Phylogenetics is the study of evolutionary relationships between organisms and how they are related through common ancestry. Phylogenetic trees graphically represent hypotheses of ancestor-descendent relationships. They can be constructed using morphological, physiological, or molecular data to identify shared derived character states that cluster organisms into monophyletic groups. Parsimony seeks to minimize evolutionary changes and identify the most parsimonious tree. Phylogenies are useful for studying questions about evolution, biogeography, and coevolution.

1. Introduction to Phylogeny
Required Reading: chapter 4 (Ignore Box 4.1)

2. Objectives
• The basics of phylogenetic trees
• How phylogenetic trees are constructed.
• How phylogenies can address questions
about evolution.

3. Phylogeny
Phylogenetics: the study of ancestor descendent
relationships. The objective of phylogeneticists is
to construct phylogenies
Phylogeny: A hypothesis of ancestor descendent
relationships.
Phylogenetic tree: a graphical summary of a
phylogeny

4. Phylogeny
All life forms are related by common ancestry and
descent. The construction of phylogenies provides
explanations of the diversity seen in the natural
world.
Phylogenies can be based on morphological data,
physiological data, molecular data or all three.
Today, phylogenies are usually constructed using
DNA sequence data

5. Review:
Introduction
to
Phylogenetic
Trees

6. Phylogenetic Characters
We use characters to construct phylogenies.
A character is any attribute of an organism
that can provide us with insights into history
(shared ancestry).
In molecular phylogenies, characters are
typically nucleotide positions in a gene
sequence, and each position can possess
four CHARACTER STATES: A,C, G, or T

7. Cladisitc Character State Definitions
• Plesiomorphy: refers to the ancestral character state
• Apomorphy: a character state different than the
ancestral state, or DERIVED STATE
• Synapomorphy: a derived character state
(apomorphy) that is SHARED by two or more taxa
due to inheritance from a common ancestor: these
character states are phylogenetically informative using
the parsimony or cladistic criterion
• Autapomorphy: a uniquely derived character state

8. Character States
After Page and Holmes 1998
we will return
to this

9. Figure 4.2, pg.113
More Synapomorphies
shared
shared

10. Definitions
Monophyletic: a group that includes ALL of the
descendents of a common ancestor. Monophyletic
groups are also known as CLADES
Non Monophyletic: Any case that does not satisfy
the above, such as:
Paraphyletic: A group that includes some, but not all
of the descendents of a common ancestor
Polyphyletic: assemblages of taxa that have been
erroneously grouped on the basis of homoplasious
characters (eg “vultures”)

11. Monophyletic Groups
•All groups circled in red are monophyletic
fig 4.1 p112

12. Examples of Synapomorphies
Figure 4.3, pg. 114
Synapomorphies identify monophyletic groups

13. Monophyly and Non-Monophyly
After Page and Holmes1998

14. Reptiles: A Paraphyletic Group
Paraphyletic – a grouping that contains some, but not all descendants
of a common ancestor
Sauropsida
Naming based on current data
Reptiles
Naming based on past data

15. Homology and Homoplasy
A character state that is shared between two
DNA sequences or taxa may be so because
they inherited it from a common ancestor,
or it is HOMOLOGOUS (a homology/
synapomorphy)
Alternatively, the shared character might
occur because they were evolved
independently, in which case they are called
a HOMOPLASY

16. Why can Homoplasy Occur?
After Page and Holmes1998

17. Homoplasy and Polyphyly
Homoplasy results in erroneous, polyphyletic groupings
such as “vultures”

18. A ‘Vulture’
“Vultures” are a polyphyletic group. New world and old world
vultures provide an example of homoplasy resulting from convergent
evolution.

19. More Examples of Convergence

20. Analogy (non homology): The fins of a whale and
the fins of a shark are another example of homoplasy
due to convergence, the independent acquisition of a
character in different lineages

21. Three Spine Stickle Back: Parallel
Evolution
• 3 spine stickle back
species pairs have evolved
independently in coastal
lakes of British Columbia
• Positive assortative mating
and disruptive selection
have been important in the
divergence of these pairs

22. Reversals & Phylogeny
Figure 4.5, pg. 116

23. Constructing Phylogenetic Trees
• We use homologous characters (synapomorphies)
to construct phylogenetic trees and to identify
groups that are monophyletic; synapomorphies are
phylogenetically informative.
• We want to avoid using homoplasious characters
to construct phylogenies

24. Homology and Homoplasy Revisited

25. Parsimony (also known as cladistics)
The Principle of Parsimony: simple explanations
are preferred over more complicated ones.
In terms of phylogenetic trees, less evolutionary
steps are better than more steps to explain
relationships. The tree with the least number of
steps is the most parsimonious.
The parsimony method minimizes the total number of
evolutionary changes required to explain relationships

