Moved plotting maps to archive, added a new buffer map

genetic_analyses/3_plot_populations_map.R → 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",

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")
+
+

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")

genetic_analyses/data_files/geographic_files/butternut_buffer.cpg

@@ -0,0 +1 @@
+ANSI 1252

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