Molecular Evolution Chapters 10 & 11
44 Questions
0 Views

Choose a study mode

Play Quiz
Study Flashcards
Spaced Repetition
Chat to lesson

Podcast

Play an AI-generated podcast conversation about this lesson

Questions and Answers

What is the definition of p-distance in the context of DNA sequence alignment?

  • The average nucleotide difference across all sequences
  • The simplest pairwise difference between sequences (correct)
  • The genetic distance between an ingroup and outgroup
  • The total number of species in the alignment

    • In the alignment provided, how many pairwise differences are estimated between species 2 and species 3?

  • 1 (correct)
  • 3
  • 4
  • 2

    • Which species in the alignment has the maximum difference compared to the outgroup species 5?

  • Species 2
  • Species 4
  • Species 3 (correct)
  • Species 1

    • If we consider species 1, what is its pairwise difference with species 4?

    <p>2</p> Signup and view all the answers

    Which of the following statements about the pairwise difference matrix is true?

    <p>Species 3 has a higher difference to species 1 than to species 4</p> Signup and view all the answers

    What is the advantage of using molecular characters in phylogenetic studies?

    <p>They reveal when taxa are mistakenly grouped together.</p> Signup and view all the answers

    Which of the following statements is true regarding honeybees and stingless bees?

    <p>Both honeybees and stingless bees have large numbers of non-reproductive workers.</p> Signup and view all the answers

    Based on DNA sequences, how were honeybees reclassified?

    <p>They were shown to be closely related to solitary orchid bees.</p> Signup and view all the answers

    What does the term 'analogous similarities' refer to in the context of taxonomic classification?

    <p>Similar traits that arise independently.</p> Signup and view all the answers

    What aspect of bee behavior is highlighted by the presence of non-reproductive workers?

    <p>They care for the queen's offspring.</p> Signup and view all the answers

    What characterizes a polyphyletic group?

    <p>It is defined by convergent features or habits.</p> Signup and view all the answers

    What is the main difference between homologous and analogous traits?

    <p>Homologous traits are similar due to common descent.</p> Signup and view all the answers

    Which of the following groups is considered monophyletic?

    <p>Plantae, Protista, and Animalia.</p> Signup and view all the answers

    What type of traits do DNA and peptide sequences help identify?

    <p>Mistaken groupings based on analogous similarities.</p> Signup and view all the answers

    What is an example of an analogous trait?

    <p>Wings of bats and birds.</p> Signup and view all the answers

    Which of the following is NOT true regarding polyphyletic groups?

    <p>They only contain species with the same ancestor.</p> Signup and view all the answers

    Which evolutionary feature is representative of a homologous trait?

    <p>The pentadactyl limbs of mammals.</p> Signup and view all the answers

    What does the term 'clade' refer to in evolutionary biology?

    <p>A subdivision that includes all descendants of a common ancestor.</p> Signup and view all the answers

    What characteristic differentiates transitions from transversions in the K80 model?

    <p>Transitions involve purine-purine or pyrimidine-pyrimidine changes</p> Signup and view all the answers

    What is the assumption regarding nucleotide proportions in the K80 model?

    <p>AT and GC pairs occur in equal proportions</p> Signup and view all the answers

    Which substitution model introduces three different substitution rates?

    <p>Kimura 3-Parameter Model (K3P)</p> Signup and view all the answers

    What are the specified substitution rates in the K81 model?

    <p>α for transitions and β for all transversions</p> Signup and view all the answers

    How does the K80 model treat the likelihood of transitions compared to transversions?

    <p>Transitions are more likely than transversions</p> Signup and view all the answers

    Which year did Motoo Kimura publish his theory on base substitution rates?

    <p>1981</p> Signup and view all the answers

    In the K81 model, how many substitution rates are proposed for the transitions relative to transversions?

    <p>One for transitions and two for transversions</p> Signup and view all the answers

    What does the transition/transversion substitution rate symbol (κ) represent?

    <p>The ratio of transitions to transversions</p> Signup and view all the answers

    Which of the following statements is true regarding the classification of the echidna?

    <p>Echidnas are classified as monotremes.</p> Signup and view all the answers

    What type of reproduction does a koala use?

    <p>Live birth with a pouch</p> Signup and view all the answers

    Which of the following animals has hair, gives milk, and does not lay eggs?

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

    Which characteristic distinguishes placental mammals from monotremes and marsupials?

    <p>Gestation period with intrauterine development</p> Signup and view all the answers

    What is the primary distinction between cormorants and the other mammals listed?

    <p>Cormorants lay eggs and have feathers.</p> Signup and view all the answers

    Which of the following animals is NOT characterized by having a pouch?

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

    Which of the following animals has a hoof?

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

    Which classification includes animals that are neither monotremes nor marsupials?

    <p>Placental mammals</p> Signup and view all the answers

    What characteristic is shared by echidnas and koalas but not by cormorants?

    <p>Both produce milk</p> Signup and view all the answers

    Which of the following is true about the reproductive strategy of a cat?

    <p>Cats give live birth without a pouch.</p> Signup and view all the answers

    What do bootstrap values represent in a phylogenetic tree?

