Using multilocus sequence data to assess population structure, natural selection, and linkage disequilibrium in wild tomatoes
Using multilocus sequence data to assess population structure, natural selection, and linkage disequilibrium in wild tomatoes
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DOI：
10.1093/molbev/msm162
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发表时间：
2007-10-01
影响因子：
10.7
通讯作者：
Staedler, Thomas
中科院分区：
文献类型：
--
作者：
Arunyawat, Uraiwan;Stephan, Wolfgang;Staedler, Thomas
我们采用了多位点的方法来研究群体细分和自然选择对2个密切相关的野生番茄物种（Solanum peruvianum和Solanum chilense）的DNA多态性的影响，使用来自大部分物种范围内的群体的8个核基因座的序列数据。这两个物种都表现出相当程度的核苷酸变异。沉默核苷酸多样性的物种范围内的水平是18%，在S。peruvianum（pi（sil）约为2.50%）比S.智利（PI（SIL）约为2.12%）。其中一个位点偏离了中性预期，显示出S.智利人。这种地理上的变异模式暗示着一种不完全的（持续的）选择性扫描，但不能完全否定中性的解释。这两种野生番茄物种表现出中等水平的群体分化（平均F-ST近似为0.20）。有趣的是，合并的样品（在不同的否认）表现出更负的田岛的D和傅和李的D值，这种显着过量的低频多态性只能解释人口（或范围）的扩张，是不太可能是由于人口结构本身。因此，我们建议，人口结构和人口/范围的扩大是最重要的进化力量塑造的核苷酸多样性的模式内和否认在这些野生番茄。种群分化模式也可能受到土壤种子库和气候周期介导的历史关联的影响。基因内连锁不平衡（LD）衰减非常迅速的物理距离，这表明高重组率和有效的人口规模在这两个物种。LD的快速下降似乎非常有希望为未来的关联研究与映射功能变异的目的在野生番茄。
We employed a multilocus approach to examine the effects of population subdivision and natural selection on DNA polymorphism in 2 closely related wild tomato species (Solanum peruvianum and Solanum chilense), using sequence data for 8 nuclear loci from populations across much of the species' range. Both species exhibit substantial levels of nucleotide variation. The species-wide level of silent nucleotide diversity is 18% higher in S. peruvianum (pi(sil) approximate to 2.50%) than in S. chilense (pi(sil) approximate to 2.12%). One of the loci deviates from neutral expectations, showing a clinal pattern of nucleotide diversity and haplotype structure in S. chilense. This geographic pattern of variation is suggestive of an incomplete (ongoing) selective sweep, but neutral explanations cannot be entirely dismissed. Both wild tomato species exhibit moderate levels of population differentiation (average F-ST approximate to 0.20). Interestingly, the pooled samples (across different denies) exhibit more negative Tajima's D and Fu and Li's D values; this marked excess of low-frequency polymorphism can only be explained by population (or range) expansion and is unlikely to be due to population structure per se. We thus propose that population structure and population/range expansion are among the most important evolutionary forces shaping patterns of nucleotide diversity within and among denies in these wild tomatoes. Patterns of population differentiation may also be impacted by soil seed banks and historical associations mediated by climatic cycles. Intragenic linkage disequilibrium (LD) decays very rapidly with physical distance, suggesting high recombination rates and effective population sizes in both species. The rapid decline of LD seems very promising for future association studies with the purpose of mapping functional variation in wild tomatoes.