It is difficult to overstate the cultural and biological impacts that the domestication of plants and animals has had on our species. Fundamental questions regarding where, when, and how many times domestication took place have been of primary interest within a wide range of academic disciplines. Within the last two decades, the advent of new archaeological and genetic techniques has revolutionized our understanding of the pattern and process of domestication and agricultural origins that led to our modern way of life. In the spring of 2011, 25 scholars with a central interest in domestication representing the fields of genetics, archaeobotany, zooarchaeology, geoarchaeology, and archaeology met at the National Evolutionary Synthesis Center to discuss recent domestication research progress and identify challenges for the future. In this introduction to the resulting Special Feature, we present the state of the art in the field by discussing what is known about the spatial and temporal patterns of domestication, and controversies surrounding the speed, intentionality, and evolutionary aspects of the domestication process. We then highlight three key challenges for future research. We conclude by arguing that although recent progress has been impressive, the next decade will yield even more substantial insights not only into how domestication took place, but also when and where it did, and where and why it did not.The domestication of plants and animals was one of the most significant cultural and evolutionary transitions in the ∼200,000-y history of our species. Investigating when, where, and how domestication took place is therefore crucial for understanding the roots of complex societies. Domestication research is equally important to scholars from a wide range of disciplines, from evolutionary biology to sustainability science (1, 2). Research into both the process and spatiotemporal origins of domestication has accelerated significantly over the past decade through archaeological research, advances in DNA/ RNA sequencing technology, and methods used to recover and formally identify changes in interactions among plants and animals leading to domestication (2-4). In the spring of 2011, 25 scholars with a central interest in domestication and representing the fields of genetics, archaeobotany, zooarchaeology, geoarchaeology, and archaeology met at the National Evolutionary Synthesis Center to discuss recent progress in domestication research and identify challenges for the future. Our goal was to begin reconsidering plant and animal domestication within an integrated evolutionary and cultural framework that takes into account not just new genetic and archaeological data, but also ideas related to epigenetics, plasticity, geneby-environment interactions, gene-culture coevolution, and niche construction. Each of these concepts is relevant to understanding phenotypic change, heritability, and selection, and they are all fundamental components of the New Biology (5) and Expanded Modern Evolutionary Synthesis (6).

Recent increases in archaeobotanical evidence offer insights into the processes of plant domestication and agricultural origins, which evolved in parallel in several world regions. Many different crop species underwent convergent evolution and acquired domestication syndrome traits. For a growing number of seed crop species, these traits can be quantified by proxy from archaeological evidence, providing measures of the rates of change during domestication. Among domestication traits, nonshattering cereal ears evolved more quickly in general than seed size. Nevertheless, most domestication traits show similarly slow rates of phenotypic change over several centuries to millennia, and these rates were similar across different regions of origin. Crops reproduced vegetatively, including tubers and many fruit trees, are less easily documented in terms of morphological domestication, but multiple lines of evidence outline some patterns in the development of vegecultural systems across the New World and Old World tropics. Pathways to plant domestication can also be compared in terms of the cultural and economic factors occurring at the start of the process. Whereas agricultural societies have tended to converge on higher population densities and sedentism, in some instances cultivation began among sedentary hunter-gatherers whereas more often it was initiated by mobile societies of hunter-gatherers or herder-gatherers.D omestication offers an ideal laboratory for understanding evolution because it is a recent phenomenon in terms of geological time scales and because the selection pressures that affect harvestability by humans are often known (1). Domestication is a product of human behaviors that regulate or increase food supply, but may also inadvertently lock humans into an increased reliance on managed taxa (2). Archaeological research provides a fossil record of past organisms undergoing domestication, often accompanied by cultural artifacts associated with habitat management or niche construction (3, 4). The effects of agriculture in terms of intensifying land productivity to support larger populations has been fundamental to the development of civilizations and the ongoing impact on and management of ecosystems (5, 6). Domestications have occurred separately on different continents and in different cultural traditions, and thus represent a set of parallel experiments from which to infer recurrent processes (Fig. 1). In some cases this represents parallelism of phylogenetically related organisms that have been subjected to similar selection pressures and developed identical or similar adaptations in different places. In others, we can consider domestication as convergent evolution, in as much as similar adaptations have evolved across crops in different plant families. These parallel adaptations have been defined as the "domestication syndrome" (7, 8). A distinction can be made between true convergence, in which analogous states have been reached from very different and unrelated starting points, versus parallelism...

