Evolutionary Biology and Phylogeny Quiz
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Questions and Answers

What does the branch length in some phylogenetic trees represent?

  • The relative chronology of branching events
  • The number of changes in a DNA sequence (correct)
  • The absolute time since the common ancestor
  • The total lifespan of the lineages

What principle suggests looking for the simplest explanation that fits the facts in phylogenetic analysis?

  • Principle of maximum parsimony (correct)
  • Principle of genetic variability
  • Maximum likelihood
  • Maximum divergence theory

In phylogenetic trees, what is generally implied by the branching pattern?

  • Precise absolute timing of events
  • Equal length of all lineages
  • Relative timing of branching events (correct)
  • Species evolution rate

If the branch length leading to Drosophila is longer than that leading to the mouse, what can be inferred?

<p>More genetic changes occurred in the Drosophila lineage (D)</p> Signup and view all the answers

How many different ways can trees be formed when analyzing data for 50 species?

<p>3 × 10^76 (C)</p> Signup and view all the answers

What type of ancestor do humans and bacteria share?

<p>A prokaryotic organism (C)</p> Signup and view all the answers

What does the principle of maximum likelihood help systematists with?

<p>Constructing phylogenetic trees (B)</p> Signup and view all the answers

What does more genetic change in a lineage indicate based on branch length?

<p>It has undergone more changes since divergence (B)</p> Signup and view all the answers

What are sister taxa?

<p>Groups that share an immediate common ancestor and are closest relatives (C)</p> Signup and view all the answers

What happens to orthologous genes after speciation?

<p>They diverge and are found in separate gene pools. (A)</p> Signup and view all the answers

What does a rooted tree represent in phylogenetics?

<p>The most recent common ancestor to all taxa in the tree (C)</p> Signup and view all the answers

What characterizes a basal taxon?

<p>A lineage that diverges early in the history of a group (A)</p> Signup and view all the answers

Which of the following best describes paralogous genes?

<p>They diverge due to being present in more than one copy in the genome. (A)</p> Signup and view all the answers

How does gene count compare to phenotypic complexity in humans and yeast?

<p>Humans have only four times as many genes as yeast despite higher complexity. (B)</p> Signup and view all the answers

What does a polytomy indicate in a phylogenetic tree?

<p>Limited understanding of certain evolutionary relationships (C)</p> Signup and view all the answers

What is the main purpose of molecular clocks in evolutionary biology?

<p>To measure the absolute time of evolutionary change. (A)</p> Signup and view all the answers

What does the sequence of branching in a phylogenetic tree signify?

<p>Patterns of descent among organisms (A)</p> Signup and view all the answers

What provides useful information about a species' phylogeny?

<p>Phylogenetic trees based on both morphological and molecular data (B)</p> Signup and view all the answers

What is true about the nucleotide substitutions in orthologous genes?

<p>They are proportional to the time since two species shared a common ancestor. (C)</p> Signup and view all the answers

What are homologies in the context of evolution?

<p>Phenotypic and genetic similarities due to shared ancestry (B)</p> Signup and view all the answers

How many genes do humans share with mice as orthologous genes?

<p>Approximately 99%. (B)</p> Signup and view all the answers

What is a common feature of living organisms regarding gene functions?

<p>They share many biochemical and developmental pathways. (A)</p> Signup and view all the answers

What accounts for morphological divergence among closely related species?

<p>Relatively few genetic differences (B)</p> Signup and view all the answers

What factors can influence the evolution of paralogous genes?

<p>Gene duplication within a species. (C)</p> Signup and view all the answers

What is the primary purpose of graphing genetic differences against evolutionary branch points?

<p>To estimate the absolute date of evolutionary events (A)</p> Signup and view all the answers

Why are some molecular clocks considered more accurate than others?

<p>They have a consistent average rate of change (B)</p> Signup and view all the answers

Which of the following statements best describes the neutral theory of molecular evolution?

<p>Much of the change in DNA sequences is selectively neutral. (A)</p> Signup and view all the answers

What can affect the rate of change in molecular clocks across different genes?

