1. The Evolutionary history of related organisms
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PHYLOGENY…
The Evolutionary history of related organisms
Photographic images within this PowerPoint
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2. Distinguishing Phylogeny vs. Taxonomy
Taxonomy – a hierarchical structure of grouping & naming or classifying organisms based on similarities and differences
Phylogeny – Depicts the evolutionary relationships of a group of organisms.
Phylogenetic trees indicate when/where species diverged from a common ancestor.

3. Phylogenetic trees show lines of descent
The branching patterns that
make up a phylogenetic tree
are not usually observed
directly, rather they are
inferred from data
Red circle – extinction.
What does this dead-end
branch depict?
Try to answer the
question before you
click again. Make
sure you do this each
time a question is
asked.
An extinction
Image adapted from: Baum, D.A. and Smith S.D. Tree thinking: an introduction to phylogenetic biology. Roberts, 2013.

4. Before we can create phylogenetic trees, we need to ask…

5. How are organisms classified?
Let’s start with a set of species named as follows… A B C D E F
We have evidence that:
B and C are more closely related to each other than to any other species
A is related to B and C, but not as closely as B and C are related to each other
D, E and F are more closely related to each other than to A, B or C
Let’s start here and learn a simple way to organize the species based on relatedness.

6. How are organisms classified?
We know:
B and C are closely related
Start by grouping the most closely related organisms together.
Use parentheses to put them together in a set…
…and a comma to show that they share a common ancestor.
B C
(B C)
(B,C)

7. How are organisms classified?
We know:
B and C are closely related
A is related to both B and C, but not as closely as B and C are related to each other
Now add the next most closely related organism
Place this organism next to the first set,
add parentheses to group them into a larger set,
and a comma to show the common ancestor.
A (B,C)
(B,C)
(A (B,C))
(A,(B,C))

8. How are organisms classified?
What about the other organisms? D E F
D, E and F are more closely related to each other than to A, B or C.
If D, E and F are equally related to each other (or you’re not sure!) put them together in a set using parentheses.
And separate them with commas to show they share a common ancestry.
D E F
(D E F)
(D,E,F)

9. How are organisms classified?
Let’s bring this all together.
Because the DEF set is more distantly related from the ABC set, we keep the 2 sets separate but put them next to each other.
Then we add a final set of parentheses to enclose all of the species as one larger set.
Don’t forget the comma, to show the common ancestor between the two sets that make up the larger set.
((A,(B,C)),(D,E,F))
(A,(B,C)) (D,E,F)

10. How are organisms classified?
One last thing!
To show that you have completed the tree, you add a semi colon to the end of the set.
((A,(B,C)),(D,E,F));

11. How are organisms classified?
((A,(B,C)),(D,E,F));
What you have just made is a phylogenetic tree!
Click to see how this can be converted into a phylogenetic tree…

12. (B,C)
Present
Don’t worry about the terms for right now…
Past

13. (A,(B,C))
Present
Past

14. (D,E,F)
Present
Past

15. ((A,(B,C)),(D,E,F));
Present
Past

16. ((A,(B,C)),(D,E,F));
Present
Past

17. Some common terminology
Branches indicate
evolutionary path
Descendants
(Current taxa)
at tips
Nodes indicate 
common ancestor
Other
terms shown
here will be
addressed later.
Past
Present

18. Now that we’ve seen how trees are put together let’s look at how to interpret them.
Past
Present

19. Unless stated otherwise, assume that absolute time is NOT representedC D α δ
Trees ONLY depict relatedness and not time unless specifically stated otherwise. Alpha happened after beta (alpha occurred closer to the present than beta). We don’t know if alpha came before or after delta. β
Was α before or after δ?
Was α before or after β?
You can’t tell

20. More terminology A cladogram indicates relatedness only!
Sister taxa are
most closely
related because
the MRCA (most recent common ancestor) that they share is more recent than the ones they share with another taxon on this tree
A cladogram shows relatedness only! Branch length is not always meaningful – Taxon B and C are not more or less evolved than taxon D, E, and F.
Sister taxa are NOT closely related because they are next to one another at the tips. A and B are NOT sister taxa, whereas B and C are, because they share an MRCA.
Branch length is not always meaningful

21. Same order – different tree?
Let’s look at these two trees. The taxa are in the same order at the tips, but the branching appears to be different.
Tree on the left: human and mouse are sister taxa - most closely related, share a common ancestor. Tree on the right: lizard and mouse are most closely related.
These circles show just
one difference. There are
more. You should identify
them. Use the Tree Thinking
Article.
What’s different?
Images via Wikimedia Commons used under Creative Commons Attribution 2.0 Generic License.

