Lecture 11a - Phylogenetics in Bioinformatics
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Questions and Answers

Which method disregards character data when constructing a phylogenetic tree?

  • Bootstrapping
  • Maximum Parsimony
  • Neighbor Joining (NJ) (correct)
  • Maximum Likelihood

    • The Randomized Trees (Skewness Test) indicates that phylogenetic datasets have a symmetrical distribution.

    False

    Name one software used for phylogenetic analysis.

    PHYLIP

    The ____ method uses the amount of dissimilarity between two aligned sequences to construct the phylogenetic tree.

    <p>distance-based</p> Signup and view all the answers

    Match the following phylogenetic tree construction methods with their descriptions:

    <p>Maximum Parsimony = Uses minimal changes to explain data Unweighted Pair Group Method with Arithmetic Mean (UPGMA) = A distance-based method Bootstrap = Gathers support from resampled datasets Maximum Likelihood = Uses statistical methods for tree construction</p> Signup and view all the answers

    What term describes sequences that have a common ancestral origin but may not have the same activity?

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

    An unrooted phylogenetic tree indicates the direction of evolution.

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

    What is the difference between orthologs and paralogs?

    <p>Orthologs are homologs created through speciation, while paralogs are created through gene duplication.</p> Signup and view all the answers

    A _______ tree helps define the root, effectively setting a baseline for evolutionary comparisons.

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

    Which of the following is true regarding homologs?

    <p>They represent shared ancestry.</p> Signup and view all the answers

    Match the terms with their definitions:

    <p>Orthologs = Homologs created through speciation Paralogs = Homologs created through gene duplication Xenologs = Homologs from horizontal gene transfer Homologs = Sequences with common ancestral origins</p> Signup and view all the answers

    Sequence variability in a sample needs to be unrepresentative of the broader group to resolve phylogenetic issues.

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

    The _______ of a rooted tree indicates which nodes or branches are more ancestral.

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

    Which of the following is a key assumption in cladistics?

    <p>Change in characteristics occurs in lineages over time.</p> Signup and view all the answers

    The length of branches in a phylogenetic tree always represents evolutionary distance.

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

    What is a clade?

    <p>A group of individuals that share a common evolutionary ancestor.</p> Signup and view all the answers

    The ______ is a bifurcating branch point in a phylogenetic tree.

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

    Match the following terms with their definitions:

    <p>Homolog = Sequences derived from a common ancestor Ortholog = Genes in different species that evolved from a common ancestor Paralog = Genes that are related by duplication within a genome Xenology = Genes transferred between organisms through horizontal gene transfer</p> Signup and view all the answers

    What is the main purpose of phylogenetic analysis?

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

    Homologous sequences are those that originate from unrelated ancestors.

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

    What is one reason why the best BLAST match may not be the most similar sequence?

    <p>Due to evolutionary divergence or the presence of homologous sequences.</p> Signup and view all the answers

    What indicates the presence of a common ancestor in a phylogenetic tree?

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

    Unrooted trees are used to depict evolutionary history.

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

    Name two software options commonly used for multiple sequence alignment.

    <p>ClustalW, T-Coffee</p> Signup and view all the answers

    Rooted trees imply a direction of __________.

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

    Which of the following is NOT a step in performing phylogenetic analysis with DNA/protein data?

    <p>Data collection</p> Signup and view all the answers

    Character weighted matrices assign the same weight to transitions and transversions.

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

    What is the main goal of the parsimony method in phylogenetics?

    <p>To find the simplest tree representing evolutionary relationships.</p> Signup and view all the answers

    Study Notes

    Lecture 11a - Phylogenetics - Bioinformatics

    • Phylogenetics is the study of evolutionary relationships, often represented by "trees" or cladistics.
    • Phylogenetic analysis infers evolutionary relationships.
    • Clades are groups of organisms sharing a common ancestor.
    • Members of a clade are closely related.

    Learning Objectives

    • Understand phylogenetic tree elements.
    • Know assumptions made when interpreting phylogenetic trees.
    • Differentiate between rooted and unrooted trees.
    • Define and understand the relationships between homolog, ortholog, paralog, and xenology.
    • Describe phylogenetic tree construction steps.

    Phylogenetics

    • Evolutionary theory forms the basis for assumptions in BLAST, multiple protein alignments, and sequence distance measurements.
    • Identifying gene families, functions, origins of diseases, and polymorphisms are important applications.
    • Best BLAST matches aren't always the most similar sequences.
    • Misinterpretations of phylogenetic data are possible.

    The Basics of Phylogenetics

    • Phylogenetics studies evolutionary relationships.
    • Phylogenetic analysis estimates these relationships, often using phylogenetic trees.
    • Cladistics is sometimes used to indicate phylogenetic relationships.
    • A clade is a group of organisms with a common ancestor.
    • Members of a clade are more closely related to each other than to members of other groups.

