## Body size at release, change in body size, and maturity analyses for juvenile ambystomatids ## Arianne Messerman, Raymond Semlitsch, and Manuel Leal ## June 2019 bod <- read.table("Body_Size2017.txt",header=T,colClasses="character") str(bod) bod$spp<-as.factor(bod$spp) bod$tag<-as.factor(bod$tag) bod$rel.svl<-as.numeric(bod$rel.svl) bod$rel.tl<-as.numeric(bod$rel.tl) bod$rel.mass<-as.numeric(bod$rel.mass) bod$june.svl<-as.numeric(bod$june.svl) bod$june.tl<-as.numeric(bod$june.tl) bod$june.mass<-as.numeric(bod$june.mass) bod$change.svl<-as.numeric(bod$change.svl) bod$change.tl<-as.numeric(bod$change.tl) bod$change.mass<-as.numeric(bod$change.mass) aman<-subset(bod,bod$spp=="AMAN") amma<-subset(bod,bod$spp=="AMMA") amte<-subset(bod,bod$spp=="AMTE") str(aman) str(amma) str(amte) all.caught<-ifelse(bod$june.svl>0,1,0) aman.caught<-ifelse(aman$june.svl>0,1,0) amma.caught<-ifelse(amma$june.svl>0,1,0) amte.caught<-ifelse(amte$june.svl>0,1,0) sum(all.caught, na.rm=TRUE)#49 sum(aman.caught, na.rm=TRUE)#21 sum(amma.caught, na.rm=TRUE)#11 sum(amte.caught, na.rm=TRUE)#17 x1<-mean(bod$rel.mass, na.rm=TRUE)#1.81g x2<-mean(bod$june.mass, na.rm=TRUE)#8.58g x3<-mean(bod$change.mass, na.rm=TRUE)#6.75g plot(bod$spp, bod$rel.mass, na.rm=TRUE) plot(bod$spp, bod$june.mass, na.rm=TRUE) plot(bod$spp, bod$change.mass, na.rm=TRUE) mean(bod$rel.mass, na.rm=TRUE) sd(bod$rel.mass, na.rm=TRUE) mean(bod$june.mass, na.rm=TRUE) sd(bod$june.mass, na.rm=TRUE) mean(bod$change.mass, na.rm=TRUE) sd(bod$change.mass, na.rm=TRUE) mod1<-aov(rel.mass~spp, bod) summary(mod1) TukeyHSD(mod1)#No significant difference mod2<-aov(rel.svl~spp, bod) summary(mod2) TukeyHSD(mod2)#AMTE longer than AMMA plot(bod$spp, bod$rel.svl, na.rm=TRUE) mean(aman$rel.svl, na.rm=TRUE) mean(amma$rel.svl, na.rm=TRUE) mean(amte$rel.svl, na.rm=TRUE) sd(aman$rel.svl, na.rm=TRUE) sd(amma$rel.svl, na.rm=TRUE) sd(amte$rel.svl, na.rm=TRUE) ((mean(amte$rel.svl, na.rm=TRUE)-mean(amma$rel.svl, na.rm=TRUE))*100)/mean(amte$rel.svl, na.rm=TRUE) mod3<-aov(rel.tl~spp, bod) summary(mod3) TukeyHSD(mod3)#AMAN=AMTE>AMMA plot(bod$spp, bod$rel.tl) mean(aman$rel.tl, na.rm=TRUE) mean(amma$rel.tl, na.rm=TRUE) mean(amte$rel.tl, na.rm=TRUE) sd(aman$rel.tl, na.rm=TRUE) sd(amma$rel.tl, na.rm=TRUE) sd(amte$rel.tl, na.rm=TRUE) mod4<-aov(june.mass~spp, bod) summary(mod4) TukeyHSD(mod4)#AMAN> AMTE and AMMA mean(amma$june.mass, na.rm=TRUE) mean(amte$june.mass, na.rm=TRUE) mean(aman$june.mass, na.rm=TRUE) sd(amma$june.mass, na.rm=TRUE) sd(amte$june.mass, na.rm=TRUE) sd(aman$june.mass, na.rm=TRUE) mod5<-aov(june.svl~spp, bod) summary(mod5) TukeyHSD(mod5)#AMAN>AMTE>AMMA