Phylogeny and Molecular Clock Hypothesis

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Questions and Answers

What is the definition of phylogeny?

Phylogeny is the inference of evolutionary relationships.

What does the Molecular Clock Hypothesis state?

The rate of molecular evolution is approximately constant in all evolutionary lineages.

What are some basic assumptions in phylogenetics?

The molecular sequence is correct, sequences are homologous, and sampling of taxa is adequate.

What are the parts of a phylogenetic tree?

Branches, nodes, clades, and the root. Signup and view all the answers

What is an operational taxonomic unit (OTU)?

An OTU is an external taxonomic unit represented at each node. Signup and view all the answers

What is the rate of amino acid substitution for myoglobin?

0.89 Signup and view all the answers

Nucleotide sequences evolve at the same rates among different positions within a codon.

False Signup and view all the answers

What does a cladogram represent?

Relationships are inferred Signup and view all the answers

What are orthologs?

Homologous genes produced through speciation that have similar functions. Signup and view all the answers

What is the main disadvantage of the molecular clock hypothesis?

Evolutionary rates depend on factors like metabolic rates and selection pressure. Signup and view all the answers

Paralogs arise from gene duplication and may have different functions from their common ancestor.

True Signup and view all the answers

Which protein has the highest rate of amino acid substitution according to the provided data?

Growth hormone Signup and view all the answers

The molecular clock hypothesis suggests that protein sequences evolve at variable rates.

False Signup and view all the answers

What is the estimated time of gene duplications according to the content?

44 million years ago (MYA) Signup and view all the answers

According to Kimura's theory, the primary cause of evolutionary change is ___________ drift of mutant alleles.

random Signup and view all the answers

Match the protein with its corresponding rate of amino acid substitution:

Growth hormone = 3.7 Lactalbumin = 2.7 Carbonic anhydrase c = 1.6 Myoglobin = 0.89 Signup and view all the answers

Which of the following factors does NOT affect the evolutionary rate according to the content?

Geographical location Signup and view all the answers

According to the molecular clock hypothesis, gene function must remain constant for the clock to work.

True Signup and view all the answers

Who introduced the Relative rate test as a method to assess the molecular clock?

Tajima Signup and view all the answers

What is the purpose of adding a third protein (C) in the Tajima Relative Rate Test?

To serve as an outgroup for comparison Signup and view all the answers

Which type of tree shows the common ancestor as a node from which all other nodes are derived?

Rooted tree Signup and view all the answers

The Tajima test uses a significance level of p < 0.01 to reject the null hypothesis.

False Signup and view all the answers

What does the molecular clock hypothesis suggest about the rates of evolution of nucleotide sequences?

All sequences should have an equal rate of evolution. Signup and view all the answers

A cladogram reflects precise evolutionary time scales.

False Signup and view all the answers

What is the purpose of the Needleman-Wunsch algorithm in phylogenetics?

To achieve multiple alignment of protein sequences and construct an evolutionary tree. Signup and view all the answers

The Tajima algorithm considers three sequences, where one is used as the __________.

out-group Signup and view all the answers

An organism similar but not from the same branch is referred to as an __________.

outgroup Signup and view all the answers

Match the terms related to evolutionary concepts with their descriptions:

Gene family identification = Understanding related genes' functions Epidemiology of pathogenic diseases = Study of disease spread and impact Polymorphism characterization = Analysis of variation within a species Common ancestor = An ancestor from which multiple lineages derive Signup and view all the answers

What statistical method is used to test the comparability of rates in the Tajima Relative Rate Test?

Chi-square test Signup and view all the answers

Match the following types of trees with their descriptions:

Cladogram = Equal branch lengths, relationships inferred Phylogram = Different branch lengths reflect evolutionary distance Dendrogram = Branched tree with a given scale Un-rooted tree = Branching relationships without common ancestor position Signup and view all the answers

What does a node in a phylogenetic tree represent?

A bifurcating branch point Signup and view all the answers

Which of the following is NOT a basic assumption in tree analysis?

Each position evolved dependent on others Signup and view all the answers

Branch lengths in a phylogenetic tree represent the number of changes between nodes.

True Signup and view all the answers

External nodes in a phylogenetic tree represent internal relationships between taxa.

False Signup and view all the answers

What is one of the uses of evolutionary theory mentioned in the content?

Gene discovery or Epidemiology of pathogenic diseases. Signup and view all the answers

What types of biological material can be used to construct phylogenetic trees?

