WEBVTT

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Prof: Very good.

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So today we're going to talk
about phylogenetics and

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systematics, and the lecture has
this kind of structure.

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I'll remind you of what the
Tree of Life looks like.

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Then I will motivate the
lecture basically by giving you

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some surprising recent results
from molecular systematics,

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and then I will go into
basically what phylogenetic

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concepts are and how to build a
phylogenetic tree.

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I won't do this in great
detail, but I hope I do enough

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of it so that you at least have
a good feel for the issues that

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are involved when you do this.

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So this is the same picture of
the Tree of Life that I used

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earlier in the course,
and basically it shows you that

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since about 3.5 billion years
ago,

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there have been three large
clades that have developed.

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<<Technical
Adjustments>>

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Take a moment and look at this
picture,

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and look at the next one--which
is a--

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this next one is essentially a
blowup of what's been going on

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since about here--
and think about how much that

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tells us about biology.

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It provides a very basic
structure, the structure of

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relationships.

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It tells you which things
shared common ancestors,

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and why we might expect them to
be one way rather than another

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way.

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It sets up thousands of
comparisons in our minds about

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questions that we might ask.

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It provides an extremely
useful, overarching structure.

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But the question is,
how did phylogenetic biologists

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actually get this picture,
and are they still changing it?

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And the answer is:
they got it with the methods of

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inference that I'm going to
sketch today,

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and they're still changing it.

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It's not written in stone and
it's been changing ever since

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the first time somebody tried to
write it down.

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So these things are working
hypotheses,

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and we are able to get a better
and better refinement of them as

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new information comes in,
but there are significant

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changes.

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Now this is what Darwin had to
say in the Origin about

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the Tree of Life.

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It's a truly wonderful fact,
the wonder of which we are apt

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to overlook from familiarity,
that all animals and all

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plants, throughout all time and
space,

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should be related to each other
in groups.

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And he goes on about how these
groups are hierarchical.

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He said, "The affinities
of all the beings of the same

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class have sometimes been
represented by a great tree.

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I believe this simile is
largely the truth."

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So in this beautiful Victorian
prose, Darwin rhapsodizes a bit

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about the Tree of Life,
and it was the only picture he

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had in his book.

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Okay?

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So he thought it was real
important.

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He made a sketch of it,
and by it, by this sketch,

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he meant to indicate that a lot
of things had gone extinct and

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that through ancestry and shared
common ancestry you could define

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relationship.

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Now he could see immediately
that the tree isn't given,

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it should be discovered.

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He said, "Our
classifications will come to be,

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as far as they can be so made,
genealogies;"

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So they will reflect what
actually happened in terms of

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evolutionary history to generate
relationship;

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"and then they will truly
give what may be called the plan

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of creation.

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The rules for classifying will
no doubt become simpler when we

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have a definite object in view.

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We possess no pedigree or
armorial bearings."

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Okay?

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That's mid-nineteenth century
code for there's no barcode on

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the species.

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Okay?

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They're not wearing their name
on the forehead and they're not

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telling you who they're related
to.

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So we have to discover and
trace these diverging lines.

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Well it actually has taken a
long time for phylogenetics to

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settle on clear logic and clear
methods.

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Up until about oh somewhere
around 19--

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the ideas were there but they
weren't really implemented until

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about 1965 to 1970,
and there ensued a huge

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controversy that lasted for
about twenty years.

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And now that all--the dust has
settled and that seems to be in

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the past,
but many people actually my age

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are still marked by it,
because we witnessed it.

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And I'm now going to more or
less summarize what came out of

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it,
but I just want to signal to

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you that this was,
in the not very distant past,

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an extremely controversial area
of science,

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and that it was revolutionized
both by the advent of DNA

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sequence data,
and by the development of

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powerful mathematical and
computer methods for determining

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relationship;
and there was an argument about

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which ones we should use.

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So the first step in that is
taken by a guy named Zimmermann,

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and it's just sketched here,
and it seems very simple:

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Sharing a more recent common
ancestor defines relationship.

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So magnolias and apple trees
are more closely related to each

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other than either is to a
gingko,

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because this point on the tree
is later in time,

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and connects them,
than this point on the tree,

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which connects them to gingkoes.

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It seems like a very simple
idea.

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It wasn't really clearly
articulated until Zimmermann

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laid it down as a principle in
1931.

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Now some of these concepts
you've already been through.

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So I'm going to simply mention
these names again,

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just so that they get repeated
and start becoming part of your

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own vocabulary.

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Monophyletic is a group that
contains all of the descendants

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from a single common ancestor
and nothing that is not

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descended from that common
ancestor;

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paraphyletic groups are groups
that do not contain all of the

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species descended from the most
recent common ancestor;

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and polyphyletic groups really
are a hodgepodge of stuff that

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shouldn't be in that sort of
bin,

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under that category at all,
because they have--

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basically independent
evolutionary lines are being

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incorrectly lumped together.

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The basis of a lot of this
inference is the concept of

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homology,
and homology and analogy--I'll

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repeat them in a minute when we
get to some slides that

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illustrate them--
but they were defined by

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Richard Owen in the early
nineteenth century,

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before Darwin's Origin of
Species.

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He was a great morphologist,
in London,

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and basically the idea of
homology is that a trait is

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identical in two or more species
because they are descended from

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a common ancestor.

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So they got it because their
ancestor had it.

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And homoplasy,
or convergence,

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is similarity for any reason
other than common ancestry.

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So convergence in morphological
traits, mutation to the same

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sequence, in DNA,
will lead to homoplasy.

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So homology is helpful,
and homoplasy is confusing in

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determining phylogenies.

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So here's a good monophyletic
group.

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Okay? This is the dogs.

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And here the dogs are.

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Here's Canis and Lycaon--so the
Lycaon is the African Hunting

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Dog--and their closest relatives
are the South American wolves.

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Canis, by the way,
Canis--the timber wolf is in

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the genus Canis,
and all domestic dogs are

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descended from wolves,
which is a nice example of

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really rapid evolution;
take a wolf,

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turn it into a Saint Bernard
and a Chihuahua.

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I give you 5000 years.

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Can you do it?

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Well it takes pretty tough
breeding to do that,

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but you can.

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And, by the way,
I had a colleague--Armand

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Kuris, who's at Santa Barbara,
decided he was going to create

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his own race;
he wanted to create the ugliest

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dog in the world.

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He was going to name it the
Louisiana Swamp Dog.

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It took him six generations.

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I mean, this dog is really ugly.

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>

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But it's registered with the
American Kennel Club.

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So you can do rapid breeding
with dogs.

