The genetic expectations of a protracted model for the origins of domesticated crops

Abstract

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.domestication ͉ phylogenetics ͉ protracted transition ͉ simulation

The Checkered Prehistory of Rice Movement Southwards as a Domesticated Cereal—from the Yangzi to the Equator

“…However, humans eventually would have planted rice seeds outside permanent wetlands, perhaps in seasonally wet terrain where the climatic regime would have imposed selection for the annual growth habit that characterizes O. sativa. Outplanting away from wild stands would also have allowed any selection towards nonshattering to be retained more easily with each successive monsoonal planting season (Allaby et al 2008). The implication here is that the very process of radiation and migration on the part of humans was an essential part of the domestication process for rice right from the start.…”

Evolution of the VvMybA gene family, the major determinant of berry colour in cultivated grapevine (Vitis vinifera L.)

“…Domestication is likely to be a protracted process (Tanno and Willcox, 2006;Fuller, 2007;Allaby et al, 2008) that occurred in multiple locations (Molina-Cano et al, 2005;Ö zkan et al, 2005). This process of domestication can be seen as a gradual succession of selection steps leading to the 'elite' crop cultivated nowadays.…”

Detecting multiple origins of domesticated crops

“…The protracted model of Allaby et al (5) differs from this classic model in that genetic drift operates not only during an initial domestication bottleneck, but also for many subsequent generations. In the simulations used for their study, an initial population bottleneck (N b ϭ 20, d ϭ 10) is followed by tens or hundreds of additional generations with 50-150 individuals, either with a single domestication event (Fig.…”

“…Allaby et al (5) have conducted a series of simulations in which they ask the following question: given a true domestication history that involves two independent events (Fig. 1B), how often do multilocus, neutral markers lead to the inference of a single domestication origin ( Fig.…”