BIOL359 Study Guide - Midterm Guide: Computational Phylogenetics, Evolutionary Taxonomy, Polyphyly
5 May 2018
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BIOL 359 Lecture Notes
Topic 7: Introduction to Phylogeny
➢ Phylogenetic the study of ancestor descendent relationships. The objective of phylogeneticists is to
construct phylogenies
➢ Phylogeny a hypothesis of ancestor descendent relationships
• Phylogenies can be based on morphological data, physiological data, molecular data or all three
• Phylogenies are usually constructed using DNA sequencing data (nucleotide/ amino acid sequencing)
➢ Phylogenetic Tree a graphical summary of a phylogeny
Phylogenetic Tree
➢ You can rotate a node 180o and that would not change the lineage
➢ Bifurcation when an ancestor divides into two
➢ Polytomy more than two lineages coming off of a node. Can happen for two reasons:
I. We do not have enough data to properly resolve the relationships coming off of that node
II. That’s actually what happened (e.g. an organism gets into an environment with no other organisms
with it and multiple lineages branch off of the same ancestor at the same time)
➢ Phylogenetic Characters
• We use characters to construct phylogenies. A character is any attribute of an organism that can
provide us with insights into history (can also be nucleotide positions, which would possess 4-
character states A, T, G, C)
• Plesiomorphy: refers to the ancestral character state
• Apomorphy: a character state different than the ancestral
state, or derived state. Must be either a synapomorphy or
an autapomorphy
• Synapomorphy: a derived character state (apomorhpy) that is
shared by two or more taxa due to inheritance from a
common ancestor. Is phylogenetically informative in that it
tells us about the phylogenetic relationships. Synapomorphies
identify monophyletic groups. Mutations can create
sunapomorphies and reversals can remove sunapomorphies
• Autapomorphy: a uniquely derived character state
• Homoplasy: independently evolved and do not share the same characteristics as the ancestor at
the base of the tree. We want to avoid using homoplasious characters to construct phylogenies
➢ Monophyletic: a group that includes all of the descendants of a common ancestor. Monophyletic groups
are known as clades
➢ Non-Monophyletic: Any case that does not satisfy the above,
such as: paraphyletic and polyphyletic
➢ Paraphyletic: A group that includes some, but not all of the
descendants of a common ancestor (e.g. reptiles are a
paraphyletic group because they contain some, but not all of
the descendants of a common ancestor since birds are
closely related to them)
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➢ Polyphyletic: assemblages of taxa that have been mistakenly grouped on the bases of the
homoplasious character. Grouping organisms that do not belong together (e.g. vultures)
➢ How does Homoplasy occur?
• Ancestral conditions are not the same as the ancestor. We are only referring to the character
state/ features possessed by the ancestors. Results in polyphyletic groupings
• Parallel evolution independent evolution of the same features from the same ancestral condition
• Convergent evolution independent evolution of the same feature from different ancestral condition
• Secondary loss reversion to ancestral condition
➢ Parsimony (A.K.A cladistics)
• The principle of parsimony: simple explanations are preferred over more complicated ones (e.g. less
evolutionary steps are better than more steps to explain relationships. The phylogenetic tree with the
least number of steps is the most parsimonious
• 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, 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)
• Example: (1) arrange into phylogenetic
trees, all possible combinations that we
can get. The more taxa we have, the
more phylogenetic trees to come up with.
(2) select characters that are
synapomorphies brown blotches on the
hind legs, dark tail, horns, face. (3) look
at the characters and determine the
simplest way they came about in the
animals
Estimating the Confidence level of a phylogeny
➢ Boostrap Method computational technique for estimating the confidence level of a phylogenetic
hypothesis.
randomly generates new data sets from the original set
computes the number of times that a particular grouping (or branch) appeared in the tree
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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 cladistics 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
Using Phylogeny
➢ Biogeography: the branch of science that seeks explanations for why organisms are found in some
regions, but not others. Often involves the use of phylogenies to test hypotheses concerning the
geographic origins of different species or groups of species (chameleons)
➢ Coevolution: the process where evolutionary changes in the traits of one species drives evolutionary
changes in the traits of another species. Can involve predators and prey, hosts and parasites, and
mutualism. Coevolution can result in co-speciation
➢ Other phylogenetic methods
• Maximum likelihood
• Bayesian methods of phylogenetic inference
Topic 8: Studying Adaptation
➢ An adaptation is a trait that increases the fitness of the individual relative to individuals that do not
possess the trait – arise by selection, but the process may be aided (or hindered) by drift
➢ Testing hypotheses concerning whether traits in organisms are adaptive is a major component of
evolutionary biology
➢ The adaptive significance of some traits is not always obvious
Testing Hypotheses about adaptations
➢ Oxpeckers (pg. 371)
• Paul Weeks divided a herd of cattle into two random groups. He allowed the oxpeckers to visit
one group and the other group he protected from the oxpeckers. He did this three times,
switching the groups each time. At the beginning and end of each trial, Weeks counted the
ticks on every ox
• Weeks found that the oxpeckers had no effect on their hosts’ tick loads and a worsened effect
on open wounds in the groups with the oxpecker visits
• Weeks found that Cattle exposed to oxpeckers had considerably less earwax which lead to the
conclusion that oxpeckers are eaters of earwax
• There was also a possibility that oxpeckers may eat enough ticks to provide a benefit for other
hosts or in other environments
➢ All hypotheses must be tested, explanations unconfirmed by hypothesis testing are best regarded as
stories
➢ When studying adaptations:
I. Differences among populations are not always adaptations
find more resources at oneclass.com
find more resources at oneclass.com
Document Summary
Phylogenetic the study of ancestor descendent relationships. The objective of phylogeneticists is to construct phylogenies. Phylogeny a hypothesis of ancestor descendent relationships: phylogenies can be based on morphological data, physiological data, molecular data or all three, phylogenies are usually constructed using dna sequencing data (nucleotide/ amino acid sequencing) Phylogenetic tree a graphical summary of a phylogeny. You can rotate a node 180o and that would not change the lineage. Bifurcation when an ancestor divides into two. Polytomy more than two lineages coming off of a node. Can happen for two reasons: we do not have enough data to properly resolve the relationships coming off of that node. That"s actually what happened (e. g. an organism gets into an environment with no other organisms with it and multiple lineages branch off of the same ancestor at the same time) Phylogenetic characters: we use characters to construct phylogenies.
