Evolution and Molecular Phylogeny
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Questions and Answers

What does the internal node in a species tree represent?

  • Gene divergence
  • Molecular clock measurement
  • Speciation (correct)
  • Concatenation of genes

What may result in an overestimated branch length in gene/protein trees?

  • Incorrect molecular clock calibration
  • Preceding speciation events (correct)
  • Using concatenated genes
  • Species reproductive isolation

What is the primary focus of a gene/protein tree compared to a species tree?

  • Concatenated DNA sequencing
  • Species divergence
  • Molecular clock usage
  • Gene/protein divergence (correct)

Which statement is true regarding the comparison between species trees and gene trees?

<p>Gene trees may have different topologies than species trees. (C)</p> Signup and view all the answers

What technique is often employed in constructing species trees?

<p>Concatenation of genes (B)</p> Signup and view all the answers

What aspect is crucial for understanding the divergence in gene/protein trees?

<p>Gene/protein sequencing depth (B)</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

In a species tree, what does reproductive isolation facilitate?

<p>Speciation events (C)</p> Signup and view all the answers

Which of the following is a potential limitation of molecular clocks in phylogenetic reconstruction?

<p>They assume constant rates of evolution. (C)</p> Signup and view all the answers

Which of the following is NOT a major consideration during the Multiple Sequence Alignments stage?

<p>Examine individual nucleotide variants (B)</p> Signup and view all the answers

During which stage of phylogenetic analysis would researchers choose a model for DNA and amino acid substitution?

<p>Stage 3: Models of DNA and AA Substitution (B)</p> Signup and view all the answers

What is an essential aspect to check in the Multiple Sequence Alignments stage?

<p>Review alignment for homologous sequences (B)</p> Signup and view all the answers

Which stage follows the Multiple Sequence Alignments in phylogenetic analysis?

<p>Models of DNA and AA Substitution (C)</p> Signup and view all the answers

What is a key factor to consider when performing a multiple sequence alignment?

<p>The evolutionary distance between sequences (A)</p> Signup and view all the answers

What is evaluated during the concluding stage of phylogenetic analysis?

<p>The quality of the constructed phylogenetic tree (C)</p> Signup and view all the answers

In the context of sequence acquisition, what does homologous refer to?

<p>Sequences derived from a common ancestor (A)</p> Signup and view all the answers

What principle of Darwinian Evolution suggests that species evolve slowly over time?

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

Which aspect of evolution explains that every organism shares a common ancestor?

<p>Common Descent (A)</p> Signup and view all the answers

In the context of Molecular Phylogeny, what is the difference between a true tree and an inferred tree?

<p>True trees reflect actual historical events, while inferred trees are hypothetical constructs. (D)</p> Signup and view all the answers

What does 'Multiplication of Species' in Darwinian Evolution primarily imply?

<p>Species can evolve into multiple new species due to geographic isolation. (B)</p> Signup and view all the answers

What does the term 'Heredity' signify in the context of evolution?

<p>The conservative transfer of features that define a species across generations. (B)</p> Signup and view all the answers

Which of the following is NOT considered a component of Darwinian Evolution?

<p>Lamarckian Inheritance (D)</p> Signup and view all the answers

In which way does Natural Selection primarily influence evolutionary processes?

<p>By favoring variation that is best suited for survival. (D)</p> Signup and view all the answers

What is the ultimate goal of Molecular Phylogeny?

<p>To deduce the evolutionary trees representing all species of life. (A)</p> Signup and view all the answers

What does the Molecular Clock Hypothesis suggest about the rate of molecular evolution?

<p>It is approximately constant for a given gene or protein. (A)</p> Signup and view all the answers

Which factor could affect the applicability of the molecular clock?

<p>The functional retention of the gene over evolutionary time. (B)</p> Signup and view all the answers

In molecular phylogeny, what does the term 'topology' refer to?

<p>The relationships defined in the evolutionary tree. (B)</p> Signup and view all the answers

What is an inherent characteristic of molecular evolution rates across different organisms?

<p>They vary among different organisms. (B)</p> Signup and view all the answers

Why are some genes or proteins not suitable for molecular clock analysis?

