1. Phylogeny: Reconstructing Evolutionary Trees
Chapter 14

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. 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. 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. 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. 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. 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. Types of homoplasy Convergence Parallelism Reversal
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. 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
ACCT
ACTT
ACCT

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

14. A tree for [dogs, humans, lizards] – 2
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. A tree for [dogs, humans, lizards] – 3
hair
backbone
dog
lizard
human
hair
backbone
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

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

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. A tree for [dogs, humans, lizards] – 5
hair
backbone
lizard
human
dog
hair
backbone
(a)
(c)
human
lizard
dog
hair
backbone
(b)
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

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

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

25. Sequence data for parsimony analysis (Fig. 14
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. 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. 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. 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. 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. 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. 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. 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. 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