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).

The exhibition of increasingly intensive and complex niche construction behaviors through time is a key feature of human evolution, culminating in the advanced capacity for ecosystem engineering exhibited by Homo sapiens. A crucial outcome of such behaviors has been the dramatic reshaping of the global biosphere, a transformation whose early origins are increasingly apparent from cumulative archaeological and paleoecological datasets. Such data suggest that, by the Late Pleistocene, humans had begun to engage in activities that have led to alterations in the distributions of a vast array of species across most, if not all, taxonomic groups. Changes to biodiversity have included extinctions, extirpations, and shifts in species composition, diversity, and community structure. We outline key examples of these changes, highlighting findings from the study of new datasets, like ancient DNA (aDNA), stable isotopes, and microfossils, as well as the application of new statistical and computational methods to datasets that have accumulated significantly in recent decades. We focus on four major phases that witnessed broad anthropogenic alterations to biodiversity-the Late Pleistocene global human expansion, the Neolithic spread of agriculture, the era of island colonization, and the emergence of early urbanized societies and commercial networks. Archaeological evidence documents millennia of anthropogenic transformations that have created novel ecosystems around the world. This record has implications for ecological and evolutionary research, conservation strategies, and the maintenance of ecosystem services, pointing to a significant need for broader cross-disciplinary engagement between archaeology and the biological and environmental sciences.biodiversity | extinctions | invasive species | novel ecosystems | Anthropocene The reshaping of global biodiversity is one of the most significant impacts humans have had on Earth's ecosystems. As our planet experiences its sixth "mass extinction event" (1), the effect of anthropogenic landscape modification, habitat fragmentation, overexploitation, and species invasions could not be more apparent (2, 3). These transformations are linked largely to the industrial economies, burgeoning populations, and dense transport networks of contemporary human societies. Accordingly, the humanmediated alteration of species distributions has been characterized as a modern phenomenon with limited, and largely insignificant, historical antecedents. This conventional understanding fails to account for several decades of archaeological, paleoecological, and genetic research that reveal a long and widespread history of human transformation of global biodiversity (4-6). The evolutionary trajectory of Homo sapiens has seen growing capacities for advanced cognition and demographic and geographic expansion, along with an exponential increase in the scope and impact of human niche constructing activities (7) that have culminated in fundamental changes to planetary ecosystems.Drawing upon findings from ...

Original multidisciplinary research hereby clarifies the complex geodomestication pathways that generated the vast range of banana cultivars (cvs). Genetic analyses identify the wild ancestors of modern-day cvs and elucidate several key stages of domestication for different cv groups. Archaeology and linguistics shed light on the historical roles of people in the movement and cultivation of bananas from New Guinea to West Africa during the Holocene. The historical reconstruction of domestication processes is essential for breeding programs seeking to diversify and improve banana cvs for the future.plant genetics | historical linguistics | archaeobotany | diploid banana cultivars | triploid banana cultivars N ew multidisciplinary findings from archaeology, genetics, and linguistics clarify the complex geodomestication pathways-the geographical configurations of hybridization and dispersalthat generated the range of modern banana cultivars (cvs). Although recent molecular research, combined with the outcomes of previous genetic studies, elucidates major stages of banana domestication, such as the generation of edible diploids and triploids, it sheds only partial light on the historical and sociospatial contexts of domestication. The geographic distributions of genotypes involved in banana domestication require human translocations of plants, most likely under vegetative forms of cultivation, across vast regions. Linguistic analyses of (traditional) local terms for bananas reveal several striking regional-scale correspondences between genetic and linguistic patterns. These multidisciplinary findings enable the relative dating of the principal events in banana geodomestication and situate banana cultivation within broader sociospatial contexts. Archaeological findings provide a timeline to anchor and calibrate the relative chronology.

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...

Multidisciplinary investigations at Kuk Swamp in the Highlands of Papua New Guinea show that agriculture arose independently in New Guinea by at least 6950 to 6440 calibrated years before the present (cal yr B.P.). Plant exploitation and some cultivation occurred on the wetland margin at 10,220 to 9910 cal yr B.P. (phase 1), mounding cultivation began by 6950 to 6440 cal yr B.P. (phase 2), and ditched cultivation began by 4350 to 3980 cal yr B.P. (phase 3). Clearance of lower montane rainforests began in the early Holocene, with modification to grassland at 6950 to 6440 cal yr B.P. Taro (Colocasia esculenta) was utilized in the early Holocene, and bananas (Musa spp.) were intensively cultivated by at least 6950 to 6440 cal yr B.P.

Environmentally transformative human use of land accelerated with the emergence of agriculture, but the extent, trajectory, and implications of these early changes are not well understood. An empirical global assessment of land use from 10,000 BP to 1850 CE reveals a planet largely transformed by hunter-gatherers, farmers and pastoralists by 3,000 years ago, significantly earlier than land-use reconstructions commonly used by Earth scientists. Synthesis of knowledge contributed by over 250 archaeologists highlighted gaps in archaeological expertise and data quality, which peaked at 2000 BP and in traditionally studied and wealthier regions. Archaeological reconstruction of global land-use history illuminates the deep roots of Earth's transformation and challenges the emerging Anthropocene paradigm that large-scale anthropogenic global environmental change is mostly a recent phenomenon.One Sentence Summary: A map of synthesized archaeological knowledge on land use reveals a planet largely transformed by hunter-gatherers, farmers and pastoralists by 3,000 years ago.

No abstract

For the last 150 y scholars have focused upon the roles of intentional breeding and genetic isolation as fundamental to understanding the process of animal domestication. This analysis of ethnoarchaeological, archaeological, and genetic data suggests that long-term gene flow between wild and domestic stocks was much more common than previously assumed, and that selective breeding of females was largely absent during the early phases of animal domestication. These findings challenge assumptions about severe genetic bottlenecks during domestication, expectations regarding monophyletic origins, and interpretations of multiple domestications. The findings also raise new questions regarding ways in which behavioral and phenotypic domestication traits were developed and maintained.reproductive isolation | selected breeding | zooarchaeology | donkey | pig Domestication resulted in diverse phenotypic and behavioral changes to wild animals, including decreased flight responses, increased sociality, earlier reproduction, and modification of endocrine and metabolic systems (1-4). Darwin's (5) seminal research, heavily influenced by European animal breeding practices during the 19th century, led subsequent scholars studying animal domestication to prioritize the central roles of human intentionality, directed or controlled breeding of individuals, and genetic isolation of captive herds from wild relatives (6). This anthropocentric legacy is evident in various widely used definitions of domestication that emphasize isolation of captive animals from wild species and total human control over breeding and animal care (6-8). However, a growing body of archaeological, genetic, and ethnohistorical evidence discussed here shows that neither reproductive isolation nor intentional breeding of individuals was as significant as traditionally thought. Our findings indicate long-term gene flow between managed and wild animal populations, and little control of breeding of domestic females. These findings challenge assumptions about severe genetic bottlenecks during domestication and interpretations of genetic variability in terms of multiple instances of domestication. The findings also raise questions about ways in which behavioral and phenotypic domestication traits were maintained.Research into dog and pig domestication over the last several decades has drawn attention to the roles of nonhuman drivers in the domestication process (9, 10)