diff --git a/genetic_analyses/3_plot_populations_map.R b/Archive/3_plot_populations_map.R similarity index 96% rename from genetic_analyses/3_plot_populations_map.R rename to Archive/3_plot_populations_map.R index 20f4831..17de024 100644 --- a/genetic_analyses/3_plot_populations_map.R +++ b/Archive/3_plot_populations_map.R @@ -109,7 +109,10 @@ coord_df_proj <- spTransform(coord_df, proj_out) setwd(butternut_drive) butternut_buffer <- readOGR(dsn = paste0(butternut_drive,"\\Genetic_Analyses\\data_files\\geographic_files") , layer = "butternut_buffer") -butternut_buffer_trans <- sp::spTransform(na_shp, proj_out) +butternut_buffer_trans <- sp::spTransform(butternut_buffer, "+proj=longlat +ellps=WGS84 +datum=WGS84") + +##calculate dist2line +butternut_dist <- dist2Line(coord_df, butternut_buffer_trans) ##list of 24 colors for populations butternut_col <- c("darkmagenta", "darkorchid3", "deeppink3", "darkviolet", "deeppink","lightpink", diff --git a/Images/geographic_images/pop_map_allind.pdf b/Images/geographic_images/pop_map_allind.pdf index 31aee82..2bef7d7 100644 Binary files a/Images/geographic_images/pop_map_allind.pdf and b/Images/geographic_images/pop_map_allind.pdf differ diff --git a/SDMs/1_create_pop_buffer.R b/SDMs/1_create_pop_buffer.R index 5882939..b6689be 100644 --- a/SDMs/1_create_pop_buffer.R +++ b/SDMs/1_create_pop_buffer.R @@ -32,6 +32,15 @@ max_lat <- max(butternut_range$Latitude) coordinates(butternut_range2) <- c('Longitude', 'Latitude') proj4string(butternut_range2) <- CRS("+proj=longlat +ellps=WGS84 +datum=WGS84") +##set working directory +setwd(butternut_drive) + +##Lon lat files +butternut_reorg_lonlat <- read.csv("Genetic_Analyses\\data_files\\after_reorg\\reorg_lon_lat.csv") + +##population names document +butternut_24pop_names <- unique(butternut_reorg_lonlat$Pop) + ######################################### ########## Calculate Buffer ############# ######################################### @@ -64,3 +73,5 @@ butternut_buff <- gBuffer(crop, width = 100000) ##write out buffer file shapefile(butternut_buff,"butternut_buffer") + + diff --git a/genetic_analyses/3_sum_stats_geneticdiversity.R b/genetic_analyses/3_sum_stats_geneticdiversity.R index e5f0763..1b82631 100644 --- a/genetic_analyses/3_sum_stats_geneticdiversity.R +++ b/genetic_analyses/3_sum_stats_geneticdiversity.R @@ -4,7 +4,7 @@ #First, we tested linkage disequilibrium, null alleles, #and Hardy Weinberg equilibrium. #Next, a data frame including expected heterozygosity, allelic richness, -#number of alleles, mean longtiude and latitude by population, and +#number of alleles, mean longtiude and latitude by population, distance to range edge, and #individual numbers. This table is included in full in the supplemental text #of this manuscript. @@ -17,6 +17,9 @@ library(poppr) library(hierfstat) library(PopGenReport) library(pegas) +library(geosphere) +library(sp) +library(rgdal) ########################################## ############# Set directories ############ @@ -41,15 +44,19 @@ butternut_reorg_lonlat <- read.csv("Genetic_Analyses\\data_files\\after_reorg\\r ##load in mean lon and lat document butternut_mean_lon_lat <- read.csv("Genetic_Analyses\\data_files\\geographic_files\\butternut_coord_df.csv") -##create population name doc -butternut_24pop_names <- unique(butternut_reorg_lonlat$Pop) - ##name individuals in genind doc rownames(butternutgen_reorg@tab) <- butternut_reorg_lonlat$Ind -##name populations in genind doc +##population names document +butternut_24pop_names <- unique(butternut_reorg_lonlat$Pop) + +##name populations in genind levels(butternutgen_reorg@pop) <- butternut_24pop_names +##load range buffer for butternut +butternut_buffer <- readOGR(dsn = paste0(butternut_drive,"\\Genetic_Analyses\\data_files\\geographic_files") , + layer = "butternut_buffer") + ############################################################################ ####### Run Genetic Diversity Checks like LD, HWE, Null Alleles ########### ############################################################################ @@ -101,12 +108,48 @@ BN_ind <- BN_poppr[1:24, 2:3] BN_alleles <-bn_sumstats$pop.n.all/length(butternutgen_reorg@loc.n.all) BN_all_rich <- colMeans(allelic.richness(butternutgen_reorg)$Ar) +####Geographic analyses for each population +##calculate mean longitude and latitude for each population +butternut_mean_lon <- matrix() +butternut_mean_lat <- matrix() + +##loops for mean lat/lon +for(pop in butternut_24pop_names){ + + butternut_mean_lon[pop] <- mean(butternut_reorg_lonlat[butternut_reorg_lonlat$Pop == pop,][,3]) + +} + +for(pop in butternut_24pop_names){ + + butternut_mean_lat[pop] <- mean(butternut_reorg_lonlat[butternut_reorg_lonlat$Pop == pop,][,4]) + +} +##now combine into dataframes +butternut_coords_df <- cbind(butternut_mean_lon, butternut_mean_lat)[-1,] + +#project range extent buffer to the same extent as population lon/lat +butternut_buffer_trans <- sp::spTransform(butternut_buffer, "+proj=longlat +ellps=WGS84 +datum=WGS84") + +##now calculate distance to butternut range edge +butternut_dist <- dist2Line(butternut_coords_df, butternut_buffer_trans) + +##add regional names +butternut_regions <- c("New Brunswick","New Brunswick", "New Brunswick", "New Brunswick", "New Brunswick", + "New Brunswick","New Brunswick", "Ontario","Quebec","Ontario","Ontario","Quebec", + "United States", "United States", "United States", "United States", "United States", + "United States", "United States", "United States", "United States", "United States", + "United States", "United States") + ##create data frame -butternut_stat_df <- signif(cbind(butternut_mean_lon_lat[,2:3], BN_ind, BN_nall, BN_all_rich, BN_hexp),3) +butternut_stat_df <- cbind(butternut_regions, signif(cbind(butternut_coords_df[,c(1:2)], (butternut_dist[,1]/1000), + BN_ind, BN_nall, BN_all_rich, BN_hexp),3)) ##name columns and rows -rownames(butternut_stat_df) <- butternut_24pop_names -colnames(butternut_stat_df) <- c("Mean Longitude", "Mean Latitude", "Number of Individuals", "MLG","Number of Alleles", "Allelic Richness", "Expected Heterozygosity") +rownames(butternut_stat_df) <- c(1:24) +colnames(butternut_stat_df) <- c("Region","Mean Longitude", "Mean Latitude", "Distance to Range Edge (km)", + "Number of Individuals", + "MLG","Number of Alleles", "Allelic Richness", "Expected Heterozygosity") ##write out csv write.csv(butternut_stat_df, "Genetic_Analyses\\genetic_analyses_results\\butternut_stat_df.csv") diff --git a/genetic_analyses/data_files/geographic_files/butternut_buffer.cpg b/genetic_analyses/data_files/geographic_files/butternut_buffer.cpg new file mode 100644 index 0000000..a70e9b0 --- /dev/null +++ b/genetic_analyses/data_files/geographic_files/butternut_buffer.cpg @@ -0,0 +1 @@ +ANSI 1252 \ No newline at end of file diff --git a/genetic_analyses/data_files/geographic_files/butternut_buffer.dbf b/genetic_analyses/data_files/geographic_files/butternut_buffer.dbf index cebbd88..722bc4b 100644 Binary files a/genetic_analyses/data_files/geographic_files/butternut_buffer.dbf and b/genetic_analyses/data_files/geographic_files/butternut_buffer.dbf differ diff --git a/genetic_analyses/data_files/geographic_files/butternut_buffer.sbn b/genetic_analyses/data_files/geographic_files/butternut_buffer.sbn new file mode 100644 index 0000000..47cdd64 Binary files /dev/null and b/genetic_analyses/data_files/geographic_files/butternut_buffer.sbn differ diff --git a/genetic_analyses/data_files/geographic_files/butternut_buffer.sbx b/genetic_analyses/data_files/geographic_files/butternut_buffer.sbx new file mode 100644 index 0000000..c8f7a9e Binary files /dev/null and b/genetic_analyses/data_files/geographic_files/butternut_buffer.sbx differ diff --git a/genetic_analyses/data_files/geographic_files/butternut_buffer.shp