Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary

Abstract

Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zones. However, the history of dromedary domestication and the influence of ancient trading networks on their genetic structure have remained elusive. We combined ancient DNA sequences of wild and early-domesticated dromedary samples from arid regions with nuclear microsatellite and mitochondrial genotype information from 1,083 extant animals collected across the species' range. We observe little phylogeographic signal in the modern population, indicative of extensive gene flow and virtually affecting all regions except East Africa, where dromedary populations have remained relatively isolated. In agreement with archaeological findings, we identify wild dromedaries from the southeast Arabian Peninsula among the founders of the domestic dromedary gene pool. Approximate Bayesian computations further support the "restocking from the wild" hypothesis, with an initial domestication followed by introgression from individuals from wild, now-extinct populations. Compared with other livestock, which show a long history of gene flow with their wild ancestors, we find a high initial diversity relative to the native distribution of the wild ancestor on the Arabian Peninsula and to the brief coexistence of early-domesticated and wild individuals. This study also demonstrates the potential to retrieve ancient DNA sequences from osseous remains excavated in hot and dry desert environments.

Keywords: Camelus dromedarius; anthropogenic admixture; demographic history; paleogenetics; wild dromedary.

Fig. 1.

Representation of the mitochondrial haplotypes retrieved from 759 modern dromedaries and 15 archaeological specimens. (A) Geographical distribution of the modern haplogroups across the species range (delimited by orange dashed line). Pie charts are proportional to sample sizes of the five distinctive regions (Dataset S1). Haplogroups were defined according to Bayesian analysis of population structure (BAPS) clustering (SI Appendix). The proportion of singletons diverging from B1 by one or two mutations (seventh cluster) is depicted by the dotted line within B1 (white). The chart in the upper right corner represents haplogroups retrieved from Southern Asian (SAS*; n = 87) and Australian (AU; n = 38) dromedaries. Stars depict locations of the archaeological sites: SG, Sagalassos, Turkey (Early Byzantine, 450–700 CE); TU, Tulln, Austria (second Ottoman–Habsburg war, ca. 1683 CE); AP, Apamea, Syria (Early Byzantine, 400–600 CE); AQ, Aqaba, Jordan (Mamluk and Ottoman periods, 1260–1870 CE). The Inset in the lower right corner shows sites in the UAE: AB, Al-Buhais (5000–4000 BCE); AS, Al-Sufouh (ca. 2400–1400 BCE); TA, Tell Abraq (Late Bronze–Iron Age, 1260–500 BCE); UN, Umm-an-Nar (Early Bronze Age, 3000–2000 BCE). (B) MJN displaying 76 haplotypes grouped into two maternal lineages, H_A (A1 and A2) and H_B (B1–4). Haplotypes diverging from A1 and A2 and from B1–4 are colored according to BAPS clustering (SI Appendix). Circles are proportional to the sample size. Small diamonds represent median vectors corresponding to missing haplotypes or homoplasies. (C) Parsimonious representation of the occurrence and sharing of mitochondrial haplotypes (531 bp) between modern (light gray) and ancient (dark red) samples. Wild dromedary samples are marked with a dagger (†). Taxonomic determinations of ancient specimens are detailed in SI Appendix. Umm-an-Nar’s sample (UN624) was represented assuming the most frequent nucleotide (nt15486: G). In the case of the alternative allele (nt15486: A), UN624 shared its haplotype with the specimen from Tell Abraq (TA623) (SI Appendix). For both networks, consensus network of all shortest trees is shown; branch lengths are proportional to number of mutations.

Fig. 2.

Individual assignment (structure) plots of 970 (global dataset) and 810 dromedaries (excluding EAF) for a theoretical number of ancestral genetic populations (K) set at 2 and 9, respectively. Optimal clustering solution determined with DeltaK is reported in SI Appendix, Fig. S2. Sample sizes of the distinctive regions and countries are presented in SI Appendix, Table S1 and Dataset S1.

Fig. 3.

BSP derived from the alignment of 759 modern with seven early-domesticated dromedary MT-CR sequences. The thick solid line depicts the median estimate of N_e, with black thin lines delimiting the 95% HPD. We used the archaeological dating of the wild and early-domesticated dromedary samples (SI Appendix, Table S4) to estimate the substitution rate µ = 1.232 × 10⁻⁰⁶ substitution⋅site⁻¹⋅y⁻¹ (95% HPD: 4.435 × 10⁻⁰⁷, 2.213 × 10⁻⁰⁶). LA, Late Antiquity; MA, Middle Ages.