It depends on the level of the hierarchy you are working on. An orthologous sequence is one that has passed the three tests of homology (Congruence, Similarity and Conjunction) and, hence, is synapomorphic in a certain point of the hierarchy. Even if in a shallower level it becomes plesiomorphyc, the relation between the sequences is not changed, so they are still orthologous.

No it is not just referring to the apomorphic state

Orthology/ Paralogy just refers to the mode of how the lineages of compared genes originated during Evolution (in a set of orthologous genes only bifurcations due to speciation are assumed to have been involved - in a set of paralogous genes at least one duplication Event was involved causing bifurcations)

So orthology paralogy assumptions are Independent of our phylogenetic hypotheses among the organisms which contain the compared genes.

Apomorphy/ Plesiomorphy Statements change dependent on our preferred phylogenetic hypothesis.

So orthology assumptions both refer to apomorphic and plesiomorphic states of a compared gene.

Nikolaus, I think we are more or less saying the same thing. I need to check Patterson 1998 again to be sure, however.

Anyway, what you said is that paralogy fails the conjunction test, in other words, there is a relation of homonomy between the regions. A orthologous sequences passed all tests and are, hence, homologous.

If I am not mistaken, you can also have duplication events followed by deletion events and what looks like a single copy will show itself paralogous only after phylogentic analysis. If my memory don't fail me, there is a Nelson paper discussing that issue.

Cheers,

Ortholog - similar genes in different species.

Paralog - similar genes within a species.

Homologs - Orthologs and Paralogs.