    <p>The percentage agreement among a set of trees for a particular clade</p> Signup and view all the answers

    What type of trees do the Neighbor-Joining method generate?

    <p>Non-rooted trees with metric distances</p> Signup and view all the answers

    Which method requires a substitution model to assess probabilities of mutations?

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

    What is a distinguishing feature of rooted trees compared to non-rooted trees?

    <p>Rooted trees have a defined common ancestor.</p> Signup and view all the answers

    Which software tools mentioned cannot visually discriminate between rooted and non-rooted trees?

    <p>MEGA and GENEIOUS</p> Signup and view all the answers

    How can one determine whether a constructed tree is rooted or not?

    <p>The method used for tree construction</p> Signup and view all the answers

    What is the main purpose of consensus trees in phylogenetic analysis?

    <p>To summarize the agreement from multiple sampled trees</p> Signup and view all the answers

    Which of the following statements about the Neighbor-Joining method is FALSE?

    <p>It requires complex substitution models.</p> Signup and view all the answers

    Study Notes

    Molecular Evolution - Chapter 10 & 11

    • The notes cover molecular evolution, specifically focusing on alignments and phylogenies.
    • Dr. Oliver taught the courses.

    Phylogeny

    • Phylogeny examines the evolutionary relationships of taxa.
    • It determines how closely or distantly groups of organisms are related.
    • These relationships are based on whether the organisms share a recent or distant common ancestor.
    • A quote from Ernst Haeckel is included about the ability to create accurate genealogical trees for kingdoms of nature.

    Constructing Phylogenies

    • Phylogenies are constructed using phylogenetic trees.
    • Morphological characters (physical traits) can be used to build these trees.
    • Molecular characters, including variation in DNA and peptide sequences, are also used to create phylogenetic trees.

    Morphological Characters

    • The slides present examples for use in constructing phylogenies:
      • Vertebrae (backbone presence)
      • Chitin (cytoskeleton)
      • Feathers
      • Fur (hair)
      • Milk production
      • Hooves
    • These characters are observed in different organisms to determine relationships.

    Phylogenetic Trees for Study

    • The note slides show images of different animals, such as a cormorant, koala, echidna, cat, and elephant.
    • This data enables construction of trees showing evolutionary relationships.

    Data Tables

    • Data tables list the presence or absence of key characteristics (e.g., feathers, fur) across different animal species.
    • The tables illustrate how these characteristics help determine the evolutionary relationships.

    DNA and Peptide Sequences

    • Molecular data, specifically DNA and peptide sequences, are valuable in examining phylogeny.
    • Analyzing these sequences helps to understand when groups of organisms are incorrectly associated due to similarities that aren't from a common ancestor.

    Phylogenies of Other Groups

    • Phylogeny of seabirds is depicted in the slides, showing the evolutionary relationships based on characteristics.
    • Phylogenic trees from the 1800s, depicting three monophyletic groups, are included.
    • Examples of monophyletic (clade), polyphyletic, and paraphyletic groups are shown on the slides, with explanations about each. A clade is a monophyletic group. Monophyletic groups include all descendants of the most recent common ancestor. Polyphyletic groups don't include the common ancestor of all members of the taxon. Paraphyletic groups consist of the most recent common ancestor and some, but not all, of its descendants.
    • The slides include a table for aligning the DNA sequence of eight different mammals. They also introduce the concept of substitution models, as used in molecular phylogenetics.
    • Different models to model the process of DNA sequence evolution across species are outlined, including Jukes-Cantor (JC69), Kimura (K2P), Kimura-3 parameter (K81), Felsenstein (F81), Hasegawa-Kishino-Yano (HKY85), and Tamura-Nei (TN93), and the 'generalized Time-Reversible' model (GTR). Each model has different assumptions, and the best model depends on the dataset.

    Rooted vs. Unrooted Trees

    • Rooted trees represent an evolutionary path, showing which lineage splits from which common ancestor.
    • Non-rooted trees do not specify this evolutionary path.
    • A graph comparing rooted and unrooted trees is presented in the slides. The UPGMA method is introduced as an approach to create phylogenetic trees.

    Molecular Clock Hypothesis

    • Molecular evolution rates can be used to estimate time since the split from a common ancestor.
    • The slides describe the molecular clock hypothesis and discuss issues of how this concept has evolved.
    • The principle behind this assumes that the rate across lineages is constant. However, more observations show different rates, depending on the gene region, type of change, complexity of the genome, etc.
    • Information on the rate of changes (mutations) across different types of organisms (e.g., viruses, bacteria, fungi, eukaryotes) is provided.

    Studying That Suits You

    Use AI to generate personalized quizzes and flashcards to suit your learning preferences.

    Quiz Team

    Related Documents

    Phylogenetics Final Powerpoint Slides PDF

    Description

    This quiz covers key concepts from Chapters 10 and 11 of Molecular Evolution, focusing on alignments and phylogenies as taught by Dr. Oliver. It explores the examination of evolutionary relationships among taxa, including the construction of phylogenetic trees based on morphological and molecular characters.

    More Like This

    Use Quizgecko on...
    Browser
    Open
    Browser
    Browser