Herded and hunted goat genomes from the dawn of domestication in the Zagros Mountains

Abstract

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.

Keywords: Neolithic; ancient DNA; archaeozoology; caprine; domestication.

Fig. 1.

Map showing selected archaeological sites of the Zagros and eastern Fertile Crescent, with sampled sites enlarged and those mentioned in the text labeled. Site key presented in SI Appendix, Table S1. Inset map shows broader geographic context.

Fig. 2.

Archaeozoological evidence for goat management at Ganj Dareh. (A) Overall and sex-specific combined survivorship curves of goat samples from Ganj Dareh Smith excavation assemblage, showing proportion of animals surviving beyond each age group across all levels and each level individually. The overall curves include material that could not be sexed and are not included in the sex-specific curves. (B) Hoofprints in mud-brick at Ganj Dareh (sample 270, context 2033, lowest level of collapse from Smith excavation); Inset displays likely individual hoof impressions.

Fig. 3.

Principal components analysis of wild and domestic goat through time. Variation (%) explained by each PC is indicated in parentheses. Two clusters are observed from the AN Zagros goat, a large group with domestic affinity and a small group with wild affinity.

Fig. 4.

Neighbor-joining tree based on pairwise IBS and with 50 bootstraps and 5-Mb windows, using genomes with ≥1X mean coverage. AN Zagros goats are highlighted, with Zagros Main in yellow and Zagros Outlier basal group in orange. Modern clades are collapsed when possible. Node support values are shown when less than 0.75. The phylogeny demonstrates that the two groups are successive sister groups to later domestic groups, and basal to domestic variation.

Fig. 5.

Simplified admixture graph modeling the ancestries of Neolithic and pre-Neolithic goats, with the inclusion of the Tur C. caucasica and sheep as an outgroup. Mixing events are represented by dotted lines, with a dash frequency proportional to the contribution of that clade. Drift statistics are present in SI Appendix, Fig. S17. Ancient wild turkey = Epipaleolithic Direkli Cave; Ancient Wild Armenia = Upper Pleistocene Hovk 1 Cave. Neolithic East Iran (Tappeh Sang-e Chakhmaq) includes a nearby contemporaneous sample from Monjukli Depe, Turkmenistan (SI Appendix, Table S12).

Fig. 6.

Goat genetic diversity through time. (A) Error-corrected transversion heterozygosity as violin plots for modern and ancient genomes downsampled to 2X. A single Zagros Outlier genome, Abdul4, is displayed as a point and symbol. Asterisk (*) indicates significant differences in medians between a group and Ganj Dareh genomes (Wilcoxon rank-sum, P value cutoff 0.05). (B) Transversion heterozygosity rate in 500-kb windows on chromosomes 1, 6, and 22 for Ganjdareh18 and Ganjdareh22. Windows called as within long ROH regions are displayed in full color. (C) F_ROH5Mb estimates for ancient and modern goats. The 80th and 90th percentiles of F_ROH5Mb values are indicated. Asterisk (*) indicates difference in group median values with Ganj Dareh. The Ganj Dareh genomes show a combination of high heterozygosity with the presence of long ROH.

Fig. 7.

Uniparental haplogroup frequencies for (A) mtDNA and (B) Y chromosomes. Zagros Outlier mtDNA are indicated by a black box. Frequencies for modern populations were obtained from refs. and . Distinct diversity patterns are seen in the AN Zagros goat uniparental markers, with greater diversity observed in the maternal mtDNA pool.