Evolution, Population Genetics, and Comparative Genomics
Evolution as a population-level process
Selection, drift, mutation, and migration
Evolutionary change results from the interaction of mutation, natural selection, genetic drift, recombination, and gene flow. Population genetics provides the mathematical framework for connecting molecular variation to adaptation and constraint.
Key distinction
Evolution is a change in allele frequency over time, whereas adaptation is a particular outcome of selection in a given environment.
Phylogenomics and comparative analysis
Inferring histories from sequences
Comparative genomics identifies conserved elements, gene family expansions, horizontal transfer, and lineage-specific innovations. Phylogenetic inference must account for rate variation, incomplete lineage sorting, and model misspecification.
Which force can cause allele frequencies to change randomly, especially in small populations?
Genetic drift is stochastic change in allele frequencies due to sampling effects.
Correct answer: Genetic drift
What is one challenge in phylogenetic inference?
Incorrect assumptions about substitution processes or lineage history can bias tree reconstruction.
Correct answer: Model misspecification
Molecular evolution and open problems
Neutrality and constraint
A major debate concerns how much of molecular evolution is shaped by neutral drift versus selection. Another frontier is integrating genotype-phenotype maps with fitness landscapes across environments.
What does a molecular clock attempt to estimate?
Molecular clocks use sequence divergence to infer timing of evolutionary splits.
Correct answer: Time since divergence from sequence changes
Name one source of bias in comparative genomics.
Incomplete genomes and lineage-specific losses can distort evolutionary conclusions.
Correct answer: Gene loss and sampling bias