DNA, RNA, or proteins Signup and view all the answers

Column residues in a phylogenetic algorithm represent the states of characters.

True Signup and view all the answers

What is a clade in the context of phylogenetics?

A monophyletic group or taxon derived from a common ancestor. Signup and view all the answers

The __________ allows the correct placement of the tree root.

out-group Signup and view all the answers

Which of the following best describes 'Operational Taxonomic Units' (OTUs)?

External taxa represented at each node Signup and view all the answers

Match the following terms with their definitions:

Clade = A monophyletic group derived from a common ancestor Node = A bifurcating branch point in a tree Branch = Represents the relationship between taxa OTU = External taxonomic unit at a terminal node Signup and view all the answers

Molecular phylogeny provides actual evolutionary events without any assumptions.

False Signup and view all the answers

What role do homologous sequences play in the context of common ancestors?

They suggest that sequences were derived from a common ancestor. Signup and view all the answers

What does speciation occur due to?

Reproductive isolation Signup and view all the answers

Orthologs are derived from gene duplication.

False Signup and view all the answers

What marks a speciation event in a species tree?

An internal node Signup and view all the answers

Homologous genes or proteins share a common __________.

ancestor Signup and view all the answers

Match the types of homologs with their characteristics:

Orthologs = Derived from speciation Paralogs = Derived from gene duplication Homologs = Share a common ancestor Gene families = Evolve before or after speciation Signup and view all the answers

Which term best describes the concept of measuring the degree of relatedness or difference?

Similarity Signup and view all the answers

Paralogs are used for constructing phylogenetic trees.

False Signup and view all the answers

What is a key use of orthologs in genomics?

Markers for homologous chromosomal regions Signup and view all the answers

Study Notes

Phylogeny

The inference of evolutionary relationships between organisms.
Traditionally, phylogeny relied on morphological or structural information.
Molecular sequence data is now used for phylogenetic analysis.

Molecular Clock Hypothesis

Proposed in 1962 & 1963 by Zuckerkandl, Pauling, and Margoliash.
States that the rate of molecular evolution is approximately constant in all evolutionary lineages.
Suggests that protein sequences evolve at constant rates, allowing for the estimation of divergence times.
Studies were conducted using human globins with known amino acid composition.
Homologous proteins have correlated rates based on divergence time from a common ancestor.

Molecular Clock Evidence

Haemoglobin consistency provides evidence for the molecular clock.
Evidence suggests that gene duplications occurred 44 million years ago (MYA) and were derived from a common ancestor 260 MYA.

Limitations of the Molecular Clock Hypothesis

The clock varies across different species, genes, and parts of individual species due to:
- Selection pressure
- Generation time
Observations of morphological evolution are not always in a steady state.
Molecular evolution may occur independently from morphological evolution.
Kimura's (1968) neutral theory suggests that the main cause of evolutionary change is random drift of selectively neutral mutant alleles.
Evolutionary rate is dependent on various factors:
- Metabolic rates
- Generation times
- Population sizes
- Mutation rates
- Selection pressure
The clock only works if gene or protein function is maintained over evolutionary time.

Tajima's Relative Rate Test (1993)

Tests the molecular clock by calculating the relative rates of evolution of two proteins or protein families.
Introduces a third protein as an outgroup for comparison.
Utilizes a common ancestor to determine rates of change.
Uses the null hypothesis to accept or reject the clock.

Evolutionary Theory Uses

Gene family identification
Gene discovery (function)
Origins of genetic diseases
Epidemiology of pathogenic diseases
Polymorphism characterization
Evolutionary theories of life

Tree Topology

Represents the relationship of tree subjects (e.g., proteins, genes, organisms).
Branch lengths reflect the degree of these relationships.
A phylogenetic tree or dendrogram is a graph with branches and nodes.
Nodes represent taxonomic units, while branches connect them.
Branch lengths can be seen as a distance scale on the tree.

Tree Nomenclature

Clade or cluster: A monophyletic group or taxon derived from a common ancestor or node.
Node: An internal node is a bifurcating branch point in a tree. An external node represents an operational taxonomic unit (OTU).
Taxon: Any named group of organisms (not necessarily arranged in a cluster).
Branch: Represents the relationship between taxa.
Root: The common ancestor of all units in a rooted tree.

Common Ancestor

If two sequences are homologous, it is assumed they were derived from a common ancestor.
A common ancestor suggests similar function.
Molecular phylogeny can only generate an inferred tree from data.

