1. RECONSTRUCTING EVOLUTIONARY TREES
RECONSTRUCTING EVOLUTIONARY TREES

2. Phylogeny Evolutionary history of a group
Evolutionary history of a group
must be inferred indirectly from data
we do not have any direct knowledge about any evolutionary histories

3. Terminology Phylogenetics- Phylogeny- Phylogenetic tree
Phylogenetics-
Study of the history of the evolution of a species or other taxon
Phylogeny-
The ancestral history of a species
Phylogenetic tree
– A diagram which shows the ancestry and descent of a group of species

4. Terminology Pleisiomorphy- Sympleisiomorphy – Apomorphy –
Terminology
Pleisiomorphy-
an ancestral character trait also called relictual
Sympleisiomorphy –
shared ancestral traits
Apomorphy –
a derived or descendant character trait
Synapomorphy –
shared derived traits used to reveal evolutionary relationships

5. Terminology Cladistics-
Terminology
Cladistics-
A classification scheme based on the possible ancestral relationships in a group which was built using relationships inferred by the presence of synapomorphies
Cladogram –
a phylogenetic tree based on synapomorphies.
Phenetics-
classification scheme based on grouping populations according to their similarities. No attempt is made to determine the derived vs. Primitive state of the characters, thus no clear reflection of the ancestral history is implied.

6. Synapomorphies
Synapomorphies are the result of genetic divergence from an ancestral species
Are homologous because they derive from a common ancestor
Must be independent and not correlated with other traits (linkage equilibrium)
Synapomorphies help to define closely related groups.

7. Synapomorphies cont.
Two key elements of synapomorphies which allow the assumption of evolutionary relationships
Synapomorphies represent evolutionary branch points
Each branch point on a cladogram represents at least one (possibly more) derived trait has arisen
Synapomorphies are nested
Figure 4.2 Page 113

8. Cladograms
A phylogenetic tree constructed by clustering synapomorphies
Synapomorphies identify evolutionary branch points
At a branch point, lineages begin evolving independently
Synapomorphies are nested so when moving from the tip of a phylogenetic tree back towards the root, each branch represents a new synapomorphy
Synapomorphies are indicated by bars across branches Figure 4.3

9. Examples of Synapomorphies
Feathers are found in all birds because they were derived from a simpler structure in their common dinosaur ancestor.
Within the birds, the passerine group all share a 3 plus 1 toe arrangement which this group shares as a synapomorphy from the 2 plus 2 arrangement in their common ancestor

10. Bird example Synapomorphies can be identified at any taxonomic level
Synapomorphies can be identified at any taxonomic level
A given series of synapomorphies can be used to define phylogenetic relationships
for example, in birds, synapomorphies can be used to identify trends in the changes in forelimbs, hind limbs, breastbones, tail, and pelvis
Example

11. Identifying Synapomorphies
Identifying Synapomorphies
Not an easy task
Need to first establish homology of the trait within the group of interest.
Accomplished by documenting and correlating structural, genetic and developmental similarities
Must be able to deduce the direction of change through time.
Which is the ancestral character state and which is the derived character state.
This happens through outgroup comparison

12. Outgroups Use outgroup– a close relative that branched off earlier.
identifying an outgroup can be challenging. It requires…
information from other phylogenies to suggest relationship between the groups
Fossil record confirmation that the proposed outgroup is older (to be sure that the outgroup is more ancestral and therefore has the ancestral form of the trait of interest).

13. If A-H represent the phylogenetic group you are proposing then ……
If you can identify group I-L as being related through a distant ancestor ( ) Then this can be your outgroup. A B C D E F G H J K L I

14. Terminology
Homoplasy- information which may cause misinterpretation of information about the evolutionary history of an organism.
Examples
Convergent evolution – similarity between species that is due to…
a character trait arising on 2 or more separate occasions in evolutionary history.
These traits are analogous may carry out similar functions but…
The origin of their structure is along different evolutionary pathways.
This type of evolution is also referred to as parallel evolution
You are already familiar with the wings of insects, birds and bats are the result of convergent evolution
Other examples

15. Homoplasy cont
Reversals- Traits which have reverted back to an ancestral form from a derived state.
p. 116
Mistakes due to homoplasy can be minimized by
Choosing characters that evolve slowly relative to the age of the group
Using characters that do not commonly show reversals or convergence
If reversals are found they do not qualify as synapomorphies

16. How to identify homoplasy
Use multiple synapomorphies and traits in identifying groups.
Follow the rule of parsimony which says that the fewest number of changes needed to explain the evolutionary relationships is most likely the correct one. Example
Also, often careful analysis of the structure itself usually reveals differences at a cellular or microscopic level.
Most often, however, we do not have
the material or
the ancestral history needed to identify Homoplasy
so most cladistic datasets do contain hidden homoplasious information.

