Molecular evolution – divergence, clocks, gene duplication - Question Bank

1. The comparison of gene order between related species (synteny analysis) can provide insights into:
A) Rates of molecular divergence
B) The timing of chromosomal rearrangements and gene duplication events
C) The functional redundancy of genes
D) The selective pressures on non-coding DNA
2. What role does recombination play in molecular evolution, especially concerning duplicated genes?
A) It typically leads to the loss of duplicated genes.
B) It can facilitate unequal crossing over, a mechanism for gene duplication.
C) It slows down the divergence of duplicated genes.
D) It is irrelevant to the fate of duplicated genes.
3. The 'molecular clock hypothesis' is primarily based on the accumulation of:
A) Chromosomal rearrangements
B) Point mutations
C) Gene duplications
D) Horizontal gene transfers
4. When analyzing molecular divergence, what is the significance of identifying 'hotspots' of molecular evolution?
A) Regions with very low mutation rates
B) Regions exhibiting unusually high rates of genetic change
C) Areas of intense positive selection
D) Regions where gene duplication is common
5. Which of the following is an example of a molecular clock calibration point derived from non-fossil evidence?
A) A known geological event that separated populations (e.g., island formation)
B) The oldest fossil of a specific lineage
C) The divergence time of a well-characterized gene duplication event
D) The first appearance of a specific protein in the fossil record
6. What is the concept of 'molecular drive' in the context of gene families?
A) The random mutation of genes
B) The non-random, concerted evolution of repetitive DNA sequences and gene families
C) The process of natural selection on individual genes
D) The rate of protein synthesis
7. The study of divergence between coding and non-coding DNA sequences can reveal:
A) Regions under different selective pressures
B) Rates of gene duplication
C) Molecular clock calibration points
D) Horizontal gene transfer events
8. What is the 'effective population size' (Ne) and how does it relate to molecular evolution?
A) It is the number of individuals in a population; it has no effect on molecular evolution.
B) It is the number of individuals contributing genes to the next generation; it influences the rate of genetic drift and fixation of mutations.
C) It is the maximum population size; it directly correlates with the rate of speciation.
D) It is the number of species in an ecosystem; it determines molecular divergence rates.
9. The process of gene family expansion and contraction over evolutionary time is driven by:
A) Gene duplication and deletion events
B) Random genetic drift
C) Environmental selection pressures
D) Horizontal gene transfer
10. Which of the following is a challenge in using molecular clocks?
A) Determining the exact rate of mutation
B) Accounting for rate variation
C) Choosing appropriate calibration points
D) All of the above
11. What is the role of 'molecular signatures' in evolutionary studies?
A) Unique patterns of genetic variation that reflect evolutionary history
B) Specific protein structures
C) Phenotypic traits
D) Environmental adaptations
12. The concept of 'molecular parallelism' refers to:
A) Independent evolution of similar traits via similar molecular changes
B) Convergent evolution at the molecular level
C) Parallel mutations occurring in different lineages
D) All of the above
13. What is the primary evolutionary consequence of gene duplication if both copies are maintained?
A) Reduced genetic diversity
B) Increased metabolic efficiency
C) Potential for novel functions and increased complexity
D) Immediate loss of function
14. A 'relaxed molecular clock' allows for:
A) A single, constant substitution rate across all branches of a phylogenetic tree
B) Variable substitution rates across different branches
C) Only synonymous substitutions
D) No mutations to occur
15. Which type of molecular clock is based on the assumption of a constant rate of substitution per lineage?
A) Global clock
B) Local clock
C) Relaxed clock
D) Strict clock
16. The study of molecular divergence patterns can reveal:
A) The evolutionary relationships between organisms
B) The relative rates of evolution in different lineages
C) The history of gene duplication events
D) All of the above
17. What does 'paralogy' refer to in molecular evolution?
A) Genes in different species that evolved from a common ancestral gene by speciation
B) Genes within the same species that arose from duplication
C) Genes that are functionally unrelated
D) Genes that are highly conserved across all species
18. What does 'orthology' refer to in molecular evolution?
A) Genes within the same species that arose from duplication
B) Genes in different species that evolved from a common ancestral gene by speciation
C) Genes that have lost their function
D) Genes that have acquired new functions
19. When comparing homologous genes in two species, a higher number of non-synonymous substitutions compared to synonymous substitutions might suggest:
