Biology Chapter on Molecular Phylogeny

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Questions and Answers

What is the primary basis for determining the degree of relatedness between organisms using molecular phylogeny?

  • Differences in their DNA sequences. (correct)
  • Comparison of homologous structures.
  • Similarities in their ecological niches.
  • Analysis of analogous structures.

Which of the following best characterizes a clade in cladistics?

  • A group of organisms that have similar functions.
  • A group of organisms descended from a single common ancestor. (correct)
  • A group of organisms sharing analogous structures.
  • A group of organisms with similar morphological features.

What is the key distinction between homologous and analogous structures?

  • Homologous structures are found in closely related species, while analogous structures are found in distantly related species
  • Homologous structures evolve independently, while analogous structures are inherited from a common ancestor.
  • Homologous structures are identical, while analogous structures are only similar in function.
  • Homologous structures share a common ancestry, while analogous structures do not. (correct)

How does the accumulation of random mutations in genetic codes relate to the divergence of closely related species?

<p>Closely related species accumulate fewer mutations over time, indicating recent divergence. (B)</p> Signup and view all the answers

Why are analogous structures considered less informative than homologous structures when determining evolutionary relationships?

<p>Analogous structures do not indicate shared ancestry. (C)</p> Signup and view all the answers

What is the best definition of phylogeny?

<p>The evolutionary history and relationships among groups of organisms. (D)</p> Signup and view all the answers

Which of the following is NOT a type of evidence mentioned that scientists use to trace evolutionary relationships?

<p>Fossil Record Evidence (A)</p> Signup and view all the answers

According to the insect cladogram in figure 1, which group is most closely related to butterflies and moths?

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

What is the primary benefit of 'tree thinking' in understanding the relationships between organisms?

<p>It helps us understand the branching evolutionary relationships between species, considering time and ancestors. (D)</p> Signup and view all the answers

According to the content, what has significantly advanced the analysis of relationships between organisms?

<p>Genetic sequencing techniques (A)</p> Signup and view all the answers

In constructing a Venn Diagram to represent a phylogeny, what purpose does the outgroup serve?

<p>To provide a point of comparison for the phylogeny being examined (D)</p> Signup and view all the answers

Why might classification systems for biological organisms change over time?

<p>As scientists acquire additional information about organisms. (B)</p> Signup and view all the answers

Based on the provided text, who developed the Three Domain System?

<p>Carl Woese (D)</p> Signup and view all the answers

What does the size of the circle represent, when beginning with the character that is shared by all the taxa on the outside?

<p>Indicating the shared characteristics among the outside taxa (A)</p> Signup and view all the answers

What would likely be written in the area of the Venn diagram only shared by frogs and cats?

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

What information is displayed as a result of genetic sequencing?

<p>A new way of analyzing relationships between organisms (C)</p> Signup and view all the answers

What is the primary distinction introduced by Linnaeus for identifying plants?

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

Which of the following best describes the 'specific epithet' in Linnaean taxonomy?

<p>An adjective describing the species. (A)</p> Signup and view all the answers

In the context of Linnaean classification, what does the name Homo sapiens signify, according to the provided information?

<p>&quot;Wise man&quot; (A)</p> Signup and view all the answers

What is the MOST accurate description of taxonomy?

<p>The science of classifying organisms. (D)</p> Signup and view all the answers

What fundamental approach did Linnaeus employ in grouping organisms?

<p>Obvious physical traits (D)</p> Signup and view all the answers

What is a key limitation of the Linnaean system of classification?

<p>It is an artificial system based on morphological similarities, not evolutionary relationships. (A)</p> Signup and view all the answers

What distinguishes each species from others within the same genus, according to Linnaeus?

<p>The specific epithet (C)</p> Signup and view all the answers

What was a significant early influence on Linnaeus's interest in taxonomy?

<p>Classifying organisms from childhood (D)</p> Signup and view all the answers

Based solely on the provided information, what is a key characteristic that distinguishes a polyphyletic group from a monophyletic group?

<p>A polyphyletic group lacks a single most recent common ancestor, unlike a monophyletic group. (A)</p> Signup and view all the answers

Given the average differences described, which grouping demonstrates the least evolutionary difference?

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

If a newly discovered species is classified into an existing phylogenetic tree, and its inclusion alters a previously defined monophyletic group, what is the MOST likely consequence?

<p>The tree may need to be restructured. Potentially requiring reclassification of species to maintain monophyletic groupings. (A)</p> Signup and view all the answers

In early classification schemes, what was a primary criterion used to categorize organisms?

<p>Habitat and body form (A)</p> Signup and view all the answers

Sequence F has an average difference of 10. Based on this information, what may be inferred about Sequence F's relationship to the other sequences?

<p>Sequence F represents an early divergence point in the evolutionary history of the sequences, since it is equally distantly related to the other sequences. (A)</p> Signup and view all the answers

Considering the definition of a paraphyletic group, which of the following scenarios BEST illustrates its formation?