<p>The significance of the gene's function (C)</p> Signup and view all the answers

What percentage of amino acid differences in Drosophila species proteins is attributed to directional natural selection?

<p>50% (D)</p> Signup and view all the answers

What is a potential explanation for fluctuations in the rate of mutation accumulation?

<p>Natural selection can impact mutation rates over time. (D)</p> Signup and view all the answers

Which of the following is NOT a factor that can influence the accuracy of molecular clocks?

<p>Geological time periods (C)</p> Signup and view all the answers

How do gene mutation rates vary among different types of genes?

<p>Some genes can evolve much faster than others. (B)</p> Signup and view all the answers

What is a primary concern of biologists regarding molecular clocks?

<p>They extrapolate conclusions beyond the calibration in the fossil record. (D)</p> Signup and view all the answers

What advantage does using many genes provide when calibrating molecular clocks?

<p>It helps average out fluctuations due to factors like natural selection. (A)</p> Signup and view all the answers

How has the molecular clock approach been applied to HIV research?

<p>To date the jump of the virus from primates to humans. (C)</p> Signup and view all the answers

What type of genetic material does HIV possess?

<p>RNA that evolves quickly. (B)</p> Signup and view all the answers

What system did early taxonomists primarily use to classify species?

<p>Two kingdoms: plants and animals. (C)</p> Signup and view all the answers

What did the discovery of genetic data reveal about the five-kingdom system?

<p>Some prokaryotes differ significantly, challenging classifications. (A)</p> Signup and view all the answers

What taxonomic system has replaced the five-kingdom system?

<p>A three-domain system including Bacteria, Archaea, and Eukarya. (A)</p> Signup and view all the answers

What supports the validity of the three-domain system?

<p>Analyses of nearly 100 completely sequenced genomes. (B)</p> Signup and view all the answers

Which domain contains most of the currently known prokaryotes?

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

What characterizes the domain Archaea compared to Bacteria?

<p>Diverse group of prokaryotes (C)</p> Signup and view all the answers

What does the kingdom Monera currently represent in taxonomy?

<p>It included organisms from both Bacteria and Archaea domains and is now considered obsolete (A)</p> Signup and view all the answers

Which of the following statements best describes the relationship between Eukaryotes and Archaea?

<p>They share a more recent common ancestor than either do with Bacteria (D)</p> Signup and view all the answers

What evidence supports the evolutionary relationships in the tree of life?

<p>Similarities in rRNA genes (A)</p> Signup and view all the answers

What is horizontal gene transfer?

<p>Transfer of genes from one genome to another across different domains (B)</p> Signup and view all the answers

What discovery is made regarding metabolic genes in yeast compared to other organisms?

<p>Many of yeast’s metabolic genes are closer to Bacterial genes than to Archaea genes (A)</p> Signup and view all the answers

Why is the study of single-celled organisms significant in evolutionary history?

<p>They dominate most evolutionary branches on the tree of life (C)</p> Signup and view all the answers

Flashcards

Sister taxa

Groups of organisms sharing an immediate common ancestor, each other's closest relatives.

Rooted tree

Phylogenetic tree including the most recent common ancestor of all taxa.

Basal taxon

Lineage diverging early in a group's history, branching near the common ancestor.

Polytomy

Branch point on a phylogenetic tree from which more than two groups emerge, due to limited understanding of relationships.

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Homologies

Phenotypic and genetic similarities due to shared ancestry.

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Phylogenetic trees

Show patterns of descent, not phenotypic similarity. Branching order reflects descent, not age.

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Phylogenetic tree use

Phylogenies can reveal closely related species with beneficial traits for genetic transfer to cultivated plants or identify illegally harvested species.

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Morphological divergence

Differences in form between closely related species, possibly due to few genetic differences or different environmental pressures.

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Phylogenetic tree branch lengths

In some trees, branch lengths represent rates of change or time, while in others, they don't hold any specific meaning.

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Relative vs. absolute chronology

Phylogenetic trees show evolutionary relationships, but their branching order only tells us which events came earlier or later, not the precise timing.

