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 (C)</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. (D)</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. (B)</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 (B)</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. (A)</p> Signup and view all the answers

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

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

What does Bayesian Methods primarily model?

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

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

<p>Bootstrap analysis (C)</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 (A)</p> Signup and view all the answers

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

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

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

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

What does Hamming Distance measure in regards to molecular sequences?

<p>The degree of divergence between sequences (A)</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 (D)</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 (C)</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) (C)</p> Signup and view all the answers

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

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

Which model adjusts for GC content during analysis?

<p>Tamura's Model (C)</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 (D)</p> Signup and view all the answers

Which model accounts for unequal substitution rates across variable sites?

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

What is the first stage of phylogenetic analysis?

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

Which stage involves aligning sequences that are homologous?

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

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

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

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

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

What is the purpose of evaluating trees in phylogenetic analysis?

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

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

<p>Data Cleaning Methods (B)</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 (D)</p> Signup and view all the answers

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

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

What does a branch in a phylogenetic tree connect?

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

What does branch length in a phylogenetic tree represent?

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

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

<p>Internal node (A)</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 (D)</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 (D)</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 (D)</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 (B)</p> Signup and view all the answers

What distinguishes a phylogram from a cladogram?

<p>Cladograms do not indicate evolutionary change (C)</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 (B)</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) (D)</p> Signup and view all the answers

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

<p>Fewer evolutionary changes (C)</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. (A)</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 (A)</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) (B)</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. (A)</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. (C)</p> Signup and view all the answers

Flashcards

Molecular Clock Hypothesis

The hypothesis that the rate of genetic change within a species is relatively constant over time.

Caveat: Rate Variation Among Organisms

The rate of molecular evolution can differ between different species.

Caveat: Rate Variation Among Genes/Proteins

The rate of molecular evolution can differ between different genes or proteins.

Caveat: Functional Gene

The molecular clock is only useful for comparing genes that have retained their function over time.

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Molecular Phylogeny

The study of evolutionary relationships between organisms or molecules using molecular biology techniques.

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Topology

The branching pattern of a phylogenetic tree, showing the relationships between organisms or molecules.

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Node

A point on a phylogenetic tree where a new lineage diverges from a common ancestor.

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Clade

A group of organisms or molecules descended from a common ancestor.

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Phylogenetic Tree

A graph representing evolutionary relationships between organisms, based on shared characteristics.

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Branch

A branch connects two nodes and represents the evolutionary path between them. Its length indicates the amount of change.

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External Node

A taxon (OTU) that is currently existing.

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Internal Node

A taxon (OTU) that is extinct and only represented by an ancestral point.

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Sequence Acquisition

The process of obtaining DNA or protein sequences from organisms to be used in phylogenetic analysis.

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Multiple Sequence Alignment (MSA)

Aligning multiple sequences to identify similarities and differences, crucial for inferring evolutionary relationships.

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Models of DNA and AA Substitution

Mathematical models used to estimate how DNA or protein sequences evolve over time, helping to create accurate phylogenetic trees.

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Tree-Building methods

Algorithms used to build phylogenetic trees based on the aligned sequences and evolutionary models.

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Evaluating Trees

Evaluating the reliability and accuracy of phylogenetic trees using statistical tests and visualization techniques.

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Homologous Sequences

Sequences used in phylogenetic analysis must share a common ancestor, meaning they are related by descent.

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MSA of Distantly Related Sequences

Distantly related sequences present challenges in MSA because aligning them accurately can be difficult. This is important when considering evolution over long periods.

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Gaps in MSA

Gaps in MSA can occur due to insertions or deletions in sequences, and must be carefully considered in phylogenetic analysis.

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Hamming Distance

A measure of the genetic distance between two DNA sequences, representing the number of nucleotide differences.

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Poisson Correction

A method that corrects for the underestimation of genetic distance caused by multiple mutations at a single site.

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Jukes-Cantor Model

A model that estimates evolutionary distance by considering the probability of all possible nucleotide substitutions.

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Kimura Two-Parameter Model

An extension of the Jukes-Cantor model that accounts for the different rates of transitions and transversions.

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Tamura's Model

A model that adjusts for variations in the GC content of DNA sequences.

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Gamma (Γ) Model

A model that acknowledges that different sites within a sequence can evolve at different rates.

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Distance-Based Methods

Methods for constructing phylogenetic trees based on the genetic distances between sequences.

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Neighbor-Joining (NJ)

A method for building phylogenetic trees that does not assume a constant rate of evolution.

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Bayesian Methods

A statistical approach to modeling uncertainty in complex models. It incorporates prior information and uses computational methods to estimate the posterior probability distribution.

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Bootstrap Analysis

A method used in molecular phylogeny to estimate the reliability of branches in the tree. It generates multiple trees from random subsets of data and compares them to the original tree.

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Maximum Likelihood Tree

The tree with the highest likelihood of being correct based on the data.

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Most Probable Tree (Bayesian Inference)

A tree generated using Bayesian inference, reflecting the most probable evolutionary relationships based on the data and prior information.

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TREE PUZZLE Program

A program for constructing phylogenetic trees that breaks down the problem into smaller groups (quartets) and then performs estimations of support for each group.

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MSA (Multiple Sequence Alignment)

A sequence alignment, which serves as input for Bayesian methods, helps to define the prior model for the tree.

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MCMC (Markov Chain Monte Carlo)

Generating the posterior probability distribution for a Bayesian method.

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Maximum Parsimony

A method of constructing a phylogenetic tree that finds the tree with the shortest total branch lengths. This method assumes all taxa evolve at the same rate and all characters contribute equally to the information. It aims to minimize the number of evolutionary changes required to explain the observed data. This method is susceptible to long-branch attraction, where rapidly evolving taxa might be incorrectly grouped together.

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Maximum Likelihood

A method of constructing a phylogenetic tree that aims to find the tree topology and branch lengths that have the highest probability of producing the observed data. It uses statistical models of evolutionary change that can vary across different parts of the tree. This method considers more complex evolutionary scenarios and is considered more accurate than parsimony methods.

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What is the starting point in distance-based methods for building phylogenetic trees?

A tree-building method that starts by calculating the pairwise distances between molecular sequences. The distances are then used to estimate branch lengths, with shorter distances indicating closer relationships.

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What is the goal of maximum parsimony?

A tree-building method that finds the tree with the shortest total branch lengths. This means it minimizes the number of evolutionary changes required to explain the observed data.

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What does maximum likelihood use to determine the most likely tree?

A tree-building method that aims to find the tree topology and branch lengths that have the highest probability of producing the observed data. It uses a statistical model of evolutionary change.

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What is UPGMA?

The Upweighted-Pair Group Method with Arithmetic Mean is a specific type of distance-based tree-building method. It is simple and fast but can be less accurate compared to other methods. It assumes a constant rate of evolution.

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What is Neighbor-Joining?

A method that does not assume a constant rate of evolution and is generally considered more accurate than UPGMA or other distance-based tree methods.

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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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