One of the things we want to do in systematics with phylogenetic relationships is to understand how those areas are related historically. This helps us understand how organisms speciate, in other words, how new species arise. We do this through a method called vicariance biogeography. It's really, at base, very simple. We have four areas: Southeastern, eastern Queensland, Atherton Plateau, and Cape York. And we look at two groups of organisms, parrots and finches and we ask how are the species that are endemic in each of these areas related to one another? In this hypothetical example we see the parrot in the southeast of Australia is related to the parrot in East Queensland. They in turn are related to the parrot on the Atherton Plateau. They, in turn, are related to another species on the Cape York Peninsula.

Now we look at finches. Let's say we find a group of finches that has species endemic in those very same areas and we discover that finch 1 in the Southeast is related to Eastern Queensland finch 2. They in turn are related to finch 3 in Atherton and then finally they are related to finch 4 on Cape York. We see that these individual cladograms, as they're called, or phylogenetic hypotheses, show parallel patterns, congruent patterns, in area relationships. We can substitute the areas for these species and lo and behold we have a hypothesis that says at time one, Cape York split off first, dividing an ancestral population into two species, one on Cape York and the other in Atherton, East Queensland, and the Southeast.

Then there was some event ‹a barrier was created‹ that split Atherton away from Southeastern Australia and Eastern Queensland. And then finally Eastern Queensland and Southeastern Australia were separated. All this hypothesis requires is three geological, climatic, or ecological events to separate the areas and allow isolated populations to diverge into new species. We know that in Australia that those events happened, because, for instance, there was climate change that reduced the size of continuous moist areas to smaller areas (these areas of endemism) that were separated by drier regions. So, in summary, we delineate patterns of endemism. We construct phylogenetic hypothesis for the different groups of organisms - the clades of organisms that are in these areas - and then we look for congruence in their area-relationships.

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