<p>They are non-functional and cannot provide reliable data. (B)</p> Signup and view all the answers

What role does molecular biology play in molecular phylogeny?

<p>It offers techniques for studying evolutionary relationships. (C)</p> Signup and view all the answers

Which statement correctly describes the variation in molecular clocks?

<p>The clock varies among different genes and proteins. (B)</p> Signup and view all the answers

What is indicated by the term 'node' in a molecular phylogenetic tree?

<p>A common ancestor shared by different sequences. (D)</p> Signup and view all the answers

What is the primary function of the TREE-PUZZLE program in tree-building methods?

<p>To reduce the problem into quartets and generate a consensus tree (A)</p> Signup and view all the answers

Which component is NOT part of the Bayesian methods in tree-building?

<p>Use of maximum likelihood estimation (B)</p> Signup and view all the answers

What does bootstrap analysis measure in tree evaluation?

<p>The accuracy, consistency, and robustness of the tree topology (C)</p> Signup and view all the answers

What is typically considered a supportive value for clade designations in bootstrap analysis?

<p>Values above 70% (A)</p> Signup and view all the answers

Which of the following accurately describes the Bayesian inference result?

<p>It provides the most probable tree based on prior information. (C)</p> Signup and view all the answers

Which method is most commonly used for assessing the robustness of tree topologies?

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

What is the first step in the Bayesian modeling process for tree estimation?

<p>Performing MSA with a prior model (B)</p> Signup and view all the answers

What does maximum likelihood report in tree-building methods?

<p>The tree with the greatest likelihood from calculated data (C)</p> Signup and view all the answers

Which of the following statements accurately describes Distance-Based Methods in tree construction?

<p>They calculate pairwise distances between molecular sequences. (A)</p> Signup and view all the answers

What is the main advantage of using the Neighbor-Joining (NJ) method over the Unweighted-Pair Group Method with Arithmetic Mean (UPGMA)?

<p>NJ does not assume a constant molecular clock. (D)</p> Signup and view all the answers

In Maximum Parsimony tree construction, what does it mean when a tree has shorter branch lengths?

<p>It suggests a more likely explanation of evolutionary relationships. (C)</p> Signup and view all the answers

What challenge does Maximum Parsimony face when analyzing rapidly evolving taxa?

<p>It may create artifacts due to long-branch attraction. (A)</p> Signup and view all the answers

How does Maximum Likelihood differ from Maximum Parsimony in determining tree topology?

<p>It incorporates a statistical model for evolutionary change. (B)</p> Signup and view all the answers

What is a potential limitation of the UPGMA method in constructing trees?

<p>It assumes the molecular clock is constant. (D)</p> Signup and view all the answers

Which tree-building method is specifically designed to maximize the likelihood of producing a given dataset?

<p>Maximum Likelihood (A)</p> Signup and view all the answers

Which of the following is NOT assumed by the Maximum Parsimony method?

<p>Rapidly evolving taxa cannot create artifacts. (A)</p> Signup and view all the answers

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Flashcards

Evolution

The theory explaining how groups of organisms change over time, leading to differences between descendants and their ancestors.

Biological Evolution

The process by which traits passed down from parents (heredity) influence the structure and function of organisms across generations.

Perpetual Change

The idea that change in the natural world is a continuous process, not static.

Common Descent

The idea that all living organisms share a common ancestor.

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Multiplication of Species

The process of creating new species, often triggered by geographical isolation.

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Gradualism

The idea that evolutionary change occurs gradually over long periods.

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Natural Selection

The mechanism that drives evolution. Organisms with traits better suited to survival reproduce more successfully.

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Molecular Phylogeny

The study of evolutionary relationships between organisms, using molecular data.

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Species Tree

A type of tree that illustrates evolutionary relationships between species, with internal nodes representing speciation events.

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Gene/Protein Tree

A type of tree that shows the evolutionary history of genes or proteins, with internal nodes representing divergence events.

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Speciation

The process by which two new species arise from a single ancestral species, usually due to reproductive isolation.

