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

描述(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。城市栖息地往往包含极高的人口密度，只有几个城市“适配器”，导致生物同质化。人为提高初级生产力、更稳定和更充足的食物供应以及从营养竞争中释放出来，导致了这些异常的种群密度。城市人口还经历了种内竞争加剧、疾病和环境污染。野生动物可能会迅速适应当地的城市条件，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信息性变异的能力。我们将使用这些新方法来研究纽约市白脚老鼠(Permyscus Leucopus)种群对城市化的适应情况。首先，我们将使用454和ABI固体下一代测序技术为来自纽约市城市和非城市人口的白足小鼠生成深层外显子组序列。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。我们将确定基因组区域，并最终确定显示城市人口选择统计特征的个别编码序列。 城市大白杨的一个初步参考外显子组已经被测序和注释，并确定了几个候选基因座。其他分析将使用可靠的外显子组数据检查城市人口基因表达水平的定量变化，并使用全基因组RAD-Seq(限制位点相关DNA测序)方法检查蛋白质编码区以外的潜在调控变化。我们还将使用景观基因组分析来检验来自城市化的选择压力是否会导致整个纽约大都会地区相关变化的“进化综合症”，或者是个体人口对当地城市条件的适应。景观要素(如土壤污染、人口密度、生境类型)和信息量变量之间的统计关系 将使用新的空间基因组技术进行研究。作为记录影响潜在适应性遗传变异的选择压力的进一步步骤，我们将在纽约大都市区建立长期研究地点，以检验候选遗传变异的适合性后果，并为未来的田间实验奠定基础。最后，我们将在我们之前的大量努力的基础上，将城市进化生物学整合到巴鲁克学院和纽约市环境研究高中的课程中。 公共卫生相关性：在城市环境中茁壮成长的哺乳动物物种经历了更高的种群密度，更多地暴露在疾病和环境污染物中，以及对有限资源的更激烈竞争。据预测，这样的条件将施加巨大的选择压力，但很少有研究考察城市人口的适应性进化变化。这项研究中的种群基因组学方法将开发一种新的哺乳动物模型系统(白脚小鼠，Permyscus leucopus)，以了解在人类主导的环境中正在迅速塑造生物生物学的进化力量。

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. Urban habitats often contain extremely high population densities of just a few urban "adapters", leading to biological homogenization. Artificially high primary productivity, a more stable and abundant food supply, and release from trophic competition result in these abnormal population densities. Urban populations also experience enhanced intraspecific competition, disease, and environmental pollution. Wildlife may rapidly adapt to these local urban 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 informative variation indicative of local adaptation. We will use these new approaches to examine adaptation to urbanization among populations of the white-footed mouse (Peromyscus leucopus), in New York City. First, we will generate deep exome sequence for white-footed mice from urban and non-urban populations in NYC using 454 and ABI SOLiD next-generation sequencing. Gene identity will be established through alignment with annotated rat, mouse, and Peromyscus genomes. We will identify genomic regions, and ultimately individual coding sequences, that exhibit statistical signatures of selection in urban populations. A preliminary reference exome for urban P. leucopus has already been sequenced and annotated, and several candidate loci have been identified. Additional analyses will examine quantitative changes in gene expression levels in urban populations using the SOLiD exome data, and potential regulatory changes outside of protein-coding regions using a genome-wide RAD-Seq (restriction site associated DNA sequencing) approach. We will also use landscape genomic analyses to examine whether selection pressures from urbanization result in an "evolutionary syndrome" of correlated change across the NYC metro area, or alternatively, adaptation to local urban conditions in individual populations. Statistical associations between landscape elements (e.g. soil pollution, population density, habitat type) and informative variants will be investigated using new spatial genomic techniques. As a further step in documenting the selection pressures influencing potentially adaptive genetic variants, we will establish long-term study sites in the NYC metro area to examine the fitness consequences of candidate genetic variants and lay the groundwork for future field experiments. Finally, we will build upon our substantial prior efforts to integrate urban evolutionary biology into courses at Baruch College and the NYC High School for Environmental Studies. PUBLIC HEALTH RELEVANCE: Mammalian species that thrive in urban environments experience higher population densities, enhanced exposure to disease and environmental pollutants, and greater competition for limited resources. Such conditions are predicted to exert substantial selective pressures, but few studies have examined adaptive evolutionary changes in urban populations. The population genomics approach in this study will develop a new mammalian model system (the white-footed mouse, Peromyscus leucopus) for understanding the evolutionary forces that are rapidly shaping the biology of organisms in human-dominated environments.