Data from: Unidirectional diploid–tetraploid introgression among British birch trees with shifting ranges shown by restriction site-associated markers

Zohren J, Wang N, Kardailsky I, Borrell JS, Joecker A, Nichols RA, Buggs RJA

Date Published: April 25, 2016

DOI: http://dx.doi.org/10.5061/dryad.815rj.2

 

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Title Genotyping method (mixed ploidy dataset)
Downloaded 15 times
Description This script allows the genotyping of a mixed ploidy data set (including polyploids). It is based on read counts and average base quality. The algorithm calculates the most likely variant configuration at each locus using a log-likelihood model.
Download genotyping.R (10.36 Kb)
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Title Beta-binomial model for allelic ratios
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Description Function to model number of reads per SNP allele as a mixture of beta-binomial distributions. The data are censored to be between two cutoff values.
Download betabinomial.R (8.11 Kb)
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Title Plotting of figures
Downloaded 14 times
Description Collection of scripts used for plotting figures in the present study.
Download plotting.R (10.17 Kb)
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Title Analyses used in present study
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Description Collection of scripts used for analyses in the present study.
Download analyses.R (10.12 Kb)
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Title Betula RAD reference sequence
Downloaded 4 times
Description These sequences were concatenated and used as a reference for the mapping of the 213 RAD individuals.
Download Betula_RAD_reference.fasta.gz (35.41 Mb)
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Title Input file for STRUCTURE analysis
Downloaded 12 times
Description This file was used to analyse the RAD data in STRUCTURE. The first row contains loci names, the first column individual names, the second column population identifiers, missing data is encoded as "-9", and the ploidy is four.
Download structure_input.txt (93.33 Mb)
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Title Input file for PCA etc.
Downloaded 5 times
Description This R object is the basis of many of the analyses performed in the present study. E.g. the Principal Component Analysis and the calculation of Fst values.
Download data_80p_genlight.rdata (5.483 Mb)
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When using this data, please cite the original publication:

Zohren J, Wang N, Kardailsky I, Borrell JS, Joecker A, Nichols RA, Buggs RJA (2016) Unidirectional diploid–tetraploid introgression among British birch trees with shifting ranges shown by restriction site-associated markers. Molecular Ecology 25(11): 2413–2426. http://dx.doi.org/10.1111/mec.13644

Additionally, please cite the Dryad data package:

Zohren J, Wang N, Kardailsky I, Borrell JS, Joecker A, Nichols RA, Buggs RJA (2016) Data from: Unidirectional diploid–tetraploid introgression among British birch trees with shifting ranges shown by restriction site-associated markers. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.815rj.2
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