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Gene/Protein Divergence

The evolutionary process by which two new genes or proteins diverge from a shared ancestor.

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Molecular Clock

The use of a rate of change in DNA or protein sequences to estimate the time of evolutionary events.

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Concatenated Genes/Proteins

The use of multiple genes or proteins in a species tree construction.

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Gene/Protein Tree Overestimation

A type of tree where the branch lengths may be overestimated due to the fact that gene/protein divergence may predate speciation.

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Tree Topology

The arrangement or pattern of branches in a tree.

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Molecular Clock Hypothesis

A hypothesis in molecular phylogeny stating that the rate of molecular evolution for a specific gene remains relatively constant over time.

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Rate Variation in Molecular Clock

The difference in evolutionary rate between different genes or proteins.

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Organism-Specific Evolutionary Rate

The observation that the rate of molecular evolution varies between different organisms.

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Topology in Phylogeny

The branching pattern in a phylogenetic tree that shows the relationships between different organisms or molecules.

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Node in Phylogeny

A point on a phylogenetic tree that represents a common ancestor of two or more lineages.

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Clade in Phylogeny

A group of organisms that share a common ancestor.

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External Node in Phylogeny

An organism or molecule that is not part of the main group being studied in a phylogeny.

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Sequence Acquisition

The first step in phylogenetic analysis involves collecting DNA or protein sequences from various organisms. This can be done through lab experiments or accessing databases like GenBank.

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Multiple Sequence Alignment (MSA)

Multiple Sequence Alignment (MSA) arranges sequences from different organisms, highlighting regions of similarity and difference. This is crucial for identifying evolutionary relationships.

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Models of DNA/AA Substitution

Models of DNA/AA Substitution estimate the rate of change in nucleotide or amino acid sequences over time. These models help build accurate trees.

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Tree-Building Methods

Tree-building methods use various algorithms to construct a phylogenetic tree based on the aligned sequences and substitution models.

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Evaluating Trees

Evaluating Trees assesses the reliability and accuracy of the constructed phylogenetic tree using statistical methods and comparing different tree topologies.

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Homologous Sequences

Homologous sequences share a common ancestor. In MSA, this means the sequences descended from the same original sequence.

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MSA Inspection

MSA should be inspected carefully to ensure the alignment is biologically plausible, considering the metadata associated with the sequences. This helps identify errors or inconsistencies.

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Gaps in MSA

Gaps in an MSA represent missing nucleotides/amino acids. Proper treatment of gaps is crucial for accurate phylogenetic analyses.

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Distance-Based Methods

This method constructs evolutionary trees by calculating the distances between molecular sequences, where shorter distances imply closer evolutionary relationships. It's computationally efficient, making it suitable for analyzing large datasets.

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UPGMA (Unweighted-Pair Group Method with Arithmetic Mean)

A simple and fast distance-based method that assumes a constant rate of evolution across all lineages (molecular clock). It is commonly used but offers less accuracy than Neighbor-Joining.

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Neighbor-Joining (NJ)

An improved distance-based method that doesn't require a constant molecular clock, providing better accuracy than UPGMA. It identifies the most closely related pairs of sequences and joins them together, building a tree.

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Maximum Parsimony

This method focuses on minimizing the number of evolutionary changes (mutations) required to explain the observed sequences, leading to trees with the shortest branch lengths. It's a simple and intuitive approach but may be biased by long-branch attraction.

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Maximum Likelihood

This approach identifies the tree and branch lengths that have the highest probability of generating the observed molecular data, taking into account the evolutionary model. It provides a statistical framework and is considered the most robust method.

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Long-Branch Attraction

When rapidly evolving lineages are grouped, they may appear closer than they truly are due to an overestimation of their similarity. This can lead to inaccurate tree construction.

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Informative Sites

Informative sites in DNA sequences are those that vary among different taxa, providing valuable data for tree construction. They help differentiate between evolutionary lineages.

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Bayesian Methods

A statistical approach to modeling uncertainty in complex models, relying on prior information and estimating the posterior probability distribution.

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TREE-PUZZLE Program

A method of generating a consensus tree, it involves dividing the data into quartets and performing quartet puzzling, followed by generating the final tree.

