Post date: Jun 03, 2020 1:2:14 PM
homoplasy = similarity in trait not explained by descent -
qualifies a trait being found in two individuals, but that does not give us an information about ancestry (this is the definition of homology: shared trait based on common ancestry). The trait was acquired independently in both individuals. In present time we see that two individuald have the same trait (mutation in DNA sequence for example). However this trait was not acquired because both individuals have a common ancestor, it was acquired for example because of similar selective pressures, or by chance (genetic drift).
It can lead us to make false conclusions we we look at present time organisms without having information on the history of both individuals.
In our case, homoplasy may not be a problem because we are studying a rather shallow phylogeny (less than 1 million years ago, as compared to deep phylogeny 60 million years ago). We look at mutations. When we see a mutation, we assume all trees having this mutation share a common ancestor. There was no double mutation (reversion to ancestral trait) because the amount of time is short thus the probability of double mutation is very low. Maybe there are one or two but we are ignoring them. Homoplasy should impact less our result than the confidence in mutation calling.