Phylogenetic Trees: Concepts and Methods

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Questions and Answers

What is the best definition of a 'synapomorphy'?

A trait that has evolved through the mechanism of natural selection.

A noncoding stretch of DNA containing short, repeated segments.

A derived trait shared by two or more related species, inherited from their immediate common ancestor. (correct)

A character state similarity due to shared descent.

Which of the following is NOT a principle or concept used in phylogeny construction?

Descent with modification

Homoplasy

Artificial Selection (correct)

Parsimony

What is the best definition of 'homoplasy'?

The independent origin of similar traits in separate lineages.

A character state similarity not due to shared descent. (correct)

The similarity of characteristics resulting from shared ancestry.

The reversion of a derived character state to a form resembling its ancestral state.

What is a 'clade'?

A single ‘branch’ in the tree of life, representing an organism and all its descendants. (A) Signup and view all the answers

What does 'polytomy' describe in a phylogeny?

An internal node with more than two branches, where the order of branching is unresolved. (A) Signup and view all the answers

What is the primary difference between 'homologous' and 'homoplastic' traits?

Homologous traits are inherited from a common ancestor, while homoplastic traits are not. (B) Signup and view all the answers

Why is Tiktaalik considered significant in understanding the evolution of tetrapods?

Tiktaalik exhibits a mosaic of characteristics found in both fish and tetrapods. (A) Signup and view all the answers

What is 'uniformitarianism'?

The idea that natural laws observable today have always been in effect. (D) Signup and view all the answers

Which of the following BEST describes the concept of 'descent with modification'?

The gradual change in species' traits over time through the passing of traits from parents to offspring. (C) Signup and view all the answers

What is the primary benefit of using 'microsatellites' in phylogenetic studies?

They are highly variable and useful for comparing populations and individuals. (A) Signup and view all the answers

Why is the construction of phylogenies in real-time important for disease epidemiology?

It allows us to track the evolution of pathogens and understand their origins. (B) Signup and view all the answers

Which of the following is the best definition of a 'theory' in science?

An overarching set of mechanisms or principles that explain major aspects of the natural world. (D) Signup and view all the answers

What is 'convergent evolution'?

The independent origin of similar traits in separate lineages. (A) Signup and view all the answers

What is the primary function of an 'outgroup' in phylogenetic analysis?

To provide a reference point for inferring the ancestral states of characters. (B) Signup and view all the answers

Which of these statements BEST describes the relationship between 'natural selection' and 'adaptation'?

Natural selection is a process that results in the development of adaptations. (C) Signup and view all the answers

Which of the following is a characteristic of a 'paraphyletic' group?

It shares a common ancestor, but does not include all descendants. (A) Signup and view all the answers

What is the best definition of a 'taxon'?

A group of organisms that a taxonomist judges to be a cohesive taxonomic unit. (D) Signup and view all the answers

Which of the following is NOT a useful character for inferring phylogenies?

Traits that all species share (B) Signup and view all the answers

What is homoplasy, and how does it affect phylogenetic analysis?

Homoplasy refers to the independent evolution of similar traits in different lineages. It makes phylogenetic analysis more complex, potentially leading to inaccurate relationships. (D) Signup and view all the answers

What is the purpose of using an outgroup in phylogenetic analysis?

An outgroup serves as an internal reference point to determine the direction of evolutionary change within the group. (B) Signup and view all the answers

Why is the search for transitional fossils important for understanding the evolution of tetrapods?

Transitional fossils help us to understand the evolutionary processes that led to the development of new characters. (D) Signup and view all the answers

How do scientists use phylogeny to understand the evolution of phenotypes?

They use phylogeny to identify homologous features in different lineages, providing insights into how different characters evolved. (B) Signup and view all the answers

Which of the following statements about phylogenetic trees is NOT accurate?

Phylogenetic trees are always based on a single gene or character. (D) Signup and view all the answers

What type of evolutionary change is responsible for homoplasy?

Convergent Evolution (A) Signup and view all the answers

What is the significance of the coelacanth in understanding the evolution of tetrapods?

