Phylogenetics (7) Flashcards
Phylogeny?
= a diagram that shows lines of evolutionary descent from a common ancestor.
Cladogram?
= a branching diagram tracing evolutionary history.
Branch?
= unbroken lines of descent.
Terminal taxa?
= extant organisms.
Apomorphies?
= derived features.
What do branches do?/What do they show? (4)
• Show evolutionary histories.
• Show lineages.
• Summarize evolution across lineages.
• Show divergence from a common ancestor (speciation).
Natural groups?
= groups that share common ancestor, ie. monophyletic.
Monophyly?
= common ancestor + all its descendants.
Paraphyly?
= common ancestor + some of its descendants.
Polyphyly?
= no recent common ancestor/group that doesn’t contain a single common ancestor of the group.
Steps for Tree Reading? (3)
• Tree tip order = not important.
• No terminal node is ancestral to any other terminal node.
• No terminal node is more evolved than any other terminal node.
Tree styles? (2)
• Mammal phylogeny.
• Rectangular cladogram.
Transition?
= interchanges of purine for purine (A-T or G-C).
Transversion?
= interchanges of purine for pyramidine (A-G or T-C).
Which is slower between transversion & transition?
Transversion.
Molecular clock?
= probabilities of where you can estimate/calculate time.
How do we obtain a cladogram? (2)
• From Morphological data.
• From Fossils.
Why are polyploids important?
Important for biodiversity.
Eg of polyploidy & biodiversity?
Grey tree frogs.
How are polyploids formed?
Via autopolyploidy.
Autopolyploidy?
= polyploid within same species.
Phylogram?
= diagram that includes evolutionary change information.
Branch length in Phylogram?
= amount of change/ diversification rates.
Eg of Phylogram?
Dwarf chameleons.
Branch length of Phylogram occurs under what?
Mutation selections.
How do we obtain a cladogram from eg. Morphological data?
Use the categorical/binary (0,1,1,2…) scores.
Steps to draw a Phylogenetic tree? (5)
• Choose the taxa.
• Select the characters.
• Determine polarity (using fossil evidence).
• Group the features by synapomorphies.
• Work through all synapomorphies & group accordingly.
How do you choose the best tree?
Via the Principle of Maximum Parsimony.
Parsimony?
= the most likely phylogeny is the simplest one/the one with the least evolutionary events.
Principle of Maximum Parsimony?
= principle where we use simplest explanation with the least assumptions & the shortest tree is the preferred hypothesis of relationships.
Why use the Principle of Maximum Parsimony? (2)
• To avoid guessing & complication.
• Has the least number of steps.
Principle of Maximum Parsimony conclusion? / What does it conclude? (2)
• That it’s much easier to lose a trait than it is to gain it a second time.
• The simplest tree with the least no. of events is the best tree.
Bayesian?
= Stats & priors.
Homologous characters?
= features that are similar in structure/position due to common ancestry.
Analogous characters?
= features similar not due to common ancestry but due to function.
Homology?
= basis of analysis (that basis being the common ancestor).
Result of analogy?
Homoplasy.
Homoplasy type?
• Convergence.
Result of homology?
Congruence.
Eg of homology?
Protea &
Egs of analogy? (2)
• Vertebrate eye & Octopus eye.
• Pitcher plants.
How do we identify homology?
• Common ancestor via same structure/position.
Egs of convergence? (3)
• Human & Octopus eye.
• Bird & Bat wings.
• Capitula in sunflowers/daisies & Protea.
Significance of rooting phylogenetic trees? (2)
• Provides evolutionary direction.
• Defines the point on a tree of a hypothetical ancestor.
Methods of Phylogenetic tree rooting? (3)
• No rooting.
• Mid-point rooting.
• Outgroup rooting.
Which rooting “system” is commonly used?
Outgroup rooting.
Outgroup rooting attributes? (3)
• Seeks to maintain monophyly.
• Selects a taxonomy related to the study group but not part of the study group.
• Gives conclusions about relatedness.
Types of data that we can use to infer a phylogeny? (2)
• Morphological data.
• Molecular data.
Polytomy?
= internal node of a cladogram that has more than 2 sister taxa/immediate descendants.
Aim in Phylogenetics?
To get informative characters to get relationships.
What can Phylogenetic trees tell us? (4)
• Enable us to visualize evolution.
• Show us patterns of speciation.
• Enable us to classify diversity in a natural way.
• Enable us to make predictions about fossils.
Apomorphy?
= derived features.
Pleisiomorphy?
= ancestral features/traits.
Autapomorphy?
= features unique to a specific group.
Synapomorphy?
= shared derived features.
What do synapomorphies do?
Provide information on relationships.
Outgroup?
= a taxon that has no shared characters with other taxa.
Eg of patterns of speciation?
Spiny leg blades of Orb-weaving spiders on Hawaiian islands.
