Data from: Chromosomes tell half of the story: the correlation between karyotype rearrangements and genetic diversity in sedges, a group with holocentric chromosomes

 

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Title R workspace with all Carex pachystachya data
Downloaded 29 times
Description R workspace with Carex pachystachya genetic and chromosome data, and geographic coordinates. Load into R using the "load" command. Two objects are contained in the workspace: (1) a table named "coordAndChrom3" that contains Whitkus's voucher numbers, diploid chromosome counts, and decimal latitude and longitude for each population; and (2) "whitkusFinal", a list of two matrices, the first a matrix of allele frequencies indexed by locus (rows) and population (columns), the second a matrix of sample sized indexed in the same manner.
Download whitkusData.Rdata (2.136 Kb)
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Title Zip file to conduct Carex scoparia analyses in R
Downloaded 47 times
Description A zip file with an R workspace and a source file that executes all analyses conducted in R to generate Table 2. To execute, unzip the files into your working directory, load the file called "scopariaWorkspace.Rdata" into R, then source the file called "27may08analyses.R". Please note that the mantel tests are set to run for 200 permutations in this file, to make life easy when you are running... these mantel tests were actually run for 20,000 permutations for the final paper. Please email me if you have trouble running this.
Download scoparia-R-analyses.zip (18.26 Kb)
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Title NEXUS file for Carex scoparia and outgroups
Downloaded 22 times
Description A nexus file for Carex scoparia and outgroups. Original binned data are in a separate file.
Download aflp_30march08_corrected-withPaupEnd.nex (69.71 Kb)
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When using this data, please cite the original publication:

Hipp AL, Rothrock PE, Whitkus R, Weber JA (2010) Chromosomes tell half of the story: the correlation between karyotype rearrangements and genetic diversity in sedges, a group with holocentric chromosomes. Molecular Ecology 19: 3124-3138. http://dx.doi.org/10.1111/j.1365-294X.2010.04741.x

Additionally, please cite the Dryad data package:

Hipp A, Rothrock P, Whitkus R, Weber J (2010) Data from: Chromosomes tell half of the story: the correlation between karyotype rearrangements and genetic diversity in sedges, a group with holocentric chromosomes. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.1435
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