A3.2 Classification and cladistics

What is the purpose of classification in biology?

Classification organizes organisms into groups based on traits or evolutionary origins, simplifying information storage and retrieval.

What is the basic level of classification in the hierarchical system?

The species is the basic level of classification.

What is the broadest group in the classification hierarchy?

The domain is the broadest group in the classification hierarchy.

Why is classification important for identifying unknown species?

Classification allows scientists to group organisms by traits, narrowing down possibilities until the species is identified.

What is taxonomy?

Taxonomy is the science of assigning organisms to classification groups.

What is a taxon?

A taxon is any classification group, such as a phylum or family.

What happens to the number of species as you move up the classification hierarchy?

The number of species increases, but they share fewer traits.

What is the boundary paradox in taxonomy?

The boundary paradox is the difficulty in determining the exact moment when groups diverge enough to form separate taxa.

What are synapomorphies?

Synapomorphies are shared traits inherited from a common ancestor.

What are the two criteria for classification to reflect evolutionary origins?

All organisms from a common ancestor are included in the group, and all species in the group share a common ancestor.

What can we predict about a newly discovered species of bat?

We can predict it has mammalian traits like a four-chambered heart, hair, mammary glands, and a placenta.

What discovery about daffodils has medical significance?

Daffodils produce alkaloids, such as galanthamine, used to treat Alzheimer’s disease.

What is a clade?

A clade is a group of organisms evolved from a common ancestor, including living and extinct species.

What determines the size of a clade?

The size of a clade depends on how many species descended from the common ancestor.

What is an example of a small clade?

Ginkgo biloba is the only living member of a small clade.

What evidence is used to identify clades?

Base sequences of genes, amino acid sequences of proteins, and morphological traits are used to identify clades.

Why is sequence data especially important for extinct species?

Extinct species lack DNA, so morphological traits from fossils are used.

What are nested clades?

Nested clades are smaller clades within larger clades based on shared ancestry.

What does the molecular clock estimate?

The molecular clock estimates the time since two species diverged based on differences in base sequences.

What assumption does the molecular clock rely on?

It assumes mutations accumulate at a roughly constant rate over time.

What factors affect the accuracy of the molecular clock?

Generation time, population size, and selective pressure affect the mutation rate and accuracy.

How was the molecular clock used to estimate human evolution?

It estimated humans diverged from a common ancestor with chimpanzees 4.5 million years ago.

What tool can be used to compare protein and DNA sequences?

The BLAST tool can compare sequences.

What does a cladogram represent?

A cladogram represents ancestor–descendant relationships in a branching diagram.

What is a node in a cladogram?

A node is a branching point where a hypothetical ancestor split into two or more clades.

What is the root of a cladogram?

The root is the base of the cladogram, representing the common ancestor of all clades.

What does the parsimony criterion assume in cladogram construction?

It assumes the smallest number of mutations explains current sequence differences.

Why should multiple cladograms be compared?

To account for potential errors in assumptions about evolutionary pathways.

What did sequence data reveal about traditional classifications?

It confirmed many but also led to reclassifications where groups didn’t share a common ancestor.

What is the modern view of domains in classification?

There are three domains: Eubacteria, Archaea, and Eukaryota.

What distinguishes Archaea from Eubacteria?

Base sequences of ribosomal RNA show significant differences between the two.

What are the three domains of life?

The three domains are Bacteria, Archaea, and Eukaryota.

What is the advantage of a hierarchical classification system?

It simplifies the organization and retrieval of biological information.

How many species of mammals are there?

There are approximately 6,500 species of mammals.

What traits place an organism in the order Carnivora?

Traits like teeth and diet adapted for meat-eating.

What is the genus and species name of the fisher?

Pekania pennanti.

What does a genus contain?

A genus contains one or more species.

What does a family contain?

A family contains one or more genera.

Why do taxonomists sometimes disagree over classifications?

Divergence over time creates uncertainty about when taxa should be split or merged.

What is the primary goal of biological classification?

The goal is to reflect the evolutionary relationships among organisms.

What allows biologists to make predictions about organisms?

Shared traits inherited from a common ancestor (synapomorphies) allow predictions.

Why do clades include extinct species?

Extinct species evolved from the same common ancestor as living species in the clade.

How is evolutionary history deduced from genomes?

Base sequence comparisons reveal evolutionary relationships.

What happens to sequence differences over time?

Sequence differences accumulate due to mutations.

What is a molecular clock used for in evolutionary studies?

It estimates divergence times between species.

What does the parsimony criterion aim to minimize?

It minimizes the number of evolutionary changes needed to explain sequence data.

What does a node with three branches on a cladogram indicate?

It indicates uncertainty about which two clades diverged first.

Why are cladograms considered hypotheses?

They are based on assumptions about mutation rates and evolutionary pathways.

What evidence supports the reclassification of prokaryotes?

Ribosomal RNA base sequences revealed two distinct groups: Eubacteria and Archaea.

How does generation time affect mutation rates?

Shorter generation times lead to faster accumulation of mutations.

What is the primary focus of cladistic analysis?

