Data from: Genetic distinction between contiguous urban and rural multimammate mice in Tanzania despite gene flow

Special conditions are required for genetic differentiation to arise at a local geographical scale in the face of gene flow. The Natal multimammate mouse, Mastomys natalensis, is the most widely distributed and abundant rodent in sub-Saharan Africa. A notorious agricultural pest and a natural host for many zoonotic diseases, it can live in close proximity to man, and appears to compete with other rodents for the synanthropic niche. We surveyed its population genetic structure across a 180 km transect in central Tanzania along which the landscape varied between agricultural land in a rural setting and natural woody vegetation, rivers, roads and a city. We sampled M. natalensis across 10 localities, and genotyped 15 microsatellite loci from 515 individuals. Hierarchical STRUCTURE analyses show a K-invariant pattern distinguishing Morogoro suburbs (located in the centre of the transect) from nine surrounding rural localities. Landscape connectivity analyses in Circuitscape and comparison of rainfall patterns suggest that neither geographical isolation nor natural breeding asynchrony could explain the genetic differentiation of the urban population. Using the Isolation-with-Migration model implemented in IMa2 we inferred that a split between suburban and rural populations would have occurred recently (<150 years ago) with higher urban effective population density consistent with an urban-source to rural-sink of effective migration. The observed genetic differentiation of urban multimammate mice is striking given the uninterrupted distribution of the animal throughout the landscape and the high estimates of effective migration (2NeM = 3.0 and 29.7), suggesting a strong selection gradient across the urban boundary.在基因流（gene flow）存在的背景下，若要在局地地理尺度上形成遗传分化（genetic differentiation），需满足特定前提条件。纳塔尔多乳鼠（Natal multimammate mouse，学名Mastomys natalensis）是撒哈拉以南非洲分布最广、种群数量最丰富的啮齿类动物。它既是臭名昭著的农业害虫，也是多种人畜共患病的自然宿主，可与人类近距离共存，且似乎会与其他啮齿类竞争人伴生生态位（synanthropic niche）。我们于坦桑尼亚中部一条180公里的样带上开展种群遗传结构调查，该样带沿线景观类型呈梯度变化，涵盖乡村农田、天然木本植被、河流、道路与一座城市。我们于10个采样点采集纳塔尔多乳鼠样本，并对515个个体的15个微卫星位点（microsatellite loci）进行基因分型。分层STRUCTURE群体结构分析显示出一种K值恒定的模式，可将样带中部的莫罗戈罗郊区与周边9个乡村采样点区分开来。通过Circuitscape软件开展的景观连通性分析以及降雨模式对比结果表明，地理隔离与自然繁殖异步均无法解释该城市种群的遗传分化现象。借助IMa2软件中实现的隔离与迁移（Isolation-with-Migration）模型，我们推断郊区种群与乡村种群的分化发生在近期（不足150年前），且城市种群的有效种群密度更高，这与有效迁移呈现城市源-乡村汇的模式相符。鉴于该物种在整个研究景观中连续分布，且有效迁移估计值较高（2NeM = 3.0与29.7），观测到的城市环境下纳塔尔多乳鼠的遗传分化现象十分显著，这表明城市边界两侧存在较强的选择梯度。