Phylogeny can be based on morphological homologies and molecular homologies. What are the advantages and limitations to using each

1. Molecular data:  

- Advantages:  

a. less susceptible to evolutionary convergence

b. huge amount of potential characters available for data comparison (each nucleotide can potentially be used to assess the state of a character)

c. useful for assessing times of divergence

- Disadvantages:  

a. multiple sequence alignments are hard to solve for sequences with high evolutionary rates

b. limitation to the number of states of the character

c. generally unuseful for comparing with data from extinct species

d. difficulties of inferring positional homology

2. Morphological data:

- Advantages:  

a. useful to understand the evolutionary significance of traits in extinct ancestral species

b. there is not limitation to the number of different states of the character

- Disadvantages:

a. susceptible to evolutionary convergence

b. limited number of characters is available

Explanation:

Morphological and molecular data are the two primary sources of information used to infer homology. In the last years, molecular data gained ground for this purpose. However, it should be stressed that molecular data only have 4 different states (i.e., 4 different types of nucleotides), while for morphological data in principle there is not limitation to the number of different states. On the other hand, morphological traits are more susceptible to evolutionary convergence, thereby leading to spurious results when assessing the homology of problematic characters. Finally, it is important to highlight that morphological data are generally more useful to understand the origin and homology of traits in extinct species.

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