Early agriculture and crop transitions at Kakapel Rockshelter in the Lake Victoria region of eastern Africa.

The histories of African crops remain poorly understood despite their contemporary importance. Integration of crops from western, eastern and northern Africa probably first occurred in the Great Lakes Region of eastern Africa; however, little is known about when and how these agricultural systems coalesced. This article presents archaeobotanical analyses from an approximately 9000-year archaeological sequence at Kakapel Rockshelter in western Kenya, comprising the largest and most extensively dated archaeobotanical record from the interior of equatorial eastern Africa. Direct radiocarbon dates on carbonized seeds document the presence of the West African crop cowpea (Vigna unguiculata (L.) Walp) approximately 2300 years ago, synchronic with the earliest date for domesticated cattle (Bos taurus). Peas (Pisum sativum L. or Pisum abyssinicum A. Braun) and sorghum (Sorghum bicolor (L.) Moench) from the northeast and eastern African finger millet (Eleusine coracana (L.) Gaertn.) are incorporated later, by at least 1000 years ago. Combined with ancient DNA evidence from Kakapel and the surrounding region, these data support a scenario in which the use of diverse domesticated species in eastern Africa changed over time rather than arriving and being maintained as a single package. Findings highlight the importance of local heterogeneity in shaping the spread of food production in sub-Saharan Africa.

Domestication as the evolution of interspecies cooperative breeding.

We propose that domestication is the result of interspecies cooperative breeding. Considering domestication as an outcome of cooperative breeding can explain how domestication occurs in both plants and animals, encompass cases of domestication that do not involve humans, and shed light on why humans are involved in so many domesticatory relationships. We review the cooperative breeding model of human evolution, which posits that care of human infants by alloparents enabled the evolution of costly human brains and long juvenile development, while selecting for tolerance of strangers. We then explore how human cooperation in the protection and provisioning of young plants and animals can explain the evolution of domestication traits such as changes in development; loss of aggressive, defensive, and bet-hedging aspects of the phenotype; and increased fertility. We argue that the importance of cooperative breeding to human societies has made humans especially likely to enter into interspecies cooperative breeding relationships.

The taming of the weed: Developmental plasticity facilitated plant domestication.

Our experiments with crop progenitors have demonstrated that these species exhibit dramatic plasticity in key traits that are affected by domestication, including seed and fruit morphology. These traits can be altered by cultivating crop progenitors for a single season, in the absence of any selection for domesticated phenotypes. We hypothesize that cultivation caused environmental shifts that led to immediate phenotypic changes in crop progenitors via developmental plasticity, similar to tameness in animals. Here we focus on the loss or reduction of germination inhibitors in an annual seed crop because seeds with high dormancy are undesirable in crops, and also present a serious barrier to selective pressures that arise from seed-saving and planting by humans. Data from four seasons of observation of the crop progenitor Polygonum erectum L. suggest that the low plant density conditions of an agroecosystem trigger a phenotypic response that reduces germination inhibitors, eliminating a key barrier to further selection. The timing of the harvest can also be used to manipulate the germinability of seed stock. These observations suggest that genetic assimilation may have played a role in the domestication of this plant. More experimental work with crop progenitors is needed to understand whether or not this phenomenon played a part in the domestication of other plants, and to accurately interpret the significance of ancient plant phenotypes in the archaeological record.

Phylogenomic analysis points to a South American origin of Manihot and illuminates the primary gene pool of cassava.

The genus Manihot, with around 120 known species, is native to a wide range of habitats and regions in the tropical and subtropical Americas. Its high species richness and recent diversification only c. 6 million years ago have significantly complicated previous phylogenetic analyses. Several basic elements of Manihot evolutionary history therefore remain unresolved. Here, we conduct a comprehensive phylogenomic analysis of Manihot, focusing on exhaustive sampling of South American taxa. We find that two recently described species from northeast Brazil's Atlantic Forest were the earliest to diverge, strongly suggesting a South American common ancestor of Manihot. Ancestral state reconstruction indicates early Manihot diversification in dry forests, with numerous independent episodes of new habitat colonization, including into savannas and rainforests within South America. We identify the closest wild relatives to Manihot esculenta, including the crop cassava, and we quantify extensive wild introgression into the cassava gene pool from at least five wild species, including Manihot glaziovii, a species used widely in breeding programs. Finally, we show that this wild-to-crop introgression substantially shapes the mutation load in cassava. Our findings provide a detailed case study for neotropical evolutionary history in a diverse and widespread group, and a robust phylogenomic framework for future Manihot and cassava research.

