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

Gryseels S, Goüy de Bellocq J, Makundi R, Vanmechelen K, Broeckhove J, Mazoch V, Šumbera R, Zima Jr. J, Leirs H, Baird SJE

Date Published: July 1, 2016

DOI: http://dx.doi.org/10.5061/dryad.n5v84

 

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Title Field data Gryseels et al. Rodent urban-rural genetic contrast
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Description Explanations 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 trap
Download Field data Gryseels et al. Rodent urban-ru....xlsx (112.3 Kb)
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Title Parameter settings for STRUCTURE clustering analyses
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Description Parameter settings for STRUCTURE clustering analyses used in the manuscript
Download Parameter settings for STRUCTURE clusteri...es.txt (1.821 Kb)
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Title Microsatellite data
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Description Explanations for datafile "Microsatellite data.xls" This datafile contains microsatellite genotype information of Mastomys natalensis. General comment: "-9" describes a missing datapoint Column headings: ID --> 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 --> 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 --> 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 --> microsatellite repeat numbers at 15 different loci (column headers = names of the loci)
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Title IMa2 input file
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Description The exact input file as used in IMa2 analyses in the manuscript.
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Title IMa2 commands
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Title Landscape Costs
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Description Explanations 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).
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When using this data, please cite the original publication:

Gryseels S, Goüy de Bellocq J, Makundi R, Vanmechelen K, Broeckhove J, Mazoch V, Šumbera R, Zima Jr J, Leirs H, Baird SJE (2016) Genetic distinction between contiguous urban and rural multimammate mice in Tanzania despite gene flow. Journal of Evolutionary Biology 29(10): 1952–1967. http://dx.doi.org/10.1111/jeb.12919

Additionally, please cite the Dryad data package:

Gryseels S, Goüy de Bellocq J, Makundi R, Vanmechelen K, Broeckhove J, Mazoch V, Šumbera R, Zima Jr. J, Leirs H, Baird SJE (2016) Data from: Genetic distinction between contiguous urban and rural multimammate mice in Tanzania despite gene flow. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.n5v84
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