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.

在基因流存在的条件下，若要在局地地理尺度上产生遗传分化，需满足特定前提条件。纳塔尔多乳鼠（Mastomys natalensis）是撒哈拉以南非洲分布最广、种群数量最多的啮齿动物；该物种既是臭名昭著的农业害兽，亦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动物竞争与人伴生的生态位（synanthropic niche）。我们在坦桑尼亚中部一条180公里长的样带上开展了种群遗传结构调查，该样带沿线的景观类型多样，涵盖乡村农田、天然木本植被、河流、道路与一座城市。我们在10个采样点采集了纳塔尔多乳鼠样本，并对515个个体的15个微卫星位点（microsatellite loci）完成了基因分型。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个乡村采样点清晰区分。通过Circuitscape软件开展的景观连通性分析，结合降雨模式比对结果可知，地理隔离与自然繁殖异步性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），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”的模式相一致。鉴于该物种在整个研究景观中分布连续，且有效迁移估计值极高（2NeM=3.0与29.7），观测到的城市纳塔尔多乳鼠遗传分化现象尤为显著，这表明城市边界两侧存在较强的选择梯度。