Final answer:
The statement 'Missing taxon often cause misaligned trees' is not a problem associated with reconstructing phylogenies. Issues mainly arise from distinguishing homologous traits from analogous traits and homoplasy, as well as the application of maximum parsimony.
Step-by-step explanation:
The correct answer is d) Missing taxon often cause misaligned trees. This is not a problem with reconstructing phylogenies because including taxonomic representation is essential for correctly aligning trees, but the absence of taxa does not typically misalign trees. Instead, it can result in incomplete or less informative trees.
The process of reconstructing phylogenies involves analyzing traits to decipher accurate evolutionary relationships. Scientists must distinguish between homologous and analogous traits, where homologies indicate common ancestry and analogies may result from convergent evolution, known as homoplasy. Homoplasy can mislead phylogenetic analysis because traits look similar due to similar selective pressures rather than shared ancestry. The principle of maximum parsimony, which chooses the simplest evolutionary pathway with the least amount of change, helps to build phylogenetic trees but might not always reflect the true complexity of evolutionary history.