Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata.
Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata.
复制标题
DOI：
10.1371/journal.pone.0002411
复制
发表时间：
2008-06-11
期刊：
影响因子：
3.7
通讯作者：
Gaut BS
中科院分区：
文献类型：
--
作者：
Ross-Ibarra J;Wright SI;Foxe JP;Kawabe A;DeRose-Wilson L;Gos G;Charlesworth D;Gaut BS
许多影响遗传多样性的过程对当地人口起作用。然而，植物核苷酸多样性的研究在很大程度上忽略了局部采样，使得难以推断种群的人口历史和评估局部适应的重要性。拟南芥（Arabidopsis lyrata）是一种自交不亲和的多年生植物，是研究种群历史和局部适应在遗传变异模式中的作用的一个很好的模型系统。本研究利用拟南芥（Arabidopsis lyrata） 6个自然居群中140条染色体的77个基因座，对其核苷酸多样性进行了研究。6个种群高度分化，FST中值为0.52，结构分析未发现混合个体。种群内平均多样性因种群而异，其中德国种群的多样性最高；这个种群的沉默多样性水平比世界范围内的拟南芥样本高3倍。我们估计了这些种群的人口模型，发现在过去19,000至47,000年间，涉及非平衡人口事件的种群分化的证据，这些非平衡人口事件减少了大多数种群的有效规模。最后，我们使用推断的人口统计学模型对局部适应进行了初步测试，并确定了几个基因，包括开花时间基因FCA和抗病位点，作为局部适应事件的候选基因。我们的研究结果强调了种群特异性、非平衡人口统计学过程在黑桫椤多样性格局中的重要性。此外，我们广泛的数据集为未来的分子群体遗传研究提供了重要的资源。
Many of the processes affecting genetic diversity act on local populations. However, studies of plant nucleotide diversity have largely ignored local sampling, making it difficult to infer the demographic history of populations and to assess the importance of local adaptation. Arabidopsis lyrata, a self-incompatible, perennial species with a circumpolar distribution, is an excellent model system in which to study the roles of demographic history and local adaptation in patterning genetic variation. We studied nucleotide diversity in six natural populations of Arabidopsis lyrata, using 77 loci sampled from 140 chromosomes. The six populations were highly differentiated, with a median FST of 0.52, and structure analysis revealed no evidence of admixed individuals. Average within-population diversity varied among populations, with the highest diversity found in a German population; this population harbors 3-fold higher levels of silent diversity than worldwide samples of A. thaliana. All A. lyrata populations also yielded positive values of Tajima's D. We estimated a demographic model for these populations, finding evidence of population divergence over the past 19,000 to 47,000 years involving non-equilibrium demographic events that reduced the effective size of most populations. Finally, we used the inferred demographic model to perform an initial test for local adaptation and identified several genes, including the flowering time gene FCA and a disease resistance locus, as candidates for local adaptation events. Our results underscore the importance of population-specific, non-equilibrium demographic processes in patterning diversity within A. lyrata. Moreover, our extensive dataset provides an important resource for future molecular population genetic studies of local adaptation in A. lyrata.
登录
查看更多内容
种群基因组学：果蝇果蝇中多态性和差异的全基因组分析。
影响因子：
9.8
作者：
Begun, David J.;Holloway, Alisha K.;Stevens, Kristian;Hillier, LaDeana W.;Poh, Yu-Ping;Hahn, Matthew W.;Nista, Phillip M.;Jones, Corbin D.;Kern, Andrew D.;Dewey, Colin N.;Pachter, Lior;Myers, Eugene;Langley, Charles H.
通讯作者：
Langley, Charles H.
影响因子：
1.5
作者：
Charlesworth, B;Nordborg, M;Charlesworth, D
通讯作者：
Charlesworth, D
影响因子：
56.9
作者：
Clark, Richard M.;Schweikert, Gabriele;Weigel, Detlef
通讯作者：
Weigel, Detlef
影响因子：
10.7
作者：
Arunyawat, Uraiwan;Stephan, Wolfgang;Staedler, Thomas
通讯作者：
Staedler, Thomas
DOI：
10.1073/pnas.0705323104
发表时间：
2007-07-17
影响因子：
11.1
作者：
Borevitz, Justin O.;Hazen, Samuel P.;Ecker, Joseph R.
通讯作者：
Ecker, Joseph R.