Genome analysis of the Jomon dogs reveals the oldest domestic dog lineage in Eastern Eurasia

Abstract

41 Dog is the oldest domesticated animal that established close relationships with humans. 42 Due to its ancient origin, when, where, and whether a single or dual domestication event 43 occurred is still under debate. The dogs in the Jomon period (Jomon dogs) in the 44 Japanese archipelago had little change in morphology from 10,000 to 3,000 years ago. 45 Therefore, we expected that the ancient genome of the Jomon dogs would provide a 46 clue to reveal the characteristics of the ancient East Asian dogs. Here, we have 47 sequenced the genomes of three 6000-year-old Jomon dogs, one 3000-4000-year-old 48 Jomon dog, and four late 8th century dogs excavated in Japan. Our analyses suggest that 49 the Jomon dogs are a distinct lineage from the previously known ancient dogs and are 50 one of the oldest among the dogs in East Eurasian lineages. In addition, the genome of 51 the Jomon dogs contained 9.5% of the genome of Japanese wolf ancestry due to a single 52 introgression event. We estimated the proportion of the Jomon dog lineage genome in 53 the genomes of dogs, which indicates that the genomic composition derived from the 54 Jomon dog lineage is one of the major sources of modern dog genomes. Furthermore, 55 we estimated the early admixture events of dogs in East Eurasia by analyzing the 56 ancient genomes of the Jomon dogs. Due to the admixture events, the Jomon 57 dog-derived genome has been one of the genomic sources of a wide range of modern 58 dogs. 59 60 61 bioRxiv preprint doi: https://doi.org/10.1101/2023.09.29.560089; this version posted October 1, 2023. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license. 62 bioRxiv preprint doi: https://doi.org/10.1101/2023.09.29.560089; this version posted October 1, 2023. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license. 63