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That's, of course,
on a timescale up here that you

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couldn't even fit onto that
little white line at the top of

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the picture.

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Interestingly,
all this stuff over here is

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extinct.

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There are a few little marks
here that are kind of

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interesting.

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Out here, on the branch going
up to the Caninae,

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is digitigrady,
which means that at that point

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they started chasing after
things that were running fast,

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and evolution,
just like it did with horses,

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started to cause them to be
selected to run on their toes.

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So they got longer legs by
running on their toe tips,

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rather than on the pads of
their feet directly.

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And bone cracking came in right
about here, so they could get

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the marrow out of bones.

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That's a good monophyletic
group.

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You probably can't see it up
there.

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I'll give you a little bit of
timeline.

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The whole thing starts taking
off about 40,000,000 years ago,

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in the Eocene.

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And Canis, the dog genus
itself, is about 5,000,000 years

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old;
it's about as old as Homo.

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Okay, here are some
paraphyletic groups.

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Reptiles is paraphyletic.

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Okay?

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It's got turtles,
lizards and crocodiles in it,

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but it doesn't have the birds.

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So reptiles is an inaccurate
term.

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This is the monophyletic
group--lizards,

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crocodiles and birds--and we
don't have an everyday language

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term for it.

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Crocodiles, by the way,
build nests and guard them,

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and when the baby crocodiles
hatch out,

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they cheep like birds:
"cheep,

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cheep."

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So there are--this relationship
between crocs and birds is well

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established.

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Here's a polyphyletic group.

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If we define a group called the
homoeothermic tetrapods,

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it contains the birds and the
mammals.

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But look at all of the things
that are more closely related to

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the birds than the mammals are.

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So if we were to define the
birds and the mammals as a

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group,
it would be a false group,

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because phylogenetically the
birds have many things which are

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more closely related to them
than the mammals do.

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And this group is polyphyletic.

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Okay?

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It has contributions from two
different sources.

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Another good example of a
polyphyletic group would be if

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you decided to link together all
of the things that look like

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cactuses in Africa and South
America.

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The ones in South America are
cactuses, but the ones in Africa

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are euphorbs;
they look just like cactuses.

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There's a nice example in the
Peabody Museum.

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You can look at them sitting
next to each other.

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Okay?

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That's a polyphyletic group.

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They are convergent,
they came together.

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Similarly, the homeothermy in
the birds and mammals is

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convergent.

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The ancestor back here did not
have warm blood.

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It evolved twice,
once in the line to mammals and

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once in the line to birds.

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I know there were some-warm
blooded dinosaurs,

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but that was later.

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Warm-bloodedness probably came
in, in this line,

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about here somewhere;
don't know exactly.

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Then this central concept,
homology.

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Here are the forelimbs of
turtles, humans,

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horses, birds,
bats and seals.

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So we've got some stuff here
that's spanning quite a bit of

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the tetrapods;
vertebrates that are living on

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land.

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And you can see that it's
possible to match up sections of

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these structures,
all the way through.

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And actually if you study that,
and you realize that they were

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all in an ancestral condition
together,

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you can see how evolution has
changed their proportions,

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changed their thickness,
but it hasn't changed their

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spatial relationships to each
other.

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And, in fact,
if you go through the

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development,
you'll discover that the same

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nerves coming out of the
backbone are running to the same

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parts of the limb,
and all of those conditions

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have been held together,
over evolutionary time.

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And if you look at the HOX
genes that are controlling their

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development,
you can see,

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as you saw in a lecture a
little bit earlier,

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that the DNA sequences in the
HOX genes,

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that are telling it whether to
make a humerus,

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a radius, an ulna or digits,
are actually homologous in

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their DNA sequence as well.

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So there's a molecular homology
that underlies the morphological

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homology.

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And if you look at molecular
sequences,

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here's a gene called aniridia
in humans,

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and a gene called eye-less in
fruit flies,

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and only six--these are not DNA
sequences,

13:54.330 --> 13:58.540
this is protein sequence;
so these are amino acids--only

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six of the sixty amino acids are
different.

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The two sequences are 90%
identical.

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There are search algorithms,
like BLAST, that go out and

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look for these sorts of
similarities.

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So that if you get a candidate
gene or a candidate protein

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sequence,
it's possible simply to put a

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search term in,
to a search engine,

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and have other genes from other
species pop up.

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So you can look for molecular
homology that way.

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A good molecular homology is
the fruit fly homeobox complex

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and the human HOX complex--
we talked about this

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earlier--where the sequence of
the genes along the chromosome,

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and the parts of the body that
are being controlled by those

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genes developmentally,
are similar in humans and in

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fruit flies,
and actually unite everything

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that you see here.

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So this sort of thing is a
signal of shared ancestry,

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and it's the kind of molecular
information used to construct

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the broader Tree of Life.

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So this is something that is
linking together arthropods,

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annelids, mollusks,
echinoderms and chordates.

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Now analogy.

15:13.639 --> 15:18.689
Analogy or convergence is a
misleading kind of information,

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because that means that natural
selection has taken things that

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were evolutionarily independent,
and which have sister groups,

15:28.457 --> 15:32.187
have relatives,
that don't look anything like

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this,
and then shaped both of those

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things to come together to a
common form.

15:38.000 --> 15:42.040
So the dolphin and the
ichthyosaur have a very similar

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fusiform body,
and this is because of strong

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selection to swim rapidly in the
ocean and to chase down fish and

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squid;
which they both did.

15:51.350 --> 15:55.110
And the analogy goes deeper
than that.

15:55.110 --> 15:59.250
As you probably know,
the dolphin has live birth,

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it's viviparous.

16:00.799 --> 16:02.659
So is the ichthyosaur.

16:06.860 --> 16:09.510
in Germany, and look at the
world's largest collection of

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pregnant ichthyosaurs,
you can see an ichthyosaur that

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was giving birth at the point
when it was fossilized.

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And they often had twins,
or triplets.

16:23.168 --> 16:28.798
So the definition of analogy is
two things that look very much

16:28.798 --> 16:31.638
alike,
even though they have many

16:31.638 --> 16:36.038
relatives that look quite
different and are distant on the

16:36.041 --> 16:36.661
tree.

16:36.658 --> 16:40.298
So the dolphin is more closely
related to a kangaroo than it is

16:40.304 --> 16:43.264
to an ichthyosaur,
and an ichthyosaur is more

16:43.259 --> 16:47.099
closely related to a hummingbird
than it is to a dolphin;

16:47.100 --> 16:48.480
nevertheless they look similar.

16:48.480 --> 16:49.570
So that's analogy.