The period from the late third millennium BC to the start of the first millennium AD witnesses the first steps towards food globalization in which a significant number of important crops and animals, independently domesticated within China, India, Africa and West Asia, traversed Central Asia greatly increasing Eurasian agricultural diversity. This paper utilizes an archaeobotanical database (AsCAD), to explore evidence for these crop translocations along southern and northern routes of interaction between east and west. To begin, crop translocations from the Near East across India and Central Asia are examined for wheat (Triticum aestivum) and barley (Hordeum vulgare) from the eighth to the second millennia BC when they reach China. The case of pulses and flax (Linum usitatissimum) that only complete this journey in Han times (206 BC–AD 220), often never fully adopted, is also addressed. The discussion then turns to the Chinese millets, Panicum miliaceum and Setaria italica, peaches (Amygdalus persica) and apricots (Armeniaca vulgaris), tracing their movement from the fifth millennium to the second millennium BC when the Panicum miliaceum reaches Europe and Setaria italica Northern India, with peaches and apricots present in Kashmir and Swat. Finally, the translocation of japonica rice from China to India that gave rise to indica rice is considered, possibly dating to the second millennium BC. The routes these crops travelled include those to the north via the Inner Asia Mountain Corridor, across Middle Asia, where there is good evidence for wheat, barley and the Chinese millets. The case for japonica rice, apricots and peaches is less clear, and the northern route is contrasted with that through northeast India, Tibet and west China. Not all these journeys were synchronous, and this paper highlights the selective long-distance transport of crops as an alternative to demic-diffusion of farmers with a defined crop package.

The Austronesian settlement of the remote island of Madagascar remains one of the great puzzles of Indo-Pacific prehistory. Although linguistic, ethnographic, and genetic evidence points clearly to a colonization of Madagascar by Austronesian language-speaking people from Island Southeast Asia, decades of archaeological research have failed to locate evidence for a Southeast Asian signature in the island's early material record. Here, we present new archaeobotanical data that show that Southeast Asian settlers brought Asian crops with them when they settled in Africa. These crops provide the first, to our knowledge, reliable archaeological window into the Southeast Asian colonization of Madagascar. They additionally suggest that initial Southeast Asian settlement in Africa was not limited to Madagascar, but also extended to the Comoros. Archaeobotanical data may support a model of indirect Austronesian colonization of Madagascar from the Comoros and/or elsewhere in eastern Africa.

Domestication is the process by which plants or animals evolved to fit a human-managed environment, and it is marked by innovations in plant morphology and anatomy that are in turn correlated with new human behaviours and technologies for harvesting, storage and field preparation. Archaeobotanical evidence has revealed that domestication was a protracted process taking thousands of plant generations. Within this protracted process there were changes in the selection pressures for domestication traits as well as variation across a geographic mosaic of wild and cultivated populations. Quantitative data allow us to estimate the changing selection coefficients for the evolution of non-shattering (domestic-type seed dispersal) in Asian rice (Oryza sativa L.), barley (Hordeum vulgare L.), emmer wheat (Triticum dicoccon (Shrank) Schübl.) and einkorn wheat (T. monococcum L.). These data indicate that selection coefficients tended to be low, but also that there were inflection points at which selection increased considerably. For rice, selection coefficients on the order of 0.001 prior to 5500 BC shifted to > 0.003 between 5000 and 4500 BC, before falling again as the domestication process ended 4000-3500 BC. In barley and the two wheats selection was strongest between 8500 and 7500 BC. The slow start of domestication may indicate that initial selection began in the Pleistocene Glacial era.