<p>A group of birds, including their common ancestor, excluding reptiles. (C)</p> Signup and view all the answers

What is the primary role of the thermostable polymerase in PCR?

<p>To survive the repeated cycles of denaturation, annealing, and extension. (C)</p> Signup and view all the answers

Suppose a researcher discovers that two species, initially thought to be closely related based on physical traits, actually have significant genetic differences indicating distant ancestry. How would this discovery MOST likely impact their taxonomic classification?

<p>Their classification would be adjusted to reflect the genetic evidence, potentially reassigning them to different taxonomic groups. (B)</p> Signup and view all the answers

During the annealing step of PCR, what determines the optimal temperature for primer binding?

<p>The melting temperature of the primers. (D)</p> Signup and view all the answers

In the context of constructing a phylogenetic tree, what does identifying a group with the 'least differences' primarily help to determine?

<p>The sequence of evolutionary events. (D)</p> Signup and view all the answers

What is the LEAST inclusive grouping in the Linnaean system of classification?

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

Which of the following is true regarding the newly synthesized DNA strands in PCR?

<p>They consist of one old strand and one new strand. (B)</p> Signup and view all the answers

What is the purpose of repeating the denaturation, annealing, and extension steps for multiple cycles in PCR?

<p>To increase the concentration of the target DNA sequence. (D)</p> Signup and view all the answers

Which characteristic defines organisms belonging to the same species in the Linnaean system?

<p>Producing fertile offspring together (A)</p> Signup and view all the answers

During PCR, at what temperature does the unwinding of the DNA template typically occur?

<p>~95°C (A)</p> Signup and view all the answers

In binomial nomenclature, what does the 'bi' in 'binomial' refer to?

<p>The two-part naming system consisting of the genus and specific epithet (B)</p> Signup and view all the answers

In the primer annealing step, what type of bonds are formed between the primers and the DNA template?

<p>Hydrogen bonds (D)</p> Signup and view all the answers

Which of the following represents the correct formatting for a species name in binomial nomenclature?

<p><em>Canis familiaris</em> (C)</p> Signup and view all the answers

What is the primary role of restriction enzymes (REs) in recombinant DNA technology?

<p>To cut DNA molecules at specific locations (D)</p> Signup and view all the answers

What is the length of the oligonucleotide sequence in the primer?

<p>~20bp (D)</p> Signup and view all the answers

What is the final number of PCR cycles typically performed?

<p>35 (C)</p> Signup and view all the answers

What is a key characteristic of the 'sticky ends' produced by restriction enzymes?

<p>They have single-stranded extensions that can form hydrogen bonds with complementary ends (C)</p> Signup and view all the answers

In the context of selective breeding, what is the primary goal when humans domesticate plants and animals?

<p>To select for and propagate desired traits (A)</p> Signup and view all the answers

Which of the following correctly describes the function of 'sticky ends' in recombinant DNA technology?

<p>Facilitating hydrogen-bonded base pairing between DNA fragments cut with the same enzyme (C)</p> Signup and view all the answers

Flashcards

Evolutionary Connections

Links between species based on their ancestry, showing divergence from a common ancestor.

Phylogeny

Study of evolutionary relationships among organisms, tracing back to a common ancestor.

Homologous Structures

Similar structures in related organisms due to inheritance from a common ancestor.

Analogous Structures

Similar traits in unrelated organisms, arising due to similar functions, not common ancestry.

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Molecular Phylogeny

Analyzing DNA and amino acid sequences to trace evolutionary relationships among organisms.

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Cladistics

A method of organizing species based on shared traits and common ancestry into clades.

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Clade

A group of organisms that share a common ancestor, formed in cladistics.

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Cladogram

A diagram showing evolutionary relationships among organisms within one or more clades.

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Tree of Life

A branching evolutionary pattern showing relationships among organisms.

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Tree Thinking

Phylogenetic thinking that helps understand evolutionary relationships.

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Phylogenetic Tree

Diagram that depicts evolutionary relationships based on characteristics.

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Three Domain System

Classification system for organisms developed by Carl Woese in 1990.

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Outgroup

A group not sharing any traits, used for comparison in phylogenetics.

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Venn Diagram

A visual tool to show the relationships between different groups.

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Genetic Sequencing

Technique for analyzing DNA to understand evolutionary relationships.

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Character Traits

Features shared by organisms used to classify them.

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Linnaeus

The scientist known as the father of taxonomy.

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Taxa

Groupings in the Linnaean classification system ranging from kingdom to species.

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Kingdom

The largest and most inclusive taxonomic grouping of organisms.

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Species

The smallest and most exclusive grouping of organisms that can reproduce fertile offspring.

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Genus

A taxonomic group that includes closely related species.

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Binomial Nomenclature

The system of naming species with two parts: genus and specific epithet.