16:49.570 --> 16:52.930


16:52.928 --> 16:59.468
So once people got their DNA
sequences and their logic under

16:59.470 --> 17:02.300
control,
and they started doing a lot of

17:02.302 --> 17:04.702
molecular systematics,
they discovered some

17:04.700 --> 17:07.290
relationships that were kind of
surprising,

17:07.288 --> 17:09.738
because analogy,
convergence,

17:09.740 --> 17:12.980
had been covering up
relationship,

17:12.980 --> 17:17.260
or because evolution had so
radically changed the external

17:17.255 --> 17:21.425
appearance of these creatures,
that it was very difficult to

17:21.430 --> 17:23.190
see who they were related to.

17:23.190 --> 17:25.520
Here are a few of these
insights.

17:25.519 --> 17:29.399
I'll bet that if I ask Alex or
Jeremy or Katie or the other

17:29.396 --> 17:32.736
teaching fellows if they've got
a favorite one,

17:32.740 --> 17:35.680
that they could probably come
up with others as well.

17:35.680 --> 17:37.800
Maybe I will in a minute;
so start thinking.

17:37.799 --> 17:39.859
Okay?

17:39.858 --> 17:44.208
Pentastomids were a mysterious
group of creatures,

17:44.212 --> 17:49.102
and they turn out to be closely
related to fish lice.

17:49.098 --> 17:52.038
I'll show you a pentastomid in
a minute.

17:52.038 --> 17:54.528
There used to be a group called
carnivorous plants,

17:54.529 --> 17:56.109
the pitcher plants and the
sundews,

17:56.108 --> 17:58.208
and people thought that the
pitcher plants and the sundews

17:58.214 --> 17:58.774
were related.

17:58.769 --> 18:02.399
These are plants that are
adapted to living under very low

18:02.403 --> 18:05.703
nitrogen conditions,
and they need nitrogen to make

18:05.696 --> 18:08.566
all of their proteins,
and they get it by killing

18:08.568 --> 18:09.978
insects and other things.

18:09.980 --> 18:13.240
Some of them can even kill a
small frog.

18:13.240 --> 18:17.140
So it was thought that it was
likely that this was a natural

18:17.144 --> 18:20.914
group and that they had all
evolved these capacities in an

18:20.914 --> 18:23.484
ancestral condition,
and that they were all related

18:23.482 --> 18:23.942
to each other.

18:23.940 --> 18:24.510
But they're not.

18:24.509 --> 18:27.969
It's happened several times.

18:27.970 --> 18:30.830
It wasn't really clear where
the whales had come from.

18:30.828 --> 18:34.708
One might have thought that
well maybe whales are related to

18:34.711 --> 18:37.931
seals, or perhaps they're
related to other aquatic

18:37.934 --> 18:39.584
mammals, like otters.

18:39.578 --> 18:41.398
But seals and otters are
carnivores,

18:41.400 --> 18:44.730
and it turns out that whales,
including the toothed whales,

18:44.730 --> 18:47.550
the active carnivorous dolphins
and sperm whales,

18:47.549 --> 18:49.729
are ungulates.

18:49.730 --> 18:50.010
Okay?

18:50.012 --> 18:53.472
So there was an ungulate that
used go around eating plants and

18:53.472 --> 18:56.652
it went into the water and it
started to eat all kinds of

18:56.648 --> 18:57.668
other things.

18:57.670 --> 18:58.040
Okay?

18:58.038 --> 19:01.808
It stopped eating plants and it
started eating fish,

19:01.805 --> 19:05.475
squid;
and some of them eat a lot of

19:05.479 --> 19:08.799
crustacea, if they filter feed.

19:08.799 --> 19:10.469
Sycamores.

19:10.470 --> 19:14.190
Sycamores, or plane trees,
are the classic tree which is

19:14.189 --> 19:16.759
used to decorate the European
plaza.

19:16.759 --> 19:17.279
Okay?

19:17.281 --> 19:23.141
If you like to sit out in the
summer, in Italy or France,

19:23.137 --> 19:29.197
and watch the people go by,
you're probably sitting under a

19:29.202 --> 19:31.192
sycamore tree.

19:31.190 --> 19:34.220
And they have a leaf that looks
like a maple leaf,

19:34.219 --> 19:37.679
and if you just look at a
sycamore--and by the way it has

19:37.680 --> 19:41.220
a kind of blotchy bark;
so it has sort of white bark

19:41.215 --> 19:44.455
but with blotches on it--
if you just look at a sycamore

19:44.464 --> 19:46.744
and you just look at the shape
of the leaf,

19:46.740 --> 19:48.050
you might think,
"Oh, these are related to

19:48.051 --> 19:48.481
maples."

19:48.480 --> 19:49.620
They aren't at all.

19:49.618 --> 19:54.308
They are in fact more closely
related to water lilies.

19:54.308 --> 19:56.958
Now those are some pretty
radical surprises.

19:56.960 --> 19:59.580
Those are things that were
buried in the DNA sequences,

19:59.578 --> 20:02.298
that were not apparent in the
morphology,

20:02.298 --> 20:05.828
and they are not only testimony
to the power of molecular

20:05.825 --> 20:08.795
systematics,
they are testimony to the power

20:08.798 --> 20:12.858
of natural selection to change
the shape of things in ways that

20:12.858 --> 20:15.868
are profoundly altering and
create all sorts of

20:15.871 --> 20:18.491
mis-impressions about
relationship.

20:18.490 --> 20:20.920
So here are some pentastomids.

20:20.920 --> 20:25.200
This set of pentastomid worms
here is actually crawling across

20:25.195 --> 20:27.575
the roof of a crocodile's mouth.

20:27.578 --> 20:32.638
They tend to live in the noses
of crocodiles and dogs.

20:32.640 --> 20:36.170
They don't tend to live in
humans, this is one of those

20:36.165 --> 20:40.075
yucky, creepy-crawlies that you
don't have to worry about too

20:40.084 --> 20:41.264
much yourself.

20:41.259 --> 20:44.489
But it looks--actually it looks
something like a beetle larva,

20:44.487 --> 20:47.707
or something like that;
it looks kind of like a

20:47.711 --> 20:48.541
mealworm.

20:48.538 --> 20:53.818
But look, it's got segments in
it, and it has some kind of

20:53.815 --> 20:56.125
funny structure inside.

20:56.130 --> 20:59.470
It turns out that it's most
closely related to this thing.

20:59.470 --> 21:06.620
Here is a fish louse on the
outside of a triggerfish,

21:06.618 --> 21:09.918
and this is an isopod.