A) Purifying selection
B) Neutral evolution
C) Positive selection
D) Gene inactivation
20. The 'molecular clock hypothesis' is most applicable to which type of genetic change?
A) Changes in gene regulation
B) Accumulation of neutral mutations
C) Positive selection events
D) Epigenetic modifications
21. What is the concept of 'molecular drive' in relation to gene families?
A) The independent evolution of duplicated genes
B) The coordinated change in copy number of genes within a family
C) The rate of mutation in non-coding regions
D) The process of speciation
22. Which type of sequence is often used for deep phylogenetic divergences due to its slow evolutionary rate?
A) Mitochondrial DNA control region
B) Nuclear ribosomal RNA genes
C) Protein-coding genes with high synonymous substitution rates
D) Transposable elements
23. The process of gene duplication can occur through:
A) Unequal crossing over
B) Retrotransposition
C) Replication slippage
D) All of the above
24. What is meant by 'molecular divergence time'?
A) The time since two species last shared a common ancestor
B) The time it takes for a gene to duplicate
C) The rate at which mutations accumulate
D) The period of evolutionary stasis
25. The study of molecular evolution helps to understand:
A) The mechanisms of adaptation
B) The history of life on Earth
C) The genetic basis of disease
D) All of the above
26. Which of these is NOT a factor that can affect the accuracy of molecular clock estimates?
A) Rate heterogeneity across the genome
B) Selection pressures acting on the gene
C) Accuracy of fossil calibration points
D) The number of genes analyzed
27. What is the significance of conserved non-coding sequences in molecular evolution?
A) They indicate regions under strong purifying selection
B) They are prone to rapid mutation
C) They are primarily involved in gene duplication
D) They represent neutral variation
28. The process where a duplicated gene evolves to become non-functional is called:
A) Neo-functionalization
B) Sub-functionalization
C) Gene inactivation
D) Positive selection
29. A 'molecular clock calibration point' is typically derived from:
A) Fossil records providing a minimum age for a lineage
B) Known speciation events
C) Assumptions about mutation rates
D) Analysis of gene expression data
30. What is the 'COGs' database used for in molecular evolution studies?
A) Estimating divergence times
B) Clustering orthologous genes
C) Identifying gene duplication events
D) Calibrating molecular clocks
31. The rate of molecular evolution is often measured as the number of:
A) Speciation events per million years
B) Substitutions per site per year
C) Changes in phenotype per generation
D) Geographical range expansions
32. Which of the following is a common method for detecting gene duplication events?
A) Sequence alignment of homologous genes
B) Analysis of gene expression levels
C) Comparative genomics
D) All of the above
33. What is the role of selective constraints in molecular evolution?
A) They accelerate the rate of molecular divergence
B) They slow down the rate of change in functionally important regions
C) They are irrelevant to molecular clock calibrations
D) They only affect neutral mutations
34. In molecular phylogenetics, what does a longer branch length typically represent?
A) A shorter evolutionary time
B) A greater number of molecular changes
C) A more recent common ancestor
D) A lower mutation rate
35. Which type of mutation is most likely to be selectively neutral?
A) Nonsense mutation
B) Frameshift mutation
C) Synonymous substitution (silent mutation)
D) Missense mutation leading to protein dysfunction
36. The molecular clock concept was first proposed by:
A) Charles Darwin
B) Gregor Mendel
C) Emile Zuckerkandl and Linus Pauling
D) Alfred Hershey and Martha Chase
37. Horizontal gene transfer is a form of molecular evolution that involves:
A) Inheritance from parent to offspring
B) Transfer of genetic material between unrelated organisms
C) Recombination within a species
D) Somatic mutations
38. What is a pseudogene?
A) A functional gene that has duplicated
B) A non-functional gene copy resulting from duplication and subsequent mutation
C) A gene with a highly conserved sequence
D) A gene involved in metabolic pathways
39. The divergence time between two species can be estimated using molecular clocks by comparing:
A) Morphological differences
B) Geographical distribution
C) Number of genetic differences in their DNA or protein sequences
D) Behavioral patterns
40. Which of the following is a limitation of the molecular clock hypothesis?
A) Rates of molecular evolution can vary between different genes
B) Rates can vary between different lineages
C) Rates can be affected by selection pressures
D) All of the above
41. Neutral theory of molecular evolution posits that:
A) Most molecular changes are driven by positive selection
B) Most molecular changes are selectively neutral
C) Mutations are always deleterious
D) Gene duplication is rare and non-impactful
42. The rate of molecular divergence can be influenced by:
A) Generation time
B) Metabolic rate
C) Selection pressures
D) All of the above
43. Sub-functionalization, following gene duplication, occurs when:
A) Each gene copy evolves to perform a subset of the original gene's functions
B) Both copies maintain the original full function
C) One copy is lost and the other duplicates its function
D) Expression patterns of the duplicated genes become identical
44. What is neo-functionalization in the context of gene duplication?
A) Both gene copies retain the original function
B) One gene copy is lost, and the other maintains the original function
C) One gene copy evolves a completely new function
D) The expression levels of both genes are reduced
45. After gene duplication, one copy of the gene can potentially:
A) Be immediately deleted
B) Undergo rapid degradation
C) Acquire new functions through mutation and selection
D) Remain identical to the original copy indefinitely
46. Gene duplication is considered a major source of:
A) Genetic drift
B) Neutral variation
C) New genetic material and evolutionary innovation
D) Epigenetic modifications
47. What type of molecular data is most commonly used to calibrate molecular clocks?
A) Protein sequences
B) Mitochondrial DNA sequences
C) Ribosomal RNA sequences
D) All of the above
48. The concept of a 'molecular clock' is based on the assumption that:
A) Evolutionary rates are constant across all genes and lineages
B) Mutations accumulate at a relatively constant rate over time
C) Speciation events are predictable and regular
D) Environmental pressures drive specific genetic changes
49. Molecular divergence refers to the process of:
A) Speciation due to geographical isolation
B) Accumulation of genetic differences between lineages over time
C) Changes in gene expression patterns
D) Development of complex multicellularity
50. What is the primary unit of molecular evolution?
A) Phenotypic changes
B) Allelic frequencies in a population
C) Changes in DNA or protein sequences
D) Ecological niche shifts
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