17. Principles for constructing a phylogenetic tree Using parsimony to resolve conflicts in data sets
Look at homologous traits across a group of species
The characteristics of traits which can be used for scoring individuals are
- Those that are variable among the taxa being studied
- Those that are heritable
- Characters must all be independent of one another
- Use traits that are similar between groups studied because this indicates a common ancestor
Use Parsimony

18. Why using parsimony is valid
Usually valid to assume that reversals and convergences are rare relative to similarities when coming from a common ancestral form
Reversals and convergences always require multiple steps and so will lead to more steps in a cladistic analysis
So Homoplasious trees will not normally be the most parsimonious trees derived.

19. However
Some homoplasy is almost always evident in evolutionary history
this means there are several ways that a cladogram may be constructed
The accepted cladogram will be the one that has the most support from several different possible treatments of the data

20. Relationships found in cladograms
Relationships found in cladograms
Monophyletic – A group which contains a common ancestor and ALL of its descendants
Paraphyletic – Groupings which include some but not all descendants of a common ancestor.
Polyphyletic- grouping ignores ancestry just groups them based on similar traits
does not use synapomorphies and
includes no ancestors.
this is a more phenetic approach

21. B D E A C F
Monophyly
Paraphyly
Polyphyly

22. Choosing characters for the analysis
Morphological traits
Essential in the case of fossils
Scoring traits on fossils is tedious and requires expertise.
Sometimes looking at embryological development of similar structures can help identify whether traits are homologous

23. Molecular characters
Nucleotides may be scored rapidly and a huge number of genes are available for comparison
Models have been developed to predict how sequences change through time
However, homoplasy is difficult to identify because differences are limited to just four character states A, G, C, and T

24. The case of the whale

25. An example from a single morphological character
Ungulates are divided into two monophyletic groups
Artiodactyla – hippos, cows, pigs, deer, giraffes, antelopes and camels
Perrisodactyla- horse and rhinos
This grouping is due to many structural characteristics of the skull and dentiton
but mainly it is determined by the shape of an ankle bone called the astragalus Fig 4.7

26. Fossil records provide evidence that suggests that whales are related to the ungulates
including horse, rhino, deer, cow, camel, and antelope
whales are most closely related to the hippo
Previously it was thought that some of the characteristics shared by whales and hippos were convergences due to their aquatic lifestyles

27. Problems with the former tree
If whales and hippos are sister groups then this morphological trait (astragalus) does not follow the most parsimonious route in evolution
The whales would have had to lose the character trait See Figure 4.8

28. Multiple Molecular characters
Molecular data are also available for the whale/hippo hypothesis.
When multiple characters are used, each trait is treated independently and mapped onto a possible cladogram
The sum of all changes required on each possible tree is totaled and the best tree is considered to be that which is most parsimonious or has the least number of changes required

29. Homework exercise

30. An exercise in constructing an evolutionary history
Figure 4.9 shows a group of DNA characters in the sequence for the gene which encodes a milk protein
Of the sequences shown, 15 of the nucleotides group at least two taxa and separate them from the rest. All of the rest are invariant and provide no information

31. Let’s use this information to choose between two possible trees
First we need to find the most parsimonious reconstruction for each character that changes (we will use positions 151, 162, 166,176,177, and 194)
Then we count up the required changes and the tree with the fewest is the best choice

32. Searching among trees
The number of alternative trees to search can quickly become impossible
4 Species
3 branching patterns
5 Species
15 branching patterns
6 Species
105
7 Species ( fig 14.4)
945
8 Species
10,395

33. Computers can automate the task
With a group of 10 or less taxa, computers can test all possible combinations
For more taxa the computer is too slow to test all possibilities

34. Evaluating trees
Bootstrapping – computer rebuilds a new data set from the existing one.
Computer randomly selects one of the data points then another and then another until you have a data set the same size as the original.
(Not all of the original are included since some will never be chosen by the random process).
Build a tree from this data set and then repeat the entire process.
This is repeated several times over and branches which occur at greater than 70% have been shown to reflect the true phylogeny

35. Two other methods do not use parsimony
Phylogenetic methods compute probability or likelihood of specific trees.
Maximum likelihood
Bayesian Analysis
Genetic Distance (more phenetic)

36. Maximum likelihood
Statistical analyses may be used to determine the best tree
Works from a mathematical formula that describes the probability that a certain nucleotide substitution will occur
(somehow computed by biologists and unique to the DNA sequence being studied).
Compare this model with a particular phylogenetic tree and determine how likely it is that a particular set of DNA sequences in a particular tree will actually occur.

37. Maximum likelihood continued
Maximum likelihood continued
A computer evaluates each tree and computes the probability of each arrangement occurring based on the specified model of character change
The probability is reported as the likelihood that each given tree explains the data
Can actually demonstrate that some potential trees really are more likely.
Then can do statistical analyses to decide how likely a tree really is.