21:09.920 --> 21:13.030
Pentastomids are related to
fish lice.

21:13.028 --> 21:17.458
They are not related to
beetles, or to nematode worms,

21:17.461 --> 21:19.971
or to a lot of other things.

21:19.970 --> 21:23.190
And, in fact,
they're nested within the fish

21:23.185 --> 21:23.705
lice.

21:23.710 --> 21:28.030
So evolution took something
that looked like that and turned

21:28.030 --> 21:29.130
it into that.

21:29.130 --> 21:33.200
And like a lot of things,
this probably was accomplished

21:33.201 --> 21:37.051
by things like crocodiles eating
things like fish.

21:37.048 --> 21:40.278
And when the parasite that was
living on the fish got ingested

21:40.279 --> 21:42.029
by the crocodile,
it was more or less,

21:42.025 --> 21:44.355
"Oh my heavens,
how am I going to adapt to the

21:44.362 --> 21:45.262
crocodile?"

21:45.259 --> 21:48.699
Well if it could fall of the
fish and stay in the mouth of

21:48.700 --> 21:51.960
the crocodile and crawl up its
nose, it can survive;

21:51.960 --> 21:53.430
which essentially is what these
things did.

21:53.430 --> 21:56.930


21:56.930 --> 21:59.650
Here are two carnivorous plants.

21:59.650 --> 22:02.140
Okay? They are polyphyletic.

22:02.140 --> 22:05.300
Pitcher plants have evolved
independently at least three

22:05.299 --> 22:07.669
times;
flypaper traps at least five

22:07.672 --> 22:08.152
times.

22:08.150 --> 22:11.090
There are two groups of pitcher
plants that are sister groups to

22:11.092 --> 22:14.852
two clades of flypaper traps;
but others have other sister

22:14.848 --> 22:15.508
groups.

22:15.509 --> 22:18.559
So these are actually deeply
cool plants.

22:18.558 --> 22:22.548
The world hotspot of pitcher
plants,

22:22.548 --> 22:25.818
if you have a deep desire to go
collect a lot of pitcher plants,

22:25.818 --> 22:31.848
is Borneo, and it is no
coincidence that Borneo is an

22:31.854 --> 22:37.054
island that has very,
very nitrogen poor soil,

22:37.048 --> 22:42.568
and the trees and all the
shrubs that live on Borneo,

22:42.568 --> 22:46.348
many of them have special
adaptations to dealing with this

22:46.348 --> 22:48.138
low nutrient environment.

22:48.140 --> 22:53.110
Things like flypaper and the
sundews, the flypaper traps,

22:53.105 --> 22:57.355
they often live in bogs,
which also are extremely

22:57.363 --> 22:58.963
nutrient poor.

22:58.960 --> 23:02.480
If you go to Bethany Bog here,
you will find these living in

23:02.482 --> 23:03.322
Bethany Bog.

23:03.318 --> 23:07.298
It's a kettle lake that was
left after the glaciers

23:07.295 --> 23:08.245
retreated.

23:08.250 --> 23:10.470
There's a mat of vegetation
growing out over it,

23:10.469 --> 23:13.209
which means that in the middle
of it, the plants are living

23:13.208 --> 23:14.198
right over water.

23:14.200 --> 23:19.230
The water is nutrient poor,
and there are flypaper traps

23:19.229 --> 23:23.709
catching flies out there,
to get their protein.

23:23.710 --> 23:27.760
This is a chunk of the Tree of
Life that shows you the

23:27.756 --> 23:29.966
radiation of the ungulates.

23:29.970 --> 23:33.290
And you can see that both the
toothed and the baleen whales

23:33.291 --> 23:36.901
are nested within the ungulates,
and their closest relatives are

23:36.900 --> 23:37.760
the hippos.

23:37.759 --> 23:41.319
So you should think that the
ancestor of the hippo went into

23:41.316 --> 23:44.936
the ocean,
probably about 35,000,000 years

23:44.940 --> 23:46.870
ago,
and right here,

23:46.865 --> 23:50.435
marked on the tree,
are some of the genes which

23:50.442 --> 23:53.752
have changed along these
particular lines and which are

23:53.748 --> 23:55.828
signals of those relationships.

23:55.829 --> 24:00.809


24:00.808 --> 24:05.478
So the take-home point is that
appearances are deceptive and

24:05.480 --> 24:07.620
detective work is needed.

24:07.618 --> 24:09.918
Now how do you do the detective
work?

24:09.920 --> 24:11.420
How do you build a phylogenetic
tree?

24:11.420 --> 24:16.100


24:16.098 --> 24:18.408
Before I do that,
do you guys have any favorite

24:18.411 --> 24:21.361
sort of phylogenetic--you have;
Jeremy what's yours?

24:21.358 --> 24:22.828
Teaching Fellow:
Yes, gnetales,

24:22.827 --> 24:25.167
not being related to flowering
plants, for me personally.

24:25.170 --> 24:27.760
Because gnetales have double
fertilization,

24:27.759 --> 24:30.719
which is a very interesting
innovation of plants,

24:30.721 --> 24:32.511
or flowering plants have.

24:32.509 --> 24:35.529
And actually ginkgos are
gnetales in the gymnosperms,

24:35.531 --> 24:36.521
the pine trees.

24:36.519 --> 24:40.569
That personally--we learned
that from Burleigh and Mathews .

24:40.568 --> 24:42.148
Prof: So how recently
was that discovered?

24:42.150 --> 24:43.640
Teaching Fellow:
Like three years ago;

24:43.640 --> 24:44.240
three or four years ago.

24:44.240 --> 24:46.350
Prof: Okay,
see, the tree keeps changing.

24:46.349 --> 24:47.289
It's a moving target.

24:47.289 --> 24:48.849
It gets better.

24:48.848 --> 24:52.118
The basic branches are not
moving too much,

24:52.116 --> 24:56.626
but out there on the tips
there's still a lot of action.

24:56.630 --> 24:57.520
So how do you get it?

24:57.519 --> 24:58.839
How do you build a phylogenetic
tree?

24:58.839 --> 25:04.709
Well this is an important point.

25:04.710 --> 25:05.790
You need to have some
characters;

25:05.789 --> 25:07.349
so those are states of traits.

25:07.348 --> 25:09.838
They could be nucleotide
sequences.

25:09.838 --> 25:13.158
It could be whether the thing
has scales or fur,

25:13.159 --> 25:17.679
or it could be whether it has a
three or four-chambered heart.

25:17.680 --> 25:19.760
It could be a lot of things.

25:19.759 --> 25:23.609
So you need characters,
and they need to have different

25:23.607 --> 25:24.247
states.