Coelacanths are a closely related group to tetrapods, providing insights into the evolutionary transition from water to land. (C) Signup and view all the answers

Study Notes

Phylogenetic Trees: Hypotheses of Relationships

Phylogenetic trees are hypotheses about relationships between taxa, constantly refined with new data.
Statistical models analyze evidence to identify the best explanations.
Goal: Determine ancestry and relationships at any taxonomic level.

Creating Phylogenetic Trees

Choose a relevant group of interest.
Select characters for classification (e.g., morphology, DNA/RNA).
Determine character states for each taxon.
Use shared derived characters (analyzed by computationally intensive algorithms) to infer relationships.

Character Selection and Homoplasy

Each nucleotide is a potential character, but homoplasy (independent evolution of similar traits) is common.
Different genes evolve at varying rates, influencing their usefulness for different relationships (distant vs. close).
Parsimony (fewest changes) is a desirable approach for tree construction.
Traits present in all species, or unique to one species, are often less informative for constructing phylogenies.
Shared derived traits (synapomorphies) are most useful.

Complicating Factors

Constructing phylogenies is complex due to homoplasy, including convergent evolution (similar traits for separate reasons), or evolutionary reversal (losing a trait that appeared later).
Molecular phylogenies allow inferences of phenotypes/characteristics

Outgroups and Homologies

Outgroups are used to root trees (a distantly related species, not directly studied).
Homology signifies shared traits due to common ancestry (e.g., coelacanth fins & tetrapod forelimbs; bones in human arms & comparative long bones).

Fossil Evidence and Transition

Researchers predict transitional fossil locations and search for them.
Identifying transitional fossils (e.g., Tiktaalik) helps trace evolutionary paths between groups.

Applications of Phylogenies

Real-time phylogenies are useful for disease epidemiology.
Phylogenetic evidence is widely used to understand origins, trait evolution, and forensics.

Key Terminology

Taxon: A group of organisms (e.g., species, order)
Taxonomy: Science of describing, naming, and classifying organisms.
Carolus Linnaeus: Founder of modern taxonomy (nested hierarchical system).
Uniformitarianism: Natural laws explain past events.
Theory: Set of mechanisms explaining natural world aspects.
Hypothesis: Tentative explanation testable through investigation.
Homology: Similarity from shared ancestry.
Homologous characteristic: Similarity inherited from a common ancestor.
Descent with modification: Traits passed from parents to offspring (over time causes gradual species change).
Natural selection: Mechanism driving adaptive evolution based on phenotypic differences.
Artificial selection: Selective breeding to encourage desirable traits in organisms such as plants, and animals.
Adaptation: Inherited trait enhancing survival/reproduction.
Branch: Lineage evolving through time.
Node: Point where lineage splits (speciation event).
Tip: Terminal end representing compared species, molecules, or populations.
Internal node: Node within the phylogeny representing ancestral populations or species.
Clade: A single “branch” of the tree of life (ancestor and ALL its descendants).
Monophyletic: Group that forms a clade.
Polyphyletic: Group not sharing an immediate common ancestor.
Paraphyletic: Group sharing a common ancestor not including all descendants of that common ancestor..
Character: Heritable aspect of organisms for comparisons.
Synapomorphy: Derived trait shared by related species.
Outgroup: Organism outside the monophyletic group (often used for inferring ancestral character states).
Homoplasy: Character similarity NOT from common descent (e.g., convergent evolution, reversals).
Convergent evolution: Independent evolution of similar traits.
Evolutionary reversal: Return of a derived character to an ancestral state.
Parsimony: Selecting the hypothesis with the fewest assumptions.
Polytomy: Node with more than two branches (splitting order unknown).
Microsatellite: Noncoding DNA with repeated segments (useful for comparing populations and individuals).

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Description

This quiz explores the concepts and methodologies used in constructing phylogenetic trees. It covers the selection of characters, the analysis of relationships among taxa, and the implications of homoplasy in phylogenetics. Test your understanding of how these trees are derived and their importance in studying evolutionary relationships.