Data from: Contrasting support for alternative models of genomic variation based on microhabitat preference: species-specific effects of climate change in alpine sedges

Massatti R, Knowles LL

Date Published: July 7, 2016

DOI: http://dx.doi.org/10.5061/dryad.ng3bv

 

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Title chal_empirical_data
Downloaded 17 times
Description Empirical SNP dataset for Carex chalciolepis. These data were used to create summary statistics in arlsumstat for comparison with modeled data in the ABC procedure. They also informed the sampling of the modeled data across the landscape (so that the modeled data had the same pattern of missing data as the empirical data). This file can be viewed and manipulated in a text editor or Excel. It was generated by converting a vcf output file from the populations program in Stacks using PGDSpider.
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Title nova_empirical_data
Downloaded 11 times
Description Empirical SNP dataset for Carex nova. These data were used to create summary statistics in arlsumstat for comparison with modeled data in the ABC procedure. They also informed the sampling of the modeled data across the landscape (so that the modeled data had the same pattern of missing data as the empirical data). This file can be viewed and manipulated in a text editor or Excel. It was generated by converting a vcf output file from the populations program in Stacks using PGDSpider.
Download nova_1186_cut.stru (714.8 Kb)
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Title changeArpAfterSim
Downloaded 10 times
Description This python script is integrated into the modeling simulations (see 'chalciolepis_ABCsampler_input_file'). After each coalescent simulation in Splatch, this script changes the resulting modeled dataset to have the same pattern of missing data as the empirical data. A companion file is needed for the script to work properly (see 'chal_missing_example'). The script can be viewed and modified in a text editor and was created by myself and members of the Knowles lab.
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Title chal_missing_example
Downloaded 18 times
Description This is an example file that describes the pattern of missing data in an empirical dataset ('chal_empirical_data'). The file is utilized by the changeArpAfterSim.py script (see script in this data archive) to create modeled datasets with the same pattern of missing data as the empirical datasets. The file can be viewed in a text editor.
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Title create_mask
Downloaded 15 times
Description This is an R script that creates a text file describing the pattern of missing data in an empirical dataset (see example mask file 'chal_missing_example' created from 'chal_empirical_data'). The resulting mask file is used by the changeArpAfterSim script to change modeled datasets into modeled datasets with the same pattern of missing data as the empirical data. This script was generated by and modified by myself and members of the Knowles lab.
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Title chalciolepis_parameters_example
Downloaded 18 times
Description This file defines the parameters and the prior ranges/distributions from which values are pulled to update the simulations at the beginning of every Splatche simulation. See the ABCSampler documentation for more information about file format and options. The file can be viewed and modified in a text editor. The file is defined in the ABCSampler input file (see 'chalciolepis_ABCsampler_input_file').
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Title chalciolepis_ABCsampler_input_file
Downloaded 5 times
Description This is an example of an input file used by the ABCsampler program. It defines the values that need to be updated at every new iteration (in capital letters - taken from the parameter file 'chalciolepis_parameters_file'), as well as the programs that need to be run (and the order in which those programs are executed). This file can be viewed and modified in a text editor. See the ABCSampler documentation for detailed information about the structure and options for this file.
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Title chalciolepis_empirical_summary_stats
Downloaded 13 times
Description This is an example of the empirical summary statistics that must be included in the simulation folder. This file was created using arlsumstat program and the empirical dataset (see 'chal_empirical_data'). The file can be viewed and modified in a text editor. See the Arlequin/arlsumstat documentation for more information.
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Title settings_chalciolepis_splatche
Downloaded 14 times
Description This is an example of a settings file for a single Splatche run. The Splatche documentation describes all of the options within the file in detail. The file can be viewed and modified in a text editor.
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Title chalciolepis_distribution_pts
Downloaded 4 times
Description File containing the distribution points used for distribution modeling in Maxent. These points come from verified herbarium records and personal collections.
Download chal.txt (7.996 Kb)
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Title nova_distribution_points
Downloaded 5 times
Description File containing the distribution points used for distribution modeling in Maxent. These points come from verified herbarium records and personal collections.
Download nova.txt (5.652 Kb)
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When using this data, please cite the original publication:

Massatti R, Knowles LL (2016) Contrasting support for alternative models of genomic variation based on microhabitat preference: species-specific effects of climate change in alpine sedges. Molecular Ecology 25(16): 3974–3986. http://dx.doi.org/10.1111/mec.13735

Additionally, please cite the Dryad data package:

Massatti R, Knowles LL (2016) Data from: Contrasting support for alternative models of genomic variation based on microhabitat preference: species-specific effects of climate change in alpine sedges. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.ng3bv
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