38. Bayesian Markov Chain Monte Carlo
This is a different angle of approaching the question of maximum likelihood.
It works with individual trees and attempts to find a probability that a particular tree is correct.
The Maximum likelihood methods are believed to work better than Parsimony but they cannot always be used.
You must have a model of likely changes in DNA before they can be used.

39. Genetic distance (Phenetic approach)
Genetic distance (Phenetic approach)
All character data is converted into one distance value that represents genetic differences between taxa.
The distance value is calculated by converting the discrete and individual data points into one number representing a measure of their similarity
For instance, the percentage of nucleotide sites that differ between two taxa may be computed. (i.e. if 18 out of 100 nucleotides are different between the two this could be represented as a genetic distance of .180

40. Genetic distance (cont)
Genetic distance (cont)
This method loses all specific information but can capture the overall degree of similarity between pairs of taxa
Taxa are clustered together based on their genetic distances and a tree is constructed from this which minimizes the total distance among taxa. Fig 4.10

41. Ways of evaluating how good a particular tree is
Produce a consensus tree with parsimony
Use statistical analyses to evaluate the best trees under ML and BMCMC
Compare the best trees under parsimony, ML and BMCMC to see how consistent they are.
Do all three and if consistent can be pretty confident you have the right tree.

42. Resolving character conflict
When conflict still exists all we can really do is wait for more data
Perhaps new techniques will arise which can help to resolve the conflict

43. A new molecular character for helping to determine phylogeny
SINEs and LINEs (Short or Long INterspersed Elements)
These are parasitic DNA sequences that insert themselves into a host’s genome
Events which lead to the insertion of parasitic DNA into the genome are rare so that convergence is unlikely (i.e. not likely that the same homologous sequence would insert into two different lineages in the exact same location)
Reversal is also unlikely to go undetected because if the parasitic DNA is lost it will undoubtedly not be cut out exactly as it entered in and will therefore take along some of the host DNA genome with it. (cont)

44. This allows geneticists to differentiate from those that never had the parasitic DNA inserted and those who secondarily lost it
Therefore, SINE and LINE are assumed to be free of homoplasy.

45. SINE and LINE Data support the whale hippo hypothesis

46. Recent fossil finds also corroborate the trees determined by cladistic analysis
Wolf-sized Pakicetus and fox-sized Ichthyolestes are both terrestrial but have whale-like ear bones and astragalus bones in their ankles
Also the more recent Ambulocetus and Rhodocetus have the same characteristics
Whale video

47. Homework exercise

48. An exercise in constructing an evolutionary history
Figure 4.9 shows a group of DNA characters in the sequence for the gene which encodes a milk protein
Of the sequences shown, 15 of the nucleotides group at least two taxa and separate them from the rest. All of the rest are invariant and provide no information

49. Let’s use this information to choose between two possible trees
First we need to find the most parsimonious reconstruction for each character that changes (we will use positions 151, 162, 166,176,177, and 194)
Then we count up the required changes and the tree with the fewest is the best choice

50. Current phylogeny of ungulates

52. What can phylogenies be used for?
What can phylogenies be used for?

53. Using phylogenies
CAN HELP ANSWER QUESTIONS ABOUT RATES OF CHANGE
Example
Rates of divergence in a protein were used to estimate the colonization time of the Hawaiian Drosophila at 42 million years
The Islands are only 5-6 million years old

54. Using phylogenies can answer questions about...
THE AGE OF CLADES
When the fossil record can provide documentation for a lineage it can help place a time scale on the branching points
Cladograms can then be used to make predictions about what we might find in future fossil discoveries

55. Using phylogenies to ...
Understand how organisms came to be where they are.... Biogeography
For instance ...can use phylogenetic trees to help establish how some taxa radiated out to their current locations when Gondwana broke up. Chameleons example in the book.
Did Chameleon species disperse or were they separated at the time that Gondwana broke up? Figure 14.13
This field of study is called phylogeography

56. Using phylogenies can document coevolution
Using phylogenies can document coevolution
Example
Ants that farm fungi or Aphids with bacterial endosymbionts have been studied. Leaf cutter ant video.
Phylogenetic analysis of the two groups which are in association may provide evidence that the species have evolved in concert.

57. Using phylogenies to answer questions
Using phylogenies to answer questions
USED TO TRACK DOWN THE TRANSMISSION HISTORY OF COMMUNICABLE DISEASES
Plague example in the book.

58. The End

59. Figure 4.3 page 114

61. Figure 4.4 p. 115

62. Figure 4.6 p. 117

63. Figure 4.7 p. 120

66. Figure 4.10 p. 126

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72. The End