define.bioregions<-function(tax.dist,geo.dist,method="average",plot=TRUE)
{
	tax.tree<-hclust(tax.dist,method=method)
	geo.tree<-hclust(geo.dist,method=method)

	if(plot==T)
	{
		par(mfrow=c(1,2))
		plot(tax.tree)
		plot(geo.tree)
	}


	geo.phylo<-as.phylo(geo.tree)
	tax.phylo<-as.phylo(tax.tree)
	geo.phylo$edge.length<-geo.phylo$edge.length*2

	tax.subtrees<-subtrees(tax.phylo)
	tax.clusters<-vector(length=length(tax.subtrees),mode="list")
	for(i in 1:length(tax.clusters))
	{
		tax.clusters[[i]]<-sort(tax.subtrees[[i]]$tip.label)
	}





	node.heights<-sort(dateNodes(geo.phylo),decreasing=F)
	test.node.heights<-node.heights[which(names(node.heights)%in%as.character(1:length(geo.phylo$tip.label))==F)]

	for(i in 1:geo.phylo$Nnode)
	{

		if(i==1)
		{
			level<-1		
			height.ranges<-vector(length=1,mode="list")
			height.ranges[[1]]<-vector(length=2)
			height.ranges[[1]][1]<-0
	
			bioregions<-vector(length=1,mode="list")
			bioregions[[1]]<-1:length(geo.phylo$tip.label)
			names(bioregions[[1]])<-sort(geo.phylo$tip.label)

		}
		else
		{
			clust.node<-as.numeric(names(test.node.heights)[i-1])
			children<-sort(geo.phylo$tip.label[Descendants(geo.phylo, clust.node, type ="tips")[[1]]])
	
			for(j in 1:length(tax.clusters))
			{
				if(identical(tax.clusters[[j]],children)==T)
				{
					level<-level+1
					
					new.bioregions<-vector(length=level,mode="list")
					new.bioregions[1:length(bioregions)]<-bioregions
					new.bioregions[[level]]<-new.bioregions[[level-1]]				
	
					change<-children[which(new.bioregions[[level]][children]!=new.bioregions[[level]][children[1]])]
					
					for(k in 1:length(change))
					{
						new.bioregions[[level]][which(new.bioregions[[level]]>new.bioregions[[level]][change][k])]<-new.bioregions[[level]][which(new.bioregions[[level]]>new.bioregions[[level]][change][k])]-1
					}
					new.bioregions[[level]][change]<-new.bioregions[[level]][children[1]]				
					bioregions<-new.bioregions
	
					new.height.ranges<-vector(length=level,mode="list")
					new.height.ranges[1:length(height.ranges)]<-height.ranges
					new.height.ranges[[level]]<-vector(length=2)
					new.height.ranges[[level-1]][2]<-test.node.heights[i-1]
					new.height.ranges[[level]][1]<-test.node.heights[i-1]
					height.ranges<-new.height.ranges

		
				}
			}
		}
	}
	height.ranges[[length(height.ranges)]][2]<-max(test.node.heights)
		
	results<-list(bioregions,height.ranges)
	names(results)<-c("bioregions","height.ranges")	
	return(results)
}