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Two equid species have been documented in the Pleistocene of the Iberian Peninsula, the horse Equus caballus, and the Eurasian hemione Equus hydruntinus. While the former survived the Holocene–Pleistocene until now, the timing for the extinction of the latter is unclear. Scarce, fragmented archaeological remains assess the presence of small equids living in the Holocene of Iberia. Those could possibly correspond to the Eurasian hemione although unambiguous morphological identification is often not possible. With the find of an equid tooth from Leceia, a Chalcolithic fortified site in Portugal, and using both morphological and mitochondrial genome analyses, we demonstrate for the first time the presence of a new equid species in Holocene Iberia, namely a donkey (Equus asinus). Radiocarbon dating of the tooth to Cal 2340–2130, and 2080–2060 BC with 95% probability, demonstrates that donkeys were present in Iberia well before the arrival of Phoenicians in the first quarter of the first millennium BC (900–750 years BC), which were considered so far as the first who introduced donkeys in the region.

In order to test the possibility of large migrations of wild horses between the North and the South of Western Europe during the Late Glacial, we addressed the population diversity in this area, especially during the Bolling/Allerod periods. We based this appreciation upon the detailed morphology of the distal part of the metapodials. Landmark approaches were applied to archaeological and palaeontological samples from three distinct areas: Switzerland Plateau, Paris Basin, and Charente (France). Little differences of isometric size characterized the three regional samples. Multivariate analyses of shape (principal component analysis, discriminant, canonical variates and neural network analyses) revealed similar sets of complex shape features on both metacarpals and metatarsals. In addition, regional groups appeared clearly differentiated by well defined shape patterns, the functional implications of which remain to be established. These results evidence the existence of a regional structuration of populations (particularly clear on the CVA of both metacarpals and metatarsals) suggesting the absence of long distance migrations. Finally, it appears that the distinction between size and shape systematically operated by geometric morphometrics can provide better insights into the study of the mobility of ancient populations. Geometric morphometrics approaches such as 3D Procrustes superimpositions, appear therefore to be of great interest for archaeological purposes.