plot(bod$spp, bod$june.svl) mean(aman$june.svl, na.rm=TRUE) mean(amma$june.svl, na.rm=TRUE) mean(amte$june.svl, na.rm=TRUE) sd(aman$june.svl, na.rm=TRUE) sd(amma$june.svl, na.rm=TRUE) sd(amte$june.svl, na.rm=TRUE) mod6<-aov(june.tl~spp, bod) summary(mod6) TukeyHSD(mod6)#AMAN> AMTE and AMMA plot(bod$spp, bod$june.tl) mean(aman$june.tl, na.rm=TRUE) mean(amma$june.tl, na.rm=TRUE) mean(amte$june.tl, na.rm=TRUE) sd(aman$june.tl, na.rm=TRUE) sd(amma$june.tl, na.rm=TRUE) sd(amte$june.tl, na.rm=TRUE) ###Calculate same models for change in body size to account for preexisting differences at release mod7<-aov(change.mass~spp, bod) summary(mod7) TukeyHSD(mod7)#AMAN> AMTE=AMMA (same result) mean(amma$change.mass, na.rm=TRUE) mean(amte$change.mass, na.rm=TRUE) mean(aman$change.mass, na.rm=TRUE) sd(amma$change.mass, na.rm=TRUE) sd(amte$change.mass, na.rm=TRUE) sd(aman$change.mass, na.rm=TRUE) mod8<-aov(change.svl~spp, bod) summary(mod8) TukeyHSD(mod8)#AMAN>AMTE=AMMA (AMTE not greater than AMMA) plot(bod$spp, bod$change.svl) mean(aman$change.svl, na.rm=TRUE) mean(amma$change.svl, na.rm=TRUE) mean(amte$change.svl, na.rm=TRUE) sd(aman$change.svl, na.rm=TRUE) sd(amma$change.svl, na.rm=TRUE) sd(amte$change.svl, na.rm=TRUE) mod9<-aov(change.tl~spp, bod) summary(mod9) TukeyHSD(mod9)#AMAN> AMTE = AMMA (Same results) plot(bod$spp, bod$change.tl) mean(aman$change.tl, na.rm=TRUE) mean(amma$change.tl, na.rm=TRUE) mean(amte$change.tl, na.rm=TRUE) sd(aman$change.tl, na.rm=TRUE) sd(amma$change.tl, na.rm=TRUE) sd(amte$change.tl, na.rm=TRUE) ########################################################### ##Maturity of animals euthanized in august mat<-read.csv("Ambystoma_Dissections_June2017.csv",header=T) str(mat) mat$mature<-as.factor(mat$mature) aman1<-subset(mat,mat$spp=="AMAN") amma1<-subset(mat,mat$spp=="AMMA") amte1<-subset(mat,mat$spp=="AMTE") mod10<-aov(svl~mature, mat) summary(mod10) #SVL does not differ by maturity mod11<-aov(svl~species, mat) summary(mod11) #SVL differs by species library(nlme) library(car) mod12<-glm(mature ~ svl * species, mat, family=binomial) summary(mod12) #With spp accounted for, no difference in svl by maturity anova(mod12) Anova(mod12) plot(mat$mature, mat$svl) mod12.0<-glm(mature~1, mat, family=binomial) anova(mod12, mod12.0) mod13<-lmer(svl ~ mature + (1|species), mat) summary(mod13) #With spp accounted for, no difference in svl by maturity Anova(mod13) plot(mat$mature, mat$svl) mod14<-lmer(svl ~ sex + (1|species), mat) summary(mod14) #With spp accounted for, no significant difference in svl by sex Anova(mod14, type="III") plot(mat$sex, mat$svl)