ppos not mesonychians, are whales’ closest living relatives — a result nailed down by retroposon (SINE) insertions and artiodactyl ankle characters mapped onto phylogenies around 2001-2005. What’s your favorite example where phylogenetic analysis overturned a morphology-based assumption because of homoplasy?
New World vultures are my pick — phylogenomics (e.g., Jarvis 2014: https://www.science.org/doi/10.1126/science.1253451) pulled them with hawks/eagles, and the “bald head” and soaring wing plan were classic homoplasy. When I’m worried about that, I map the obvious adaptive traits onto the molecular backbone and see if they rack up extra steps versus neutral-ish characters, then downweight them before re-running morphology. That same trick helped me make sense of the artiodactyl ankle set you cited from 2001–2005 alongside the SINE insertions.
Flamingos + grebes for me: phylogenomics (Hackett et al… 2008: https://www.science.org/doi/10.1126/science.1163283) pulled flamingos from storks and grebes from loons, reinterpreting those wader/diver traits as homoplasy, and the flip led to overlooked cranial and eggshell synapomorphies being recognized. Small caveat: morphology-only matrices now often recover the same clade after recoding — like realizing the lawn flamingo was wearing a wetsuit all along.
I’ll go with Afrotheria: tenrecs and golden moles grouping with elephants and manatees blew up the old “Insectivora” junk drawer — molecular trees beat look-alike teeth shaped by diet. @esanchez, it’s another case where “small + eats bugs” was homoplasy in disguise; got a favorite Afrotherian oddball?