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

Globally destructive crop pathogens often emerge by migrating out of their native ranges. These pathogens are often diverse at their center of origin, and may exhibit adaptive variation in the invaded range via multiple introductions from different source populations. However, source populations are generally unidentified or poorly studied compared to invasive populations. Phytophthora infestans, the causal agent of late blight, is one of the most costly pathogens of potato and tomato worldwide. Mexico is the center of origin and diversity of P. infestans and migration events out of Mexico have enormously impacted disease dynamics in North America and Europe. The debate over the origin of the pathogen, and population studies of P. infestans in Mexico, have focused on the Toluca Valley, whereas neighboring regions have been little studied. We examined the population structure of P. infestans across central Mexico, including samples from Michoacán, Tlaxcala, and Toluca. We found high levels of diversity consistent with sexual reproduction in Michoacán and Tlaxcala, and population subdivision that was strongly associated with geographical region. We determined that population structure in Central Mexico has contributed to diversity in introduced populations based on relatedness of U.S. clonal lineages to Mexican isolates from different regions. Our results suggest that P. infestans exists as a metapopulation in Central Mexico, and this population structure could be contributing to the repeated re-emergence of P. infestans in the U.S. and elsewhere.Read_Me_FirstPlease 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.Pinf9_full_MSN_DAPC_3alleles_info_checkedAnalysis 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.Pinf9_full_STRUCTURE_regular_recessive_SpearmanCorrelation_checkedAnalysis details of Spearman correlation tests between two different Q-matrix generated from the regular and recessive coding of STRUCTURE analysis.Pinf9_lineage_correction_checkedAnalysis details demonstrating how the lineage-correction data sets was obtained from the full data set including 197 P. infestans isolates.Pinf3Mexpops_full_and_LC_farthest_AMOVA_checkedAnalysis details of AMOVA based on full and lineage-correction data sets of Michoacán, Tlaxcala and Toluca isolates.Pinf3Mexpops_Full_and_LC_farthest_Migrate_checkedInference results of gene flows based on full and lineage-corrected data sets of Michoacán, Tlaxcala and Toluca calculated by software Migrate-n.Pinf3MexpopsLC_farthest_ADZE_correct_checkedMean allelic richness calculation based on lineage-corrected data sets of Michoacán, Tlaxcala and Toluca using software ADZE.Pinf3Mexpops_diploid_popprsummarystats_checkedAnalysis details of summary statistics of diversity based on data set of diploid Michoacán, Tlaxcala and Toluca populations.Pinf3MexpopsLC_farthest_LD_HWE_checkedAnalysis details of linkage disequilibrium and Hardy-Weinberg equilibrium tests based on lineage-correctted data set of Michoacán, Tlaxcala and Toluca populations.Pinf3MexpopsLC_farthest_diploid_LD_HWE_Fis_checkedAnalysis 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.Toluca3regionsLC_farthest_LD_HWE_checkedAnalysis details of linkage disequilibrium and Hardy-Weinberg equilibrium tests based on lineage-corrected data sets of Toluca isolates by region/host.Toluca3regionsLC_farthest_diploid_LD_HWE_checkedAnalysis details of linkage disequilibrium and Hardy-Weinberg equilibrium tests based on data set includinglineage-corrected and diploid Toluca isolates by region/host.Pinf9_full_popprsummarystats_checkedThe completely original data set and analysis details of summary statistics of diversity based on this full data set