Phylogeny Practice Test Practice

These questions are part of the practice quiz. Start practicing

• Explain the neighbor-joining algorithm and its assumptions.
• According to the material, reptiles form what kind of group?
• Which statement correctly defines homoplasy traits?
• What is the primary basis for organizing taxa in cladistics?
• What is a confidence metric?
• Which of the following is a commonly used nucleotide substitution model?
• In bootstrap analysis, how is support for a clade quantified?
• Homoplasy refers to traits that are what?
• What is a character matrix and how are characters coded?
• Which term best describes a group formed from members with different ancestry and not including their most recent common ancestor?
• What is the gamma distribution in rate variation modeling used for?
• Which statement describes a polyphyletic group?
• Which statement correctly defines homologous traits?
• Which method explicitly uses shared derived characters to infer evolutionary relationships among taxa?
• What does apomorphy refer to in phylogenetics?
• Compare maximum likelihood Bootstrap support to Bayesian posterior probabilities for tree confidence, including interpretation caveats.
• Which statement is true about homologous traits in distant lineages?
• What evidence helps identify homologous traits beyond superficial similarity?
• Define homoplasy and explain a common cause.
• What is the key distinction between maximum parsimony and maximum likelihood phylogenetic methods?
• Under what circumstance is a phylogenetic network preferred over a tree?
• Which statement correctly defines a synapomorphy and its role in identifying monophyletic groups?
• What does label A represent on this tree?
• A group that includes a common ancestor and all of its descendants is best described as:
• Cladistics classifications are based on what kind of characters?
• What is the saturation problem in molecular data and how does it affect tree inference?
• In maximum likelihood phylogenetics, what criterion defines the best tree?
• Why might you partition phylogenetic data by gene or codon position?
• A 99% confidence level means you can ______ the null hypothesis and accept your alternative hypothesis 99 times out of 100.
• Where can everything swivel on trees?
• Which of the following is a strategy to mitigate long-branch attraction beyond simply choosing a different method?
• Cladistics is best described as?
• Which of the following is a clear homologous trait across tetrapods?
• What does a distance matrix indicate in distance methods?
• Data partitioning and why researchers might combine nuclear and mitochondrial data.
• In Bayesian phylogenetics, what is a prior and how does it influence results?
• What does the term 'character state' refer to?
• What factor contributes to several equal-optimal trees in practice?
• Which taxon is the outgroup?
• Which statement is true about the GTR model and potential extensions?
• Are Taxon B and Taxon D the same lineage on the tree?
• What distinguishes a strict consensus from a majority-rule consensus when summarizing across multiple trees?
• What is the purpose of model selection in maximum likelihood phylogenetics?
• What is the typical trade-off when coding indels as binary characters in a data matrix?
• A grouping in a phylogeny that includes a common ancestor and all its descendants is called a:
• What does a root on a phylogenetic tree represent?
• Synapomorphies are best described as what?
• What do the CI and RI indicate in parsimony analysis?
• If two species share a trait due to common ancestry, what does that imply?
• What is the impact of compositional bias on phylogenetic inference and how can it be mitigated?
• Which statement is true about homologous traits?
• In Bayesian phylogenetics, what does posterior probability represent?
• What is homology in the context of phylogenetic characters?
• What is the circled piece called, and what does it represent?
• Which approaches detect model misspecification in phylogenetic analyses?
• Midpoint rooting places the root halfway between the two most distant taxa.
• B and C are described as which of the following in the tree?
• Which statement best differentiates a strict molecular clock from a relaxed clock?
• What is the difference between a gene tree and a species tree, and why can they differ?
• Where is the bootstrap support value labeled after bootstrapping?
• What is model averaging in phylogenetics and why use it?
• On a phylogenetic tree, which groups are the descendants of a given node?
• Which statement describes a paraphyletic group?
• How do fossils assist in rooting phylogenetic trees?
• What is pleiomorphy (plesiomorphy) in phylogenetics?
• How do bootstrap and jackknife support values differ in phylogenetics?
• In a phylogenetic diagram, the blue line represents which concept?
• Which statement accurately describes homologous vs analogous?
• What is a character?
• How do we resolve conflicts caused by homoplasy in cladistics?
• Explain outgroup rooting and its purpose in phylogenetic analysis.
• In maximum parsimony analysis, which objective determines the preferred tree?
• In phylogenetics, what is an apomorphy?
• Which statement correctly defines a clade?
• Which of the following is an example of a character state?
• Define parsimony in phylogenetics.
• Biogeography in phylogenetics studies geographic distributions; when integrated with phylogeny, what processes can it reveal?
• What is a clade and how is it determined on a phylogenetic tree?
• Which pairing is correct?
• Which of the following statements about rooted phylogenetic trees is true?
• Which of the following is a plausible indicator that a trait is homologous rather than analogous?
• What do cladistics classifications reflect?
• What is a posterior predictive check in Bayesian phylogenetics and what does it assess?
• Which label represents the past on the tree?
• Which taxon is identified as the outgroup in this tree?