25:24.250 --> 25:29.260
And the characters that are
informative are shared derived

25:29.257 --> 25:30.397
characters.

25:30.400 --> 25:33.210
I will go into this issue with
a full slide,

25:33.209 --> 25:37.079
because this is a key point;
the characters that give you

25:37.077 --> 25:41.367
phylogenetic information are the
ones that everything in a group

25:41.369 --> 25:44.829
shares with each other,
and it's different from the

25:44.828 --> 25:45.428
ancestor.

25:45.430 --> 25:51.130


25:51.130 --> 25:55.580
Well, you can only define
derived by comparison with

25:55.582 --> 25:56.632
primitive.

25:56.630 --> 25:56.940
Okay?

25:56.942 --> 26:00.642
So primitive is like what it
used to be, and derived is what

26:00.635 --> 26:04.015
it is now, somewhere on the
tree, and you can't do that

26:04.017 --> 26:05.267
without a tree.

26:05.269 --> 26:07.309
So there's kind of a paradox.

26:07.308 --> 26:10.688
You don't have a tree,
and if you don't have it,

26:10.690 --> 26:13.760
you don't have a way to
determine what came first,

26:13.759 --> 26:16.969
and therefore you don't know
about character polarization.

26:16.970 --> 26:21.890
Character polarization means
knowing which state is primitive

26:21.892 --> 26:26.922
and which is derived;
that polarizes that series of

26:26.915 --> 26:28.425
trait states.

26:28.430 --> 26:31.140
So there are number of ways out
of this logical dilemma.

26:31.140 --> 26:35.610
One is you look at all possible
trees--

26:35.608 --> 26:38.318
this is, by the way,
a huge computational problem,

26:38.318 --> 26:40.468
as you'll see at the end--and
you choose the ones that are

26:40.473 --> 26:40.893
simplest.

26:40.890 --> 26:43.940
So that's the principle of
parsimony.

26:43.940 --> 26:46.650
And it's a logical principle;
it's not an empirical

26:46.647 --> 26:49.037
principle, and it's not
necessarily the way that

26:49.039 --> 26:50.159
evolution operates.

26:50.160 --> 26:55.340
But given that there are many,
many possible trees,

26:55.338 --> 26:59.168
choosing the simplest one
basically is a way of saying,

26:59.170 --> 27:03.440
"This is how we're dealing
with our ignorance."

27:03.440 --> 27:06.970
Or you could choose the tree
that would make it most likely

27:06.965 --> 27:10.855
that you would have observed the
character data that you actually

27:10.856 --> 27:14.206
did observe;
that's called the principle of

27:14.211 --> 27:15.801
maximum likelihood.

27:15.798 --> 27:19.518
And, in fact,
in the computer programs and in

27:19.516 --> 27:24.326
the theoretical arguments that
go on in phylogenetics,

27:24.328 --> 27:28.478
these are two of the main
themes, and many of the methods

27:28.482 --> 27:33.212
combine them,
in various ways.

27:33.210 --> 27:37.930
Okay, so a bit about
shared-derived characters.

27:37.930 --> 27:40.690
Remember that picture with the
different colors,

27:40.686 --> 27:43.206
with the different parts of the
forelimb?

27:43.210 --> 27:44.760
Having a forelimb that has a
humerus,

27:44.759 --> 27:47.399
a radius, an ulna,
carpals and metacarpals,

27:47.400 --> 27:50.660
in that sequence,
really doesn't help us to

27:50.656 --> 27:53.136
distinguish bats from turtles.

27:53.140 --> 27:54.940
Okay?

27:54.940 --> 27:59.140
That trait's shared among all
tetrapods.

27:59.140 --> 28:02.840
So the fact that you're looking
at a thing, that's got those

28:02.839 --> 28:06.669
parts to it, doesn't help you to
distinguish bats from turtles

28:06.665 --> 28:08.355
from whales from seals.

28:08.358 --> 28:10.598
Sure, they've all got it,
but that's not telling you

28:10.599 --> 28:13.059
whether they're closely related
to each other or not,

28:13.058 --> 28:16.328
because they all got it from a
common ancestor;

28:16.329 --> 28:18.589
it's not derived.

28:18.588 --> 28:23.148
However, that structure
distinguishes the tetrapods from

28:23.153 --> 28:25.233
the lobe-finned fishes.

28:25.230 --> 28:29.040
So at that point on the tree it
becomes useful as a

28:29.042 --> 28:31.792
shared-derived marker,
of a group;

28:31.788 --> 28:33.998
which is why,
one of the reasons why,

28:34.000 --> 28:36.710
we're pretty confident that the
tetrapods is a good group,

28:36.710 --> 28:41.440
and that things didn't- that
the vertebrates didn't come out

28:41.442 --> 28:43.852
of the water multiple times.

28:43.848 --> 28:47.148
In this context it's marking a
trait that originated once in

28:47.147 --> 28:49.827
their common ancestor;
it's shared by all of them;

28:49.828 --> 28:52.588
it's not found in their closest
relatives.

28:52.588 --> 28:54.808
The jargon is derived from the
Greek.

28:54.808 --> 28:57.638
This thing is called a
synapomorphy.

28:57.640 --> 29:01.600
Syn means shared;
apo means derived;

29:01.599 --> 29:03.119
and morph means trait.

29:03.118 --> 29:08.098
So a shared-derived trait is a
synapomorphy.

29:08.098 --> 29:12.518
Now there's a bunch of
important stuff here.

29:12.519 --> 29:19.669
Just looking the same isn't
very helpful.

29:19.670 --> 29:22.300
The informative traits are the
ones that are shared and

29:22.301 --> 29:22.791
derived.

29:22.788 --> 29:25.918
And what is shared and what is
derived, and therefore what is

29:25.923 --> 29:27.913
informative, depends on the
context;

29:27.910 --> 29:29.810
it depends on the part of the
tree that you're sitting in.

29:29.809 --> 29:33.059


29:33.058 --> 29:37.008
Okay, now a little bit about
building trees.

29:37.009 --> 29:41.079
You can think--evolution is
real complex and a lot of stuff

29:41.077 --> 29:42.057
is going on.

29:42.058 --> 29:47.068
But let's suppose that A has
the ancestral state of a trait,

29:47.065 --> 29:51.725
and that between A and B and C,
a new state of the trait

29:51.730 --> 29:52.750
evolves.

29:52.750 --> 29:57.460
So Ancestral is blue and New is
red.

29:57.460 --> 30:01.440
And this marks the point where
that trait started to change,

30:01.440 --> 30:05.560
and then it spread through the
population and by this point it

30:05.555 --> 30:06.495
was fixed.

