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Tree thinking - PlantED Digital Learning Library
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Phylogenetic or evolutionary trees are
diagrams that are used throughout
biology in studies ranging from
conservation to epidemiology.
They contain a great deal of information
about the evolutionary relationships and
diversification within and among
different kinds of organisms.
This video will address the following
questions about phylogenetic trees:
What are the parts?
How are they constructed?
And finally, how are they interpreted?
Although phylogenetic trees can be used for any taxonomic group,
species will be used in this video
for clarity.
To begin with, phylogenetic trees can be drawn a number of different ways.
Whether sloped with
angled branches or even showing a
slightly circular type of diagram,
these phylogenies all show the same
relationship among the Species A through E
because they have the same branching pattern.
You can even draw the phylogeny
with a different angle of orientation
and it still shows the same
relationships among these species.
Regardless of how the phylogeny is drawn,
they are all made of the same parts.
The ends are called the tips. The base is the
root. The lines are branches or clades.
And the points where the branches
diverge from one another called nodes.
The "out-group" is a sister species that's
used as a basis for comparison.
Species that are the focus of the study are
called the "in-group".
Another important nuts-and-bolts kind of thing to know
about phylogenetic trees is that you can
rotate them around the nodes that
doesn't change the relationship shown in them.
For example, in all three of the
trees shown here, the relationships among
species A, B and C are the same.
B and C are more closely related to one another
than either is to species A because B and C
share more recent node with one another.
Now, let's compare
the tree on the left with this
tree showing a different relationship of
branching patterns among A, B and C.
This tree shows a different relationship among the
species because A and C share a more
recent node with one another than either
one does with B.
So, while rotating around notes doesn't matter their sequence does.
Let's now focus on
interpreting trees in more detail.
In the example shown here, we have four species:
one shown by a square and then three circles.
There is a time component of
phylogenetic trees, and in them, the root
indicates the past and the tips indicate
the present.
In this tree, the three circle species
are joined at a note that indicates the
most recent common ancestor, and the
different branches represent lineages of
organisms that gave rise to the species
at the tips.
What this means is that at some point
along these lineages, new characteristics
arose and were passed on to all the
descendants in that lineage.
So, as indicated by the traits of round, blue and
stripe in this tree,
those traits arose due to some mutation that then became
established in those lineages.
Let's zoom in on the phylogeny to consider what that means.
Starting with a lineage, we
have each branch and it's composed of
many different populations, which are
indicated by these blue lines.
Populations exist independently from one
another but they are genetically united
by movement of individuals among them,
a process called gene flow.
Inside each of these populations are individuals who
mate, reproduce, and pass their DNA from
ancestors to descendants over time
as is indicated by these pedigrees.
And so, a lineage is actually a representation of
many different populations composed of
reproducing individuals over time.
Let's now consider what is represented by a node.
Now, I want you to think about
what is being drawn here as a
cross-section through the lineage just
below the node with each population
represented by a circle.
Looking inside one of these populations, we can see the
different individuals that compose it.
Suppose a mutation arises in one of these
individuals. Let's also have this
population with our new red mutation
become isolated from the other
populations of the species, so there's no
more gene flow between them.
Either due to conferring some survival advantage or
completely random processes, the red
trait becomes more common and, ultimately,
becomes the only trait found
in this population.
If other changes occur so that red individuals are reproductively
isolated and can no longer mate with
blue individuals when they come into
contact with them,
this results in genetic separation of
the blue and red individuals and leads to
the evolution of a new species, or speciation.
So, nodes represent reproductive isolation of lineages and
ultimately speciation.
These concepts about nodes and lineages are the basis
of how modern biologist group species
into larger groupings.
For example, grouping species B, C and E into
a genus that excludes D would be called
a paraphyletic group because it is
excluding one of the descendants of
these four species' most recent common ancestor.
Biologist prefer to include
all the descendants of a common ancestor
in their groupings, so by including D in
this genus we now have what biologists
call a monophyletic group, meaning
that this genus now contains all the
descendants of the four species' most
recent common ancestor.