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Maximum Parsimony

The principle of selecting the simplest explanation that fits observed data when reconstructing evolutionary relationships.

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Shared derived characters

Characteristics that were present in an ancestor and then changed in its descendants, being a unifying feature when comparing phylogenies.

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Base changes in phylogenies

Comparing base changes in DNA sequences (e.g., A, T, G, C) helps to determine relationships among groups.

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Phylogenetic tree complexity

As data (e.g. DNA sequences) increases, the possible tree shapes multiply exponentially, making accurate analysis challenging.

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Common ancestry survival

All lineages, despite the long stretches of time, have a common ancestor.

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Fossil/Genetic evidence

Fossils and DNA information combine to understand the history of life on Earth.

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Orthologous genes

Genes found in different species which diverged after speciation, though they may have similar functions.

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Paralogous genes

Genes within the same species that diverged after gene duplication, potentially carrying out distinct tasks.

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Molecular clock

A method to estimate evolutionary time based on the rate of genetic change in orthologous genes.

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Evolutionary change rate

The rate at which genes and genomes change over time, important for understanding evolutionary relationships.

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Divergence time

The time elapsed since two species shared a common ancestor, revealed through molecular comparisons.

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Orthologous gene similarity

High percentage similarity between orthologous genes in different species indicates a shared evolutionary history and ancestry, reflecting conserved roles.

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Human and yeast gene similarity

A substantial proportion of human genes have orthologs in yeast, demonstrating the fundamental conservation of biological processes across vastly different life forms.

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Gene duplication

A process where a section of DNA is copied, leading to an extra copy of a gene which then can evolve different functions.

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Neutral Theory

The idea that many genetic changes are neutral and have little or no impact on fitness, leading to a clock-like rate of change.

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Genetic Drift

Random changes in the frequency of genes in a population, affecting the molecular clock.

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Selective Neutrality

The assumption that most changes used in the molecular clock are not influenced by natural selection.

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Rate of Genetic Change

The speed at which genetic differences accumulate in a gene, influencing the molecular clock.

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Directional Selection

Natural selection favoring a specific trait, potentially affecting the accuracy of the molecular clock.

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Importance of the Gene

The impact of a gene's function on survival determines its rate of change, affecting the molecular clock.

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Long-Term Fluctuations

Over long evolutionary periods, fluctuations in the rate of genetic change due to natural selection tend to even out.

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Molecular Clock Skepticism

Biologists are wary of conclusions derived from molecular clocks for time spans beyond fossil record calibration, as these clocks assume consistent rates over vast periods, introducing uncertainty.

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Molecular Clock Calibration

Using a multitude of genes to construct molecular clocks can minimize the impact of variable evolutionary rates, leading to more accurate estimates of divergence times.

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HIV-1 M Origin

Molecular clock analysis suggests that the most common HIV strain, HIV-1 M, likely infected humans in the 1930s, based on viral samples collected over time.

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Three-Domain System

The three domains—Bacteria, Archaea, and Eukarya—represent a higher taxonomic level than kingdoms, encompassing all life forms. This system recognizes the deep evolutionary split between prokaryotes.

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Early Kingdoms

Historically, organisms were classified into two kingdoms: plants and animals. Later, a five-kingdom system emerged, adding Monera (prokaryotes), Protista, Fungi, and Animalia.

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Prokaryotic Diversity

Genetic analyses revealed that some prokaryotes differ as much from each other as they do from eukaryotes, prompting a reevaluation of the five-kingdom system.

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Genomic Support for Domains

Analyses of numerous fully sequenced genomes provide strong evidence for the validity of the three-domain system, supporting the profound separation between Bacteria, Archaea, and Eukarya.

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Revising the Tree of Life

Our understanding of the tree of life is constantly being updated as new data emerges, leading to modified classifications and a deeper appreciation for the relationships among all living things.

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Three Domains of Life

The three primary branches of life on Earth: Bacteria, Archaea, and Eukarya. Each domain possesses unique cellular structures, biochemical processes, and evolutionary histories.

