Ancient DNA reveals the timing and persistence of organellar genetic bottlenecks over 3,000 years of sunflower domestication and improvement.

Here, we report a comprehensive paleogenomic study of archaeological and ethnographic sunflower remains that provides significant new insights into the process of domestication of this important crop. DNA from both ancient and historic contexts yielded high proportions of endogenous DNA, and although archaeological DNA was found to be highly degraded, it still provided sufficient coverage to analyze genetic changes over time. Shotgun sequencing data from specimens from the Eden's Bluff archaeological site in Arkansas yielded organellar DNA sequence from specimens up to 3,100 years old. Their sequences match those of modern cultivated sunflowers and are consistent with an early domestication bottleneck in this species. Our findings also suggest that recent breeding of sunflowers has led to a loss of genetic diversity that was present only a century ago in Native American landraces. These breeding episodes also left a profound signature on the mitochondrial and plastid haplotypes in cultivars, as two types were intentionally introduced from other Helianthus species for crop improvement. These findings gained from ancient and historic sunflower specimens underscore how future in-depth gene-based analyses can advance our understanding of the pace and targets of selection during the domestication of sunflower and other crop species.

Storytelling and story testing in domestication.

The domestication of plants and animals marks one of the most significant transitions in human, and indeed global, history. Traditionally, study of the domestication process was the exclusive domain of archaeologists and agricultural scientists; today it is an increasingly multidisciplinary enterprise that has come to involve the skills of evolutionary biologists and geneticists. Although the application of new information sources and methodologies has dramatically transformed our ability to study and understand domestication, it has also generated increasingly large and complex datasets, the interpretation of which is not straightforward. In particular, challenges of equifinality, evolutionary variance, and emergence of unexpected or counter-intuitive patterns all face researchers attempting to infer past processes directly from patterns in data. We argue that explicit modeling approaches, drawing upon emerging methodologies in statistics and population genetics, provide a powerful means of addressing these limitations. Modeling also offers an approach to analyzing datasets that avoids conclusions steered by implicit biases, and makes possible the formal integration of different data types. Here we outline some of the modeling approaches most relevant to current problems in domestication research, and demonstrate the ways in which simulation modeling is beginning to reshape our understanding of the domestication process.

Particularism and the retreat from theory in the archaeology of agricultural origins.

The introduction of new analytic methods and expansion of research into previously untapped regions have greatly increased the scale and resolution of data relevant to the origins of agriculture (OA). As a result, the recognition of varied historical pathways to agriculture and the continuum of management strategies have complicated the search for general explanations for the transition to food production. In this environment, higher-level theoretical frameworks are sometimes rejected on the grounds that they force conclusions that are incompatible with real-world variability. Some of those who take this position argue instead that OA should be explained in terms of local and historically contingent factors. This retreat from theory in favor of particularism is based on the faulty beliefs that complex phenomena such as agricultural origins demand equally complex explanations and that explanation is possible in the absence of theoretically based assumptions. The same scholars who are suspicious of generalization are reluctant to embrace evolutionary approaches to human behavior on the grounds that they are ahistorical, overly simplistic, and dismissive of agency and intent. We argue that these criticisms are misplaced and explain why a coherent theory of human behavior that acknowledges its evolutionary history is essential to advancing understanding of OA. Continued progress depends on the integration of human behavior and culture into the emerging synthesis of evolutionary developmental biology that informs contemporary research into plant and animal domestication.

Current perspectives and the future of domestication studies.

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.

Human behavioral ecology, phenotypic (developmental) plasticity, and agricultural origins: insights from the emerging evolutionary synthesis.

The fields of human behavioral ecology (HBE) and evolutionary developmental biology (evo-devo) both stand to make significant contributions to our understanding of agricultural origins. These two approaches share a concern with phenotypic-plasticity and its evolutionary significance. HBE considers the adaptive plasticity of the human phenotype in response to resource distribution in time and space and has helped to advance understanding of the economic costs and benefits of food production. However, evo-devo and the associated subject of phenotypic (developmental) plasticity have so far been largely neglected as sources of insight into the domestication of plants, despite growing evidence for their evolutionary importance in nature and their roles in the origins of novel traits. We argue that it is important to consider environmentally induced phenotypic variation resulting directly from both natural- and human-induced ecological change as a source of the distinctive morphologies of domesticated plants.