Sanaz Beizaee Doost

Southwest and Central Asia were pivotal regions for the domestication and dispersal of domestic herbivores. Here we investigate long-term variation in bony labyrinth morphology of domestic bovids (sheep, goats and cattle) across the last 10 000 years. We focused on the osseous cavity of the inner ear, located within the petrous bone. We analysed semicircular canal (SC) size and shape using micro-computed tomography and geometric morphometrics (GMM) on 78 modern reference specimens and 234 archaeological petrous bones from 51 sites spanning the Iranian Plateau, Central Asia, the Caucasus and the Indus Valley. Bony labyrinth morphometrics yielded a strong taxonomic signal, enabling species-level identification of 228 out of 234 specimens and revealing greater diversity than anticipated. Comparative analyses further documented contrasting, nonlinear diachronic trajectories in SC size and shape among sheep, goats and cattle, reflecting species-specific responses to domestication and long-term herd management. Together, these results demonstrate that bony labyrinth GMM provides a robust, non-destructive framework for taxonomic identification and evolutionary inference and underscore how long-term, interdisciplinary approaches can capture the complex, nonlinear dynamics of animal domestication across the longue durée.

The origins and prehistory of domestic sheep ( Ovis aries ) are incompletely understood; to address this, we generated data from 118 ancient genomes spanning 12,000 years sampled from across Eurasia. Genomes from Central Türkiye ~8000 BCE are genetically proximal to the domestic origins of sheep but do not fully explain the ancestry of later populations, suggesting a mosaic of wild ancestries. Genomic signatures indicate selection by ancient herders for pigmentation patterns, hornedness, and growth rate. Although the first European sheep flocks derive from Türkiye, in a notable parallel with ancient human genome discoveries, we detected a major influx of Western steppe–related ancestry in the Bronze Age.

The Aceramic Neolithic (∼9600 to 7000 cal BC) period in the Zagros Mountains, western Iran, provides some of the earliest archaeological evidence of goat (Capra hircus) management and husbandry by circa 8200 cal BC, with detectable morphological change appearing ∼1,000 y later. To examine the genomic imprint of initial management and its implications for the goat domestication process, we analyzed 14 novel nuclear genomes (mean coverage 1.13X) and 32 mitochondrial (mtDNA) genomes (mean coverage 143X) from two such sites, Ganj Dareh and Tepe Abdul Hosein. These genomes show two distinct clusters: those with domestic affinity and a minority group with stronger wild affinity, indicating that managed goats were genetically distinct from wild goats at this early horizon. This genetic duality, the presence of long runs of homozygosity, shared ancestry with later Neolithic populations, a sex bias in archaeozoological remains, and demographic profiles from across all layers of Ganj Dareh support management of genetically domestic goat by circa 8200 cal BC, and represent the oldest to-this-date reported livestock genomes. In these sites a combination of high autosomal and mtDNA diversity, contrasting limited Y chromosomal lineage diversity, an absence of reported selection signatures for pigmentation, and the wild morphology of bone remains illustrates domestication as an extended process lacking a strong initial bottleneck, beginning with spatial control, demographic manipulation via biased male culling, captive breeding, and subsequently phenotypic and genomic selection. Significance Goats were among the first domestic animals and today are an important livestock species; archaeozoological evidence from the Zagros Mountains of western Iran indicates that goats were managed by the late ninth/early eighth millennium. We assess goat assemblages from Ganj Dareh and Tepe Abdul Hosein, two Aceramic Neolithic Zagros sites, using complementary archaeozoological and archaeogenomic approaches. Nuclear and mitochondrial genomes indicate that these goats were genetically diverse and ancestral to later domestic goats and already distinct from wild goats. Demographic profiles from bone remains, differential diversity patterns of uniparental markers, and presence of long runs of homozygosity reveal the practicing and consequences of management, thus expanding our understanding of the beginnings of animal husbandry.