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Prokaryotes

Organisms lacking a true nucleus and membrane-bound organelles. Bacteria and Archaea are prokaryotes.

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Eukaryotes

Organisms with cells containing a true nucleus and membrane-bound organelles. Plants, animals, fungi, and protists are all eukaryotes.

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Horizontal Gene Transfer (HGT)

The transfer of genetic material between organisms that are not direct ancestors or descendants. This process can occur through mechanisms like transposable elements, plasmid exchange, and viral infection.

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The 'Tree of Life' - What does it show?

A diagram that depicts the evolutionary relationships between all living organisms. The branching pattern represents the evolutionary history and common ancestry of different species.

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rRNA Genes

Genes that code for ribosomal RNA, a crucial component of ribosomes involved in protein synthesis. rRNA genes are used extensively in phylogenetic analysis.

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What makes Eukarya & Archaea closer than to Bacteria?

Phylogenetic studies based on rRNA genes, as well as other genetic analyses, suggest that Eukarya and Archaea are more closely related to each other than either is to Bacteria.

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Early Life: Gene Swaps

During the early stages of life, horizontal gene transfer was prevalent, leading to significant exchange of genetic material between different domains. This resulted in a more complex and dynamic evolutionary landscape.

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Study Notes

Evolutionary Biology

  • Evolutionary biology investigates both the process and pattern of evolution
  • Processes include natural selection and other mechanisms changing population genetics
  • Patterns are the products of evolution over time

Phylogeny

  • Phylogeny is the evolutionary history of species or groups
  • Systematics is an analytical approach to classify diversity and determine evolutionary relationships between living and extinct organisms
  • Evidence for reconstructing phylogeny involves fossil record, morphological, biochemical, and genetic similarities
  • Scientists are continuously refining the universal tree of life based on new data

Taxonomy

  • Taxonomy is the science of naming and classifying organisms
  • The Linnaean system, proposed by Carolus Linnaeus, uses two-part names (binomial) for organisms, organized hierarchically (e.g., species, genera, family, order, class, phylum, kingdom, domain)

Phylogenetic Trees

  • Phylogenetic trees are diagrams illustrating evolutionary relationships
  • Branch points (nodes) represent evolutionary divergence from common ancestors
  • Sister taxa are groups sharing an immediate common ancestor
  • Rooted trees show the most recent common ancestor of all taxa
  • Basal taxa diverge early in the history of a group
  • Polytomies represent unresolved evolutionary relationships

Inferring Phylogenies

  • Homologies are similarities due to shared ancestry
  • Organisms with similar morphologies or DNA sequences are likely closely related
  • Analogies are similarities due to convergent evolution
  • Analogy is due to similar environmental pressures leading to similar adaptations
  • Identifying homologies is crucial for accurate phylogenetic reconstruction
  • Molecular data can help resolve phylogenetic relationships, especially in cases with limited fossil record

Molecular Clocks

  • Molecular clocks use constant rates of gene evolution to estimate absolute time of evolutionary events
  • Maximum parsimony and maximum likelihood are principles used to infer phylogenies based on molecular and morphological data
  • Maximum parsimony considers the simplest explanation (fewest evolutionary changes)
  • Maximum likelihood models likely sequence of evolutionary events with given probability rules
  • Molecular clocks can estimate divergence times, but they may not be entirely accurate due to deviations or fluctuations in rates over time

Phylogenetic Tree of Life

  • Early classifications grouped species into plants and animals
  • Modern classification systems now use three domains: Bacteria, Archaea, and Eukarya
  • Horizontal gene transfer has played a significant role in evolution, particularly early on
  • Some data have been interpreted as suggesting that a 'ring of life' might be more accurate than a simple tree

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Phylogeny & Tree of Life Outline PDF

Description

Test your knowledge on evolutionary biology, including the processes and patterns of evolution. Dive into phylogeny and taxonomy, exploring how species are classified and the significance of phylogenetic trees. Understand the foundational concepts that shape our understanding of life on Earth.

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