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Study Questions for Classification and Phylogenies (Chapter 20) Learning Objectives - Define taxonomy, phylogeny, and phylogenetic systematics - Explain why we use scientific nomenclature instead of common names and know how to correctly write binomial scientific names - Understand how to read a phylogenetic tree - Explain the relationships between homologous traits, analogous traits, convergent evolution, divergent evolution, and shared ancestry - Explain the differences between a derived and an ancestral trait - Recognize and demonstrate the differences between monophyly, polyphyly, and paraphyly - Explain the molecular clock Define: Taxonomy, Taxon (Taxa), Binomial Nomenclature, Phylogenetic Systematics, Phylogeny, Root, Branch Point, Basal Taxon, Sister Taxa, Polytomy, Homologous Characters, Analogous Characters, Evolutionary Divergence (Divergent Evolution), Evolutionary Convergence (Convergent Evolution), Ancestral Characters, Derived Characters, Monophyly (Monophyletic), Paraphyly (Paraphyletic), Polyphyly (Polyphyletic), Clade, Synapomorphy Neutral DNA Sequences (i.e., why do we call them “neutral”?), Molecular Clock Explain: - What is the only taxon below Domain, for which biologists have a clear definition? - Elk are classified in the species canadensis and the genus cervus. Red Deer are classified in the species elaphas and the genus cervus. Correctly write the binomial names for both elk and red deer. Why are they classified in the same genus (i.e., interpret what this means)? - You find an introductory biology textbook published in 2007 and notice that the phylogenetic trees differ from the ones in a more recent textbook published in 2023. Why would the textbooks differ like this? - Why do we use homologous traits and not analogous traits when constructing phylogenies? - What role does the “outgroup” serve in a phylogeny? - Four lineages differ by 16 nucleotide bases for a neutral DNA sequence that mutates every 7 million years. How long ago did the four lineages diverge from a common ancestor? - Two lineages diverged from a common ancestor 60 million years ago. If they differ from one another by 8 nucleotide bases, how frequently does the neutral DNA sequence undergo mutation? - On the Rooted Phylogenetic tree (slide #14 in the lecture notes for Jan. 22) would represent an adaptive radiation?

          Study Questions for Classification and Phylogenies (Chapter 20)
Learning Objectives
- Define taxonomy, phylogeny, and phylogenetic systematics
- Explain why we use scientific nomenclature instead of common names and know how to correctly write binomial scientific names
- Understand how to read a phylogenetic tree
- Explain the relationships between homologous traits, analogous traits, convergent evolution, divergent evolution, and shared ancestry
- Explain the differences between a derived and an ancestral trait
- Recognize and demonstrate the differences between monophyly, polyphyly, and paraphyly
- Explain the molecular clock

Define:
Taxonomy, Taxon (Taxa), Binomial Nomenclature, Phylogenetic Systematics, Phylogeny, Root, Branch Point, Basal Taxon, Sister Taxa, Polytomy, Homologous Characters, Analogous Characters, Evolutionary Divergence (Divergent Evolution), Evolutionary Convergence (Convergent Evolution), Ancestral Characters, Derived Characters, Monophyly (Monophyletic), Paraphyly (Paraphyletic), Polyphyly (Polyphyletic), Clade, Synapomorphy Neutral DNA Sequences (i.e., why do we call them “neutral”?), Molecular Clock

Explain:
- What is the only taxon below Domain, for which biologists have a clear definition?
- Elk are classified in the species canadensis and the genus cervus. Red Deer are classified in the species elaphas and the genus cervus. Correctly write the binomial names for both elk and red deer. Why are they classified in the same genus (i.e., interpret what this means)?
- You find an introductory biology textbook published in 2007 and notice that the phylogenetic trees differ from the ones in a more recent textbook published in 2023. Why would the textbooks differ like this?
- Why do we use homologous traits and not analogous traits when constructing phylogenies?
- What role does the “outgroup” serve in a phylogeny?
- Four lineages differ by 16 nucleotide bases for a neutral DNA sequence that mutates every 7 million years. How long ago did the four lineages diverge from a common ancestor?
- Two lineages diverged from a common ancestor 60 million years ago. If they differ from one another by 8 nucleotide bases, how frequently does the neutral DNA sequence undergo mutation?
- On the Rooted Phylogenetic tree (slide #14 in the lecture notes for Jan. 22) would represent an adaptive radiation?

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