Phylogenetic trees reconstruct evolutionary relationships by grouping taxa with shared derived characteristics inherited from recent common ancestors. This document discusses methods for building phylogenetic trees, including cladistics which uses shared derived homologies (synapomorphies) to determine relationships. It also examines evidence for the evolutionary relationships of whales. Molecular studies of transposable elements and additional fossil evidence support whales evolving from artiodactyl ancestors, rather than being the sister group to artiodactyls.

1. 1
Phylogeny:
Reconstructing Evolutionary Trees
Chapter 14

2. 2
Phylogenetic trees
• The phylogeny of a group of taxa (species, etc.) is
its evolutionary history
• A phylogenetic tree is a graphical summary of this
history — indicating the sequence in which
lineages appeared and how the lineages are related
to one another
• Because we do not have direct knowledge of
evolutionary history, every phylogenetic tree is an
hypothesis about relationships
• Of course, some hypotheses are well supported by
data, others are not

3. 3
Questions
• How do we make phylogenetic trees?
– Cladistic methodology
– Similarity (phenetics)
• What kinds of data do we use?
– Morphology
– Physiology
– Behavior
– Molecules
• How do we decide among competing alternative
trees?

4. 4
Similarity
• The basic idea of phylogenetic reconstruction is simple:
– Taxa that are closely related (descended from a relatively recent
common ancestor) should be more similar to each other than taxa
that are more distantly related — so, all we need to do is build
trees that put similar taxa on nearby branches — this is the
phenetic approach to tree building
– Consider, as a trivial example, leopards, lions, wolves and coyotes:
all are mammals, all are carnivores, but no one would have any
difficulty recognizing the basic similarity between leopards and
lions, on the one hand, and between wolves and coyotes, on the
other, and producing this tree; which, it would probably be
universally agreed, reflects the true relationships of these 4 taxa
leopard lion wolf coyote

5. 5
Causes of similarity
• Things are seldom as simple as in the
preceding example
• We need to consider the concept of
biological similarity, and the way in which
similarity conveys phylogenetic
information, in greater depth:
– Homology
– Homoplasy

6. 6
Homology
• A character is similar (or present) in two taxa because their
common ancestor had that character:
• In this diagram, wings are homologous characters in hawks
and doves because both inherited wings from their common
winged ancestor
cat hawk dove
wings

7. 7
Homoplasy
• A character is similar (or present) in two taxa because of
independent evolutionary origin (i.e., the similarity does
not derive from common ancestry):
• In this diagram, wings are a homoplasy in hawks and bats
because their common ancestor was an un-winged tetrapod
reptile. Bird wings and bat wings evolved independently.
hawk bat cat
wings

8. 8
Types of homoplasy
• Convergence
– Independent evolution of similar traits in distantly
related taxa — streamlined shape, dorsal fins, etc. in
sharks and dolphins
• Parallelism
– Independent evolution of similar traits in closely
related taxa — evolution of blindness in different cave
populations of the same fish species
• Reversal
– A character in one taxon reverts to an earlier state (not
present in its immediate ancestor)

9. 9
Reversal
• A character is similar (or present) in two taxa because a
reversal to an earlier state occurred in the lineage leading
to one of the taxa:
• In this diagram, hawks and cats share the ancestral
nucleotide sequence ACCT, but this is due to a reversal on
the lineage leading to cats
hawk bat cat
ACTT
ACCT
ACCT

10. 10
Cladistics
• By definition, homology indicates evolutionary
relationship — when we see a shared homologous
character in two species, we know that they share
a common ancestor
• Build phylogenetic trees by analyzing shared
homologous characters
• Of course, we still have the problem of deciding
which shared similarities are homologies and
which are homoplasies (to which we shall return)

11. 11
Two kinds of homology – 1
• Shared ancestral homology — a trait found in all
members of a group for which we are making a
phylogenetic tree (and which was present in their
common ancestor) — symplesiomorphy
– For example: a backbone is a shared ancestral
homology for dogs, humans, and lizards
– Symplesiomorphies DO NOT provide phylogenetic
information about relationships within the group being
studied

12. 12
Two kinds of homology – 2
• Shared derived homology — a trait found in some
members of a group for which we are making a
phylogenetic tree (and which was NOT present in the
common ancestor of the entire group) — synapomorphy
– For example: hair is (potentially) a shared derived homology in the
group [dogs, humans, lizards]
– Synapomorphies DO provide phylogenetic information about
relationships within the group being studied
– In this particular case, if hair is a synapomorphy in dogs and
humans, then dogs and humans share a common ancestor that is
not shared with lizards, and the common dog-human ancestor must
have lived more recently than the common ancestor of all three
taxa

13. 13
A tree for [dogs, humans, lizards] – 1
lizard human dog
hair
backbone
• The TWO major assumptions that we are making
when we build this tree are:
1) hair is homologous in humans and dogs
2) hair is a derived trait within tetrapods

14. 14
A tree for [dogs, humans, lizards] – 2
lizard human dog
hair
backbone
• In the absence of other information, the assumption of
homology of hair in humans and dogs is justified by
parsimony (fewest number of evolutionary steps is
most likely = simplest explanation)
• Also we can check to see that hair is formed in the
same way by the same kinds of cells, etc.