Eg of evolutionary relationships?
Mammals.
How do we classify organisms in a natural way?
Via natural groups, which should be monophyletic.
What are the 3 natural groups that organisms are classified under?
• Monophyly.
• Paraphyly.
• Polyphyly.
Eg of enables us to make predictions about fossils?
Whale’s ankles.
Root of Phylogenetic trees?
= oldest common ancestor.
How do you determine which organisms are more closely related than other organisms?
They share a more recent common ancestor.
Sister taxa?
= groups that are more closely related to each other than either is to another group.
Homoplasy types? (3)
• Parallel homoplasy.
• Convergent homoplasy.
• Reversion homoplasy.
Parallel homoplasy?
= ancestral condition of a variable trait (plesiomorphy) is present in common ancestor but derived state (apomorphy) has evolved independently.
Convergent homoplasy?
= trait is absent in common ancestor (analogous traits).
Reversion homoplasy?
= transition within a lineage that goes back to the ancestral state.
Phylogenetic tree?
= branching diagram representing the pattern of relatedness of organisms.
Other definition of Phylogeny?
= a hypothesis about how organisms are related & how groups diversified.
What does a phylogeny show us?
Shows us the relationship between different species or genes.
What do Phylogenetic trees show us?
The patterns of descent of organisms from their ancestors.
What do we mean by “if we use different parts of the genome, we can determine the different evolutionary processes”?
Main components of a phylogeny? (4)
• Branches.
• Nodes.
• Tips.
• Root.
Thing to note for the main components of a phylogeny?
Know these & how they fit into different parts of the time.
Bifurcating tree?
= a tree that diverges/branches.
Where do terminal taxa originate from?
They came from a common ancestor, ie., their common ancestor are species events.
What do the branch length tells us? (2)
• How many changes occurred in the evolutionary history.
• How long the time frame of the evolutionary history of events is.
Node attribute?
Can rotate.
Other points to note under the 1st Reading trees tip? (2)
• Adjacent taxa aren’t necessarily more closely related to each other than taxa placed further away.
• Phylogenies are all identical but the ordering isn’t the same.
Eg of 2nd tree reading tip?
You & your cousins vs your aunts & grandparents.
Egs of 3rd tree reading tip? (2)
• Dogs & wolves.
• Chimpanzees & humans.
Differences between phylogeny, phylogenetic tree, cladogram & phylogram?
● Phylogeny = same as phylogenetic tree.
● Phylogenetic tree = same as phylogeny.
● Phylogram = shows changes/relatedness with inclusion of time.
● Cladogram = shows relatedness with exclusion of time.
Types of Phylogenetic trees? (2)
• Phylogram.
• Cladogram.
Important thing to note about branches?
They are non-temporal UNLESS branched with time.
How did homologous characters evolve?
Due to a common ancestor.
What is a basis for analysis of traits/trait changes?
Homology.
How are Orb-weaving spiders an eg of Patterns of speciation?
They are known to show the largest radiation on Hawaiian islands.
Phylogeny principles? (2)
• Must be based on homology/homologous characters.
• Trees must be rooted to give evolutionary direction.
Parsimony basis?
Okhan’s Razor.
Parsimony’s goal?
To reduce homoplasy when constructing a tree.
Difference between homoplasy & synapomorphy regarding definition?
● Homoplasy = shared characters due to separate mutations.
● Synapomorphy = shared characters due to common ancestor.
Homoplasy?
= share characters due to separate mutations.
Difference between homoplasy & synapomorphy relatedness?
● Homoplasy = same character but not related (analogy).
● Synapomorphy = same character but related (homology).
Incorrect assumption of homoplasy?
Misleading about relationships.
Eg of Homoplasy due to convergence?
Wings arising twice.
What do branch length tell us? (2)
• Time (if tree is dated).
• Trait changes.
Mid-point rootingmethod attributes? (3)
• Doesn’t use outgroup as a root.
• Character changes are more clock-like.
• Focuses on how characters are changing through time.
What do we mean by “Character changes are more clock-like”?
We mean that character changes happen at about the same speed/are relatively the same.
What does a dated phylogeny tell us?
Tells us when groups originated & went extinct.
How can a phylogeny be dated? (2)
• Fossils.
• Rate of mutation in DNA sequence data.
Egs of how a phylogeny can be dated using fossils? (2)
• Oldest angiosperm fossil.
• Oldest Asteraceae (daisy family) pollen.
Explain how the rate of mutation in DNA sequence data can be used to date a phylogeny?
Through one assuming a constant rate within a group (molecular clock) or adjusting for rate differences in groups.
Based on phylogeny, are Brown bears & Polar bears distinct species?
No.
3 types of genome/gene?
• Chloroplastic gene.
• Mitochondrial gene.
• Nuclear gene.
