RECONSTRUCTING EVOLUTIONARY TREES

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RECONSTRUCTING EVOLUTIONARY TREES
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Phylogeny
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• Evolutionary history of a group
• must be inferred indirectly from data
• we do not have any direct knowledge about any
  evolutionary histories

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Terminology
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• 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

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Terminology
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• 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

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Terminology
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• 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.

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Synapomorphies
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• 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.

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Synapomorphies cont.
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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

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Cladograms
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• 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

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Examples of Synapomorphies
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• 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

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Bird example
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• 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

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Identifying Synapomorphies
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• 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

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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).

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If you can identify group I-L as being related
through a distant ancestor ( ) Then this can
be your outgroup.
If A-H represent the phylogenetic group you are
proposing then
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Terminology
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• 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

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Homoplasy cont
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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

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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.

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Principles for constructing a phylogenetic
treeUsing parsimony to resolve conflicts in data
sets
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• 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

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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.

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However
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• 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

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Relationships found in cladograms
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• 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

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B
D
E
A
C
F
Monophyly
Paraphyly
Polyphyly
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Choosing characters for the analysis
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• 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

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Molecular characters
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• 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

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The case of the whale
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An example from a single morphological character
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• 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

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Fossil records provide evidence that suggests
that whales are related to the ungulates
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• 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

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Problems with the former tree
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• 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

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Multiple Molecular characters
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• 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

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Homework exercise
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An exercise in constructing an evolutionary
history
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• 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

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Lets use this information to choose between two
possible trees
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• 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

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Searching among trees
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• The number of alternative trees to search can
  quickly become impossible

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Computers can automate the task
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• 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

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Evaluating trees
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• 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

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

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Maximum likelihood
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• 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.

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Maximum likelihood continued
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• 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.

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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.

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Genetic distance (Phenetic approach)
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• 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

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Genetic distance (cont)
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• 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

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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.

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Resolving character conflict
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• 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

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A new molecular character for helping to
determine phylogeny
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• SINEs and LINEs (Short or Long INterspersed
  Elements)
• These are parasitic DNA sequences that insert
  themselves into a hosts 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)

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• 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.

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SINE and LINE Data support the whale hippo
hypothesis
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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

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Homework exercise
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An exercise in constructing an evolutionary
history
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• 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

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Lets use this information to choose between two
possible trees
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• 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

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Current phylogeny of ungulates
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What can phylogenies be used for?
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Using phylogenies .......
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• 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

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Using phylogenies can answer questions about...
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• 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

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Using phylogenies to ...
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• 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

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Using phylogenies can document coevolution
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• 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.

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

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The End
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Figure 4.3 page 114
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Figure 4.4 p. 115
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Figure 4.6 p. 117
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Figure 4.7 p. 120
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Figure 4.10 p. 126
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The End
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