Biology Department, University of Massachusetts, Amherst, 01003, USA.
BMC Evol Biol. 2010 Jun 15;10:180. doi: 10.1186/1471-2148-10-180.
Weedy rice (red rice), a conspecific weed of cultivated rice (Oryza sativa L.), is a significant problem throughout the world and an emerging threat in regions where it was previously absent. Despite belonging to the same species complex as domesticated rice and its wild relatives, the evolutionary origins of weedy rice remain unclear. We use genome-wide patterns of single nucleotide polymorphism (SNP) variation in a broad geographic sample of weedy, domesticated, and wild Oryza samples to infer the origin and demographic processes influencing U.S. weedy rice evolution.
We find greater population structure than has been previously reported for U.S. weedy rice, and that the multiple, genetically divergent populations have separate origins. The two main U.S. weedy rice populations share genetic backgrounds with cultivated O. sativa varietal groups not grown commercially in the U.S., suggesting weed origins from domesticated ancestors. Hybridization between weedy groups and between weedy rice and local crops has also led to the evolution of distinct U.S. weedy rice populations. Demographic simulations indicate differences among the main weedy groups in the impact of bottlenecks on their establishment in the U.S., and in the timing of divergence from their cultivated relatives.
Unlike prior research, we did not find unambiguous evidence for U.S. weedy rice originating via hybridization between cultivated and wild Oryza species. Our results demonstrate the potential for weedy life-histories to evolve directly from within domesticated lineages. The diverse origins of U.S. weedy rice populations demonstrate the multiplicity of evolutionary forces that can influence the emergence of weeds from a single species complex.
杂草稻（红米）是栽培稻（Oryza sativa L.）的同种杂草，是全世界的一个重大问题，也是以前不存在该杂草的地区的一个新出现的威胁。尽管杂草稻与驯化稻及其野生亲缘种属于同一物种复合体，但杂草稻的进化起源仍不清楚。我们利用广泛的杂草稻、栽培稻和野生稻的地理样本中的全基因组单核苷酸多态性（SNP）变异模式来推断影响美国杂草稻进化的起源和种群动态过程。
我们发现美国杂草稻的种群结构比以前报道的更为复杂，而且多个遗传上分化的种群有各自的起源。两个主要的美国杂草稻种群与美国没有商业化种植的栽培稻品种群具有相同的遗传背景，表明杂草稻起源于驯化的祖先。杂草稻群体之间以及杂草稻与当地作物之间的杂交也导致了独特的美国杂草稻种群的进化。种群动态模拟表明，主要杂草稻群体在瓶颈效应对其在美国建立的影响以及与栽培亲缘种分化的时间上存在差异。
与先前的研究不同，我们没有发现美国杂草稻明确源自栽培稻和野生稻种间杂交的证据。我们的结果表明，杂草的生活史有可能直接从驯化的谱系中进化而来。美国杂草稻种群的多样化起源表明，多种进化力量可以影响一个单一的物种复合体中杂草的出现。
