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变化的最普遍力量之一。超过50%的人口现在居住在城市地区，大多数生态系统将在不久的将来经历城市化。残存的城市栖息地斑块通常包含极高的人口密度，只有少数城市“适应者”或“开发者”，导致生物同质化。城市适应者由于人为的高初级生产力而实现高人口密度，由于“热岛”效应而不太严重的温度波动，人类补充剂更稳定和丰富的食物供应，以及从城市环境中的营养竞争中释放出来。孤立的城市人口经历上述生态条件可能会迅速适应当地条件，但很少有研究探讨这种可能性。新兴的群体基因组学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”测序的出现使得相对便宜且快速地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性（SNP）的能力。我们将使用这些新的方法来研究当地适应城市化之间的隔离人口的城市适应者在纽约市，白足鼠（Peromyscus leucopus）。首先，我们将使用454焦磷酸测序法生成来自城市和非城市人群的白足小鼠的深度转录组序列。将通过与注释的大鼠、小鼠和鹿鼠基因组的比对来确定基因同一性（目的1）。然后，我们将确定编码序列，在城市人群中的非同义SNPs的选择表现出统计签名。我们将在多个群体中研究这些地区，以研究城市化的选择压力是否会导致景观相关变化的“进化综合征”（目标2）。很难事先预测哪些基因将被选择，但有助于处理来自高种内竞争、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与非城市人群之间的其他基因组变异。我们将在Illumina下一代测序平台上使用RNA-seq方法来鉴定选择性剪接变体并量化人群中的转录本丰度（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).