Final answer:
Not all options listed are problems in reconstructing phylogenies, with the exception of 'missing taxa causing misaligned trees.' Accurately describing phylogenies involves distinguishing between homologous and analogous traits, applying maximum parsimony, and utilizing DNA mutation data.
Step-by-step explanation:
The question addresses the challenges in reconstructing phylogenies, which is the process of deciphering the evolutionary relationships between different species. Among the issues listed, all are recognized problems except for "Missing taxa often cause misaligned trees," which does not reflect a typical concern in the reconstruction of phylogenies.
To describe phylogenies accurately, scientists must distinguish between homologous traits (traits shared due to common ancestry) and analogous or homoplasies (similar traits that evolved independently and are not due to common ancestry). This is important because homologous traits reflect evolutionary relationships, while analogous traits do not. The principle of maximum parsimony suggests that the phylogenetic tree with the fewest evolutionary changes is preferred, but sometimes this method may not accurately reflect the true complexities of evolution. Moreover, advances in DNA sequencing have allowed scientists to identify mutations in DNA codes, thereby providing deeper insights and leading to revisions in the reconstruction of phylogenies.