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29Apple is an iconic tree and major fruit crop worldwide. It is also a model species for the study of the 30 evolutionary processes and the genomic basis underlying the domestication of clonally propagated 31 perennial crops. Multidisciplinary evidence from across Eurasia has documented the pace and 32 process of cultivation of this remarkable crop. While population genetics and genomics have 33 revealed the overall domestication history of apple across Eurasia, untangling the evolutionary 34 processes involved, archeobotany has helped to document the transition from gathering and using 35 apples to the practice of cultivation. Further studies, integrating archeogenetics and -genomics 36 approaches, will definitively bring new insights about key traits involved in apple domestication. 37 Such knowledge has potential to boost innovation in present-day apple breeding. 38 39 40 41 42 43 Keywords: Adaptive introgression, self-incompatibility, rootstock, pathogen, Silk Road, targeted 44 sequencing, plant remains, paleogenetics. 45 46 47 Glossary 48 Archeobotany: The study of plant remains (seeds, fruits, wood, leaves, pollen, etc.) found in 49 archeological deposits with the aim of reconstructing the paleo-environment and the management of 50 plant resources (including the domestication of wild plants), their uses, and the waste disposal 51 practices of ancient societies. 52 Archeo/paleogenetics and -genomics: Research fields that use the genetic information gathered 53 from archeological plant or animal remains (ancient DNA; aDNA) to address questions about the 54 evolution, domestication and history of use and cultivation of plants and animals (e.g. [1-8]). 55 Balancing selection: Selection regimes that result in increased genetic diversity relative to neutral 56 expectations in populations of living organisms. 57 Crabapple [9]: Wild apple species that usually blossom profusely and produce small, acidic fruits. 58 The word crab comes from the Old English 'crabbe' meaning bitter or sharp tasting. Many 59 crabapples are cultivated as ornamental trees. In Western Europe the term crabapple is often used to 60 refer to Malus sylvestris (the European crabapple), in the Caucasus to M. orientalis (the Caucasian 61 crabapple) and, in Siberia, to M. baccata (the Siberian crabapple). The native North American 62

In the coastal area of the northwestern part of the Netherlands, dozens of sites dating to the Single Grave culture (or Corded Ware culture; 2850-2450 cal BC) have been located. Some of the sites have been excavated in the last decades of the 20th century. Within the framework of the Odyssey project of the Netherlands Organisation for Scientific Research, the excavated materials from three sites (Keinsmerbrug, Mienakker and Zeewijk) could be fully analysed. The results of archaeobotanical research, including the combined botanical and chemical analyses of organic residues (crusts) in ceramics, as well as the study of isolated remains of processed plant food and charred remains of parenchymatous tissue are presented. It is extremely challenging to find out what kind of food people prepared in the past and to determine actual prehistoric vessel use, to understand what kind of meals people prepared in ceramic vessels, what pots they used for what kind of foods, and if they used the same types of pots for the same foods all the time. The results obtained for the three sites are compared to the existing, dichotomous model developed for habitation of the Single Grave culture in the area, with small special activity sites and large permanent settlements.

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