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Nomenclature

The practice of assigning scientific names to organisms.

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Restriction Enzymes (REs)

Enzymes used to cut DNA at specific sites for genetic engineering.

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Taxonomy

The science of classifying organisms based on shared traits and relationships.

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Linnaean System

A classification system developed by Carolus Linnaeus that ranks organisms into groups like kingdom, phylum, class, and so on.

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Binomial Name

A scientific name for a species consisting of its genus and specific epithet.

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Homo sapiens

The binomial nomenclature for humans; 'sapiens' means wise.

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Morphological Similarities

Physical traits used to classify organisms in taxonomy.

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Superficial Similarities

Shallow or obvious traits that may mislead classification.

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Epithet

An adjective part of the binomial name that describes a species.

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Systema Naturae

A series of publications by Linnaeus detailing organisms he classified.

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PCR

Polymerase Chain Reaction, a method to amplify DNA.

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Denaturation

The first step in PCR where DNA unwinds at ~95°C.

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Primer Annealing

The process of primers attaching to ssDNA around ~54°C.

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Extension

The process of DNA strand elongation at ~72°C.

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Thermostability of Polymerase

The ability of DNA polymerase to withstand high heat in PCR.

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Semiconservative Replication

Each new DNA strand contains one old and one new strand.

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N cycles

The number of repeated PCR cycles, typically 35.

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Gene Detection

Using PCR to identify the presence of a specific gene.

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Average Difference in Phylogeny

The computed mean of genetic differences between groups in a phylogenetic analysis.

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Paraphyletic Group

A group containing a most recent common ancestor and some, but not all, of its descendants.

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Polyphyletic Group

An unnatural grouping of organisms that do not share a most recent common ancestor.

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Monophyletic Group

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

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Early Classification by Aristotle

The classification system organized by Aristotle based on habitat and body form.

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Function of Early Taxonomy

To categorize organisms based on their safety, usefulness, or harmfulness to humans.

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Study Notes

Evolutionary Relationships of Organisms

  • Homo luzonensis is a newly discovered species of ancient human.
  • Fossils dated to approximately 67,000 years ago were found in Callao Cave, Luzon, Philippines.
  • The species demonstrates a small stature, similar to Homo floresiensis.
  • Island isolation likely played a role in the evolutionary divergence of this species.
  • Some scientists question whether Homo luzonensis deserves its own species status, given the limited fossil sample.
  • Comparison with Homo floresiensis is relevant given shared characteristics of small stature suggested by their remains.

Human Evolution: A Branching Tree

  • The evolutionary history of humans is now understood as more complex than a simple linear tree.
  • Overlap between various ancient human species is evident, with some coexisting for significant periods.
  • Southeast Asia was once home to multiple human species in the past, including Homo erectus.
  • The presence of Denisovans (a relative of Neanderthals) in this region is noteworthy.

Homo Species Discovery

  • The discovery of Homo luzonensis highlights the complexity of early human migration patterns.
  • The ability of early humans to traverse seas and colonize island environments was often called into question.
  • The discovery of Homo floresiensis provided early evidence that humans could colonize isolated areas.

Cladistics

  • Cladistics organizes organisms' traits to determine their evolutionary relationships.
  • Cladistics sorts organisms into "clades," groups that descended from a single common ancestor.
  • Cladograms graphically represent evolutionary relationships, using branching patterns.
  • Branch points (nodes) on cladograms mark the divergence of lineages from a common ancestor.
  • Characteristics used to create cladograms include morphology, DNA, or protein sequences.

Phylogenetic Trees

  • Phylogenetic trees illustratively show the relationship between organisms.
  • The branching patterns of trees indicate various divergence points through evolutionary time.
  • Phylogenetic trees help understand the evolutionary history of organisms
  • Evolutionary relationships among species can be visualized and analyzed by cladograms.

Recombinant DNA Technology

  • Recombinant DNA technology involves joining DNA molecules from different species.
  • This is vital for creating genetically modified organisms (GMOs).
  • Techniques like heat shock and electroporation facilitate plasmid DNA insertion into host organisms.
  • Scientists employ methods like PCR (Polymerase Chain Reaction) to confirm gene presence and amplification following genetic modification.

Molecular Phylogeny

  • Molecular phylogeny examines DNA or protein sequences to understand evolutionary relationships.
  • Closely related species typically have more similar DNA or protein sequences.
  • This approach aids in inferring taxonomic relationships and constructing phylogenetic trees.

Taxonomy

  • Early classification schemes prioritized observable traits for organism classification.
  • Modern taxonomy relies on a combination of morphological and molecular data.
  • The Linnaean system, a hierarchical taxonomic method, categorises organisms into kingdoms, phyla, classes, and other levels of decreasing inclusivity
  • The 'Three Domain' System is a recent update including Archaea, Bacteria, and Eukarya to denote the three distinct main branch lineages of life on Earth.

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