10 Questions
What is the aim of phylogeny?
To deduce the correct trees for all species of life and estimate the time of divergence between organisms.
Define branches in the context of phylogenetic analysis.
Branches represent the relationship between organisms, species, or genomic sequences.
What is the difference between cladograms and phylograms?
Cladograms have branch lengths that hold no meaning, while phylograms have branch lengths that represent evolutionary change.
Explain the concept of an unrooted tree.
An unrooted tree does not have a specified origin of evolution (root) and is used to show relationships between entities without indicating a common ancestor.
What is the Newick format used for in phylogenetics?
The Newick format is used to represent phylogenetic trees in a compact, nested parentheses format.
What is the difference between character-based and distance-based methods in tree building?
Character-based methods use aligned sequences directly, while distance-based methods transform sequence data into pairwise distances.
How do distance-based methods calculate the distances between molecular sequences?
Distance-based methods calculate the distances using some distance metric, then use a clustering method to infer the tree from the pairwise distance matrix.
What does UPGMA stand for and what is its advantage in tree construction?
UPGMA stands for Unweighted Pair Group Method with Arithmetic Mean. Its advantage is that it is the simplest algorithm for tree construction, making it fast.
How is the Hamming distance calculated for pairwise sequences?
The Hamming distance is calculated by aligning pairs of sequences and counting the number of differences, then dividing by the length of the alignment.
Why is rRNA often used for constructing species trees?
rRNA is often used because it provides a phylogenetic signal that is less predominant in proteins, making it better for constructing species trees.
Study Notes
Phylogenetic Analysis
- Phylogeny is the inference of evolutionary relationships among organisms, species, or genomic sequences.
Key Terms
- Root: the origin of evolution
- Leaves: current organisms, species, or genomic sequences
- Branches: relationships between organisms, species, or genomic sequences
- Branch length: evolutionary time
- Unrooted tree: a tree without a root, representing relationships between organisms without a common ancestor
- Rooted tree: a tree with a root, representing evolutionary relationships between organisms
Types of Rooted Trees
- Cladograms: branch length has no meaning
- Phylograms: branch length represents evolutionary change
- Ultrametric: branch length represents time, with the same length from the root to the leaves
Representing Trees
- Newick format: a standard format for representing trees
Phylogenetic Tree Construction
- Step 1: Selection of sequences for analysis
- Step 2: Multiple sequence alignment
- Step 3: Tree building
- Step 4: Tree evaluation
Selecting Sequences for Analysis
- DNA: higher phylogenetic signal, synonymous vs. non-synonymous substitutions detect negative and positive selection
- Protein: phylogenetic signal less predominant than in DNA, better for constructing trees for evolutionary distant species or genes
- RNA: often used for constructing species trees, rRNA
Tree Building Methods
- Character-based methods: use aligned sequences directly during tree inference
- Distance-based methods: transform sequence data into pairwise distances, then use the matrix during tree building
Distance-Based Methods
- Calculate distances between molecular sequences using a distance metric
- Use a clustering method (UPGMA, Neighbor Joining) to infer the tree from the pairwise distance matrix
- Treat sequences from a horizontal perspective, calculating a single distance between entire sequences
- Advantage: fast, allows using evolutionary models
Distance Calculation
- Align pairs of sequences and count the number of differences (Hamming distance)
- Formula: D = (n/N*100)
UPGMA (Unweighted Pair Group Method with Arithmetic Mean)
- Originally developed for numeric taxonomy in 1958 by Sokal and Michener
- Simplest algorithm for tree construction, fast
- How to construct a tree with UPGMA: align pairs of sequences, calculate distances, and build the tree using the UPGMA method
Learn the fundamentals of phylogenetic analysis and how to infer evolutionary relationships among different species based on genetic data. Understand how phylogenetic trees represent the evolutionary history of life forms and the estimation of divergence times between organisms.
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