Lecture 23 - Phylogenetic's Flashcards
What do taxonomic ranks imply in phylogenetic trees?
They imply a tree structure, e.g., the order Nymphaeales contains families like water lilies.
What is a phylogenetic tree?
A hypothesis about evolutionary ancestry reflecting the flow of genetic information through time.
What are the main components of a phylogenetic tree?
Direction, branches (edges), nodes (taxa), and clades.
What is UPGMA used for?
Clustering taxa based on pairwise distances to build phylogenetic trees.
What is the limitation of UPGMA trees?
They might produce incorrect topology due to assuming constant rates of evolution.
What is the principle of maximum parsimony?
It minimises the number of evolutionary changes needed to explain data.
What issues arise with parsimony-based trees?
Not all changes are equally likely, and tree space is vast.
What is maximum likelihood used for?
To find the tree that maximises the probability of the observed sequence data.
Why is convergent evolution problematic in phylogenetics?
It causes unrelated species to appear similar, complicating evolutionary inferences.
Why is tree space considered vast?
The number of possible trees increases exponentially with the number of taxa.
What does the Kimura two-parameter model account for?
It differentiates between transitions and transversions in mutation rates.
Why are transitions more frequent than transversions?
They involve changes between similar chemical structures (purines or pyrimidines).
What do cladograms represent?
Phylogenetic trees without branch length information.
What is the best guess for divergence time in phylogenies?
The average number of mutations observed.
Why is substitution modelling critical in phylogenetics?
It predicts the likelihood of sequences given evolutionary processes.
How can phylogenetic trees be represented differently?
The orientation of branches around nodes can vary, but the topology remains the same.
Why does this variability not affect interpretation?
The evolutionary relationships are preserved regardless of branch orientation.
What is the first step in UPGMA clustering?
Identify the pair of taxa with the smallest distance.
How does UPGMA build a tree?
By iteratively combining pairs of taxa or groups based on their average distance.
What is the significance of Darwin’s “I think” diagram?
It illustrates the branching nature of evolutionary history and shared ancestry.
Why are molecular characters preferred over morphological ones?
They are more abundant, objective, and allow for precise distance calculations.
Give an example of convergent evolution in animals.
Sharks and dolphins look similar but are distantly related.
Why does convergence occur frequently at the molecular level?
Similar environmental pressures lead to the evolution of analogous traits.
Why are some mutations not parsimoniously informative?
They occur in only one taxon and do not provide information about shared ancestry.
What is a “parsimony-informative site”?
A site with at least two types of nucleotides, each shared by at least two taxa.
How does maximum likelihood differ from parsimony?
It accounts for different probabilities of mutation types and branch lengths.
Why do molecular sequences often provide better resolution?
They are less subjective and capture evolutionary changes at finer scales.
What can phylogenies reveal about species?
Shared ancestry, divergence times, and rates of evolution.
Why are branch lengths important in phylogenies?
They represent evolutionary time or the number of changes along a branch.
What is the purpose of substitution models?
To estimate the likelihood of observed sequences given evolutionary parameters.
Why might UPGMA produce inaccurate phylogenies?
It assumes a constant rate of evolution (molecular clock) across all taxa.
Why are transitions more frequent than transversions?
Transitions involve changes within the same nucleotide type (purine to purine or pyrimidine to pyrimidine).
How are mutation rates incorporated into phylogenies?
By calibrating branch lengths using fossil records or known divergence times.
How is confidence in a phylogenetic tree measured?
By using bootstrap analysis to test the stability of tree topology.
What is a “bootstrap value” in phylogenetics?
A measure of support for a given branch, expressed as a percentage.
How do cladograms differ from phylograms?
Cladograms show relationships without branch lengths, while phylograms include evolutionary distances.
Why is the root of a tree significant?
It represents the most recent common ancestor of all taxa in the tree.
How do sister taxa help interpret trees?
They share a more recent common ancestor with each other than with other taxa.