30:06.500 --> 30:10.720
Well this is a cartoon,
and this is a cartoon of a

30:10.718 --> 30:11.578
cartoon.

30:11.578 --> 30:11.928
Okay?

30:11.926 --> 30:16.166
We're just marking where that
happened, and the only important

30:16.165 --> 30:20.465
thing about this mark is that it
is between this point and this

30:20.474 --> 30:22.174
point;
other than that,

30:22.165 --> 30:24.595
we don't really know exactly
where it is.

30:24.599 --> 30:26.709
Okay?

30:26.710 --> 30:32.010
Now A, B and C would normally
be species.

30:32.009 --> 30:32.249
Okay?

30:32.247 --> 30:33.767
But they could be other things.

30:33.769 --> 30:36.599
They could be genes,
or they could be genera or

30:36.597 --> 30:38.687
families or something like that.

30:38.690 --> 30:41.380
And 1,2, and 3 are characters.

30:41.380 --> 30:45.250
They could be morphological;
they could be molecular.

30:45.250 --> 30:49.210
And, as a convention,
the ancestral state of that

30:49.205 --> 30:53.895
character will be denoted 0,
and the derived state will be

30:53.904 --> 30:57.334
denoted 1;
and the arrow indicates going

30:57.333 --> 30:59.453
from ancestral to derived.

30:59.450 --> 31:03.550
And basically what this picture
is telling you is that Trait 1

31:03.545 --> 31:06.025
changed from ancestral to
derived,

31:06.028 --> 31:09.628
between A and B,
and then after B split off from

31:09.626 --> 31:13.626
C,
two more things changed in C.

31:13.630 --> 31:17.940
Okay, so that's the information
that picture is trying to give

31:17.944 --> 31:18.374
you.

31:18.368 --> 31:23.128
And if you put down a real
interesting vertebrate

31:23.130 --> 31:26.790
phylogeny,
like this, a vertebrate

31:26.787 --> 31:31.417
phylogeny which has some
unfortunate names,

31:31.420 --> 31:36.140
for certain groups on it--okay?;
like reptiles aren't real--and

31:36.144 --> 31:39.244
we use these characters,
having a vertebral column,

31:39.243 --> 31:41.413
having lungs,
having an amniotic egg,

31:41.414 --> 31:43.834
having lactation,
eggshell absent,

31:43.832 --> 31:48.052
chorioallantoic placenta,
hooves on distal phalanges,

31:48.051 --> 31:50.601
a petrosal bulla,
in the skull,

31:50.597 --> 31:54.617
then what we can see from
plotting those along the line

31:54.623 --> 31:58.943
basically is which characters
here are distinguishing which

31:58.944 --> 32:01.694
groups;
what's going on when you go out

32:01.694 --> 32:04.394
into the ungulates,
the horses and the cows.

32:04.390 --> 32:10.080
The vertebral column is a
synapomorphy of the vertebrates,

32:10.076 --> 32:12.766
of this whole bunch here.

32:12.769 --> 32:17.099
But if we just look at the
mammals, which are from here on

32:17.103 --> 32:21.143
out, it's an ancestral trait;
it's not a derived trait,

32:21.143 --> 32:25.123
it's a shared-primitive trait,
and that's a symplesiomorphy,

32:25.117 --> 32:26.597
not a synapomorphy.

32:26.598 --> 32:31.118
The lungs, which come in right
here, at 2, are a synapomorphy

32:31.117 --> 32:34.277
of the tetrapods,
but they are an ancestral

32:34.280 --> 32:37.670
trait, a symplesiomorphy of the
amniotes;

32:37.670 --> 32:42.600
okay, so the amniotes are back
here--excuse me,

32:42.596 --> 32:45.486
the amniotes are up here.

32:45.490 --> 32:48.340
So whether you call a trait one
or the other depends on where it

32:48.343 --> 32:50.883
sits in the tree and what it
allows you to do with it.

32:50.880 --> 32:54.820


32:54.818 --> 32:59.348
This is a bit of the
relationship between trees and

32:59.354 --> 33:00.084
names.

33:00.078 --> 33:03.888
Ideally we would like that
relationship to be totally clear

33:03.894 --> 33:07.384
and unambiguous so that if I
just give you a name,

33:07.380 --> 33:10.330
you know where that thing sits
in the tree.

33:10.329 --> 33:12.559
This is a hard thing to do.

33:12.558 --> 33:16.978
It is so hard to do that there
is now a complete overturning of

33:16.978 --> 33:20.468
the Linnaean System of
Classification going on.

33:20.470 --> 33:23.760
It's being led by a couple of
guys here, Michael Donoghue and

33:23.758 --> 33:24.798
Jacques Gauthier.

33:24.798 --> 33:28.018
Michael is in our department,
and he's also vice-president of

33:28.017 --> 33:30.427
the university,
and Jacques Gauthier is a prof

33:30.430 --> 33:32.200
in G&G - in Paleontology.

33:32.200 --> 33:36.550
And they have worked a lot on
how to get a way to name things

33:36.551 --> 33:40.981
that actually tells you their
complete position on the Tree of

33:40.977 --> 33:41.627
Life.

33:41.630 --> 33:41.890
Okay?

33:41.885 --> 33:43.835
It's going to be a big computer
code.

33:43.838 --> 33:47.648
It's not going to be something
nice like Homo sapiens.

33:47.650 --> 33:48.090
Okay?

33:48.085 --> 33:51.125
Homo sapiens is the Linnaean
name.

33:51.130 --> 33:54.630
The new method will contain a
lot more information in it,

33:54.630 --> 33:57.970
and will probably only be
something that you can store on

33:57.973 --> 34:00.303
your iPhone,
or whatever else it is that you

34:00.304 --> 34:01.604
use to replace your memory.

34:01.599 --> 34:04.969


34:04.970 --> 34:10.970
But ideally these terms would
map onto natural relationships;

34:10.969 --> 34:13.449
and these terms actually do map
onto these natural

34:13.449 --> 34:14.259
relationships.

34:14.260 --> 34:14.570
Okay?

34:14.572 --> 34:17.832
So this is the primates,
and these are the ungulates,

34:17.831 --> 34:21.091
and they are nested within the
eutherian mammals.

34:21.090 --> 34:24.450
The therian mammals include the
marsupials, and the mammals

34:24.449 --> 34:27.579
include the monotremes,
which are the spiny echidna and

34:27.577 --> 34:29.197
the duckbilled platypus.

