Final answer:
Classification schemes face challenges such as aligning with new genetic evidence and accounting for complex evolutionary events like endosymbiosis, which can lead to updates in the phylogenetic tree that better reflect evolutionary relationships.
Step-by-step explanation:
Two problems inherent in using classification to support evolution include the misalignment of phylogenetic classifications with genetic evidence and the difficulty in accounting for convergent evolution and horizontal gene transfers such as endosymbiotic events. Classification schemes, while striving for accuracy, often require updates as new genetic data becomes available, which may contradict previous assumptions based on physical morphology. Another challenge is that traditionally hierarchy-based or cladistic systems may not handle complexities like endosymbiosis well, as these events involve the merging of lineages rather than just bifurcating branches.
For instance, despite their superficial resemblances to other animals, genetic studies have led to surprising connections, like the close evolutionary relationship between hippopotamuses and whales, which would not be evident based solely on morphological data. Moreover, the reliance on morphological data can lead to the erroneous grouping of organisms into evolutionary relationships that do not reflect their actual histories.