• Which sequence best describes bootstrap analysis for phylogenetic trees?
• What is the function of the outgroup on a phylogenetic tree?
• What is the purpose of data partitioning in phylogenetic analysis?
• What is reconciliation in phylogenomics and why is it important?
• Which statement distinguishes a paraphyletic group from a polyphyletic group?
• Which of the following is a feature of distance methods?
• Which is a homologous trait across mammals?
• What is the primary assumption of the molecular clock concept?
• What does the frequency of a clade across trees represent?
• In phylogenetic trees, what distinguishes a rooted tree from an unrooted tree?
• Which labels represent the present groups on the tree?
• Bootstrapping is a ______ used to assess node support.
• What does the term homologous mean in evolutionary biology?
• The purpose of an outgroup is to root the tree by providing a reference outside the ingroup.
• Which statement describes an analogous trait?
• Which of the following is a classic example of a homologous trait?
• What must be specified before evaluating trees in a likelihood-based method?
• Bootstrap support values are typically displayed at the node.
• Differentiate likelihood ratio test and AIC for model selection in phylogenetics.
• Differentiate monophyly, paraphyly, and polyphyly with clear examples.
• What is the branching point on a phylogenetic tree called?
• Relative dating versus absolute dating in a phylogenetic context. Which statement is true?
• Incomplete lineage sorting affects phylogenetic inference by causing what?
• Which is a problem associated with distance methods?
• Which statement best defines strict consensus?
• What is a symplesiomorphy?
• Which label represents the ancestral root in this description?
• What is a back-mutation and how does it affect parsimony?
• In phylogenetics, a phylogeny is technically a ______.
• What is the difference between a rooted and an unrooted phylogenetic tree?
• Which of the following is an analog example?
• A phylogeny is technically a ______.
• How is rate heterogeneity among sites modeled in phylogenetic analyses?
• What is 'tree space' and why can multiple optimal trees exist?
• Which roles do fossils play in phylogeny reconstruction?
• A polyphyletic group is best described as:
• Which is a common limitation of phylogenetic networks compared to trees?
• What concept is central to cladistics?
• Which statement is true about cladistics?
• Long-branch attraction can mislead phylogenetic inference. What does it primarily result from?
• What are the two meanings of distance in distance-based methods?
• How are character states typically coded in a character matrix?
• What best describes the aim of cladistic classifications?
• Which statement best captures the essence of phylogenetic systematics?
• Differentiate autapomorphy and synapomorphy.
• Vestigial traits are best explained by which idea?
• Which statement best distinguishes homologous traits from analogous traits?
• Phenetics is defined as classification based on what?
• How can model misspecification bias phylogenetic inference and what strategies mitigate it?
• In cladistics, which type of characters are used to infer relationships?
• Which term describes a trait that is shared due to common ancestry?
• Which term defines a shared derived trait that defines a clade?
• An outgroup is known to lie outside the ingroup; believed to be ancestral.
• Which statement best defines the outgroup?
• One accepted definition of lineage is:
• Midpoint rooting places the root halfway between the two most divergent taxa.
• What does positional homology refer to in sequence alignment?
• What is a calibration density in Bayesian dating and why is it used?
• What best describes the role of fossil data in defining character polarity and depth in trees?
• Which term is commonly used as a synonym for monophyletic group?
• What is a synapomorphy?
• What is a calibration point in molecular dating and how is it used?
• If node C is included in the reptile group, the group is considered what?
• Which term best describes the explanation that minimizes changes when mapping traits on a tree?
• In gene family analyses, what are orthologs and paralogs, and why is misidentifying them problematic?
• Which term describes a trait that serves the same function but has different lineage?
• Which of the following is an example of a character?
• Which term describes a trait that is unique to a single lineage?
• Which statement describes bootstrap resampling in phylogenetics?
• What are the two confidence metrics?
• What role do base frequencies play in substitution models?
• What term describes an ancestral trait?
• What is an autapomorphy?
• What term describes two taxa that share the most recent common ancestor and are each other’s closest relatives?
• Which term best describes a trait that is shared, derived, and defines a clade?
• What is a phylogeny?
• Why include a proportion of invariant sites when modeling rate variation?
• Which term describes similarity due to convergent evolution?
• Which concept explains similarities due to convergent evolution rather than shared ancestry?
• Which methods exist to assess whether a character is homologous across taxa?
• Which statement defines a paraphyletic group?
• What does the General Time Reversible (GTR) model specify?
• What is the primary purpose of sequence alignment in phylogenetic analysis?
• How can indels be treated in phylogenetic data matrices?
• Which statement best defines a monophyletic group?
• Phylogenetic systematics uses what to organize relationships among taxa?
• Which term emphasizes the actual historical path of descent through time?
• How does a clade differ from a lineage?
• What is bootstrap support value and how is it interpreted?
• Which statement best captures the concept of homology?
• In Bayesian dating, what is a relaxed clock model?
• Which statement about parsimony in tree reconstruction is true?
• How do fossils contribute to time calibration in phylogenetic analyses?
• Which term describes a derived trait that is unique to a single lineage?