Significant presence/absence of plant species
I am not quite sure what you mean by "significant presence". If you observe any non-zero number of plants of a given species in a cluster, then the rate at which this plant occur in this cluster is different from zero. No stats required to infer such thing. You should clarify your post.

Logistic Regression

It sounds like you would like to do a logistic regression with presence / absence as response and the nominal variable cluster as solo explanatory variable. In R you could for example do something like

# Dummy data
d = data.frame(
 presence = sample(0:1, 120, replace=TRUE),
 cluster =  rep(LETTERS[1:4], 30)
)

# Logistic Regression
m = glm(data= d, formula = presence ~ cluster, family = binomial(link="logit"))
summary(m)


You can find here another example of logistic regression in R

Phylogenetic signal and pseudoreplication

You might want to make sure to decorrelate your variable from the phylogeny to avoid pseudoreplication. There, the solution you might end up going with will depend on your genetic data. If you have a genetic PCA, you could go with using the first 2 axes as simple covariates in a type I sum of squares kind of model (which is probably the default of the logistic regression I performed above). If you have a kinship matrix you could use it with lmekin or MCMCglmm (see here for adding a kinship matrix). There would have many different statistical tools for such decorrelation depending on your data.