    Assumptions of Cladistics

    • Organisms are related through descent from a common ancestor.
    • Evolution follows a branching pattern (cladogenesis).
    • Characteristics change over time within lineages.

    Phylogenetic Trees - Elements

    • Clades include the most recent common ancestor (MRCA) and all its descendants.
    • Taxons are named groups of organisms.
    • Branch lengths may not directly reflect evolutionary distances but always signify divergence.
    • Nodes are branching points.

    Phylogenetic Tree Example (and Data)

    • Specific examples and data are provided in the examples. Please refer to the images for this data.

    Assumptions of Molecular Phylogenetic Methods

    • Sequences must be correct.
    • Sequences are homologous, descending from a common ancestor.
    • Each position in a multiple sequence alignment (MSA) is homologous to others.
    • Multiple sequences in an alignment share a common phylogenetic history.
    • Sampling of taxa is adequate.
    • Sequence variation reflects the broader group.
    • Sufficient sequence variability exists to resolve the issue.

    More Assumptions

    • Sequences may not always evolve according to one stochastic process.
    • All positions in a sequence may not evolve according to the same process.
    • Sequence positions often evolve independently.

    Some Definitions

    • Homologs share a common ancestor but may not have similar activities.
    • Homology refers to shared ancestry, while similarity is quantifiable.
    • Orthologs are homologs arising from speciation, usually exhibiting similar functions.
    • Paralogs arise from gene duplication and often have differing functions.
    • Xenologs are obtained from horizontal gene transfer, typically with similar function.

    Rooted Phylogenetic Trees

    • Rooted trees have a root node representing the common ancestor of all sequences/species.
    • The root indicates evolutionary direction and ancestral/derived nodes/branches.
    • Rooted trees help infer evolutionary time.
    • Outgroups (more distantly related sequences/species) define the root in rooted trees.

    Rooted Tree of Protein Domains (and Data)

    • A specific example and data are presented in the examples. Please refer to the image for this data.

    Unrooted Phylogenetic Trees

    • Unrooted trees lack a root, thus not defining evolutionary direction or a common ancestor.
    • They emphasize pairwise relationships and similarities/distances between sequences.
    • Unrooted trees are common when the evolutionary path is unclear.

    Unrooted Tree of a Gene Family (and Data)

    • A specific example and data are presented in the examples. Please refer to the image for this data.

    Rooted vs Unrooted Trees - Key Differences

    • Rooted trees indicate common ancestry, unrooted trees do not.
    • Rooted trees define an evolutionary direction, unrooted trees do not.
    • Rooted trees depict ancestry/timelines, unrooted trees only show relationships based on similarity/distance.

    How To Construct a Tree (Steps)

    • Construct a multiple sequence alignment.
    • Determine the substitution model.
    • Build the tree.
    • Evaluate the tree.

    Alignment

    • Start with a multiple sequence alignment of genes.
    • Assume aligned positions (sites) share a common ancestor.
    • Determine which base/gap represents the character state.
    • Homologous sites are ones where evolution has occurred.
    • Choose suitable software for alignment (e.g., ClustalW, ClustalX, T-Coffee, MALIGN).
    • Subsets of the alignment can be used to construct the tree.

    Alignment (Additional Details)

    • Alignment editing (deletion/insertion of gaps) can be necessary.
    • The goal is to create an alignment that best represents evolutionary processes.

    Phylogenetic Data Model

    • Substitution models describe how base rates change.
    • Parsimony aims to find the simplest evolutionary tree.
    • Weighted matrices (e.g., transition=1, transversion = 2) score distances between characters.
    • Substitution matrices (e.g., PAM, BLOSSUM) reflect rate changes between characters derived from multiple sequence alignments.

    Tree Building Methods

    • Distance-based methods use sequence dissimilarities.
    • Character-based methods use character data throughout the analysis.
    • Include methods like UPGMA (unweighted pair group method with arithmetic mean) and NJ (neighbor joining).
    • Other methods like Maximum Parsimony and Maximum Likelihood are used.

    Tree Evaluation

    • Assess tree correctness with Randomized Trees (Skewness Test) to analyze MP tree lengths distribution.
    • Bootstrapping creates many datasets with substitution, to determine how often a specific branch is recreated.

    Phylogenetic Software

    • List of software like PHYLIP, PAUP, FASTDNAml, PUZZLE, and other tools such as Clustal, Treeview are part of phylogenetic analysis. Note: Specific names of software will vary.

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    Lecture 11a - Phylogenetics PDF

    Description

    This quiz covers the essentials of phylogenetics, focusing on evolutionary relationships and their representation through trees. Students will explore concepts such as clades, tree construction, and the various types of evolutionary relationships. It aims to enhance understanding of phylogenetic analysis in bioinformatics applications.

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