Data from: High levels of diversity and population structure in the potato late blight pathogen at the Mexico center of origin

Wang J, Fernândez-Pavía SP, Larsen MM, Garay-Serrano E, Gregorio-Cipriano R, Rodríguez-Alvarado G, Grünwald NJ, Goss EM

Date Published: January 12, 2017

DOI: http://dx.doi.org/10.5061/dryad.262qq.2

 

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Title Read_Me_First
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Description Please read this Read_Me_First.txt file first. This file introduced the specific descriptions and important notes about all the files in Dryad for this paper.
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Title Pinf9_full_MSN_DAPC_3alleles_info_checked
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Description Analysis details of MSN and DAPC, in addition to the information pertaining to number of Mexican P. infestans isolates with three alleles by region and locus.
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Title Pinf9_full_STRUCTURE_regular_recessive_SpearmanCorrelation_checked
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Description Analysis details of Spearman correlation tests between two different Q-matrix generated from the regular and recessive coding of STRUCTURE analysis.
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Title Pinf9_lineage_correction_checked
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Description Analysis details demonstrating how the lineage-correction data sets was obtained from the full data set including 197 P. infestans isolates.
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Title Pinf3Mexpops_full_and_LC_farthest_AMOVA_checked
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Description Analysis details of AMOVA based on full and lineage-correction data sets of Michoacán, Tlaxcala and Toluca isolates.
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Title Pinf3Mexpops_Full_and_LC_farthest_Migrate_checked
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Description Inference results of gene flows based on full and lineage-corrected data sets of Michoacán, Tlaxcala and Toluca calculated by software Migrate-n.
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Title Pinf3MexpopsLC_farthest_ADZE_correct_checked
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Description Mean allelic richness calculation based on lineage-corrected data sets of Michoacán, Tlaxcala and Toluca using software ADZE.
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Title Pinf3Mexpops_diploid_popprsummarystats_checked
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Description Analysis details of summary statistics of diversity based on data set of diploid Michoacán, Tlaxcala and Toluca populations.
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Title Pinf3MexpopsLC_farthest_LD_HWE_checked
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Description Analysis details of linkage disequilibrium and Hardy-Weinberg equilibrium tests based on lineage-correctted data set of Michoacán, Tlaxcala and Toluca populations.
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Title Pinf3MexpopsLC_farthest_diploid_LD_HWE_Fis_checked
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Description Analysis details of linkage disequilibrium and Hardy-Weinberg equilibrium tests based on data set including lineage-corrected and diploid isolates only of Michoacán, Tlaxcala and Toluca populations; and global inbreeding coefficient calculation for each locus.
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Title Toluca3regionsLC_farthest_LD_HWE_checked
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Description Analysis details of linkage disequilibrium and Hardy-Weinberg equilibrium tests based on lineage-corrected data sets of Toluca isolates by region/host.
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Title Toluca3regionsLC_farthest_diploid_LD_HWE_checked
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Description Analysis details of linkage disequilibrium and Hardy-Weinberg equilibrium tests based on data set includinglineage-corrected and diploid Toluca isolates by region/host.
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Title Pinf9_full_popprsummarystats_checked
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Description The completely original data set and analysis details of summary statistics of diversity based on this full data set.
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When using this data, please cite the original publication:

Wang J, Fernández-Pavía SP, Larsen MM, Garay-Serrano E, Gregorio-Cipriano R, Rodríguez-Alvarado G, Grünwald NJ, Goss EM (2016) High levels of diversity and population structure in the potato late blight pathogen at the Mexico centre of origin. Molecular Ecology 26(4): 1091-1107. http://dx.doi.org/10.1111/mec.14000

Additionally, please cite the Dryad data package:

Wang J, Fernândez-Pavía SP, Larsen MM, Garay-Serrano E, Gregorio-Cipriano R, Rodríguez-Alvarado G, Grünwald NJ, Goss EM (2016) Data from: High levels of diversity and population structure in the potato late blight pathogen at the Mexico center of origin. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.262qq.2
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