This brings us to the question of how does one draw the
correct phylogenetic tree for a group of species?
Once again, let's return to our example with the circles and square.
There are several possible arrangements of this
"in-group" with the circles and the red
square as the comparator "out-group" species.
Two are shown here.
Now, a phylogenetic tree is a graphical
hypothesis of the relationship among species.
So, as with any scientific
hypothesis, we need to see which ones are
rejected by our data and which ones do
we fail to reject.
In a simple phylogenetic study, our data are the
traits that we collect from the different species.
So, let's make a simple
data matrix for these four species
usingy the traits: shape, color and fill.
Let's further assume that the traits are
independent of each other, and each
transition in character state represents
a unique individual change in characteristics.
In the tree on the left,
we can place these traits on the tree
showing how each trait changed or
evolved once, and there's no more than
one trait change per branch.
In the tree on the right, there are two changes on the
first branch from red square to blue circle
the change in the fill pattern
from solid stripe and a final change
from blue stripe back to solid red.
So, the arrangement of species in the tree
on the left required three trait changes
while the tree on the right required five.
Biologist would therefore consider
the tree on the left to be the most
likely pattern of relationship among
these species given these data because
it requires fewer trait changes, or it's
more parsimonious than the tree on the right.
For phylogenetic studies,
researchers will often code the data
numerically which makes analysis easier.
In this example, the ancestral traits are
coded with a 0 and derived or
traits that have changed are coded with 1.
Let's now consider a slightly more
complex tree.
In the phylogenetic tree
shown here, Species P through V
form a single monophyletic clade
Members of this clade are unified by a shared ancestral
trait called a plesiomorphy.
Each clade however is defined by a unique
derived trait called an apomorphy.
And as the lines in this diagram show,
apomorphies are found throughout the
tree defining and characterizing each
unique clade.
In this phylogeny, P and Q
share recent common ancestor and they
both share recent common ancestor with
species R.
Likewise, in the other clade,
the other species show their own
patterns of common ancestry among them.
Lines being drawn on the right show how
different groupings of these species are
united different shared common ancestors.
The ability to read phylogenetic trees
and interpret the information in them is
called tree thinking.
So let's look at some examples and test your tree thinking skills.
For the phylogeny shown here,
who is species C more closely related to?
Species D or Species F?
The correct answer is that C is equally related to both.
If you said that C was
more closely related to D because it is
closer to it on the phylogeny,
then you're likely reading across the tips
which is not a correct way to read these
types of diagrams.
What matters are the nodes, and as this
diagram shows, species C shares the same
common ancestor with D and F
and is, therefore, equally related to both of them.
Now, let's look at another example.
Who is C more closely related to A or F?
If you chose A, you may be reading across
the tips again. Although C is closer to
A in this phylogeny, it shares a more
recent common ancestor with F and is,
therefore, more closely related to that
species.
You may have also chosen A because there
are fewer nodes between C and A then
there are between C and F.
This is something called node counting,
and it is also an incorrect way to
interpret a phylogeny.
All that matters
are the pattern of most recent common ancestors.
So, to interpret trees correctly,
don't read across the tips or
use node counting to determine
relationships.
Let's look at one last example.
This phylogeny shows the hypothesized
relationships among five different
clades of animals.
Based on this tree,
who would you say that fish are more
closely related to,
snails or humans?
The correct answer is humans, because fish
share more recent common ancestor with the human clade.
Here's another tree.
Does it indicate a different relationship
among these five species?
The correct answer is no. Both trees show exactly the
same relationships despite the node rotations.
To summarize,
the ability to correctly
apply tree thinking allows one to
interpret and explain the information
about the patterns of evolutionary
relationships that are contained in
phylogenetic tree diagrams.
Biologists use these diagrams extensively to
identify monophyletic groups using
shared ancestral traits that show unity
and common ancestry among clades and
derive traits that help to differentiate
and identify unique evolutionary traits
and lineages.
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