Cladistic analysis focuses on evolutionary relationships based on shared traits and sequence data.

What is a potential issue with morphological traits in cladistics?

Convergent evolution can make unrelated species appear similar.

Why are nested clades important in classification?

Nested clades show how smaller groups evolved within larger groups.

What does the root of a cladogram represent?

It represents the most recent common ancestor of all included species.

How are traditional and molecular classifications reconciled?

Molecular data is used to confirm or revise traditional groupings.

Why is reclassification sometimes necessary?

New evidence may show groups do not share a common ancestor.

What is the significance of the discovery of alkaloids in daffodils?

It highlights the use of classification to predict useful traits in related species.

What is the importance of cytochrome oxidase in evolutionary studies?

Its sequence is highly conserved and used to compare evolutionary relationships.

What does a cladogram with scaled branches represent?

Scaled branches show estimated divergence times based on sequence differences.

What happens as species diverge further?

They accumulate more sequence differences and may form new taxa.

What is the role of selective pressure in mutation rates?

Selective pressure can accelerate or slow mutation accumulation.

Why is sequence data preferred over morphological traits for extinct species?

Morphological traits are more subjective and can be influenced by convergent evolution.

How has DNA sequencing changed classification?

It provides objective data for evolutionary relationships and reclassification.

What did sequence data reveal about prokaryotic diversity?

It showed prokaryotes are divided into two distinct domains: Eubacteria and Archaea.

What are the two types of evidence used in cladistics?

Base/amino acid sequences and morphological traits.

What is the purpose of using the BLAST tool?

To compare DNA or protein sequences and identify evolutionary relationships.

Why do clades vary in size?

Clades vary based on the number of species descended from their common ancestor.

What makes the molecular clock an estimate?

Mutation rates can vary, affecting accuracy.

How do researchers analyze clades with large sequence data?

They use computer software to determine evolutionary pathways with the least changes.

What does the term phylogeny refer to?

Phylogeny refers to the evolutionary history and relationships of a species or group.

What is the main limitation of cladograms?

They are hypotheses based on assumptions that may not always be correct.

What is the evolutionary significance of shared traits within a clade?

Shared traits indicate inheritance from a common ancestor.

What is a key assumption in using base sequences for evolutionary studies?

Mutations accumulate over time at a roughly constant rate.

What is the relationship between nodes on a cladogram and divergence?

Nodes represent points where an ancestral species split into two or more clades.

What is the main challenge in identifying clades based on fossils?

Fossils lack DNA, so only morphological traits can be analyzed.

What is a clade?

A group of organisms evolved from a common (shared) ancestor, including all species alive today, the ancestral species, and any extinct species that evolved from the common ancestor.

How are clades defined?

Clades are identified based on shared characteristics inherited from a common ancestor.

Can clades vary in size?

Yes, clades can be very large (e.g., birds with about 10,000 species) or very small (e.g., Ginkgo biloba with only one living member).

What is the best evidence for determining clades?

Base sequences of genes or amino acid sequences of proteins provide the most objective evidence.

What evidence is used to assign extinct species to clades?

Morphological traits and fossil evidence are used when sequence data is not available.

What is the concept of nested clades?

Smaller clades are nested within larger clades based on shared ancestry.

What is the molecular clock?

A method of estimating the time since two species diverged from a common ancestor by comparing differences in DNA or protein sequences.

What assumption is made for the molecular clock to work?

It assumes mutations accumulate at a roughly constant rate over time.

What factors can affect the mutation rate in the molecular clock?

Generation time, population size, selective pressure, and other factors.

How long ago did humans split from their nearest living relatives?

Approximately 4.5 million years ago.

When did common chimpanzees and bonobos diverge?

About one million years ago.

What is mitochondrial DNA used for?

It is used to estimate when the most recent common ancestor of all humans existed.

When did the most recent common ancestor of all humans live?

Approximately 150,000 years ago.

What is the NCBI website used for?

It is used for comparing protein and DNA sequences to study evolutionary relationships.

What is BLAST?

A tool on the NCBI website that allows sequence alignment to compare DNA or protein sequences.

How can sequence comparison resolve classification controversies?

It can identify differences in base or protein sequences to determine evolutionary relationships.

How does comparing base sequences estimate divergence times?

Fewer sequence differences indicate recent divergence, while more differences suggest older divergence.

What is the parsimony criterion in cladistics?

It suggests the most probable pattern of evolution involves the smallest number of sequence changes.

What is a cladogram?

A branching diagram that represents ancestor–descendant relationships in a clade.

What does the root of a cladogram represent?

The hypothetical common ancestor of all the clades in the diagram.

What are nodes in a cladogram?

Branching points that represent where a hypothetical ancestral species split to form two or more clades.

What do the terminal branches in a cladogram represent?

Individual clades, which may be species or groups of species.

What do numbers on a cladogram sometimes indicate?

The number of sequence differences between species.

Are cladograms always drawn to scale?

Not always; some are drawn based on estimates of time since each split occurred, while others are not.

What is the primary assumption of cladograms?

That the smallest possible number of mutations occurred to account for current sequence differences.