26. Making Inferences With Parsimony:
Evolution of the Camera Eye

27. Constructing Trees with Parsimony
Outgroup: When constructing a phylogeny for a
group of organisms, we need to employ an
outgroup, which is not part of the group of interest
(the ingroup), but also not too distantly related to
it.
The outgroup is used to polarize the character
states, or infer change. The character state
possessed by the outgroup is defined a priori as
ancestral (pleisiomorphic)

28. Whale Evolution
Ambulocetus

29. The Artiodactyla
The artiodactyla are a group of hoofed mammals
that possess an even number of toes, and includes
camels, pigs, peccaries, deer, the hippopotamus,
cattle and giraffes. The perissodactyla are hoofed
mammals that possess an odd number of toes (e.g.
horses, rhinos, tapirs).
Are whales really a member of the artiodactyla?

30. Selecting Phylogenetic Trees with
Parsimony
Figure 4.8, pg. 121
Whales early Whales late

31. Parsimony
using
morphology
Figure 14.5, pg. 558
Outgroup is a Perissodactyl

32. Parsimony
using
molecular
characters
Figure 14.6, pg. 559
• Site 142 is plesiomorphic (uninformative)
• Site 192 is a autapomorphic (uninformative)
• Sites 162, 166 & 177 are synapomorphies (informative)

33. What do the informative sites tell us
about whale phylogeny?
• Site 162 & 166
conflict with site 177
• Hence there is
homoplasy in the data
set.
• What is the most
parsimonious tree
looking at all
characters?
– Whales early – 47 nt
changes
– Whales late – 41 nt
changes
•Whales late has less evolutionary steps to explain relationships: the
most parsimonious explanation

34. Assessing Confidence in Phylogeny
• Bootstrap Method
– Computational technique for
estimating the confidence
level of a phylogenetic
hypothesis.
• Randomly generates new data
sets from the original set (1000
replicates is most common)
• Computes the number of times
that a particular grouping (or
branch) appeared in the tree.

35. Phylogeny and Taxonomy
• Taxonomic groups can be:
– Monophyletic – contain all descendants of a common
ancestor
– Paraphyletic – contain some but not all descendants of a
common ancestor, or polyphyletic (erroneous
homoplasious groupings)
– The goal of cladistic taxonomy is to only recognize
monophyletic groups as valid taxa, but traditional
taxonomy has not always done this
• Cladistics- the use of parsimony to construct
evolutionary relationships
• cladistic taxonomy= evolutionary taxonomy

36. Basics of Taxonomy
Super group Unikonta
Kingdom Animalia
Phylum Chordata
Class Mammalia
Order Primata
Family Hominidae
Genus Homo
Species sapiens
Three domains of life: Archaea, Bacteria, Eukarya. The Eukarya
are hierarchically divided as follows:

37. Example: The Amniota
All aminotic eggs possess several membranes (the amnion, chorion and
allantois) that protect the developing embryo. The amniotic egg was
an important evolutionary innovation and adaptation for life on land,
and protects the developing embryo from desiccation

38. Paraphyletic Groups: many taxonomic groups that were
recognized by traditional taxonomy are paraphyletic (eg fish)
Prokaryotes, Fish and
Dicots (in addition to
‘reptiles’) are all examples
of paraphyletic groups

39. Based on current data
Cetartiodactyla
Based on past data
Artiodactyla
The Artiodactyla are another example of a paraphyletic grouping

40. Using Phylogenies: Chameleons
Biogeography is the branch of science that seeks
explanations for why organisms are found in some regions,
but not others. This very often involves the use of
phylogenies to test hypotheses concerning the geographic
origins of different species, or groups of species such as
the Chameleons (we will consider biogeography in much
more detail later in the course)

41. Using Phylogenies: Chameleons

42. Using Phylogenies: Coevolution
Coevolution: The process where evolutionary changes in the
traits of one species drives evolutionary changes in the
traits of another species. Coevolution can involve predators
and prey, hosts and parasites, and mutualisms, such as
aphids and their endosymbiotic bacteria (above).
Coevolution can result in co-speciation.

43. Phylogeny & Coevolution
Figure 4.17, pg 136

44. Other Phylogenetic Methods
We have discussed the method of Parsimony, or Cladistics in
phylogenetic reconstruction. However, other more
powerful methods are available for use with DNA
sequence data.
These are collectively referred to as frequency probability
methods, and include Maximum Likelihood, and Bayesian
methods of phylogenetic inference. These are
computationally intensive, and have only been in frequent
use for the past 12 years or so, when computers became
powerful enough to accommodate them
These methods are covered in Biol 366 and Biol 480

45. Phylogeny Summary
• We must use characters that are homologous
(synapomorphies) and avoid homoplasies in
phylogeny construction
• Parsimony seeks the simplest explanation that
requires the least amount of change (fewest
steps).
• Phylogenetic reconstruction is a powerful tool
that can be used to answer many evolutionary
questions