Exaptation Traits for Megafaunal Mutualisms as a Factor in Plant Domestication.

Megafaunal extinctions are recurring events that cause evolutionary ripples, as cascades of secondary extinctions and shifting selective pressures reshape ecosystems. Megafaunal browsers and grazers are major ecosystem engineers, they: keep woody vegetation suppressed; are nitrogen cyclers; and serve as seed dispersers. Most angiosperms possess sets of physiological traits that allow for the fixation of mutualisms with megafauna; some of these traits appear to serve as exaptation (preadaptation) features for farming. As an easily recognized example, fleshy fruits are, an exaptation to agriculture, as they evolved to recruit a non-human disperser. We hypothesize that the traits of rapid annual growth, self-compatibility, heavy investment in reproduction, high plasticity (wide reaction norms), and rapid evolvability were part of an adaptive syndrome for megafaunal seed dispersal. We review the evolutionary importance that megafauna had for crop and weed progenitors and discuss possible ramifications of their extinction on: (1) seed dispersal; (2) population dynamics; and (3) habitat loss. Humans replaced some of the ecological services that had been lost as a result of late Quaternary extinctions and drove rapid evolutionary change resulting in domestication.

Grazing animals drove domestication of grain crops.

In addition to large-seeded cereals, humans around the world during the mid-Holocene started to cultivate small-seeded species of herbaceous annuals for grain, including quinoa, amaranth, buckwheat, the millets and several lost crops domesticated in North America. The wild ancestors of these crops have small seeds with indigestible defences and do not germinate readily. Today, these wild plants exist in small fragmentary stands that are not appealing targets for foragers. This combination of traits has led many to argue that they must have been a food of last resort. We propose a new explanation: the domestication of small-seeded annuals involved a switch from endozoochoric dispersal (through animal ingestion) to human dispersal. Humans encountered these plants in dense stands created by grazing megafauna, making them easy to harvest. As humans began to cultivate these plants they took on the functional role of seed dispersers, and traits associated with endozoochory were lost or reduced. The earliest traits of domestication-thinning or loss of indigestible seed protections, loss of dormancy and increased seed size-can all be explained by the loss of the ruminant dispersal process and concomitant human management of wild stands. We demonstrate, by looking at rangeland ecology and herd animal herbivory patterns, that the progenitors of all of these species evolved to be dispersed by megafaunal ruminants and that heavy herbivory leads to dense homogenous clusters of endozoochoric plants. Hence, easily harvested stands on nitrogen hot spots near water sources would have existed in regions where these plants were domesticated. Future experimental and ecological studies could enhance our understanding of the relationships between specific crops and their possible ruminant dispersers.

Growing the lost crops of eastern North America's original agricultural system.

Thousands of years before the maize-based agriculture practiced by many Native American societies in eastern North America at the time of contact with Europeans, there existed a unique crop system only known through archaeological evidence. There are no written or oral records of how these lost crops were cultivated, but several domesticated subspecies have been identified in the archaeological record. Growth experiments and observations of living progenitors of these crops can provide insights into the ancient agricultural system of eastern North America, the role of developmental plasticity in the process of domestication, and the creation and maintenance of diverse landraces under cultivation. In addition, experimental gardens are potent tools for public education, and can also be used to conserve remaining populations of lost crop progenitors and explore the possibility of re-domesticating these species.

Agricultural origins from the ground up: archaeological approaches to plant domestication.

The timing, geographical locations, causes, and consequences of crop domestication have long been major concerns of archaeologists, and agricultural origins and dispersals are currently more relevant than ever to scientists seeking solutions to elusive problems involving food insecurity and global health disparities. Perennial research issues that archaeologists continue to tackle include (1) thinking outside centers of origin that were based on limited and insufficient past knowledge; (2) distinguishing between single and multiple domestications of specific crops; (3) measuring the pace of domestication; and (4) decoupling domestication from agricultural economies. Paleoethnobotanists have expanded their toolkits to include analysis of ancient and modern DNA and have added increasingly sophisticated techniques in the field and the laboratory to derive precise chronological sequences to assess morphological changes in ancient and often fragmentary archaeobotanical remains and to correctly interpret taphonomy and context. Multiple lines of archaeological evidence are ideally brought together, and whenever possible, these are integrated with information from complementary sources. We discuss current perspectives and anthropological approaches to research that have as their goals the fuller and broader understanding of ancient farming societies, the plants that were domesticated, the landscapes that were created, and the culinary legacies that were passed on.