Signatures of positive selection and local adaptation to urbanization in white-footed mice (Peromyscus leucopus).
Signatures of positive selection and local adaptation to urbanization in white-footed mice (Peromyscus leucopus).
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DOI：
10.1111/mec.14369
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发表时间：
2017-11
影响因子：
4.9
通讯作者：
Munshi-South J
中科院分区：
文献类型：
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作者：
Harris SE;Munshi-South J
城市化显著改变了自然生态系统，并在全球范围内加速。城市野生动物种群往往被人类基础设施高度分散，与世隔绝的种群可能会适应当地的城市压力。然而，相对较少的研究确定了城市动物适应的基因组特征。我们使用景观基因组学方法来检查纽约市城市白足老鼠(Permyscus Leucopus)种群的选择特征。我们分析了从转录组数据中识别的154,770个SNPs，这些SNPs来自三个城市和三个农村人口的48个白纹伊蚊个体，并使用异常值测试来识别城市适应的证据。我们通过模拟一个中性的SNP数据集来解释人口学，在推断的人口学历史下将其作为异常值分析的空模型。我们还测试了候选基因是否与城市化相关的环境变量有关。我们总共检测了381个异常基因座，经过严格的过滤，识别并注释了19个候选基因座。许多候选基因参与代谢过程，并在代谢脂肪和碳水化合物方面发挥着公认的作用。我们的结果表明，纽约市的白足小鼠正在生物分子水平上适应城市栖息地的局部选择压力。对离群点的注释表明，选择作用于城市人口的新陈代谢途径，这可能与城市中与较不受干扰地区的饮食不同有关。
Urbanization significantly alters natural ecosystems and has accelerated globally. Urban wildlife populations are often highly fragmented by human infrastructure, and isolated populations may adapt in response to local urban pressures. However, relatively few studies have identified genomic signatures of adaptation in urban animals. We used a landscape genomics approach to examine signatures of selection in urban populations of white-footed mice (Peromyscus leucopus) in New York City. We analyzed 154,770 SNPs identified from transcriptome data from 48 P. leucopus individuals from three urban and three rural populations, and used outlier tests to identify evidence of urban adaptation. We accounted for demography by simulating a neutral SNP dataset under an inferred demographic history as a null model for outlier analysis. We also tested whether candidate genes were associated with environmental variables related to urbanization. In total, we detected 381 outlier loci and after stringent filtering, identified and annotated 19 candidate loci. Many of the candidate genes were involved in metabolic processes, and have well-established roles in metabolizing lipids and carbohydrates. Our results indicate that white-footed mice in NYC are adapting at the biomolecular level to local selective pressures in urban habitats. Annotation of outlier loci suggest selection is acting on metabolic pathways in urban populations, likely related to novel diets in cities that differ from diets in less disturbed areas.
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影响因子：
10.7
作者：
Chapman MA;Hiscock SJ;Filatov DA
通讯作者：
Filatov DA
影响因子：
4.9
作者：
De Kort, Hanne;Vandepitte, Katrien;Mergeay, Joachim
通讯作者：
Mergeay, Joachim
DOI：
10.1152/ajpendo.00332.2001
发表时间：
2002-04-01
影响因子：
5.1
作者：
Burcelin, M;Crivelli, V;Thorens, B
通讯作者：
Thorens, B
影响因子：
3.3
作者：
Coop, Graham;Witonsky, David;Pritchard, Jonathan K.
通讯作者：
Pritchard, Jonathan K.
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
作者：
通讯作者：
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