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Bootstrap Analysis

A method assessing the robustness of a tree's topology by generating replicates from a random dataset derived from the original alignment.

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Most Probable Tree (Bayesian Inference)

The most probable tree identified by Bayesian inference, often considered the most reliable result.

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Maximum Likelihood Tree

The tree with the highest likelihood value based on the data, reflecting the best fit to the observations.

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Tree Accuracy

A common metric used to evaluate the accuracy of a phylogenetic tree, focusing on consistency (reliability), efficiency (speed), and robustness (stability) of the inferred relationships.

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Bootstrap Support Value

Values above 70% in bootstrap analysis are often considered to support clade designations, suggesting a high probability of the group representing a true evolutionary relationship (p < 0.05 level).

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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 a biological process where organisms inherit morphological and physiological features defining a species.
  • Heredity generally maintains features, yet body structure and function change through generations.
  • Darwinian evolution explains this process:
    • Perpetual Change: the world is constantly changing.
    • Common Descent: all organisms have a common ancestor.
    • Multiplication of Species: geographic isolation leads to new species.
    • Gradualism: change occurs slowly.
    • Natural Selection: variations best suited for survival thrive and multiply.

Molecular Phylogeny

  • Its goal is to deduce the correct evolutionary trees for all life forms.
  • A "true tree" represents actual evolutionary history; an "inferred tree" is a hypothesis.
  • Molecular phylogeny studies the evolutionary relationships of organisms or molecules using molecular biology techniques.
  • Topology: defines the relationships of proteins or other objects in the tree.
  • Branch Lengths: represent the evolutionary relatedness of objects within the tree.
  • A phylogenetic tree is a graph composed of branches (edges) and nodes (points in the tree).

Molecular Clock Hypothesis

  • This hypothesis states that the rate of molecular evolution for a gene (or protein) remains relatively constant.
  • However, rates of molecular evolution vary among different organisms and genes.
  • The molecular clock is not consistently applicable in situations where a gene loses its function during an evolutionary time period.

Types of Trees

  • Species Trees: Created by speciation events, identifying when two species arise from a single ancestor. Reproductive isolation is crucial. Internal Nodes represent speciation.
  • Gene/Protein Trees: Created by divergence events, representing when a gene or a protein diverges from an ancestral sequence. Internal Nodes represent divergence.

Five Stages of Phylogenetic Analysis

  1. Sequence Acquisition: Gathering genetic material (DNA, RNA, or protein).
  2. Multiple Sequence Alignments: Aligning sequences to identify similarities and differences.
  3. Models of DNA and Amino Acid (AA) Substitution: Choosing a model to correct for the evolutionary differences between sequences.
  4. Tree-Building Methods: Constructing phylogenetic trees using various methods like Distance-Based Methods (e.g.,UPGMA, NJ – Neighbor-joining) or Character-Based Methods (e.g., Maximum Parsimony, Maximum Likelihood, Bayesian).
  5. Evaluating the Trees: Assessing the robustness and accuracy of the resulting phylogenetic tree using methods like Bootstrap Analysis.

Stage 4: Tree-Building Methods (Continued)

  • Maximum Parsimony: The best tree has the fewest evolutionary changes.
  • Maximum Likelihood: The tree that most likely produced the observed dataset.
  • Bayesian Methods: A statistical approach to handling uncertainty in evolutionary models.

Stage 5: Evaluating Trees

  • Bootstrap Analysis: Used to assess the robustness of a phylogenetic tree using random datasets generated from the multiple sequence alignment data. Bootstrap Values greater than 70% suggest the strength of the branch support.
  • Maximum Likelihood: A method that assesses how likely a tree is based upon the model of molecular evolution.
  • Bayesian Inference: A statistical approach used to build the most probable tree.

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LO8 Molecular Phylogeny and Evolution PDF

Description

This quiz explores the fundamental concepts of evolution, including Darwin’s theories and the process of natural selection. It also delves into molecular phylogeny, focusing on how evolutionary relationships are deduced among organisms. Test your understanding of these key biological principles!

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