).
      • UPGMA (rooted tree).

    UPGMA

    • UPGMA is a distance-based clustering method that builds a guide tree by clustering distances.
    • The steps involved in UPGMA are:
      1. Multiple alignments based on all-against-all pairwise comparisons.
      2. Building a distance matrix of all compared sequences.
      3. Disregarding the actual sequences.
      4. Constructing a guide tree by clustering distances iteratively.

    Evaluating Phylogenetic Methods

    • None of the phylogenetic reconstruction methods guarantee a single true tree.
    • There is currently no statistical method to compare trees obtained from different phylogenetic methods.

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    Description

    This quiz covers the basics of phylogenetic trees, including the difference between unrooted and rooted trees. Learn about the structure and representation of these trees.

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