Operational Taxonomic Units (OTUs)

External taxa or units represented at each terminal node.

Outgroup

An organism similar but not part of the tree branch.
Allows for accurate placement of the tree root.

Rooted vs. Unrooted Trees

Rooted trees: Show the common ancestor as a node from which all other nodes are derived.
Unrooted trees: Show the branching relationships between nodes but not the position of the common ancestor.
Unrooted trees can be rooted by selecting an edge and re-drawing a rooted tree in relation to that branch.

Cladogram vs. Phylogram (Phenogram)

Cladogram: Branch lengths are equal and do not reflect precise evolutionary time scales. Relationships are inferred.
Phylogram (Phenogram): Branch lengths and time scales reflect distances from a common ancestor or similarity relationships.

Feng and Doolittle (1987)

Used the Needleman-Wunsch alignment algorithm to construct evolutionary trees.
Assumed sequences shared a common ancestor.
Constructed trees from different matrices derived from a multiple sequence alignment (MSA).

Multiple Sequence Alignment (MSA) and Phylogenetics

The fundamental basis of a phylogenetic tree.
Each column is a character in a phylogenetic algorithm.
Each residue (unit) in the column represents the state of the character.

Basic Assumptions in Tree Analysis

The molecular sequence is correct and originates from a specific source.
Sequences are homologous.
Each position in the alignment is homologous with every other position.
The sampling of taxa is adequate to resolve the query of interest.
Each position in the sequence sample evolved independently.

Species vs. Gene Trees

Species trees depict speciation events and the divergence of species.
Gene trees depict gene divergence events and the duplication or evolution of genes.
The topology of a gene or protein tree may differ from a species tree.

Homology and Similarity

Homology: Implies shared ancestry.
Similarity: Independent of historical data, measures the degree of relatedness or difference.

Orthologs

Homology produced through speciation.
Genes are derived from a common ancestor due to divergence.
Have similar functions.
Gene phylogeny generally matches the organism’s general phylogeny.

Uses of Orthologs

Markers for homologous chromosomal regions in comparative mapping.
Phylogenetic footprinting.
Operon prediction.

Paralogs

Homology derived by gene duplication.
Genes derived from a common ancestor due to duplication followed by divergence.
May have different functions from the common ancestor or from each other.
Gene phylogeny does not follow the organism’s general phylogeny.
Generally not used for phylogeny.

Uses of Paralogs

Identification of paralogs is a prerequisite for studying gene duplication processes.

Xenologs

Homology resulting from horizontal gene transfer between two organisms.
May be determined by the %G+C ratio.
Gene functions are usually similar.
Gene phylogeny does not match the organism’s general phylogeny when other genes do.

References

Baxevanis, A.D. and Oulette, B.F. Bioinformatics: A practical guide to the analysis of genes and proteins. 3rd ed. Wiley.
Pevsner, J. Bioinformatics and Functional Genomics; Wiley, 2009.
Tajima, F. (1993) Simple Methods for Testing the Molecular Evolutionary Clock Hypothesis, Genetics, 135: 599-607.

Molecular Clock

Protein sequences evolve at a constant rate. This can be used to estimate the time when two protein sequences diverged.
The rate of evolution varies across proteins
Some examples of protein evolutionary rates are:
- Growth hormone: 3.7 PAM (substitutions per 100 amino acids per 10^9 years).
- Lactalbumin: 2.7 PAM.
- Carbonic anhydrase c: 1.6 PAM.
- Lysozyme: 0.98 PAM.
- Myoglobin: 0.89 PAM.
- Cytochrome C: 0.22 PAM.
- Ubiquitin: 0.10 PAM.
Nucleotide sequences evolve at different rates within codons.
The rate of evolution can vary among species or genes, due to selection pressures and generation times.
Molecular evolution may not always correlate with morphological evolution.

Neutral Theory of Molecular Evolution

Kimura's theory of neutral selection suggests that the main cause of evolutionary change is random drift of selectively neutral mutations.
Evolutionary rate depends on factors like metabolic rates, generation times, mutation rates, and selection pressures.
The molecular clock only functions reliably if the gene or protein maintains its function over evolutionary time.

Tajima's Relative Rate Test

Introduced in 1993, this test compares the evolutionary rates of two proteins (A and B) or protein families.
A third protein (C) is used as an outgroup for comparison.
The test uses a common ancestor (O) to determine the rates of change.
It applies a chi-square test with a significance level of p<0.05 to determine if the rates are comparable (null hypothesis) or if the null hypothesis should be rejected.

