The complexity of maize domestication: Maize originated in what is now central Mexico about 9000 years ago and spread throughout the Americas before European contact. Kistler et al. applied genomic analysis to ancient and extant South American maize lineages to investigate the genetic changes that accompanied domestication (see the Perspective by Zeder). The origin of modern maize cultivars likely involved a “semidomesticated” lineage that moved out of Mexico. Later improvements then occurred among multiple South American populations, including those in southwestern Amazonia. Science , this issue p. 1309 ; see also p. 1246

Until recently, domestication has been interpreted as a rapid process with little predomestication cultivation and a relatively rapid rise of the domestication syndrome. This interpretation has had a profound effect on the biological framework within which investigations into crop origins have been carried out. A major underlying assumption has been that artificial selection pressures were substantially stronger than natural selection pressures, resulting in genetic patterns of diversity that reflect genetic independence of geographic localities. Recent archaeobotanical evidence has overturned the notion of a rapid transition, resulting in a protracted model that undermines these assumptions. Conclusions of genome-wide multilocus studies remain problematic in their support of a rapid-transition model by indicating that domesticated crops appear to be associated by monophyly with only a single geographic locality. Simulations presented here resolve this conflict, indicating that the results observed in such studies are inevitable over time at a rate that is largely influenced by the long-term population size. Counterintuitively, multiple origin crops are shown to be more likely to produce monophyletic clades than crops of a single origin. Under the protracted transition, the importance of the rise of the domestication syndrome becomes paramount in producing the patterns of genetic diversity from which crop origins may be deduced. We identify four different interacting levels of organization that now need to be considered to track crop origins from modern genetic diversity, making crop origins a problem that could be addressed through system-based approaches.

The origins of agriculture involved pathways of domestication in which human behaviours and plant genetic adaptations were entangled. These changes resulted in consequences that were unintended at the start of the process. This paper highlights some of the key innovations in human behaviours, such as soil preparation, harvesting and threshing, and how these were coupled with genetic ‘innovations’ within plant populations. We identify a number of ‘traps’ for early cultivators, including the needs for extra labour expenditure on crop-processing and soil fertility maintenance, but also linked gains in terms of potential crop yields. Compilations of quantitative data across a few different crops for the traits of non-shattering and seed size are discussed in terms of the apparently slow process of domestication, and parallels and differences between different regional pathways are identified. We highlight the need to bridge the gap between a Neolithic archaeobotanical focus on domestication and a focus of later periods on crop-processing activities and labour organization. In addition, archaeobotanical data provide a basis for rethinking previous assumptions about how plant genetic data should be related to the origins of agriculture and we contrast two alternative hypotheses: gradual evolution with low selection pressure versus metastable equilibrium that prolonged the persistence of ‘semi-domesticated’ populations. Our revised understanding of the innovations involved in plant domestication highlight the need for new approaches to collecting, modelling and integrating genetic data and archaeobotanical evidence.

The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time may be due to a bulk diffusion process in many cases, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation. This model of DNA degradation is largely based on mammal bone samples due to published genomic dataset availability. Continued refinement to the model to reflect diverse biological systems and tissue types will further improve our understanding of ancient DNA breakdown dynamics.

The origins of agriculture in the Near East has been associated with a ‘core area’, located in south-eastern Turkey, in which all major crops were brought into domestication within the same local domestication system operated by a single cultural group. Such an origin leads to a scenario of rapid invention of agriculture by a select cultural group and typically monophyletic origins for most crops. Surprisingly, support for a core area has never been directly tested with archaeological evidence. Over the past decade a large amount of new archaeological and genetic evidence has been discovered which brings new light on the origins of agriculture. In this review, this new evidence was brought together in order to evaluate whether a core region of origin is supported. Evidence shows that origins began earlier than previously assumed, and included ‘false starts’ and dead ends that involved many more species than the typical eight founder crops associated with the core area. The rates at which domestication syndrome traits became fixed were generally slow, rather than rapid, and occurred over a geographically wide range that included the North and South Levant as well as the core area. Finally, a survey of the estimated ages of archaeological sites and the onset of domestication indicates that the domestication process was ongoing in parallel outside of the core area earlier than within it. Overall, evidence suggests a scenario in which crops were domesticated slowly in different locations around the Near East rather than emanating from a core area.

Domesticated crops show a reduced level of diversity that is commonly attributed to the “domestication bottleneck”; a drastic reduction in the population size associated with subsampling the wild progenitor species and the imposition of selection pressures associated with the domestication syndrome. A prediction of the domestication bottleneck is a sharp decline in genetic diversity early in the domestication process. Surprisingly, archaeological genomes of three major annual crops do not indicate that such a drop in diversity occurred early in the domestication process. In light of this observation, we revisit the general assumption of the domestication bottleneck concept in our current understanding of the evolutionary process of domestication.