You can obtain genome sequences from environmental sequencing
Orthology can be a many-to-many relation
Gene families are dynamic with recurring duplications and losses
strict tree reconciliation is very errorprone and other solutions exist with gene trees (that are generally imperfect)
an annotated gene tree corresponds to events on a species tree
Orthologs between human and mouse, or between human and zebrafish, have very different levels of conservation
The acceptor taxon is clustered within the donor taxon
Profile searches are better able to distinguish homologs from non-homologs than pairwise sequence searches
Expanded gene families reflect taxon/species adaptation