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_First
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.
Pinf9_full_MSN_DAPC_3alleles_info_checked
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.
Pinf9_full_STRUCTURE_regular_recessive_SpearmanCorrelation_checked
Analysis details of Spearman correlation tests between two different Q-matrix generated from the regular and recessive coding of STRUCTURE analysis.
Pinf9_lineage_correction_checked
Analysis 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_checked
Analysis details of AMOVA based on full and lineage-correction data sets of Michoacán, Tlaxcala and Toluca isolates.
Pinf3Mexpops_Full_and_LC_farthest_Migrate_checked
Inference 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_checked
Mean allelic richness calculation based on lineage-corrected data sets of Michoacán, Tlaxcala and Toluca using software ADZE.
Pinf3Mexpops_diploid_popprsummarystats_checked
Analysis details of summary statistics of diversity based on data set of diploid Michoacán, Tlaxcala and Toluca populations.
Pinf3MexpopsLC_farthest_LD_HWE_checked
Analysis 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_checked
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.
Toluca3regionsLC_farthest_LD_HWE_checked
Analysis 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_checked
Analysis 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_checked
The completely original data set and analysis details of summary statistics of diversity based on this full data set.