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.

Probing Low-Level Acoustic Attribute Encoding in CLAP Audio Embeddings

Audio foundation models are widely adopted as general-purpose feature extractors, yet the internal structure of their learned representations remains insufficiently understood. In this work, we analyze CLAP audio embeddings through a probing framework, studying the encoding of three fundamental perceptual dimensions: reverberation (RT60), loudness (LUFS), and spectral content, measured via spectral centroid (SC) and relative pitch (RP). Probes of increasing complexity are trained to predict each attribute from frozen embeddings across five datasets spanning noise, speech, monophonic musical notes, and music mixtures. Our primary finding is that all of these attributes are reliably recoverable from the CLAP embedding space across the examined datasets. Within this global picture, two encoding regimes emerge: RT60, LUFS, and RP are approximately linearly encoded, while SC requires non-linear probes. Both regimes generalize across eight additional audio foundation models, with the notable exception that amplitude-invariant architectures discard loudness entirely by construction. The identified linear feature directions are geometrically consistent across datasets for RT60 and LUFS, while highly domain-specific for RP. Finally, we provide a qualitative demonstration of cross-modal consistency, showing that text embeddings of acoustic descriptors align geometrically with the identified RT60 feature direction.

Beyond task performance: Decoding bioacoustic embeddings with speech features

Pretrained audio embeddings are standard in bioacoustics, yet little is known about which acoustic features these models encode, nor which are useful for a given task. This hinders transparency and limits extension to rare species or data-scarce domains. Here we reveal which speech-like features are encoded in bioacoustic representations. Using the 88~eGeMAPS features across six taxonomic groups, we apply linear and nonlinear regression probes to quantify which acoustic properties each model captures. Results confirm a ``no free lunch'' pattern: no single model captures the full feature space. A concatenated embedding achieves the highest performance, suggesting complementary acoustic space coverage across models. Loudness features are best encoded ($R^2 = 0.76$) while F0 is hardest to recover ($R^2 = 0.33$). By cross-referencing recoverability with per-species feature salience (NMI), we derive data-driven model selection guidance for bioacoustics.