34:29.199 --> 34:32.519
And between them and the
marsupials is where the female

34:32.523 --> 34:35.783
reproductive tract evolved,
because the monotremes are

34:35.784 --> 34:37.144
still laying eggs.

34:37.139 --> 34:42.149
And then the amniotes would
include the so-called reptiles;

34:42.150 --> 34:45.340
that would actually be
crocodiles, lizards,

34:45.342 --> 34:46.712
snakes, turtles.

34:46.710 --> 34:49.560
The tetrapods include the
amphibians, and then the

34:49.561 --> 34:51.891
vertebrates include the fish,
as well.

34:51.889 --> 34:55.559
So this is a natural
classification,

34:55.559 --> 35:01.219
and that's the way all
taxonomic nomenclature should be

35:01.224 --> 35:05.004
related to all good systematics.

35:05.000 --> 35:09.670
Now, how do you actually infer
a tree from a character matrix?

35:09.670 --> 35:12.630
So here we're just trying to
figure out if things are related

35:12.626 --> 35:13.066
or not.

35:13.070 --> 35:14.340
We don't have a tree yet.

35:14.340 --> 35:15.520
Okay?

35:15.518 --> 35:21.348
And we have three species and
we have three characters;

35:21.349 --> 35:27.009
and in this case ancestral is
going to be 0 and 1 is going to

35:27.012 --> 35:28.242
be derived.

35:28.239 --> 35:32.329
Well this particular character
matrix is consistent with

35:32.327 --> 35:35.967
drawing a tree this way,
and then marking down the

35:35.969 --> 35:37.529
transitions here.

35:37.530 --> 35:43.260
So when 1 went from ancestral
to derived, it changed here in

35:43.262 --> 35:47.052
both B and C,
and when 2 and 3 went from

35:47.052 --> 35:51.622
ancestral to derived,
it changed only in C.

35:51.619 --> 35:56.659
So can you see how the tree
relates to the matrix?

35:56.659 --> 35:58.139
Okay?

35:58.139 --> 36:00.809
Any question about that at this
point?

36:00.809 --> 36:02.429
I've made the simplest one I
could.

36:02.429 --> 36:05.479


36:05.480 --> 36:13.250
Now if we did it with overall
similarity, A and B share five

36:13.248 --> 36:15.748
ancestral counts.

36:15.750 --> 36:16.720
Okay?

36:16.719 --> 36:21.569
In three traits,
1,2 and 3, A has got the

36:21.568 --> 36:23.748
ancestral state.

36:23.750 --> 36:25.800
In two traits,
two of those,

36:25.802 --> 36:29.682
in B--B has also got the
ancestral trait in 2 and 3,

36:29.677 --> 36:32.487
and that would suggest this
tree.

36:32.489 --> 36:37.449
But if we go by derived
similarity, then we get this

36:37.449 --> 36:38.129
tree.

36:38.130 --> 36:40.150
And you can see what it does to
the tree.

36:40.150 --> 36:43.330
So this is overall similarity,
which is misleading,

36:43.329 --> 36:47.329
and this is shared derived
trait phylogenetics,

36:47.329 --> 36:51.819
which yields this tree,
and it shifts the sister of B

36:51.820 --> 36:53.030
from A to C.

36:53.030 --> 36:56.160


36:56.159 --> 36:59.519
Now if life were only so simple.

36:59.519 --> 37:01.079
Life is never simple.

37:01.079 --> 37:05.409
Traits can conflict with each
other in the information they

37:05.409 --> 37:07.649
give you, and they often do.

37:07.650 --> 37:10.860
So here is a character matrix
with no conflict,

37:10.864 --> 37:14.084
and here's a character matrix
with conflict.

37:14.079 --> 37:14.899
Okay?

37:14.900 --> 37:17.660
So everything was looking
pretty good, as long as we'd

37:17.663 --> 37:19.753
only measured Trait 1 and 2 down
here.

37:19.750 --> 37:24.890
But then we measured Trait 3,
and Trait 3 seemed to indicate

37:24.887 --> 37:28.717
that C had this ancestral trait
over here.

37:28.719 --> 37:32.909
It was beginning to look like C
was going to be a highly derived

37:32.905 --> 37:33.565
species.

37:33.570 --> 37:36.250
But then we've looked at
another trait and it wasn't like

37:36.253 --> 37:36.593
that.

37:36.590 --> 37:37.760
What do you do?

37:37.760 --> 37:38.320
Right?

37:38.320 --> 37:39.180
What do you do?

37:39.179 --> 37:42.979
Well you can choose the
simplest tree.

37:42.980 --> 37:45.660
You can choose the one that
implies the least change.

37:45.659 --> 37:51.719
So here are all trees which are
consistent with this character

37:51.715 --> 37:52.605
matrix.

37:52.610 --> 37:59.110
And if you go back and try,
I think you will see that you

37:59.112 --> 38:03.992
can plot all of these changes
onto here.

38:03.989 --> 38:08.219
So basically this tree is
saying that third trait down

38:08.215 --> 38:12.015
here, it changed twice;
it changed once in A and it

38:12.023 --> 38:13.303
changed once in B.

38:13.300 --> 38:17.160
So it went from an ancestral
state up to a derived state,

38:17.163 --> 38:18.753
along these branches.

38:18.750 --> 38:22.110
And these traits up here,
1 and 2, they changed between

38:22.106 --> 38:24.836
A, on the one hand,
and B and C on the other,

38:24.840 --> 38:25.400
here.

38:25.400 --> 38:28.480
So you could do that also,
and you would find that all of

38:28.480 --> 38:31.450
these trees are actually
consistent with that character

38:31.449 --> 38:35.159
matrix,
but this one takes five changes

38:35.161 --> 38:38.411
and these only take 4:
1,2, 3,4;

38:38.409 --> 38:40.839
1,2, 3,4, 5.

38:40.840 --> 38:45.400
Therefore, we come to the
conclusion that one of these

38:45.404 --> 38:49.454
traits, one of these trees,
is probably correct,

38:49.451 --> 38:52.811
just by the principle of
parsimony.

38:52.809 --> 38:56.449
And the only way that we really
resolve this kind of issue is by

38:56.445 --> 38:57.595
getting more data.

38:57.599 --> 39:00.529
The more data you get,
the more likely it is that that

39:00.532 --> 39:02.362
will converge on the real tree.

39:02.360 --> 39:05.640
I would like to point out that
there probably is not enough

39:05.641 --> 39:09.041
data in the world to do that,
for all of the creatures on the

39:09.036 --> 39:09.656
planet.

39:09.659 --> 39:11.239
In other words,
at the end of the process there

39:11.237 --> 39:12.537
will still be some unresolved
stuff.

