Phylogenetic signal in marine mammal and bird vocalizations captured by audio foundation models: the limited benefit of domain-specific pretraining
Do learned audio embeddings encode structure that nobody told them to encode? We probe four large pretrained audio models (AST, CLAP, BEATs-bio and BirdNET) with a downstream task none of them saw during training: recovering phylogenetic distance from species vocalizations. If the geometry of the embedding space tracks the tree of life, the representation is picking up something deeper than the labels the model was optimized for. We run Mantel tests across two independent radiations. In 32 marine mammal species (1,754 recordings from the Watkins Marine Mammal Sound Database) the foundation models recover strong phylogenetic signal within the 26 cetaceans (CLAP r=0.82, BEATs-bio r=0.82, AST r=0.74; all p<0.001), among the highest acoustic-phylogenetic correlations reported for any taxon. Hand-crafted MFCC features (105d) find nothing (r=0.040, p=0.338). The gap survives after PCA-projecting every embedding down to 105 dimensions, so it is not an artefact of representation size. It also survives a partial Mantel test controlling for dominant frequency (partial Mantel r=0.404, keeping 97% of the variance explained), so it is not just pitch in disguise. We repeat the analysis on 20 bird species using the Jetz et al. (2012) phylogeny, and this time add BirdNET, a classifier trained end-to-end on around 6,000 bird species. The general-purpose foundation models recover the signal again (AST r=0.55, CLAP r=0.52). The unexpected result is that neither BirdNET nor the bioacoustic BEATs-bio beat them (r around 0.32 to 0.36). Matching the training domain to the target taxon does not, by itself, help. Pretrained audio embeddings carry evolutionary information across two independent radiations, and domain-specific pretraining is not required for it to emerge.