Adaptive Evolutionary Responses of White-footed Mice (Peromyscus leucopus) to Urb

描述(由申请人提供)： 城市化是上个世纪人类活动变化最普遍的力量之一。现在超过50%的人口居住在城市地区，在不久的将来，大多数生态系统将经历城市化。残留的城市生境斑块往往包含极高的人口密度，只有几个城市“适配者”或“剥削者”，导致生物同质化。由于人为提高初级生产力，城市适配器实现了较高的人口密度，“热岛”效应导致的温度波动较小，人类补充的食物供应更稳定和丰富，城市环境中的营养竞争得以释放。经历上述生态条件的与世隔绝的城市人口可能会迅速适应当地条件，但很少有研究检验这种可能性。人口基因组学的新兴领域使用计算方法来识别大量正在选择的基因座中的统计异常值。最近，“下一代”测序技术的出现使得以相对廉价和快速的方式产生数百万个序列成为可能，从而极大地提高了检测指示局部适应的单核苷酸多态(SNPs)的能力。我们将使用这些新方法来研究纽约市一种城市适配器--白脚鼠(Permyscus Leucopus)--与世隔绝的人口对城市化的本地适应。首先，我们将使用454焦磷酸测序为来自城市和非城市人口的白足小鼠产生深层转录组序列。基因识别将通过与注释的大鼠、小鼠和Permyscus基因组的比对来建立(目标1)。然后，我们将确定在城市人口中非同义SNPs上表现出选择统计特征的编码序列。我们将在多个种群中研究这些地区，以检查来自城市化的选择压力是否会导致整个景观相关变化的“进化综合症”(目标2)。很难预先预测哪些基因将被选择，但有助于处理种内高度竞争、疾病和长期暴露于污染物的生理压力的基因座可能是例子。接下来，我们将研究由于选择性剪接和差异表达而导致的城市和非城市人群之间的额外基因组变异。我们将在Illumina下一代测序平台上使用RNA-SEQ方法来识别可选的剪接变体并量化不同种群的转录本丰度(目标3)。

DESCRIPTION (provided by applicant): Urbanization represents one of the most pervasive forces of anthropogenic change over the last century. More than 50% of the human population now occupies urban areas, and most ecosystems will experience urbanization in the near future. Remnant urban habitat patches often contain extremely high population densities of just a few urban "adapters" or "exploiters", leading to biological homogenization. Urban adapters achieve high population densities due to artificially high primary productivity, less severe temperature fluctuations due to the "heat island" effect, a more stable and abundant food supply from human supplementation, and release from trophic competition in urban environments. Isolated urban populations experiencing the ecological conditions described above may rapidly adapt to local conditions, but few studies have examined this possibility. The emerging field of population genomics uses computational approaches to identify statistical outliers among large numbers of loci that are under selection. Recently, the advent of "next generation" sequencing has made it possible to generate millions of sequences relatively cheaply and quickly, thus vastly improving the power to detect single nucleotide polymorphisms (SNPs) indicative of local adaptation. We will use these new approaches to examine local adaptation to urbanization among isolated populations of an urban adapter in New York City, the white-footed mouse (Peromyscus leucopus). First, we will generate deep transcriptome sequence for white-footed mice from urban and non-urban populations using 454 pyrosequencing. Gene identity will be established through alignment with annotated rat, mouse, and Peromyscus genomes (Aim 1). We will then identify coding sequences that exhibit statistical signatures of selection at non-synonymous SNPs in urban populations. We will examine these regions in multiple populations to examine whether selection pressures from urbanization result in an "evolutionary syndrome" of correlated change across the landscape (Aim 2). It is difficult to predict a priori which genes will be under selection, but loci that facilitate dealing with physiological stress from high intraspecific competition, disease, and chronic exposure to pollutants are likely examples. Next, we will examine additional genomic variation between urban vs. non-urban populations due to alternative splicing and differential expression. We will use RNA-seq methodology on the Illumina next-generation sequencing platform to identify alternative splice variants and quantify transcript abundance across populations (Aim 3).