Table 1.

Finding molecular convergence in convergent phenotypes

Convergent adaptation	Target species I* and II†	Top convergent term	Total convergent sites (genes) in top term	Top-term convergence enrichment (q-value, fold enrichment)	Total divergent sites (genes) in top term	Top-term divergence enrichment (q-value, fold enrichment)	Convergence (✓) or relaxation (×)
Echolocation	Bottlenose dolphin*	Cochlear ganglion degeneration	25 (18)	q = 2.2e-03 fold = 3.2	15 (11)	q = 1 fold = 1.3	✓
	Killer whale*
	Big brown bat†
	Microbat†
	David’s myotis bat†
Aquatic	Bottlenose dolphin*	Scaly skin	27 (15)	q = 3.9e-06 fold = 4.1	12 (10)	q = 1 fold = 1.6	✓
	Killer whale*
	Manatee†
High altitude	Alpaca*	Abnormal lung weight	25 (16)	q = 1.9e-02 fold = 2.7	10 (5)	q = 1 fold = 0.8	✓
	Bactrian camel*
	Pika†
Subterranean	Cape golden mole*	Short photoreceptor inner segment	15 (6)	q = 3.9e-02 fold = 3.7	42 (8)	q = 3.9e-17 fold = 6.2	×
	Star-nosed mole†
Subterranean	Naked mole rat*	Abnormal eye electrophysiology	73 (46)	q = 6.0e-07 fold = 2.3	103 (49)	q = 4.2e-08 fold = 2.1	×
	Star-nosed mole†
Subterranean	Cape golden mole*	Retinal photoreceptor degeneration	30 (22)	q = 2.9e-02 fold = 2.4	57 (23)	q = 1.1e-09 fold = 3	×
	Naked mole rat†

Each row describes the test for a different phenotypic convergence. To test positive for molecular convergence, the top enriched MGI phenotype term (of more than 4,000 tested) for convergent substitutions must not also be enriched for divergent substitutions. We discovered mostly novel convergent positions in cochlear, skin, and lung genes in echolocating, aquatic, and high-altitude mammals, respectively—while correctly identifying convergence accumulation in subterranean mammals’ vision genes as resulting from molecular relaxation (see main text).