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

白足小鼠 (Peromyscus leucopus) 对 Urb 的适应性进化反应

• 批准号: 8367359
• 负责人: Jason Munshi-South
• 金额: $ 10.82万
• 依托单位: BERNARD M. BARUCH COLLEGE
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-10 至 2013-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8367359
• 关键词: Area; Biological; Biological Models; Biology; Characteristics; Chronic; Code; DNA Sequence; Data; Disease; Ecosystem; Elements; Environment; Environmental Pollutants; Environmental Pollution; Exhibits; Exposure to; Food Supply; Functional RNA; Future; Gene Expression; Genes; Genetic; Genome; Genome Scan; Genomics; Genotype; Habitats; Human; Individual; Linear Regressions; Link; Longitudinal Studies; Modeling; Mus; Mutation; Nature; New York City; Open Reading Frames; Organism; Peromyscus; Physiological; Pollution; Population; Population Density; Productivity; Rattus; Regulatory Element; Relative (related person); Resources; Sampling; Scanning; Shapes; Single Nucleotide Polymorphism; Site; Syndrome; Techniques; Testing; Transcript; Trees; Urban Population; Urbanization; Variant; White-Footed Mouse; anthropogenesis; base; college; density; exome; experience; fitness; genetic variant; genome wide association study; genome-wide; high school; improved; next generation; novel; novel strategies; pressure; research study; response; soil pollution; urban area

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.

描述（由申请人提供）：城市化是上个世纪人类变化中最普遍的力量之一。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。城市生境往往只有极高的人口密度，只有少数城市“适应者”，导致生物同质化。较高的初级生产力、较稳定和丰富的食物供应以及从营养竞争中解脱出来是导致这些异常种群密度的原因。城市人口还经历了更强的种内竞争、疾病和环境污染。野生动物可能会迅速适应当地的城市环境，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”测序的出现使得可以相对便宜和快速地生成数百万个序列，从而极大地提高了检测指示局部适应的信息性变化的能力。我们将使用这些新的方法来研究适应城市化的白足鼠（Peromyscus leucopus），在纽约市的人口。首先，我们将使用454和ABI SOLiD下一代测序技术为来自纽约市城市和非城市人群的白足小鼠生成深度外显子组序列。将通过与注释的大鼠、小鼠和Peromyscus基因组比对来确定基因同一性。我们将确定基因组区域，并最终个人的编码序列，表现出在城市人口的选择统计签名。 一个初步的参考外显子组的城市P. leucopus已经测序和注释，并已确定了几个候选基因座。其他分析将使用SOLiD外显子组数据检查城市人群基因表达水平的定量变化，以及使用全基因组RAD-Seq（限制性位点相关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，以检查是否选择压力，从城市化的结果在整个纽约市都会区的相关变化的“进化综合征”，或者，适应当地的城市条件，在个别人群。景观要素（例如土壤污染、人口密度、生境类型）与信息变量之间的统计关联 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，我们将在纽约市市区建立长期研究地点，以研究候选遗传变异的适应性后果，并为未来的实地实验奠定基础。最后，我们将建立在我们之前的大量努力，将城市进化生物学融入巴鲁克学院和纽约市环境研究高中的课程。 公共卫生关系：在城市环境中茁壮成长的哺乳动物物种经历了更高的人口密度，更高的疾病和环境污染物暴露，以及对有限资源的更大竞争。这种情况下，预计将产生巨大的选择压力，但很少有研究探讨城市人口的适应性进化的变化。本研究中的群体基因组学方法将开发一种新的哺乳动物模型系统（白足鼠，白足鼠），以了解在人类主导的环境中迅速塑造生物体生物学的进化力量。