39:12.539 --> 39:15.989


39:15.989 --> 39:19.589
Now what about--let me just put
that in--what about this?

39:19.590 --> 39:21.390
Where does the root come from?

39:21.389 --> 39:24.889
Well these are unrooted trees,
up here,

39:24.889 --> 39:29.599
and the choice of where you
decide the ancestral state is

39:29.597 --> 39:34.217
actually makes quite a bit of
difference to the tree.

39:34.219 --> 39:37.049
I'm sorry that in translating
this has gotten screwed up a

39:37.047 --> 39:37.937
little bit here.

39:37.940 --> 39:41.740
This is actually A over here,
and then it goes D,

39:41.742 --> 39:43.092
B, C over here.

39:43.090 --> 39:46.310
Choosing this as the root,
rather than this,

39:46.309 --> 39:50.129
changes the relationship from B
and D to B and C;

39:50.130 --> 39:54.550
this is B and this is C;
this is B and this is D.

39:54.550 --> 39:57.910
So where do you get the
outgroup, how do you decide

39:57.907 --> 39:59.717
where the root should be?

39:59.719 --> 40:08.879
Well, that issue can only be
decided in the context of a

40:08.878 --> 40:11.208
bigger tree.

40:11.210 --> 40:14.780
So you must have some other
kind of information to suggest

40:14.777 --> 40:16.717
what your out group might be.

40:16.719 --> 40:19.369
And, when this is actually
done, sometimes people see

40:19.373 --> 40:22.233
whether the choice of an
outgroup is actually going to be

40:22.231 --> 40:24.631
changing the shape of their tree
very much.

40:24.630 --> 40:26.710
They will report,
"We tried this and this

40:26.706 --> 40:29.146
and this as the out group,
and these were the results,

40:29.153 --> 40:30.173
to our tree."

40:30.170 --> 40:33.410
Okay?

40:33.409 --> 40:36.829
Now, you get your trait matrix,
you want to find the simplest

40:36.829 --> 40:37.229
tree.

40:37.230 --> 40:41.020
One of them is to do an
exhaustive search.

40:41.018 --> 40:45.758
So here are two terminal taxa,
B and C.

40:45.760 --> 40:46.670
Okay?

40:46.670 --> 40:49.410
We've chosen A as the ancestral
condition;

40:49.409 --> 40:51.549
it's not an existing species
now.

40:51.550 --> 40:54.170
A, we say, is going to be the
out group;

40:54.170 --> 40:56.580
that's going to be link to the
ancestors.

40:56.579 --> 40:58.909
Only one tree possible.

40:58.909 --> 41:05.569
If we have three terminal taxa,
we can have either B as the

41:05.565 --> 41:10.195
closest relative of D;
C as the closest relative of D;

41:10.199 --> 41:12.469
or B and C as being their
closest relative.

41:12.469 --> 41:14.829
So there are three
possibilities there.

41:14.829 --> 41:17.769
If we have four terminal taxa,
oh my goodness,

41:17.766 --> 41:19.656
suddenly we have this many.

41:19.659 --> 41:21.449
Oh that's confusing.

41:21.449 --> 41:27.449
If we have 500 terminal taxa,
we have 1 times 10^(1280

41:27.445 --> 41:29.365
)possibilities.

41:29.369 --> 41:33.029
This is a combinatorial
explosion of possibilities.

41:33.030 --> 41:38.640
And about, oh say about
2003,2004,

41:38.639 --> 41:44.849
it took nine months of runtime
on a supercomputer to sort out

41:44.847 --> 41:51.257
all of the possible trees for a
reasonable number of characters

41:51.262 --> 41:54.162
for something like this.

41:54.159 --> 41:57.049
So if you have 500 species and
you wanted--

41:57.050 --> 41:59.570
and you had a reasonable number
of characters,

41:59.570 --> 42:03.470
you would only get a tiny
fraction of those trees covered,

42:03.469 --> 42:05.859
and you would wait nine months
to get your answer.

42:05.860 --> 42:08.420
It's gotten a little better
than that recently,

42:08.422 --> 42:09.262
but not much.

42:09.260 --> 42:09.850
Okay?

42:09.849 --> 42:11.509
So there are ways to get around
this problem.

42:11.510 --> 42:13.820
There are all kinds of
heuristic ways to get around

42:13.824 --> 42:14.154
this.

42:14.150 --> 42:17.360
There are ways of jumping into
tree space and doing local

42:17.358 --> 42:20.338
approximations and then
branching things together.

42:20.340 --> 42:23.080
So that, for example,
when the New York Times

42:23.077 --> 42:25.887
reported last week,
on Darwin's birthday,

42:25.887 --> 42:30.377
that biologists had recently
been able to publish a tree of

42:30.382 --> 42:33.372
11,000 plant species,
which was done here,

42:33.367 --> 42:35.827
by Stephen Smith and Michael
Donoghue's group;

42:35.829 --> 42:39.379
he did that as a super-tree,
using these approximation

42:39.375 --> 42:42.915
techniques to patch together
lots of smaller trees.

42:42.920 --> 42:46.440
And there are all kinds of
criteria that get applied to how

42:46.438 --> 42:47.348
good that is.

42:47.349 --> 42:49.759
By the way, one of the things
that Stephen turned up is that

42:49.760 --> 42:51.560
hey, the ferns are still
evolving rapidly;

42:51.559 --> 42:52.599
which is kind of neat.

42:52.599 --> 42:53.589
Lots of other stuff is in that.

42:53.590 --> 42:57.010


42:57.010 --> 43:00.310
So, the Tree of Life is not
given.

43:00.309 --> 43:03.239
We have to discover it.

43:03.239 --> 43:06.219
The informative characters in
the Tree of Life are those that

43:06.217 --> 43:07.457
are shared and derived.

43:07.460 --> 43:09.430
So appearances deceive.

43:09.429 --> 43:13.639
Simply looking similar is
insufficient information.

43:13.639 --> 43:16.819
You can make a lot of trees
with the same character matrix.

43:16.820 --> 43:18.420
You would prefer either the
simplest,

43:18.420 --> 43:22.150
which implies the least change,
or the tree that maximizes the

43:22.150 --> 43:25.210
probability of observing what
you actually see,

43:25.210 --> 43:27.230
or some combination of those
criteria.

43:27.230 --> 43:28.410
Okay?

43:28.409 --> 43:31.879
Next time we'll take these
methods and see how we can infer

43:31.876 --> 43:32.946
history with them.

43:32.952 --> 43:33.672


43:33.670 --> 43:40.000