22. Don’t be distracted by morphological similarity
It can be tempting to think about what organisms look like when interpreting these trees, but you really only want to focus on branching patterns. Lizards and frogs have many similar morphological features –four legs, they might go in water and live on land, they both eat insects, etc. But, this tree shows us that lizards are more closely related to mice and humans. While they do share an MRCA with frogs, that ancestor lived farther in the past that the MRCA circled in red and it is the SAME common ancestor shared with humans.
Use the fish in this tree as the outgroup – to help root the tree; we know fish are distantly related, as they are not tetrapods.
Most Recent Common Ancestor (MRCA)
Is a lizard more closely related to a frog or a human?
Images via Wikimedia Commons used under Creative Commons Attribution 2.0 Generic License

23. Assembling a Tree: Practice #2
Let’s practice putting that tree together ourselves,
using the set method from earlier in this tutorial
Five organisms – How are they related?
We know that the human and the mouse are most closely related. So let’s group them together in a set. We’ll do this one with pictures!
( , )

24. Assembling a Tree: Practice #2
Let’s practice putting that tree together ourselves,
using the set method from earlier in this tutorial
Five organisms – How are they related?
Next, we know that lizards
are related most closely to the human/mouse set…
( ,( , ))

25. Assembling a Tree: Practice #2
Let’s practice putting that tree together ourselves,
using the set method from earlier in this tutorial
Five organisms – How are they related?
And frogs
are related most closely to the human/mouse/lizard set…
( ,( ,( , ))))

26. Assembling a Tree: Practice #2
Let’s practice putting that tree together ourselves,
using the set method from earlier in this tutorial
Five organisms – How are they related?
Finally, we add the fish in.
( ,( ,( ,( , ))))

27. Assembling a Tree: Practice #2
What’s missing from this tree?
( ,( ,( ,( , )))) ;
The semi-colon at the end. This indicates that the tree is complete.
If we wanted to write this out using names, so that we could enter it into a phylogeny-making computer program, it would look like this:
(Fish,(Frog,(Lizard,(Human,Mouse))));

28. Trees can be drawn in various ways yet contain the same phylogenetic information
The taxa at the tips of all 4 trees are in the same order – are the evolutionary relationships the same?
All of these trees depict the exact same evolutionary relationships among taxa A through F. For example, all trees show that F and C are sister taxa, along with E and D. B is equally closely related to C and F. The BCF clade shares an MRCA with the ED clade.
Phylogenetically, these
trees are identical.
Gregory Evo Edu Outreach 1:

29. Rotation around the nodes does not change the information in a tree.
These three trees are identical 4 3 2
If you rotate tree 1 at node 1 only, you get tree 2! If you rotate node 1, 2, and 3 you get tree 3.
If you rotate tree 1 at nodes 1, 2, and 4, you get tree 3! 1
Tree 1
Tree 3
Tree 2
If we rotate around the first node…
…we get this
…we get this
If we rotate around the 1st, 2rd 4th nodes…

30. There are no “main lines” in evolution
Just because the human has a “straight shot” does not mean it is more related to the common ancestor than the others.
The “straight shot” also does not imply that the human (or the shark) is more advanced than the other taxa.
Images via Wikimedia Commons used under Creative Commons Attribution 2.0 Generic License

31. Clades can be expanded or collapsed
If we collapse these two regions…
…we get this tree
…we get this tree
We call this “pruning” the tree. If you prune tree (a) by collapsing taxa A, B, C and D into M and collapsing E and F into K, you wind up with tree (b). If you prune (a) by collapsing EFGH into N, collapsing C and D into J, and rotating at each node, you get tree (c).

32. A tree can depict polytomy
plant
animal
fungi
If we are unsure which of these is most likely:
plant
fungi
animal
Rearranging them to meet at a common point shows uncertainty about how lineages relate to each other.
This arrangement is a called a polytomy.

33. Monophyletic groups (clades)
Monophyletic group (clade)
A clade is a grouping that includes a common ancestor and all the descendants (living and extinct) of that ancestor
Scientists try and make sure that each taxon (a named group of organisms) corresponds to a clade
Clades = branch-systems have a special importance in understanding diversity. They are monophyletic.
Monophyletic groups include an ancestor and all of their descendants. (all members are most-closely related).

