The first societies that began to domesticate plants and animals in the Southern Cone inhabited a diversity of environments in both the highlands and lowlands. In the highlands these environments include deserts, quebradas, river valleys, and the subtropical forest of the eastern slope of the Andes (the sierras subandinas). The first practice related to animal domestication is linked with camelids, medium-sized animals that are adapted to arid environments. This family has four South American species: two non-domesticated (guanaco (Lama guanicoe) and vicufia (Vicugna vicugna)) and two domesticated (llama (Lama glama) and alpaca (Lama pacos)). Recent genetic studies suggest that the llama descended from the guanaco and the alpaca resulted from an interbreeding between guanaco and vicuna. The llama had a central place in the Andes not only for its meat and wool but also for its capacity for carrying burdens.
Related to this domestication process in the highlands, during the archaic period (10 000 to 3000-2500 years BP), important changes occurred: reduction in the range of mobility, the development of residential areas with the emergence of the first villages, and the adoption of new technologies. However, many societies, especially the llama herders, maintained some dimension of mobility in order to move their herds on a seasonal basis. The domestication of camelids in the highlands implied a long process of intensification which includes predation-protection-domestication before the full establishment of agro-pastoral societies. Some evidence from northern Chile and northwest Argentina suggest an independent center of camelid domestication, between 5000 to 3000 years BP, probably earlier than in the Central Andes. In sites such as Quebrada Seca 3, Inca Cueva 7, Huachichocana III, Tultin 52, Puripica 1, camelid bones, fibers, guano, and corrals for maintaining them in captivity, have all been found. Clear evidence of agro-herder societies in the puna and quebrada are dated at c. 2500 to 1200 years BP. However, the archaeological record of caves in the Argentine northwest suggests that the process started earlier at c. 5000 years BP in places with extreme aridity but with a diversity of microenvironments. In northern Chile there is also early evidence at sites such as Chiu Chiu 200 and Turi-Toconte which suggests a pastoral way of life with seasonal mobility between the high vegas and caftadones, and the precordillera and puna.
The incorporation of domesticated camelids produced important changes in settlement patterns which generated some degree of sedentarism although at the same time maintaining a high logistic dynamic. Hunting and fishing remained an important economic complement on the coast.
While camelid domestication would have a local development in the southern Andes, plant domestication had a strong alochtonous influence since the first domesticated species are from the tropical lowlands east of the cordillera. The domestication of plants was a complex process which becomes visible archaeologically at around 4000 years BP in caves of the high quebradas. However, both the domestication of wild species and introduction of already domesticated plants appeared at different times in each region and they also included a variety of species. Evidence is found in sites such as Casa Chiivez Monticulo and Tebenquiche in the southern puna, and in Quebrada de Inca Cueva-IC c.7-(more than 4000 years BP) in the headwater regions of quebradas and valleys above 3000 m a. s.l.. Remains of squash (Lagenaria sicer-aria), which were used as containers, together with textiles and basketry were found at these sites. At the Huachichocana cave site, remains of chilli (Capsicum baccatum), beans (Phaseolos vulgaris), and maize (Zea mays) where found. In the Cuyo region (south central Andes) remains of squash (Cucurbita sp.) and quinoa (Chenopodium quinoa) were dated at c. 4500-3700 years BP (i. e., sites of Los Morrillos, Agua de la Tinaja, and Gruta del Indio). Only around 2300 years BP did maize arrive in this region. In central Chile, there is evidence for Chenopodium sp. at around 3000 years BP. After this period, there are remains of domesticated plants on the Pacific coast, in the valleys, and within the cordillera.
In the Pacific coastal valleys (Chile) between 9000 and 4000 years BP, there is certain continuity and stability in societies along with a clear maritime economy. This is represented by the world famous Tradition of Chinchorro, whose elaborated human burials are extremely well preserved due to aridity in this area. After 4000 years BP, these people began to slowly experiment with plants. In this context, there was a shift toward the settlement of valleys, suggesting a search for new residential space and better land for cultivation in a desert environment. NiUfiez Atencio proposed that the first cultivars were adopted from primary domestication centers in the tropical lowlands and adapted to the narrow slopes of the mesothermic valleys west of the Andes. This is the case for bean remains found at the site of San Pedro Viejo de Pichasca dating between 8000 and 6000 years BP. However, other sites on the coast of Arica such as the cemetery Morro 2/2 (dated c. 2800 years BP) still maintained a subsistence based on marine resources. Around 1700 years BP, complex cemeteries are recorded in tumuli such as Alto Ramirez, in the Azapa valley, where several cultivated plants (squash, chilli, cotton, manioc, maize, and beans) are found placed as offerings.