The origin and evolution Zea mays of domesticated plants has intrigued the scientific communityfor centuries. Even though the history of domestication is unique to each species,two broad groups of domesticated plants have been defined on the basis of their reproductioncycles: perennial and annual plants. While annual plants have a one-year (or shorter)life cycle, perennials are long-lived plants. Their intrinsic differences make them distinctin terms of the mechanisms that have shaped their domestication history.Maize (Zea mays ssp. mays) is a model plant that has been used to study the domesticationprocess of annuals, in part because it is one of the most commercially important crops, butalso because it harbours vast phenotypic and genotypic diversity. During the last decade,substantial knowledge has been obtained regarding to the domestication, distribution, anddiversity of maize through the study of modern maize genomes. However, understandingthe complete history of maize domestication remains challenging, as its genome is a productof natural and human selection, with the added complication of genetic introgressionfrom wild conspecifics. Ancient DNA research represents a crucial tool for understandingthe early stages of domestication of maize. Chapters 1 and 2 of this thesis presenttwo studies in which we look directly into the maize genome during its early stages ofdomestication. In the first study, we obtained the complete genome sequence of a 5,310-year-old maize cob recovered from the Tehuac´an Valley in Mexico. The Tehuac´an Valleyarchaeological assemblage is key to understanding maize domestication as it holds someof the most ancient maize remains in the Americas. We show that the Tehuac´an maize cobderives from the same lineage that gave rise to all modern maize landraces sequenced todate, which in turn diverged from the wild maize subspecies parviglumis. Additionally,we find that genes associated with domestication traits were present in a mosaic state inthe 5,310-year-old sample; some of them were more similar to the domesticated state andsome other were more similar to the wild state. These results highlight the gradual natureof the domestication process in maize. In the second study, we obtained whole genomesequencing data from 24 ancient maize samples ranging in age from 70-2,700 years old,from three archaeological sites located north from the domestication centre: the RomeroCave near Ocampo Tamaulipas, Mexico, the Three Fir Shelter in northern Arizona, UnitedStates (US) and the Ozarks Shelter in northwestern Arkansas, US. We show that maizediffused via two northward expansions: one that reached the US Southwest and dispersedthrough the Central Plains, ultimately reaching the US Southeast, and a second one thatgave rise to maize in East Mexico and Central America. Furthermore, we show that modernmaize landraces in the US Southeast are the result of crossing native landraces withrecently introduced landraces most closely related to Caribbean maize.Grapevine (Vitis vinifera L.) represents one of the most important model systems to studydomestication in perennial plants. Today, grapes are propagated vegetatively, thus individualsof the same variety represent genetically identical clones, with only minor differencesowing to somatic variation. Still, their genetic diversity is comparable with that of annualplants, with thousands of different cultivars that have been described in modern andhistorical records. However, the origin and antiquity of such cultivars is mostly unknown.Chapter 3 presents the first attempt to identify the grape varieties used during the Medievaland Roman period in France using whole genome data from ancient seeds. By sequencing28 ancient seeds at ten thousand diagnostic sites and comparing them with modern cultivars,we show that the ancient seeds derived from domesticated grapes, and not from wildgrapes gathered from the wild. Importantly, we show that these ancient grapes and moderngrapes grown nearby bear similar genetic ancestry components and that people transportedcultivars across different regions in the form of cuttings. Furthermore, we present geneticevidence of clonal propagation over at least one thousand years, which gave rise to theSavagnin cultivar, and some other important cultivars in the region.