BiSSE

One-sentence definition. BiSSE (Binary State Speciation and Extinction) is a phylogenetic model that jointly estimates speciation and extinction rates for each state of a binary trait, testing whether the trait causes lineage diversification to differ between the two states.

One-sentence analogy. BiSSE is like trying to determine whether left-handed vs. right-handed boxers win more bouts, using only the tournament bracket — but if the tournament has dramatic seeding biases, you’ll find handedness “matters” even when it’s coin-flipped.

Why it matters. BiSSE is widely used but catastrophically prone to false positives on real phylogenies with heterogeneous diversification dynamics. On the cetacean phylogeny, >77% of datasets simulated under a neutral character (no state-dependent effect) return a significant association at p < 0.05; even taxon name length — which cannot cause anything — shows significant speciation correlations in >69% of vertebrate subtrees. This means most published BiSSE results on real diversified trees require skepticism and model-adequacy testing.

Where you meet it in the wiki.

• BiSSE — detailed treatment of the false-positive problem.
• Trait-dependent diversification — broader context of methods linking traits to macroevolution.
• Phylogenetic comparative methods — BiSSE in context.

Primary citation.

“More than 77% of the 400 character sets showed a significant (p < 0.05) association between character state and speciation rate, and 58% rejected the character-independent model with great confidence (p < 0.001).” — Rabosky & Goldberg, Finding 1

Prerequisites: Mk model, ancestral state reconstruction Next, learn about: SIMMAP, ancestral state reconstruction