Final answer:
The morphological species concept has issues differentiating between inter and intraspecific variation, can be deceived by mimicry and cryptic species, largely ignores asexual reproduction, and struggles with classifying organisms based on physical traits alone without considering breeding compatibility.
Step-by-step explanation:
The morphological species concept faces some noteworthy challenges. These include difficulties in distinguishing interspecific variation from intraspecific variation when examining morphological traits, especially in the fossil record. For example, looking at two sets of bones with different heights doesn't readily indicate if they belong to the same species. Morphology can be misleading due to mimicry, life-cycle changes, and cryptic species, which appear almost identical but are genetically distinct. Moreover, defining species based merely on physical traits without considering breeding behavior can lead to misclassification, as organisms that look similar might not be able to interbreed, while ones that differ greatly might still be part of the same species.
Additionally, this concept fails to effectively encapsulate the complexity of organisms that reproduce asexually, as they do not rely on interbreeding, yet must be classified. To address these and other issues, the phylogenetic species concept proposes the use of unique shared characteristics for determining species, providing a more genetic and evolutionary categorization approach.