So what are some of the assumptions in making phylogenetic trees?

One is we're looking at the summation of relationships over time.

I love this figure.

This comes from a paper by David Balm who's a friend of mine as well.

So here we have four butterflies.

You could add the parents there, and

you see that there's some relationships among them.

That this one has these two parents, this one has these two parents, etc.

You can add earlier generations, you get this web of relationships.

You can then look at the whole population; you see that this web gets more scattered.

You can look at the whole species, and

ultimately you get to this evolutionary tree.

So what we're looking at is the sum of relationships.

Think of it as the family tree of every organism that is ever lived.

It is possible to generate that family tree.

But it's going to be very, very, very dense.

There's going to be a lot of different relationships.

It's going to take a long, long time to go back to this evolutionary tree.

And that's essentially what is reflected in the evolutionary tree.

This summation of relationships over time.

It is reflecting the evolutionary history.

Most importantly just history.

We are assuming common ancestry of all the species that are being studied

are generating the phylogenetic tree.

That is an assumption that we're putting into there.

We're assuming there are clean splits into two or more taxa.

In other words the tree bifurcates, it splits.

It doesn't have to be just two it could actually split in three ways all at once.

But we're assuming these sorts of splits over time.

We're assuming the formation of new lineages.

We're also assuming that once species do diverge,

they don't actually come back together.

OKay.

So here's a sample evolutionary tree that I'd like you to look at,

as well as some terms that I'd like you to know.

So, first just look at the tree itself.

And, this is a tree that you've seen before, so we have the wolf and the fox,

which are canines, or sort of in the dog family I guess you'd say.

We have our cat, wolf and fox which are all carnivores.

And, we have our human, cat, wolf and fox which are all mammals.

So what are the branches of this tree?

Well, the branches of this tree are basically

these lines coming out from a point.

These are all branches, just like if you're looking at a actual plant tree.

So these are all branches along the evolutionary tree.

The nodes.

Nodes are intersecting points of branches.

So right here we have an intersection between the branch going to cat the branch

going to the canines.

Here we have a node that intersects the branch going to wolves.

Oh I'm sorry the branch going to foxes and the branch going to wolves.

And of course we have a node back here.

So what do these nodes represent?

Well let's think about this for a second.

The nodes represent the branching

point where you have a lineage that goes on to evolve into the modern fox, and

a branch that goes on to evolve into the modern wolf.

So this is the point where foxes and

wolves share their most recent common ancestor.

So back here, those entities that

eventually would have offspring that go on to become foxes and wolves were the same.

They had a single ancestor at the node and anytime before that node.

Same over here, at this point in time the evolutionary tree.

Some individuals may have descendants that go on to be cats, and

some descendants that go on to be wolves or foxes.