Data from: Impacts of selective logging on inbreeding and gene flow in two Amazonian timber species with contrasting ecological and reproductive characteristics

Vinson CC, Kanashiro M, Harris SA, Boshier DH

Date Published: November 20, 2014

DOI: http://dx.doi.org/10.5061/dryad.3k506

 

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Title Input for Fdash for Dipteryx odorata
Downloaded 16 times
Description Source of information: Genotypes from lab experiments, here is the input for Fdash software for genetic diversity of polyploid analysis. Input contains genotypes of pre- and post-logging adults, pre- and post-logging progenies. First column contains id of population, second column onwards contains genotypes of Do03, Do17, Do18, Do25, Do08, Do19 and Do20 loci. abbreviations: adultos corresponds to pre-logging adults sample, adultospos (post-logging adults sample), filhotespre (pre-logging progenies sample) and filhotespos (post-logging progenies sample).
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Title Input for Spagedi for Dipteryx odorata
Downloaded 21 times
Description Source of information: Genotypes from lab experiments. Here is the input for Spagedi software for spatial genetic diversity analysis, divide into two parts, first part contains pre-logging adult input and second part contains post-logging adult input. First column contains id of sample, second and third column contains x and y coordinates, forth column onwards contains genotypes of Do03, Do17, Do18, Do25, Do08, Do19 and Do20 loci.
Download Do_InputSpagedi.txt (14.44 Kb)
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Title Input for paternity software for pre-logging Dipteryx odorata
Downloaded 8 times
Description Source of information: Genotypes from lab experiments. Here is the input for Orchard software for paternity analysis, divide into two parts, first part contains pre-logging progenies input and second part contains pre-logging candidate father input. Pre-logging progenies input contains first column contains id of progeny, second column onwards contains genotypes of Do03, Do17, Do18, Do25, Do08, Do19 and Do20 loci and last column contains name of known mother. Pre-logging candidate father input contains first column contains id of individual, second column onwards contains genotypes of Do03, Do17, Do18, Do25, Do08, Do19 and Do20 loci and last two columns contains X and Y coordinates.
Download DoPre_InputOrchard.txt (36.77 Kb)
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Title Input for paternity software for post-logging Dipteryx odorata
Downloaded 7 times
Description Source of information: Genotypes from lab experiments. Here is the input for Orchard software for paternity analysis, divide into two parts, first part contains post-logging progenies input and second part contains post-logging candidate father input. Post-logging progenies input contains first column contains id of progeny, second column onwards contains genotypes of Do03, Do17, Do18, Do25, Do08, Do19 and Do20 loci and last column contains name of known mother. Post-logging candidate father input contains first column contains id of individual, second column onwards contains genotypes of Do03, Do17, Do18, Do25, Do08, Do19 and Do20 loci and last two columns contains X and Y coordinates.
Download DoPost_InputOrchard.txt (30.43 Kb)
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Title Input for MLTR software for Jacaranda copaia
Downloaded 25 times
Description Source of information: Genotypes from lab experiments. Here is the input for MLTR software for mating system analysis. Input contains genotypes of pre- and post-logging progenies. First column contains id of known mother, second column contains group id (a=pre-logging, b=post-logging), third column onwards contains genotypes of the progeny of JC03, JC09, JC21, JC05, JC28 loci.
Download JcInputMltr.txt (48.22 Kb)
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Title Input for Spagedi software for Jacaranda copaia
Downloaded 14 times
Description Source of information: Genotypes from lab experiments. Here is the input for Spagedi software for spatial genetic diversity analysis, divide into two parts, first part contains pre-logging adults input and second part contains post-logging adults input. First column contains id of individual, second column contains field id, third column contains measure of diameter at breast height (DBH) in cm, and fifth column onwards contains genotypes of JC03, JC09, JC21, JC05, JC28 loci.
Download JcInputGdaSpagedi.txt (27.93 Kb)
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Title Input for Cervus software for Jacaranda copaia
Downloaded 36 times
Description Source of information: Genotypes from lab experiments. Here is the input for Cervus software for paternity analysis, divide into three parts. First part contains pre-logging progenies and pre-logging adults genotypes first column contains id of individual, second column onwards contains genotypes of JC03, JC09, JC21, JC05, JC28 loci. Second part contains list of progenies with known mother and third part is the list of candidate fathers.
Download JcPreInputCervus.txt (33.67 Kb)
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Title Input for Cervus software for Jacaranda copaia
Downloaded 94 times
Description Source of information: Genotypes from lab experiments. Here is the input for Cervus software for paternity analysis, divide into three parts. First part contains post-logging progenies and post-logging adults genotypes first column contains id of individual, second column onwards contains genotypes of JC03, JC09, JC21, JC05, JC28 loci. Second part contains list of progenies with known mother and third part is the list of candidate fathers.
Download JcPostInputCervus.txt (59.39 Kb)
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When using this data, please cite the original publication:

Vinson CC, Kanashiro M, Harris SA, Boshier DH (2015) Impacts of selective logging on inbreeding and gene flow in two Amazonian timber species with contrasting ecological and reproductive characteristics. Molecular Ecology 24(1): 38-53. http://dx.doi.org/10.1111/mec.13002

Additionally, please cite the Dryad data package:

Vinson CC, Kanashiro M, Harris SA, Boshier DH (2014) Data from: Impacts of selective logging on inbreeding and gene flow in two Amazonian timber species with contrasting ecological and reproductive characteristics. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.3k506
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