Phylogenetics Flashcards
What is a phylogeny?
The evolutionary history of a group of species, including when current species and past lineages speciated and the relatedness of extant species and even extinct species.
What is a phylogenetic tree?
A graphical representation of a phylogeny.
What is a clade?
A monophyletic group = Includes an ancestral taxon and all of its descendants
What is the basic logic behind phylogenies?
More closely related taxa should share more traits/characters in common than distantly related taxa.
What types of traits can phylogenies be based on?
- Morphology
- Behaviour
- Physiology
- Steps in development of an embryo or juvenile
- Nucleotides in a gene
What two traits are most common today for basing phylogenies off of?
Morphology
Nucleotides
Why is morphology useful for phylogenies?
especially skeletal morphology is often well-conserved through macroevolution, offering insights into the evolutionary history of group of species
Why is DNA helpful to phylogenies?
large amounts of data can be generated
o Each nucleotide is a character
o Provides insight into homology when modeled appropriately
For studies on phylogenies, how many species tend to be used?
50+
What are the only characters that are useful in estimating phylogenetic trees?
Homologous characters
What is a synapomorphy?
A synapomorphy is a homologous trait that represents a shared derived character
What are the two reasons for why synapomorphies help to infer phylogenetic trees?
o They identify evolutionary branch points; All species formed after the origin of the synapomorphy share the trait
o Synapomorphies are nested; As you move through time and trace a tree from its root to its tips, each branching event adds one or more shared, derived traits
What does identification of the best phylogeny rely on?
relies on finding a method that maximizes groups based on synapomorphies and reduces groups based on homoplasy
What is homoplasy?
convergent evolution where two similar characteristics evolve independently
Describe maximum parsimony.
- The “best” tree is the one that minimizes the total amount of evolutionary change in the characters
o Thus, finds the simplest explanation
Describe maximum likelihood.
The “best” tree is the one with the highest likelihood at explaining the data given a specific mathematical model that describes the probability that different types of character changes (e.g., nucleotide substitutions) occur
What type of data does maximum likelihood usually use?
DNA sequence data
How does maximum likelihood estimate lengths of brances?
Estimates lengths of branches according to number of substitutions between nodes
Give the equation for determining the likelihood of a tree under maximum likelihood.
L(tree)=P(data|tree, branch lengths, model)
Who introduced the Bayesian Markov Chain Monte Carlo method and when?
Thomas Bayes
1763
Describe the Bayesian method.
- There is no single best tree
- There are many possible trees with variation in probability in explaining the observed sequence variation, given a statistical model of character evolution and prior assumptions about the values of the model
What is the formula for determining the posterior probability of a tree?
P(tree|data)=P(data├tree)*P(tree)/P(data)
How are the trees formed under the Bayesian method represented?
Operationally reported as a single tree, and probability of observing each node and corresponding monophyletic grouping of species based on its frequency among the posterior distribution of possible trees
Differentiate between maximum likelihood and Bayesian methods.
Likelihood = What is the probability of seeing the observed data (D) given the phylogenetic tree?
Bayesian = What is the probability that the phylogenetic tree is correct given the data (D)?
What method is best for determining a phylogenetic tree?
Hotly debated. Bayesian inference is preferred by many, but most purely phylogenetic papers will report results from all methods.
Give examples of applications of phylogenetics. (6)
- Defining species
- DNA barcoding
- Classification, taxonomy and nomenclature
- When did events happen in the past?
- Where and how did a virus arise?
- What is the origin of whales?
