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Understanding Phylogenetic Trees
A tutorial for
Biology of the Vertebrates
EEB 2214
Note: best viewed in PowerPoint as a “slide show,” as slides are animated
Credits: Animal icons used in this presentation are from Microsoft Clipart (Microsoft Corporation 2006), unless
otherwise indicated. The content is based on information (e.g., definitions of terms, main concepts, phylogenetic
relationships, etc.) obtained from Pough et al. 1999 and Kardong 2002. This work was spawned from the ideas of
E. Jockusch and M. Rubega, based on their experience with students’ difficulties with some important concepts.
Presentation was created by Diego Sustaita.
In their simplest forms, phylogenies are clusters of closely related organisms <next slide>
which in turn are clustered with other closely
related clusters… <next slide>
Vertebrates
“fish”
chelicerates
amphibians
“reptiles”
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insects
Tetrapods
mammals
birds
“Invertebrates”
…and clustered yet again with other
related clusters <next slide>
But in actuality they go much further, in that they portray evolutionary relationships
(relationships among organisms which reflect their historical origin). Species are
arranged into monophyletic groups (groups of two or more taxa having a common
ancestor). For example, consider the group below <next slide>
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Monophyletic lineages comprise a common ancestor and all of its
descendants; here there are five such groupings <next slide>
One comprises frogs and salamanders, and the ancestor common to both of
them (depicted here as a red dot, or “node”; these nodes are actual species –
usually extinct – whose names you will come to know) <next slide>
Another comprises lizards, crocs, and birds (you’ll come to understand why
later), and the ancestor common to all of them. What are the other three?
So what are these monophyletic relationships based on? I mean, what could a
bird, a croc, and a lizard possibly have in common, other than that they are all
tetrapods? <next slide>
Well, there are several morphological, behavioral, and molecular (e.g., DNA)
attributes which are indicative of relationships among species. In phylogenetics
jargon, these are referred to as “synapomorphies,” which are shared, derived
characters. In other words, they are characters which have evolved along the
branch leading to the most recent common ancestor, and serve to distinguish one
group from all others. Synapomorphies unite groups together, and form the basis
of the branching patterns in phylogenetic trees. For example, consider the clade
below <next slide>
diapsid skull
The members of the lineage containing lizards, crocs, and birds possess “diapsid”
skulls (two pairs of temporal openings, as opposed to one pair in mammals, or
none, in turtles, which results in increased flexibility of the skull during feeding)
<next slide>
But wait; I still don’t get how crocs are more closely related to birds than they are
to lizards. I thought crocs and lizards were both reptiles, and birds were, well,
birds…? <next slide>
feathers
A
B
If you are having trouble deciphering who’s related to who, try thinking about it as
“which groups share a common ancestor more recently.” Lizards and crocs both
share a common ancestor (B), but crocs share a more immediate one with birds (A).
So by extension, birds could be considered “reptiles” too... <next slide>
But we don’t typically consider birds “reptiles”, because, more formally, they are
feathered “archosaurs.” In fact, you learned that the term “reptiles” does NOT
represent a monophyletic grouping, because it doesn’t include birds (remember: a
monophyletic group must include an ancestor, and ALL of its descendants; the
term “fish” presents a similar problem [why???]). You’ll find that – often
counterintuitively – conventional ways of grouping organisms aren’t always very
descriptive or accurate <next slide>
Question: given what has just been presented, with which of the three groups of
organisms depicted below is the turtle most closely related? <next slide>
How about now?
A
B
C
Your answer should be the same - turtles share a common ancestor with B (the common
ancestor to lizards + A [the common ancestor to birds and crocs]), so they are most
closely related to all the groups depicted, through common ancestor “C” <next slide>
Wait… what just happened? Branches in phylogenies are free to spin around each
node, so you can’t infer phylogenetic relationships among groups based on their
proximity on a tree, unless they are bracketed together <next slide>
(Note: may not animate properly in Macs)
<next slide>
While we are on the topic of presentation, you should know that there are different
ways of presenting the same information. Convince yourself that this… <next slide>
<next slide>
… is identical to this…
Now remember that this
could be equally presented…
<next slide>
like this… <next slide>
Or even like this…, so it’s
important not to think of
whatever’s on the right-hand
side (birds, in the top
example) as the “pinnacle” of
evolution <next slide>
Also note that phylogenies vary in their degree of detail, and may be collapsed or
expanded at any given point, provided that there is enough information about
relationships among organisms <next slide>
In this phylogeny, for instance, the branch containing birds & crocs can be
collapsed into the term “archosaurs” – the group containing birds,
crocodiles, and dinosaurs <next slide>
You could go further and summarize the whole right-hand
branch as “amniotes” (in reference to organisms that
produce amniotic eggs) <next slide>
Archosaurs
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Amniotes
By the same token, each group depicted below can be expanded into its own
phylogeny <next slide>
Plethodontidae
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Mueller et al. 2004
Now take one family, and consider
the diversity of genera (this should
look familiar too…) <next slide>
Now you try. Which of the following terms would you collapse the right-hand side
of the following phylogeny into: Archosaurs, Tetrapods, Reptiles, Saurapsids, or
Dinosaurs? <next slide>
?
