Horses and donkeys have had a far-reaching impact on human history, providing mechanical power for agriculture and transportation. Their F1-hybrids, especially mules, have also been of considerable importance due to their exceptional strength, endurance and resistance. The reconstruction of the respective role that horses, donkeys and mules played in past societies requires prior identification of their osseous elements in archaeological assemblages. This, however, remains difficult on the basis of morphological data alone and in the absence of complete skeletal elements. While DNA sequencing provides almost certain identification success, this approach requires dedicated infrastructure and sufficient ancient DNA (aDNA) preservation. Here, we assessed the performance of a cost-effective alternative approach based on geometric morphometric (GMM) analysis of the bony labyrinth, a structure carried within the petrosal bone. This extremely compact osseous structure provides good aDNA preservation and is frequently found in archaeological assemblages. To assess the GMM performance, we first used High-throughput DNA sequencing to identify 41 horses, 24 donkeys, 36 mules and one hinny from 11 archaeological sites from France and Turkey spanning different time periods. This provided a panel of 102 ancient equine remains for micro-computed tomography (microCT) and GMM assessment of the variation of the bony labyrinth shape, including the cochlea and the semicircular canals. Our new method shows good-to-excellent prediction rates (85.7%–95.2%) for the identification of species and hybrids when considering the cochlea and semicircular canals together. It provides a cheap, non-destructive alternative to aDNA for the taxonomic identification of past equine assemblages.

马和驴对人类历史产生了深远的影响，为农业和交通运输提供了机械动力。它们的F1杂种（尤其是mu子）也具有相当重要的意义，因为它们具有出色的强度，耐力和抵抗力。重建过去的社会中马，驴和mu子所扮演的角色，需要事先确定其在考古组合中的骨质元素。然而，仅根据形态学数据并且在没有完整的骨骼元素的情况下，这仍然是困难的。尽管DNA测序几乎可以确保一定的鉴定成功，但是这种方法需要专用的基础结构和足够的古代DNA（aDNA）保存。这里，我们根据对骨迷路（一种在骨骼中携带的结构）的几何形态计量学（GMM）分析，评估了一种经济有效的替代方法的性能。这种极为紧凑的骨质结构提供了良好的aDNA保存，并经常在考古组合中发现。为了评估GMM的性能，我们首先使用高通量DNA测序技术，从法国和土耳其的11个考古遗址中，跨越不同时间段，鉴定出41匹马，24头驴，36 and子和1个小动物。这提供了一组102个古马遗迹，用于显微计算机断层扫描（microCT）和GMM评估包括迷耳蜗和半规管在内的骨迷路形状的变化。我们的新方法显示出优良的预测率（85.7％–95。2％），以便在同时考虑耳蜗和半圆形管时识别物种和杂种。它为过去的马群的分类学鉴定提供了一种廉价，无损的aDNA替代品。