Lecture 7- reconstructing and using phylogenies 1 Flashcards
What is phylogeny?
A description of the evolutionary history of relationships among organisms
What is a phylogentic tree?
A diagram that portrays a reconstruction of the history of the evolutionary relationships among organisms
What does a split or node on a phylogenetic tree represent?
The point at which lineages diverge
What is the name of the common ancestor of all the organisms in the tree?
The root
What is a taxon?
A group of species that are designated a name
What is a clade?
A taxon that consists of all of the evolutionary descendants of a common ancestor.
What are two species/clades that are each others closest relatives called?
Sister species/clades
What is systematics?
The study of biodiversity
Where are phylogentic trees used?
In all fields of biology
What do biologists use phylogenies to do?
Make comparisons and predictions about shared traits across genes populations and species.
How do comparisons among species require an evolutionary perspective?
Biologists determine traits that differ within a group of interest then try to determine when these traits evolved and how the trait was influenced by environmental conditions
What are features shared by two or more groups that were inherited from a common ancestor called?
Homogenous
Give an example of a homogenous trait.
The vertebral column is homologous among vertebrates.
What have phylogenetic analyses been used to discover?
Changes in the genome of HIV that confer resistance to particular drug treatments
What does the association of a particular genetic change in HIV with a particular treatment provide?
A hypothesis about resistance that can be tested experimentally.
What is a trait that differs from its ancestral form called?
A derived trait
What is a trait that was present in the ancestor of the group called?
An ancestral trait
What are derived traits that are shared among a group of organisms and are viewed as evidence of the common ancestry of the group called?
Synapomorphies
Why do similar traits evolve in unrelated groups of organisms?
- Convergent evolution
- Evolutionary reversal
What is convergent evolution?
Independently evolved traits subjected to similar selection pressures may become superficially similar
Give an example of convergent evolution.
Bones of wing and bats are homologous (inherited from common ancestor)
Wings are not homologous- evolved independently from forelimbs of different non-flying ancestors.
What is evolutionary reversal?
A character reverts back from a derived state to an ancestral state.
Give an example of an evolutionary reversal.
Frogs lack teeth in lower jaw- ancestor had teeth
Teeth have been regained in lower jaw of genus Amphignathodon
What is the genus of the frogs that have regained teeth in their lower jaw?
Amphignathodon
What are traits that are similar for reasons other than inheritance from a common ancestor called? (for example, because of convergent evolution or evolutionary reversal.)
Homoplasies
What are traits ancestral or derived depending on?
The point of reference for that phylogeny.
What assumptions are made when constructing phylogenetic trees?
No convergent evolution
No derived traits have been lost
What is a species outside the group of interest when constructing a phylogenetic tree called?
The outgroup
What do comparisons with the outgroup show?
Which traits of the ingroup are derived and which are ancestral
What is used to construct a phylogenetic tree?
Information about synapomorphies
What is the parsimony principle?
The preferred explanation of the observed data is the simplest explanation
How is it determined which traits are homoplasies and which are synapomorphies?
Using the parsimony principle
The best hypothesis when constructing a phylogentic tree is the one that involves the fewest…
homoplasies
What is Occam’s razor?
The idea that the best explanation is the one that fits the data best and makes the fewest assumptions
Phylogenetic trees are continuously…
modified
How has tree construction been revolutionized?
Computer software for trait analysis and tree construction
Process more data
What traits can be used in phylogenetic analysis?
Genetically determined traits
Evolutionary relationships can be revealed through studies of what?
Morphology Development Fossil record Behavioral triats Molecular traits (DNA and protein sequences)
What is morphology?
Presence, size, shape and other attributes of body parts
How do sytematists analyze morphological structures in finer detail?
New technological tools: electron microscope, CT scans
Why is there a wealth of recorded morphological data?
Living organisms have been studied for centuries- very comprehensive
Give an example of the features of morphology that are important for phylogenetic analysis being specific to a particular group of organisms.
Presence, development, shape and size of skeletal system is important in vertebrate phylogeny, whereas floral structures are important in studying relationships of flowering plants.
What are limitations of the morphological approach to phylogenetic analysis?
- Taxa with little morphological diversity
- Few morphological traits can be compared between distantly related species
- Morphological variation that is environmental
Why are observations of similarities in developmental patterns used to reveal evolutionary relationships?
Similarities in early developmental stages may be lost during later development
Give an example of similarities in early developmental stages may be lost during later development that are used to infer evolutionary relationships.
Larvae of marine creatures called sea squirts have a notochord that dissapears as they develop
All vertebrate animals have a notochord at some point in development
Shared structure infers closer relationship
What do fossils reveal about organisms?
Where and when organisms lived
What they looked like
What do fossils help distinguish between?
Ancestral and derived traits
What else do fossil records reveal?
When lineages diverged and began independent evolutionary histories
What do fossil records reveal about groups that have few species that have survived to the present?
Information on extinct species is critical to understanding large divergences between surviving species
What are the limitations of fossil records?
Few or no fossils for some groups
Fossil record is fragmentary
What type of behavior does not reflect evolutionary relationships?
Culturally transmitted behavior
Give an example of a behavior that is genetically determined.
Frog calls
What genome is used extensively in phylogenetic studies of plants?
cpDNA
The chloroplast genome
How does cpDNA change over time and why is this useful?
Slowly
To study ancient phylogenetic relationships
What type of DNA changes rapidly in animals?
mtDNA
Mitochondrial DNA
What is comparisons between mtDNA used for?
Studying evolutionary relationships between closely related species
What do mathematical models to describe how DNA changes over time account for?
