DOI: 10.5061/dryad.n5v84
title: Data from: Genetic distinction between contiguous urban and rural multimammate mice in Tanzania despite gene flow

description: 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 (&lt;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.
description: Field data Gryseels et
 al. Rodent urban-rural genetic contrastExplanations for
 datafile "Field data Gryseels et al. Differentiation of M.natalensis
 in synanthropy.xls" This datafile contains trapping and location
 information of small mammals captured as described in the manuscript
 "Genetic distinction between contiguous urban and rural multimammate
 mice in Tanzania despite gene flow" ID: Unique ID code of each
 captured animal Project: the samples used in the manuscript originate from
 2 different projects (see details in manuscript) Locality: Unique code of
 the locality (which consists of a set of 100 traps placed in a grid for 1
 night) where the animal is captured Town: town, village or community where
 the animal is captured Date: the date the animal was captured Species:
 morphological identification of the animal (in case of Mastomys
 natalensis: confirmed by cytochrome b DNA sequence data) Latitude and
 longitude: the exact GPS location the animal was captured inside its
 trapParameter settings for
 STRUCTURE clustering analysesParameter settings for
 STRUCTURE clustering analyses used in the manuscriptMicrosatellite
 dataExplanations for
 datafile "Microsatellite data.xls" This datafile contains
 microsatellite genotype information of Mastomys natalensis. General
 comment: "-9" describes a missing datapoint Column headings: ID
 --&gt; unique code of a captured and genotyped animal. For field
 information, see file "Field data Gryseels et al. Rodent urban-rural
 genetic contrast.txt" Info for STRUCTURE: Sample location information
 --&gt; A number code depicting the location (at the village level) the
 genotyped animal was captured. This information is used in the clustering
 algorithm in the software STRUCTURE. Info for STRUCTURE: Putative
 population origin --&gt; A number code depicting the location the
 genotyped animal was captured. This information is used in the clustering
 algorithm in the software STRUCTURE. Remaining columns --&gt;
 microsatellite repeat numbers at 15 different loci (column headers = names
 of the loci)IMa2 input
 fileThe exact input file as
 used in IMa2 analyses in the manuscript.IMa2
 commandsLandscape
 CostsExplanations for
 datafile "Landscape costs.xls" This datafile contains the
 classes of the landscape elements present in the "Transect"
 study area of the manuscript and their associated "cost values"
 for Mastomys natalensis. Landscape cover data was gathered from the
 Africover Spatially Aggregated Multipurpose Landcover database of Tanzania
 from the Food and Agriculture Organization of the UN (available at
 http://www.africover.org). Details on the land cover classification used
 can be found in Di Gregorio & Jansen (2000). These landscape elements
 were then translated into "landscape cost" values for Mastomys
 natalensis by 10 specialists, which indicates the ease of movement and the
 quality of the habitat for M. natelensis for that landscape element. This
 cost layer was then further used as a "habitat layer" in the
 software Circuitscape (see manuscript for details).