Adegenet PCA - location in color, species by shape

General
1

I am currently using a script that lets me input a fasta file, add a population trait, and plot a PCA.
I now need to modify this script so that I can input location and species information and plot a PCA with both of those factors. I would like my location to be colorful, and my species to be different shapes.
Here is the script I have so far (I put in individual population descriptors for all of my sequences)

library("ape")
library("adegenet")
setwd("~/Documents/R")
MyDNA <- read.FASTA("NoKIRGMB.fas")
MyDNA

class(MyDNA)
MyDNA <- as.matrix(MyDNA)

obj <- DNAbin2genind(MyDNA, polyThres=0.01)

sum(is.na(obj$tab))
X <- scaleGen(obj, NA.method="mean")

###Add Pops
pop(obj) <- c(INPUT)

col <- c("M" = "deepskyblue2" , "B" = "yellow1" , "O" = "springgreen")

pca1 <- dudi.pca(X,cent=FALSE,scale=FALSE,scannf=FALSE,nf=3)
barplot(pca1$eig[1:50],main="PCA eigenvalues", col=heat.colors(50))

pca1

s.class(pca1$li, pop(obj),xax=1,yax=2 , col=transp(col,.9), axesell=FALSE,
cstar=0, cpoint=1.3, grid=FALSE)
title("PCA\naxes 1-2")

s.class(pca1$li, pop(obj),xax=1,yax=3, col=transp(col,.9), axesell=FALSE,
cstar=0, cpoint=1.3, grid=FALSE)
title("PCA\naxes 1-3")

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