Uses of Evolutionary Theory

Evolutionary theory plays a crucial role in:
- Identifying gene families
- Discovering gene functions
- Understanding the origins of genetic diseases
- Analyzing the epidemiology of pathogenic diseases
- Characterizing polymorphism
- Contributing to evolutionary theories of life

Types of Evolutionary Tree Diagrams

Evolutionary tree diagrams represent evolutionary relationships.
They are also known as phylogenetic trees or dendrograms.
Key features include:
- Topology: Represents the relationships between the subjects of the tree.
- Branch lengths: Indicate the degree of relationship.
- Nodes: Represent taxonomic units.

Tree Nomenclature

Clade or cluster: A monophyletic group of taxa derived from a common ancestor.
Node: An internal node is a branch point that bifurcates. An external node represents an operational taxonomic unit (OTU).
Taxon: Any named group of organisms.
Branch: Represents the relationship between taxa.
Root: The common ancestor of all units in a rooted tree.

The Common Ancestor

If two sequences are homologous, they are assumed to be derived from a common ancestor.
Homology suggests a similar function.
Molecular phylogeny can only generate inferred trees from data.

Operational Taxonomic Units (OTUs)

OTUs are the external taxa or units represented at each node.
They are found at the terminal nodes.

Outgroups

An outgroup represents a similar organism that is not from the same branch as the rest of the tree.
It helps to position the root of the tree correctly.

Rooted vs. Unrooted Trees

Rooted trees: Show the common ancestor as a node from which all other nodes are derived.
Unrooted trees: Show the branching relationships between nodes, but don't show the position of the common ancestor. Unrooted trees can be rooted by selecting an edge and re-drawing the tree in relation to that branch.

Phylogenetic Trees

Cladogram: Branch lengths are equal and don't reflect precise evolutionary time scales. Relationships are inferred.
Phylogram or phenogram: Branch lengths and time scales reflect the distance from a common ancestor or similarity relationships.

Feng and Doolittle's Algorithm (1987)

Used the Needleman-Wunsch algorithm to achieve multiple alignment of protein sequences and construct evolutionary trees.
Based on the assumption that the sequences share a common ancestor.
Constructed trees from different matrices derived directly from a multiple sequence alignment (MSA).

Multiple Sequence Alignment (MSA) and Phylogenetics

The basis of a phylogenetic tree.
A tree can still be generated from a misaligned MSA.
Each column in a MSA represents a character in a phylogenetic algorithm.
Each residue or unit in the column represents the state of the character.

Basic Assumptions of Phylogenetic Tree Analysis

The following assumptions are crucial for accurate phylogenetic tree analysis:
1. The molecular sequence is correct and originates from a specific source.
2. The sequences are homologous.
3. Each position in the alignment is homologous with every other in the alignment.
4. The sampling of taxa is adequate to resolve the query of interest and is representative of the broader group.
5. Each position in the sequence sample evolved independently.

Species and Gene Trees

DNA, RNA, or proteins can be used to construct trees.
Speciation occurs when a species becomes reproductively isolated.
In a species tree, each internal node represents a speciation event.
Gene duplication can occur before or after a speciation event.
The topology of a gene or protein tree may differ from the corresponding species tree.

Homology and Similarity

Homology: Sequences share a common ancestor. Does not necessarily refer to similarity levels.
Similarity: Independent of historical data. A quantifiable measure of relatedness or difference.

Orthologs

Orthologs are homologous genes or proteins produced through speciation.
They are derived from a common ancestor due to divergence.
Orthologous genes or proteins have similar functions.
In identification, gene phylogeny matches the organism's general phylogeny.
Genomic variation typically occurs after speciation.

Ortholog Uses

Orthologs are useful in:
- Identifying homologous chromosomal regions for comparative mapping.
- Phylogenetic footprinting.
- Operon prediction.

Paralogs

Paralogs are homologous genes or proteins derived by gene duplication.
They are derived from a common ancestor due to duplication followed by divergence.
Paralogous genes may have different functions from the common ancestor or from each other.
In identification, gene phylogeny does not follow the organism's general phylogeny.
Paralogs are not typically used for phylogeny.

Paralog Uses

Identifying paralogs is essential for studying gene duplication processes.

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Description

Explore the concepts of phylogeny and the molecular clock hypothesis, which explains how evolutionary relationships can be inferred from molecular data. This quiz covers the historical development of these ideas, the evidence supporting them, and their limitations in understanding evolutionary timelines.