Assess students' ability to identify and analyze principal sources of uncertainty in phylogenetic trees inferred from genomic data—including sequencing and assembly errors, alignment ambiguity, model misspecification, rate heterogeneity, paralogy and gene duplication, incomplete lineage sorting, horizontal gene transfer, recombination, missing data and taxon sampling—and to evaluate their effects on topology, branch lengths, and support metrics; design diagnostic tests and recommend mitigation and sensitivity-analysis strategies across concatenation and coalescent frameworks.