Multiple changes at given position in a DNA sequence
Different rates of change at different positions in a codon and among different nucleotides
What type of changes in DNA are more likely?
Transitions (changes between 2 purines or 2 pyrimidines) are more likely than transversions
What are transversions?
Changes between a purine and a pyrimidine
What can mathematical models be used to compute?
Maximum likelihood solutions for phylogenetic estimations
How is a likelihood score for a tree determined?
The probability of the observed data evolving from a specific tree
What are maximum likelihood methods used for mostly and why?
Molecular data
Explicit mathematical models of evolutionary change are easier to develop
What are the advantages to the maximum likelihood analyses?
They incorporate more information about evolutionary change than parsimony methods
Easier to treat in a statistical framework
What are the disadvantages to the maximum likelihood analyses?
Computationally intensive and require explicit models of evolutionary change
Why is it a disadvantage that maximum likelihood analyses require explicit models of evolutionary change?
Explicit models may not be available for some kinds of character change
Describe how the hypothesis that evolutionary history can be correctly reconstructed from the DNA sequences of living organisms using phylogenetic analysis can be tested.
- Single viral bacteriophage culture T7 was selected (this was the common ancestor)
- Lineages were able to evolve in the presence of mutagen
What does mutagen do?
Increase the rate of mutation
What happened when the bacteriophage cultures were evolving?
Every 400 generations each ingroup lineage were split into two
What was the final step in the experiment to determine the accuracy of phylogenetic methods?
Isolate and sequence viruses from the end points of each lineage (8 in group, one outgroup)
Phylogenetic analysis
What were the results of the experiment to determine the accuracy of phlogenetic methods?
The evolutionary history of the lineages and the ancestral sequences of the viruses were reconstructed successfully
Why was mutagen added to the experiment that determined the accuracy of phylogenetic analysis?
Increase mutation rate so degree of homoplasy would be typical of organisms analyzed in average phylogenetic analyses.
In the experiment to determine accuracy of phylogenetic methods, what percent of amino acids changes and nucleotide positions were reconstructed accurately?
100% amino acid changes in viral proteins
Over 98% nucleotide positions
The experiment described did not take into account…
All possible conditions, for example:
- sensitivity to phylogenetic analysis to convergent environments
- highly variable rates of evolutionary change
How else has the effectiveness of phylogenetic analysis been shown?
- Other experimental studies that account for other possible conditions
- Computer simulations based on evolutionary models
Other than inferring evolutionary relationships among lineages, phylogenetic trees can be used to…
Reconstruct:
morphology, behavior, nucleotide and amino acid sequence
What was phylogenetic analysis used to reconstruct?
An opsin protein in the ancestral archosaur
What is an archosaur?
The last common ancestor of birds, dinosaurs and crocodiles
What are opsins?
Pigment proteins involved in vision
How do opsins differ?
Different opsins have different amino acid sequences
Different opsins are excited by different wavelengths
What does knowledge about opsin sequences reveal?
Clues about the animals visual capabilities and some probable behaviors
How was the opsin sequence on archosaurs determined?
Phylogenetic analysis of opsin from living vertebrates to estimate amino acid sequence of opsin in archosaurs
Once the amino acid sequence of archosaurs was determined what happened?
The protein was reconstructed in a lab
Testing showed shift towards the red end of the spectrum (compared with modern opsins)
What does a shift towards the red end of the spectrum in opsin sensitivity infer?
Nocturnal vision
In 1965, what did Emile Zuckerkandl and Linus Pauling hypothesize?
The molecular clock hypothesis
What is the molecular clock hypothesis?
Rates of molecular change are constant enough that they can be used to predict evolutionary divergence times
What can effect the molecular clock hypothesis?
- Different genes evolve at different rates
- Different evolutionary rates depending on generation times, environments, efficiencies in DNA repair etc.
Despite different rates of evolution, why can the molecular clock theory still be used?
Among closely related species a given gene evolves at a reasonably constant rate
What is the rate of evolution being used as a metric to gauge time of divergence for a split in phylogeny called?
Molecular clocks
How are molecular clocks calibrated?
Independent data such as fossil record, known time of divergence, biogeographic dates
What are biogeographic dates?
Such as dates of separation of continents
Studies of what animals provide an example of molecular clocks?
Cichlid fish in Lake Victoria, eastern Africa
How many species cichlid of fish in one group did the evolutionary radiation in Lake Victoria produce?
More than 500 species
When was it originally assumed the evolutionary radiation of cichlid fish in Lake Victoria occur?
750,000 years ago (presumed age of lake basin)
What does recently discovered geological data suggest about Lake Victoria?
It dried up between 15600 years ago and 14700 years ago
What effect did the fact that Lake Victoria dried up have on the theory of the evolutionary radiation of cichlid fish?
The fish could not have evolved in such a short time so other hypothesis were made
How were theories about the cichlid fish tested?
Phylogenetic analysis based on molecular data of 300 species
What type of molecular data was used to construct phylogenetic trees of cichlid fish in Lake Victoria and other lakes in the region?
Mitochondrial DNA sequences
What did phylogenetic analysis of cichlids in and around Lake Victoria suggest about the origins of the cichlids in the lake?
Ancestors of Lake Vicotria cichlids come from geologically older Lake Kivu
How many species of cichlid live in Lake Kivu?
15
How did cichlids from Lake Kivu colonize Lake Victoria?
Colonized on 2 different occasions
What else did phylogenetic analysis of cichlids reveal about Lake Victoria?
Some cichlid lineages found only in Lake Victoria split 100,000 years ago- thus Lake Victoria did not completely dry 15000 years ago
