I found this partial solution. At first I though it was what I was looking for but after further inspection it only works if you start at the top of the tree. It doesn't populate the Parent nodes if you start in the middle.
How to assign parent reference to a property in a child with AutoMapper
public static void ConfigureMappings()
{
Mapper.CreateMap<TreeNodeDto, Taxonomy>()
.AfterMap((s, d) =>
{
//WCF service calls to get parent and children
d.Children = Mapper.Map<TreeNodeDto[], TreeNode[]>(client.GetTreeChildren(s)).ToList();
foreach( var child in d.Children)
{
child.Parent = d;
}
}