15. 15
A tree for [dogs, humans, lizards] – 3
• These trees (in which hair is considered a homoplasy
in dogs and humans) are less parsimonious than the
one on the previous slide, because they require two
independent evolutionary origins of hair
human lizard dog
hair
backbone
hair
dog lizard human
hair
backbone
hair

16. 16
Character Polarity
• What’s the basis for our second major
assumption – that hair is a derived trait
within this group (and that absence of hair
is primitive)?
– Fossil record
– Outgroup analysis

17. 17
Outgroups – 1
• An outgroup is a taxon that is related to, but not
part of the set of taxa for which we are
constructing the tree (the “in group”)
• Selection of an outgroup requires that we already
have a phylogenetic hypothesis
• A character state that is present in both the
outgroup and the in group is taken to be primitive
by the principle of parsimony (present in the
common ancestor of both the outgroup and the in
group and, therefore, homologous)

18. 18
Outgroups – 2
• In the present example, [dog, human, lizard] are
all amniote tetrapods. The anamniote tetrapods
(amphibia) make a reasonable outgroup for this
problem
• No amphibia have hair, therefore absence of hair
[amphibia, lizards] is primitive (plesiomorphic)
and presence of hair [dogs, humans] is derived
(apomorphic)
• So, presence of hair is a shared derived character
(synapomorphy), and dogs and humans are more
closely related to each other than either is to
lizards

19. 19
A tree for [dogs, humans, lizards] – 4
• The presence of hair is apomorphic (derived) because
no amphibians have hair
lizard human dog
hair
backbone
Amphibia
amniotic egg

20. 20
Cladistic methodology
• Determine character state polarity by
reference to outgroup or fossil record
• Construct all possible trees for the taxa in
the in group
• Map evolutionary transitions in character
states onto each tree
• Find the most parsimonious tree — the one
with the fewest evolutionary changes
• Only synapomorphies are informative

21. 21
A tree for [dogs, humans, lizards] – 5
• Tree (a) is most parsimonious, so we’ll take that as our best
estimate of the true phylogeny of [dog, human, lizard]
• Of course, if we studied different characters, or used a different
outgroup, our phylogenetic tree could change
human lizard dog
hair
backbone
hair
dog lizard human
hair
backbone
hair
lizard human dog
hair
backbone
(a)
(b)
(c)

22. 22
The phylogeny of whales
• Based on skeletal characteristics, several
studies have placed whales (Cetaceans) as
close relatives of ungulates (hoofed
mammals) – Cetaceans are possibly the
sister group of the even-toed ungulates
(Artiodactyla) – “Artiodactyla hypothesis”

23. 23
The
Artiodactlya
hypothesis
for the
evolutionary
relationships
of Cetacea
(Fig. 14.4 a)
Odd-toed
ungulates
(Perissodactyla
[horses, rhinos])
are the outgroup

24. 24
The whale +
hippo
hypothesis
for the
evolutionary
relationships
of Cetacea
(Fig. 14.4 a)
This tree was
proposed based on
nucleotide
sequence of a milk
protein gene

25. 25
Sequence
data for
parsimony
analysis
(Fig. 14.6)
Blue shaded bars
represent invariant
(uninformative
sites, but note error
for site 192), and
red shaded bars
represent
synapomorphies
(note, site 177 does
not agree with tree
as drawn). Tree is
based on parsimony

26. 26
Which phylogeny for whales, if either, is
correct?
• According to the whale + hippo hypothesis,
whales are artiodactyls – not the sister group to
artiodactyls
• Artiodactyls are defined by a particular adaptation
of the astragalus, an ankle bone
• Since modern whales don’t have legs, they don’t
have ankle bones, so without more data it’s hard to
resolve the conflict between these two
phylogenetic hypotheses

27. 27
Whale phylogeny – more molecular data
(Nikaido et al. 1999)
• SINEs and LINEs — Short Interspersed Elements
and Long Interspersed Elements
• Transposable elements present in hundreds of
thousands of copies in mammalian genomes –
transposition is relatively infrequent
• Independent transposition into the same location
in two different genomes is unlikely (homoplasy)
• Therefore, if SINEs and LINEs are present at the
same location in two taxa, it is most likely
homologous.

28. 28
Presence/absence of SINEs and LINEs at 20 loci in a whale
(Baird’s beaked whale) and six artiodactyls
(Nikaido et al. 1999) (Fig. 14.8)

29. 29
Presence/absence of SINEs and LINEs at 20 loci in a whale
(Baird’s beaked whale) and six artiodactyls
(Nikaido et al. 1999) (Fig. 14.8)

30. 30
Presence/absence of SINEs and LINEs at 20 loci in a whale
(Baird’s beaked whale) and six artiodactyls
(Nikaido et al. 1999) (Fig. 14.8)

31. 31
Presence/absence of SINEs and LINEs at 20 loci in a whale
(Baird’s beaked whale) and six artiodactyls
(Nikaido et al. 1999) (Fig. 14.8)

32. 32
Presence/absence of SINEs and LINEs at 20 loci in a whale
(Baird’s beaked whale) and six artiodactyls
(Nikaido et al. 1999) (Fig. 14.8)

33. 33
Whale
phylogeny –
more fossils
Ichthyolestes, Pakicetus,
Ambulocetus,
Rhodocetus: whale-like
ear bones; artiodactyl-like
astragalus
Whales are an
evolutionary line of
artiodactyls
The whale + hippo tree is
supported by additional
data