RE: The code that is DNA
December 19, 2019 at 12:09 pm
(This post was last modified: December 19, 2019 at 12:10 pm by John 6IX Breezy.)
(December 19, 2019 at 11:12 am)Mister Agenda Wrote: Are you familiar with endogenous retroviruses? And the difference between assumption and inference?
Homoplasy, in biology and phylogenetics, is when a trait has been gained or lost independently in separate lineages over the course of evolution. This is different from homology, which is the similarity of traits can be parsimoniously explained by common ancestry.
I'm lightly familiar with retroviruses; what about them should I take into consideration?
Yes, homology is the general assumption made when two organism share similar traits or genotypes. Only once that assumption leads you up a garden path, and oddities and inconsistencies begin to emerge, can homoplasy be identified. That's the only reason why homplasy is "challenging" to phylogeny, because they remind you that you are chasing an assumption not an inference.
Even parsimony, which you yourself mentioned in your description, is full of assumptions that are not always met (see Felsenstein, 1983).
Reference: Felsenstein, J. 1983. Parsimony in systematics: Biological and statistical issues. Annual Review of Ecology and Systematics 14: 313–333.