Even if you don’t know what some of these are, you should be able to immediately rule
out 3 choices: “Archosaurs” is too restrictive, as we learned a few slides back that it
refers to the clade containing birds, crocs, and dinosaurs - (which would be even more
restrictive). “Tetrapods” is too broad, as it includes mammals as well. Reptiles, as we
just learned, is not monophyletic, so although it includes the common ancestor, it fails
to include all of its descendants (which were not depicted, such as birds). The only one
left is “saurapsids,” which in fact refers to the clade containing all of these animals
(including birds).
By now you’ve been introduced to the major concepts, but we left out a few
important details. The lengths of the branches were depicted somewhat arbitrarily
here, but sometimes they do mean something. Occasionally we’ll encounter a tree
in which branch lengths are drawn proportional to time <next slide>
A
B
C
D
100 million years ago
present
In this scenario, A and B
diverged from their
common ancestor much
more recently than did C
and D <next slide>
Also, the goal of a phylogeny is to break everything down into dichotomous,
monophyletic sister groups, but this doesn’t always happen. If there is a lack of
information about relationships among species – either because there has been
minimal divergence among a set of species, or the group simply has not been studied
(or both) – polytomies (= a node with more than two immediate descending branches)
often emerge (right-hand clade containing species C-D-E, below). <next slide>
D
C
A
B
C
D
E
E
D
This trichotomy represents three possible
resolutions, because no pair of taxa is
depicted as a sister group to the third taxon.
With more information, one of the three
possibilities may become better supported.
Note that phylogenies are essentially working
hypotheses, which are continuously updated
with new findings <next slide>
E
C
C
E
D
OK. Now its your turn. Here is an array of organisms to be assembled into a
phylogeny. So, where do you start? Well, you could probably get most of the way
just by gestalt. But eventually, you will need to now some key pieces of info –
remember those synapomorphies from Biology 108???? <next slide>
Match the letter of each group with the number of
the its corresponding position on the cladogram:
a
1
b
2
c
d
3
e
4
f
5
g
6
h
7
i
8
Once you think you have it,
go onto the next slide…
9
You should have come up with something like this: <next slide>
And
grouping
snakesand
andsea
lizards
– you’ll recall
The
oyster
(a mollusc)
startogether
(an echinoderm)
were a cheap
Afrom
few
trickier
points
are
the
distinction
between
marsupial
lecture
that
lizards,
snakes,
and
tuataras
form
the molluscs are
trick
from Biology
108 – they
are&both
invertebrates,
but
(kangaroo)
and
placental
(bear
squirrel)
mammals
<next slide>
“lepidosaur”group
<next slide> and chordates are deuterostomes
protostomes,
and enchinoderms
4=d
1=f
2=b
3=a
6=h
5=e
7=g
8=c
9=i
How else might have you correctly
arranged these species? <next slide>
One more time just to make sure it sank in:
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a
1
b
2
c
d
3
4
e
5
f
6
g
7
h
i
8
Once you think you have it,
go onto the next slide…
9
This is what you should have (right out of your lecture notes…)
Mammalia
Myxinoidea
1=e
Petromyzo Chondrich
-ntoides
-thyes Amphibians
(Urodela)
2=f
3=h
4=b
(Artiodactyla)
5=a
6=d
(Cetacea)
7=i
Aves
8=g
Lepido
-sauria
9=c
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Epilogue: We’ve shown you the appropriate phylogenetic groupings of the taxa
portrayed throughout the tutorial, however we haven’t really described the
synapomorphies that form the bases of the groupings. You should review your
notes and make sure you have a handle on the major synapomorphies which
characterize the major groups we are covering, as a starting point to
determining their relationships.

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