Molecular Evolution Chapters 10 & 11
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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 (B)</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 (A)</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. (A)</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. (C)</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. (A)</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. (B)</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. (A)</p> Signup and view all the answers

What characterizes a polyphyletic group?

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

Which of the following groups is considered monophyletic?

<p>Plantae, Protista, and Animalia. (C)</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. (D)</p> Signup and view all the answers

What is an example of an analogous trait?

<p>Wings of bats and birds. (D)</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. (C)</p> Signup and view all the answers

Which evolutionary feature is representative of a homologous trait?

<p>The pentadactyl limbs of mammals. (C)</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. (B)</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 (A)</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 (D)</p> Signup and view all the answers

Which substitution model introduces three different substitution rates?

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

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

<p>1981 (B), 1980 (C)</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 (C)</p> Signup and view all the answers

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

<p>The ratio of transitions to transversions (A)</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. (B)</p> Signup and view all the answers

What type of reproduction does a koala use?

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

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

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

Which characteristic distinguishes placental mammals from monotremes and marsupials?

<p>Gestation period with intrauterine development (C)</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. (D)</p> Signup and view all the answers

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

<p>Cat (A), Elephant (D)</p> Signup and view all the answers

Which of the following animals has a hoof?

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

Which classification includes animals that are neither monotremes nor marsupials?

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

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

<p>Both produce milk (A), Both are mammals (B)</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. (A)</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 (A)</p> Signup and view all the answers

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

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

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

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

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

<p>MEGA and GENEIOUS (A)</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 (A)</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 (D)</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. (D)</p> Signup and view all the answers

Flashcards

Homology in DNA sequences

DNA or peptide sequences can show evolutionary relationships between species (taxa).

Phylogeny based on molecular data

Using DNA/protein sequences to group species based on evolutionary relationships, rather than just physical similarities.

Analogous similarities

Physical similarities that arise independently due to similar functions, not shared ancestry.

Misleading morphological similarities

Physical similarities that may incorrectly group species together because they have similar traits for similar functions.

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Reclassification based on DNA sequences

Grouping species according to their evolutionary relationship based on DNA/protein analysis, often correcting previous morphological groupings.

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Echidna characteristics

Echidnas are mammals that lay eggs, have hair, and produce milk.

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Koala characteristics

Koalas are mammals that have hair, produce milk, and live in pouches.

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Cat characteristics

Cats are mammals with hair, produce milk, and have placentas.

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Elephant characteristics

Elephants are mammals with hair, produce milk, and have placentas.

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Monotreme

A group of mammals that lay eggs.

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Placental mammal

Mammals that develop the fetus inside the mother's body, connected to the placenta.

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Marsupial

Mammals that have a pouch for carrying their young.

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Cormorant characteristics

Cormorants are birds, and not mammals.

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Mammals features

Mammals have hair or fur and produce milk to feed their young.

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Phylogeny

The evolutionary relationships between organisms.

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Polyphyletic Group

A group of organisms that share similar traits but do not share a common ancestor.

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Convergent features

Similar features that have evolved independently in different lineages.

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Monophyletic group

A group of organisms that includes a common ancestor and all of its descendants.

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Homologous traits

Similar traits shared by related organisms because of a common ancestor.

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Analogous traits

Similar traits that evolved independently in different lineages.

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Evolutionary Tree

A diagram that illustrates the evolutionary relationships among different organisms.

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Molecular characters

Traits based on DNA or peptide sequences used to study phylogeny.

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Pairwise Differences

Comparing the differences in DNA sequences between two species.

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p-distance

The simplest method to find evolutionary relationships based on DNA sequences.

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DNA sequence alignment

Arranging DNA sequences of different species to identify correspondences and variations.

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Outgroup

A related but not directly comparable species in a comparison of more closely related species (ingroup).

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Rooted tree

A phylogenetic tree that shows the ancestral lineage from a common ancestor. It has a specific root node representing the common ancestor.

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Non-rooted tree

A phylogenetic tree that does not show the ancestral lineage. It only shows the relationships between species without a specific common ancestor node.

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Bootstrap values

Percentages representing the confidence level in a particular clade or grouping within a phylogenetic tree. They indicate how often a clade is found across many bootstrap replicates, which are random sampling of the data.

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Neighbor-Joining (NJ) method

A method for constructing unrooted phylogenetic trees based on genetic distances between species. It finds the closest pairs of species and joins them together.

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Maximum Likelihood (ML) Tree

A phylogenetic tree built using a statistical model to find the tree that best explains the observed DNA sequences. It considers probabilities of mutations to assign the most likely evolutionary relationships.

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UPGMA

A method for constructing rooted phylogenetic trees based on the average genetic distance between species. It assumes a constant rate of evolution for all species.

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Substitution Model

A mathematical model used in phylogenetic analysis to calculate the probabilities of different mutations (e.g., K2P, K3P, HKY85). It helps determine the likelihood of specific changes in DNA sequences over time.

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Consensus Tree

A phylogenetic tree summarizing results from multiple trees generated from different bootstrap replicates or different methods. It combines the most supported relationships across these trees, indicating stronger confidence in the evolutionary relationships.

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K80 (K2P) Model

A model that estimates evolutionary rates based on the assumption that transitions (purine-purine or pyrimidine-pyrimidine) are more likely than transversions (purine-pyrimidine), with a single rate for transitions and another for transversions. It also assumes equal base frequencies (50% GC, 50% AT).

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Transitions

Changes in DNA sequences from one purine (A or G) to another purine, or from one pyrimidine (C or T) to another pyrimidine.

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Transversions

Changes in DNA sequences from a purine (A or G) to a pyrimidine (C or T) or vice versa. They are considered less likely than transitions.

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K81 (K3P) Model

A more complex model that refines K80 by introducing three distinct rates for substitutions. It assumes one rate for transitions (α) and two separate rates for transversions (β and γ). It also assumes equal base frequencies (50% GC, 50% AT).

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What is the difference between K80 (K2P) and K81 (K3P) models?

K80 (K2P) simplifies evolutionary rate estimation by assuming two substitution rates (one for transitions and one for transversions), while K81 (K3P) accounts for the possibility that there are three distinct rates (one for transitions and two for transversions). Both models assume equal base frequencies.

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What is the significance of equal base frequencies in K80 and K81?

Both models assume that the four nucleotides (A, C, G, T) occur with equal frequencies (50% GC, 50% AT). This assumption simplifies the calculation of substitution rates and allows for more efficient comparisons between different sequences. However, it may not always reflect reality, as the actual frequency can vary across species and genomic regions.

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Why are transitions more likely than transversions?

Transitions involve changing a purine to another purine or a pyrimidine to another pyrimidine, which often involve less drastic changes to the chemical structure of the base. Transversions, on the other hand, require a change between purines and pyrimidines, which involve more substantial structural changes and are therefore less likely to occur during evolution.

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What are the limitations of the Kimura models (K80 and K81) for estimating evolutionary rates?

The models are based on the assumption of equal base frequencies, which may not always be true in reality. They also do not account for factors like the variation in substitution rates across different lineages or different genomic regions.

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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.

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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.

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