## PERMANOVA OF GUT CONTENT DATA # Written by: Jun Ying Lim and Susan Kennedy # From publication: # Kennedy, S. R., Lim, J. Y., Clavel, J., Krehenwinkel, H., and Gillespie, R. G. 2019. Spider webs, stable isotopes and molecular gut content analysis: Multiple lines of evidence support trophic niche differentiation in a community of Hawaiian spiders. Functional Ecology. #Set "main.dir" to your own directory containing subfolders: main.dir <- setwd() #Insert your file path in parentheses data.dir <- file.path(main.dir, "raw_data") fig.dir <- file.path(main.dir, "figures") res.dir <- file.path(main.dir, "results") #### loading packages #### library(vegan) #### load data #### # load order data # Note that this dataset is randomly subsampled to 5 indivs per web species, and 6 indivs per Spiny Leg species ord <- read.csv(file.path(data.dir, "gutES.csv"), header = TRUE, stringsAsFactors = FALSE) env_ord <- ord[ , 1:4] ord <- ord[ , -c(1:4)] # Broad stroke: sig diffs by clade? adonis(ord ~ env_ord$clade) # Sig diffs by species? adonis(ord ~ env_ord$species) # Pairwise PERMANOVA in web-builders acueur <- c("acuta", "eurychasma") ord_acueur <- ord[which(env_ord$species %in% acueur), ] env_acueur <- env_ord[which(env_ord$species %in% acueur), ] adonis(ord_acueur ~ env_acueur$species) acufil <- c("acuta", "filiciphilia") ord_acufil <- ord[which(env_ord$species %in% acufil), ] env_acufil <- env_ord[which(env_ord$species %in% acufil), ] adonis(ord_acufil ~ env_acufil$species) acuste <- c("acuta", "stelarobusta") ord_acuste <- ord[which(env_ord$species %in% acuste), ] env_acuste <- env_ord[which(env_ord$species %in% acuste), ] adonis(ord_acuste ~ env_acuste$species) acutri <- c("acuta", "trituberculata") ord_acutri <- ord[which(env_ord$species %in% acutri), ] env_acutri <- env_ord[which(env_ord$species %in% acutri), ] adonis(ord_acutri ~ env_acutri$species) eurfil <- c("eurychasma", "filiciphilia") ord_eurfil <- ord[which(env_ord$species %in% eurfil), ] env_eurfil <- env_ord[which(env_ord$species %in% eurfil), ] adonis(ord_eurfil ~ env_eurfil$species) eurste <- c("eurychasma", "stelarobusta") ord_eurste <- ord[which(env_ord$species %in% eurste), ] env_eurste <- env_ord[which(env_ord$species %in% eurste), ] adonis(ord_eurste ~ env_eurste$species) eurtri <- c("eurychasma", "trituberculata") ord_eurtri <- ord[which(env_ord$species %in% eurtri), ] env_eurtri <- env_ord[which(env_ord$species %in% eurtri), ] adonis(ord_eurtri ~ env_eurtri$species) filste <- c("filiciphilia", "stelarobusta") ord_filste <- ord[which(env_ord$species %in% filste), ] env_filste <- env_ord[which(env_ord$species %in% filste), ] adonis(ord_filste ~ env_filste$species) filtri <- c("filiciphilia", "trituberculata") ord_filtri <- ord[which(env_ord$species %in% filtri), ] env_filtri <- env_ord[which(env_ord$species %in% filtri), ] adonis(ord_filtri ~ env_filtri$species) stetri <- c("stelarobusta", "trituberculata") ord_stetri <- ord[which(env_ord$species %in% stetri), ] env_stetri <- env_ord[which(env_ord$species %in% stetri), ] adonis(ord_stetri ~ env_stetri$species) # Pairwise PERMANOVA in Spiny Legs brekam <- c("brevignatha", "kamakou") ord_brekam <- ord[which(env_ord$species %in% brekam), ] env_brekam <- env_ord[which(env_ord$species %in% brekam), ] adonis(ord_brekam ~ env_brekam$species) brequa <- c("brevignatha", "quasimodo") ord_brequa <- ord[which(env_ord$species %in% brequa), ] env_brequa <- env_ord[which(env_ord$species %in% brequa), ] adonis(ord_brequa ~ env_brequa$species) brewai <- c("brevignatha", "waikamoi") ord_brewai <- ord[which(env_ord$species %in% brewai), ] env_brewai <- env_ord[which(env_ord$species %in% brewai), ] adonis(ord_brewai ~ env_brewai$species) kamqua <- c("kamakou", "quasimodo") ord_kamqua <- ord[which(env_ord$species %in% kamqua), ] env_kamqua <- env_ord[which(env_ord$species %in% kamqua), ] adonis(ord_kamqua ~ env_kamqua$species) kamwai <- c("kamakou", "waikamoi") ord_kamwai <- ord[which(env_ord$species %in% kamwai), ] env_kamwai <- env_ord[which(env_ord$species %in% kamwai), ] adonis(ord_kamwai ~ env_kamwai$species) quawai <- c("quasimodo", "waikamoi") ord_quawai <- ord[which(env_ord$species %in% quawai), ] env_quawai <- env_ord[which(env_ord$species %in% quawai), ] adonis(ord_quawai ~ env_quawai$species) #load OTU data # Note that this dataset is subsampled to 5 indivs per web species, and 6 indivs per Spiny Leg species otu <- read.csv(file.path(data.dir, "otuES.csv"), header = TRUE, stringsAsFactors = FALSE) env_otu <- otu[ , 1:4] otu <- otu[ , -c(1:4)] # Broad stroke: sig diffs by clade? adonis(otu ~ env_otu$clade) # Sig diffs by species? adonis(otu ~ env_otu$species) # Pairwise PERMANOVA in web-builders acueur <- c("acuta", "eurychasma") otu_acueur <- otu[which(env_otu$species %in% acueur), ] env_acueur <- env_otu[which(env_otu$species %in% acueur), ] adonis(otu_acueur ~ env_acueur$species) acufil <- c("acuta", "filiciphilia") otu_acufil <- otu[which(env_otu$species %in% acufil), ] env_acufil <- env_otu[which(env_otu$species %in% acufil), ] adonis(otu_acufil ~ env_acufil$species) acuste <- c("acuta", "stelarobusta") otu_acuste <- otu[which(env_otu$species %in% acuste), ] env_acuste <- env_otu[which(env_otu$species %in% acuste), ] adonis(otu_acuste ~ env_acuste$species) acutri <- c("acuta", "trituberculata") otu_acutri <- otu[which(env_otu$species %in% acutri), ] env_acutri <- env_otu[which(env_otu$species %in% acutri), ] adonis(otu_acutri ~ env_acutri$species) eurfil <- c("eurychasma", "filiciphilia") otu_eurfil <- otu[which(env_otu$species %in% eurfil), ] env_eurfil <- env_otu[which(env_otu$species %in% eurfil), ] adonis(otu_eurfil ~ env_eurfil$species) eurste <- c("eurychasma", "stelarobusta") otu_eurste <- otu[which(env_otu$species %in% eurste), ] env_eurste <- env_otu[which(env_otu$species %in% eurste), ] adonis(otu_eurste ~ env_eurste$species) eurtri <- c("eurychasma", "trituberculata") otu_eurtri <- otu[which(env_otu$species %in% eurtri), ] env_eurtri <- env_otu[which(env_otu$species %in% eurtri), ] adonis(otu_eurtri ~ env_eurtri$species) filste <- c("filiciphilia", "stelarobusta") otu_filste <- otu[which(env_otu$species %in% filste), ] env_filste <- env_otu[which(env_otu$species %in% filste), ] adonis(otu_filste ~ env_filste$species) filtri <- c("filiciphilia", "trituberculata") otu_filtri <- otu[which(env_otu$species %in% filtri), ] env_filtri <- env_otu[which(env_otu$species %in% filtri), ] adonis(otu_filtri ~ env_filtri$species) stetri <- c("stelarobusta", "trituberculata") otu_stetri <- otu[which(env_otu$species %in% stetri), ] env_stetri <- env_otu[which(env_otu$species %in% stetri), ] adonis(otu_stetri ~ env_stetri$species) # Pairwise PERMANOVA in Spiny Legs brekam <- c("brevignatha", "kamakou") otu_brekam <- otu[which(env_otu$species %in% brekam), ] env_brekam <- env_otu[which(env_otu$species %in% brekam), ] adonis(otu_brekam ~ env_brekam$species) brequa <- c("brevignatha", "quasimodo") otu_brequa <- otu[which(env_otu$species %in% brequa), ] env_brequa <- env_otu[which(env_otu$species %in% brequa), ] adonis(otu_brequa ~ env_brequa$species) brewai <- c("brevignatha", "waikamoi") otu_brewai <- otu[which(env_otu$species %in% brewai), ] env_brewai <- env_otu[which(env_otu$species %in% brewai), ] adonis(otu_brewai ~ env_brewai$species) kamqua <- c("kamakou", "quasimodo") otu_kamqua <- otu[which(env_otu$species %in% kamqua), ] env_kamqua <- env_otu[which(env_otu$species %in% kamqua), ] adonis(otu_kamqua ~ env_kamqua$species) kamwai <- c("kamakou", "waikamoi") otu_kamwai <- otu[which(env_otu$species %in% kamwai), ] env_kamwai <- env_otu[which(env_otu$species %in% kamwai), ] adonis(otu_kamwai ~ env_kamwai$species) quawai <- c("quasimodo", "waikamoi") otu_quawai <- otu[which(env_otu$species %in% quawai), ] env_quawai <- env_otu[which(env_otu$species %in% quawai), ] adonis(otu_quawai ~ env_quawai$species)