b/genetic_analyses/data_files/geographic_files/butternut_buffer.shp index 50ceba4..f86a2e9 100644 Binary files a/genetic_analyses/data_files/geographic_files/butternut_buffer.shp and b/genetic_analyses/data_files/geographic_files/butternut_buffer.shp differ diff --git a/genetic_analyses/data_files/geographic_files/butternut_buffer.shx b/genetic_analyses/data_files/geographic_files/butternut_buffer.shx index f3d3e5e..ee5f4d9 100644 Binary files a/genetic_analyses/data_files/geographic_files/butternut_buffer.shx and b/genetic_analyses/data_files/geographic_files/butternut_buffer.shx differ diff --git a/genetic_analyses/data_files/geographic_files/butternut_buffer_map.jpg b/genetic_analyses/data_files/geographic_files/butternut_buffer_map.jpg new file mode 100644 index 0000000..2216f41 Binary files /dev/null and b/genetic_analyses/data_files/geographic_files/butternut_buffer_map.jpg differ diff --git a/genetic_analyses/genetic_analyses_results/butternut_stat_df.csv b/genetic_analyses/genetic_analyses_results/butternut_stat_df.csv index 4ce7770..239f5cd 100644 --- a/genetic_analyses/genetic_analyses_results/butternut_stat_df.csv +++ b/genetic_analyses/genetic_analyses_results/butternut_stat_df.csv @@ -1,25 +1,25 @@ -"","Mean Longitude","Mean Latitude","Number of Individuals","MLG","Number of Alleles","Allelic Richness","Expected Heterozygosity" -"31",-66.1,46.6,92,91,122,7.26,0.79 -"568",-67.7,46.7,110,109,131,7.89,0.83 -"1014",-65.6,45.7,112,112,143,8.19,0.821 -"7917",-67.7,46.1,102,102,139,8.15,0.835 -"9101113a",-66.4,45.9,227,225,144,7.71,0.819 -"9101113b",-66.7,46,126,126,140,7.99,0.828 -"151",-78.5,44.6,24,24,112,8.51,0.839 -"170",-77.1,45.4,20,20,90,7.36,0.78 -"125147",-79.4,44.1,35,35,131,9.18,0.852 -"126147",-80.1,44,55,55,143,8.91,0.848 -"171188",-75.5,45,61,61,135,8.33,0.834 -"APA12PACb",-79.3,41.6,114,114,168,9.16,0.846 -"BV",-85.9,35.9,136,136,157,8.41,0.835 -"BVT",-73,44.4,21,21,101,8.05,0.818 -"BVTGMVT2",-72.7,44,33,33,126,8.74,0.841 -"CNF",-88.6,45.5,27,27,86,6.7,0.774 -"FKN",-79.4,38.6,28,28,121,8.73,0.837 -"GMVT1",-72.6,43,21,21,105,8.31,0.815 -"MC",-86.1,37.2,61,61,155,9.31,0.851 -"OZ12",-91.3,37.1,121,121,165,8.74,0.83 -"SFNF12",-90.7,34.6,30,30,117,8.34,0.798 -"WHWI",-88.8,42.8,39,39,94,6.47,0.751 -"WWI",-89.1,44.5,18,18,83,6.8,0.757 -"VSH123",-78.5,38.4,22,22,121,9.23,0.839 +"","Region","Mean Longitude","Mean Latitude","Distance to Range Edge (km)","Number of Individuals","MLG","Number of Alleles","Allelic Richness","Expected Heterozygosity" +"1","New Brunswick",-66.1,46.6,95.8,92,91,130,7.51,0.799 +"2","New Brunswick",-67.7,46.7,110,24,24,112,8.51,0.839 +"3","New Brunswick",-65.6,45.7,161,20,20,90,7.36,0.78 +"4","New Brunswick",-67.7,46.1,168,110,109,138,8.07,0.834 +"5","New Brunswick",-66.4,45.9,168,112,112,151,8.49,0.826 +"6","New Brunswick",-66.7,46,160,102,102,146,8.32,0.838 +"7","New Brunswick",-78.5,44.6,285,35,35,135,9.41,0.857 +"8","Ontario",-77.1,45.4,180,55,55,151,9.22,0.857 +"9","Quebec",-79.4,44.1,359,61,61,141,8.53,0.837 +"10","Ontario",-80.1,44,373,227,225,152,8.03,0.829 +"11","Ontario",-75.5,45,257,126,126,148,8.34,0.834 +"12","Quebec",-79.3,41.6,517,114,114,170,9.19,0.846 +"13","United States",-85.9,35.9,451,136,136,159,8.42,0.835 +"14","United States",-73,44.4,316,21,21,101,8.05,0.818 +"15","United States",-72.7,44,273,33,33,126,8.74,0.841 +"16","United States",-88.6,45.5,186,27,27,86,6.7,0.774 +"17","United States",-79.4,38.6,353,28,28,123,8.8,0.838 +"18","United States",-72.6,43,237,21,21,105,8.31,0.815 +"19","United States",-86.1,37.2,573,61,61,155,9.31,0.851 +"20","United States",-91.3,37.1,328,121,121,167,8.76,0.83 +"21","United States",-90.7,34.6,278,30,30,118,8.37,0.798 +"22","United States",-88.8,42.8,454,39,39,94,6.47,0.751 +"23","United States",-89.1,44.5,291,18,18,84,6.88,0.758 +"24","United States",-78.5,38.4,274,22,22,121,9.23,0.839