Topic 7 Phylogeny

Introduction to Phylogeny
Required Reading: chapter 4 (Ignore Box 4.1)
• The basics of phylogenetic trees
• How phylogenetic trees are constructed.
• How phylogenies can address questions
about evolution.
Phylogenetics: the study of ancestor descendent
relationships. The objective of phylogeneticists is
to construct phylogenies
Phylogeny: A hypothesis of ancestor descendent
Phylogenetic tree: a graphical summary of a
All life forms are related by common ancestry and
descent. The construction of phylogenies provides
explanations of the diversity seen in the natural
Phylogenies can be based on morphological data,
physiological data, molecular data or all three.
Today, phylogenies are usually constructed using
DNA sequence data
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
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
Character States
we will return
to this
After Page and Holmes 1998
More Synapomorphies
Figure 4.2, pg.113
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”)
Monophyletic Groups
fig 4.1 p112
•All groups circled in red are monophyletic
Examples of Synapomorphies
Synapomorphies identify monophyletic groups
Figure 4.3, pg. 114
Monophyly and Non-Monophyly
After Page and Holmes1998
Reptiles: A Paraphyletic Group
Naming based on past data
Naming based on current data
Paraphyletic – a grouping that contains some, but not all descendants
of a common ancestor
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/
Alternatively, the shared character might
occur because they were evolved
independently, in which case they are called
Why can Homoplasy Occur?
After Page and Holmes1998
Homoplasy and Polyphyly
Homoplasy results in erroneous, polyphyletic groupings
such as “vultures”
A ‘Vulture’
“Vultures” are a polyphyletic group. New world and old world
vultures provide an example of homoplasy resulting from convergent
More Examples of Convergence
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
Three Spine Stickle Back: Parallel
• 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
Reversals & Phylogeny
Figure 4.5, pg. 116
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
Homology and Homoplasy Revisited
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
Making Inferences With Parsimony:
Evolution of the Camera Eye
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
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)
Whale Evolution
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?
Selecting Phylogenetic Trees with
Whales early
Figure 4.8, pg. 121
Whales late
Figure 14.5, pg. 558
Outgroup is a Perissodactyl
Figure 14.6, pg. 559
• Site 142 is plesiomorphic (uninformative)
• Site 192 is a autapomorphic (uninformative)
• Sites 162, 166 & 177 are synapomorphies (informative)
What do the informative sites tell us
about whale phylogeny?
• Site 162 & 166
conflict with site 177
• Hence there is
homoplasy in the data
• What is the most
parsimonious tree
looking at all
– Whales early – 47 nt
– Whales late – 41 nt
•Whales late has less evolutionary steps to explain relationships: the
most parsimonious explanation
Assessing Confidence in Phylogeny
• Bootstrap Method
– Computational technique for
estimating the confidence
level of a phylogenetic
• 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.
Phylogeny and Taxonomy
• Taxonomic groups can be:
– Monophyletic – contain all descendants of a common
– 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
Basics of Taxonomy
Three domains of life: Archaea, Bacteria, Eukarya. The Eukarya
are hierarchically divided as follows:
Super group
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
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
Based on past data
Based on current data
The Artiodactyla are another example of a paraphyletic grouping
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)
Using Phylogenies: Chameleons
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.
Phylogeny & Coevolution
Figure 4.17, pg 136
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
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
• Phylogenetic reconstruction is a powerful tool
that can be used to answer many evolutionary
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