Department of Ecology and Evolutionary Biology, 80 Waterman Street, Box G-W, Brown University, Providence, RI 02912, USA.
Integr Comp Biol. 2012 Sep;52(3):418-29. doi: 10.1093/icb/ics099. Epub 2012 Jul 4.
Understanding the patterns of genetic variation within and among populations is a central problem in population and evolutionary genetics. We examine this question in the acorn barnacle, Semibalanus balanoides, in which the allozyme loci Mpi and Gpi have been implicated in balancing selection due to varying selective pressures at different spatial scales. We review the patterns of genetic variation at the Mpi locus, compare this to levels of population differentiation at mtDNA and microsatellites, and place these data in the context of genome-wide variation from high-throughput sequencing of population samples spanning the North Atlantic. Despite considerable geographic variation in the patterns of selection at the Mpi allozyme, this locus shows rather low levels of population differentiation at ecological and trans-oceanic scales (F(ST) ~ 5%). Pooled population sequencing was performed on samples from Rhode Island (RI), Maine (ME), and Southwold, England (UK). Analysis of more than 650 million reads identified approximately 335,000 high-quality SNPs in 19 million base pairs of the S. balanoides genome. Much variation is shared across the Atlantic, but there are significant examples of strong population differentiation among samples from RI, ME, and UK. An F(ST) outlier screen of more than 22,000 contigs provided a genome-wide context for interpretation of earlier studies on allozymes, mtDNA, and microsatellites. F(ST) values for allozymes, mtDNA and microsatellites are close to the genome-wide average for random SNPs, with the exception of the trans-Atlantic F(ST) for mtDNA. The majority of F(ST) outliers were unique between individual pairs of populations, but some genes show shared patterns of excess differentiation. These data indicate that gene flow is high, that selection is strong on a subset of genes, and that a variety of genes are experiencing diversifying selection at large spatial scales. This survey of polymorphism in S. balanoides provides a number of genomic tools that promise to make this a powerful model for ecological genomics of the rocky intertidal.
了解群体内和群体间遗传变异的模式是群体和进化遗传学的核心问题。我们以橡果藤壶(Semibalanus balanoides)为研究对象来探讨这个问题，在该物种中，同工酶基因座 Mpi 和 Gpi 由于在不同空间尺度上受到不同选择压力的影响，被认为受到平衡选择的作用。我们回顾了 Mpi 基因座的遗传变异模式，将其与 mtDNA 和微卫星的种群分化水平进行了比较，并将这些数据置于从跨越北大西洋的种群样本中高通量测序得到的全基因组变异的背景下进行分析。尽管 Mpi 同工酶的选择模式在地理上存在很大差异，但该基因座在生态和跨洋尺度上的种群分化水平相对较低(F(ST)约为 5%)。在罗德岛(RI)、缅因州(ME)和英国绍斯沃尔德(Southwold)的样本中进行了群体测序。对超过 6.5 亿个读取的分析在藤壶的 1900 万个碱基对的基因组中确定了大约 33.5 万个高质量 SNP。大西洋两岸有大量的变异，但 RI、ME 和 UK 的样本之间存在显著的种群分化。对超过 22000 个重叠群的 F(ST)异常值筛选为解释同工酶、mtDNA 和微卫星的早期研究提供了全基因组背景。同工酶、mtDNA 和微卫星的 F(ST)值接近随机 SNP 的全基因组平均值，但 mtDNA 的跨大西洋 F(ST)值除外。大多数 F(ST)异常值在个体种群对之间是独特的，但有些基因表现出共享的过度分化模式。这些数据表明基因流很高，选择在一组基因上很强，并且在大的空间尺度上有许多基因正在经历多样化选择。本研究对藤壶的多态性进行了调查，提供了许多基因组工具，有望使该物种成为岩质潮间带生态学基因组学的有力模型。
