Background: Persian walnut, Juglans regia, occurs naturally from Greece to western China, while its closest relative, the iron walnut, Juglans sigillata, is endemic in south‑west China; both species are cultivated for their nutswood. Here, we infer their demographic historiesthe timedirection of possible hybridizationintrogression between them.
Results: We use whole-genome resequencing data, diferent population-genetic approaches (PSMCGONE),isolation-with-migration models (IMa3) on individuals from Europe, Iran, Kazakhstan, Pakistan,China. IMa3 analyses indicate that the two species diverged from each other by 0.85 million years ago, with unidirectional gene fow from eastern J. regiaits ancestorJ. sigillata, including the shellthickness gene. Within J. regia, a western group, located from Europe to Iran,an eastern group with individuals from northern China, experienced dramatically declining population sizes about 80 generations ago (roughly 2400 to 4000 years), followed by an expansion at about 40 generations, while J. sigillata had a constant population size from about 100 to 20 generations ago, followed by a rapid decline.
Conclusions: Both J. regiaJ. sigillata appear to have sufered sudden population declines during their domestication, suggesting that the bottleneck scenario of plant domestication may well apply in at least some perennial crop species. Introgression from introduced J. regia appears to have played a role in the domestication of J. sigillata.