34. How can we reconstruct phylogenies?
Many methods, some quite sophisticated
Simplest is to apply the principle of parsimony:
Occam’s Razor - All other things being equal, the simplest solution is the best.
Can be done on Morphological or Molecular data
The rest of this activity
will focus on parsimony analysis
with molecular data

35. THE PARSIMONY CRITERION
Select the tree that implies the minimum number of character changes summed across all characters of interest

36. Let’s use molecular data
RW A A C G A T T C T A A A G G A T T
BW A G C G C T T C T A A A G G A T T
MW A G C G C T T A T A A A G G A T T
LBW A G C G C T T A T A T A G G G T T
RW A A C A A
BW G C C A A
MW G C A A A
LBW G C A T G
RW = Rock Wren (outgroup)
BW = Banded Wren
MW = Moustached Wren
LBW = Long-Billed Wren
First we need to align the DNA (or RNA) sequence data. For each species, we have nucleotide data at 5 positions in the DNA sequence.
First, we align the gene sequences that we want to compare and look for places where they differ

37. Three possible trees Tree 1 Tree 2 Tree 3
We already know that RW is the outgroup.
There are three phylogenies (trees) that we would like to test.
Only one of these can be correct.
There are three possible trees shown here.
For each tree, RW is acting as the outgroup – this is the organism we think is most distantly related to the group of interest – we are trying to figure out the phylogenetic relationship between the moustached wren, the banded wren, and the long-billed wren.
Tree 3
Image via Wikimedia Commons used under Creative Commons Attribution 2.0 Generic License.

38. Three possible trees ( ,( ,( , ))); ( ,( ,( , ))); Tree 1 Tree 2
( ,( ,( , )));
( ,( ,( , )));
Tree 1
Tree 2
Here we’ve included the parentheses and commas we would have used to develop the top two trees.
Tree 3
Image via Wikimedia Commons used under Creative Commons Attribution 2.0 Generic License.

39. Map the characters onto tree 1
These sequences from four different wren species are aligned. Each column (1, 2, 3…) can be considered a
character trait. We will therefore analyze each sequence position (“character”) separately. 1 2 3 4 5
LBW MW BW RW A A C A A RW 4 5 3 BW G C C A A T G MW 1 2
LBW
Note the first two character states could be mapped onto two different branches (either branch leading to RW or the branch leading to (LBW, MW,BW).  For example, RW could have evolved an A from a G (1 step) or A could have evolved to a C on the branch to (LBW, MW, BW) (Also 1 step). Because these first two characters are uninformative as all they do is define the outrgroup, regardless of which branch it is placed on. It does not change the length of the tree or the topology.  We prefer to map characters that define the outgroup on that branch to address the misconception that outgroup lineages do not change and evolve.  
The number mapped above on the tree depicts
the “character” change to the left. For 1, the rock
wren “character” changed from a G (guanine)
to an A (adenine). For 2, the rock wren
“character” changed from a C (cytosine) to an
A (adenine).
Let’s map the remaining character changes
Total cost (length) =
6 steps

40. Actually there is more than one way to map character 31 2 3 4 5
LBW MW BW RW 3 A A C A A RW 3 3 BW G C C A A T G MW
LBW
Either way the character contributes 2 steps to the overall cost
i.e. – you can map this character change in two different ways,
each for the same cost (two separate changes needed).

41. Map the characters onto tree 21 2 3 4 5 MW BW
LBW RW A A C A A RW 3 4 5 BW G C C A A T G 3 MW 1 2
LBW
Length = 6 steps

42. Map the characters onto tree 31 2 3 4 5 BW MW
LBW RW A A C A A RW 4 5 BW G C C A A T G 3 MW 1 2
LBW
Length = 5

43. What was the cost of each tree?
Tree 1: length = 6
Tree 2: length = 6
It is most likely that of the 3 possible trees we looked at, for this sequence data, tree 3 is the most likely tree. So, long-billed and moustached wrens are sister taxa (share a common ancestor).
Note that these are only 3 of the many possible trees; thankfully, we can use a computer program to do this work for us when we have more taxa and longer sequences.
Tree 3 has the lowest
cost, is therefore the
most parsimonious tree
and the one that we
believe to be the most likely
tree based on Occam’s
Razor.
Tree 3: length = 5

44. This is just the beginning . .