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In the ground pattern approach, the coded states for clades above the species level are assumed to refer to:
In the ground pattern approach, the coded states for clades above the species level are assumed to refer to:
Polymorphic character states can only specify intraspecific variation.
Polymorphic character states can only specify intraspecific variation.
False
What is the primary advantage of using species as terminal taxa in the exemplar approach?
What is the primary advantage of using species as terminal taxa in the exemplar approach?
They represent the basic 'entities of generalisation' in biology.
In cladistic analyses, inapplicable and missing states are treated in the same _____
In cladistic analyses, inapplicable and missing states are treated in the same _____
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Match the following coding strategies to their descriptions:
Match the following coding strategies to their descriptions:
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What is one reason molecular data is considered more advantageous than morphological data in cladistics?
What is one reason molecular data is considered more advantageous than morphological data in cladistics?
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The phylogenetic tree analysis suggests multiple colonizations of Darwin's finches.
The phylogenetic tree analysis suggests multiple colonizations of Darwin's finches.
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What supports the Out-of-Africa model of human origins?
What supports the Out-of-Africa model of human origins?
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The genetic code comprises four possible character states: A, T, C, and ______.
The genetic code comprises four possible character states: A, T, C, and ______.
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Match the following models of human origins with their descriptions:
Match the following models of human origins with their descriptions:
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What is a characteristic of slowly evolving genes?
What is a characteristic of slowly evolving genes?
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Homoplasy occurs when character states are similar due to common ancestry.
Homoplasy occurs when character states are similar due to common ancestry.
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What is one implication of the phylogenetic evidence surrounding HIV?
What is one implication of the phylogenetic evidence surrounding HIV?
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Which of the following genetic markers is more likely to be used for higher-ranking taxa analysis?
Which of the following genetic markers is more likely to be used for higher-ranking taxa analysis?
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Only paralogous genes are used in phylogenetic reconstruction to study species splits.
Only paralogous genes are used in phylogenetic reconstruction to study species splits.
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What is the purpose of using a molecular clock in phylogenetic analysis?
What is the purpose of using a molecular clock in phylogenetic analysis?
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Alleles in populations coalesce to a common __________.
Alleles in populations coalesce to a common __________.
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Match the terms with their definitions:
Match the terms with their definitions:
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What is the first step in a phylogenetic analysis?
What is the first step in a phylogenetic analysis?
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Homology of genes indicates that they have evolved independently from a common ancestor.
Homology of genes indicates that they have evolved independently from a common ancestor.
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How can orthologs be identified in large genomic datasets?
How can orthologs be identified in large genomic datasets?
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What is the total number of possible sets of ancestral states for a tree with 3 internal nodes?
What is the total number of possible sets of ancestral states for a tree with 3 internal nodes?
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Dynamic programming approaches are not necessary for solving the small likelihood problem.
Dynamic programming approaches are not necessary for solving the small likelihood problem.
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What is the purpose of the hill climbing algorithm in finding optimal parameter values?
What is the purpose of the hill climbing algorithm in finding optimal parameter values?
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Given n input sequences, the number of internal nodes is _____ and the number of possible sets of ancestral states is _____ .
Given n input sequences, the number of internal nodes is _____ and the number of possible sets of ancestral states is _____ .
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Match the following terms with their definitions:
Match the following terms with their definitions:
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Which algorithm is used to find the best scoring local alignment for a pair of sequences?
Which algorithm is used to find the best scoring local alignment for a pair of sequences?
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The gap opening cost is typically lower than the gap elongation cost.
The gap opening cost is typically lower than the gap elongation cost.
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What does Ɣ(g) represent in gap scoring?
What does Ɣ(g) represent in gap scoring?
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The __________ method attempts to find a good solution that comes close to the best alignment in a short amount of time.
The __________ method attempts to find a good solution that comes close to the best alignment in a short amount of time.
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Match the following alignment terms with their definitions:
Match the following alignment terms with their definitions:
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What are Indels in the context of sequence alignment?
What are Indels in the context of sequence alignment?
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Name one possible problem associated with multiple alignments.
Name one possible problem associated with multiple alignments.
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Different sequence alignments can result in different scoring metrics.
Different sequence alignments can result in different scoring metrics.
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Which method is characterized by selecting the tree hypothesis that minimizes the number of changes?
Which method is characterized by selecting the tree hypothesis that minimizes the number of changes?
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In a cladogram, branch lengths convey important evolutionary information.
In a cladogram, branch lengths convey important evolutionary information.
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What does the BLAST tool use to compare sequence queries against database entries?
What does the BLAST tool use to compare sequence queries against database entries?
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An __________ tree reflects time of branching at internal nodes.
An __________ tree reflects time of branching at internal nodes.
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Match the following tree types with their descriptions:
Match the following tree types with their descriptions:
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What is a characteristic of the maximum likelihood method?
What is a characteristic of the maximum likelihood method?
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Regions with many gaps in sequence data should always be included in the analysis.
Regions with many gaps in sequence data should always be included in the analysis.
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What approach assesses the simplest explanation in phylogenetics?
What approach assesses the simplest explanation in phylogenetics?
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Study Notes
Species Definitions
- Species are defined as binomial, composed of genus and specific epithet.
- Aristotelian definition uses genus proximum and differentia specifical.
- Genus-differentia definitions have two parts:
- Genus: Existing definition forming part of the new definition. Members with the same genus are considered part of that set.
- Differentia: Portion of a definition not provided by the genus.
- Carl Linnaeus (1707-1778) is the nomenclatural author of Homo sapiens and described species in Systema Naturae (1758).
- Species descriptions must be publicly available and accompanied by voucher/type material deposited in a museum or collection.
Universal Meter
- A copy of a "provisional" meter, measuring 1 meter in length, was installed in a Paris building in 1796-1797.
- A platinum bar of 1 meter in length was deposited in the Museum National d'Histoire Naturelle in Paris for universal reference.
Taxonomy
- Taxonomy is an information science, based on hypothesis testing.
- Key aspects include:
- Characteristics and character distribution
- Species delimitation
- Phylogenetic relationship
- Intersubjective testability
- Species are communities or related communities with distinctive and definite characters, allowing naming using a competent systematist. Biological species produce fertile offspring in natural conditions.
- Species are important for generalisation.
- Different concepts for species exist
- Aristotelian (350 BC) based on resemblance.
- Regan (1878-1943) based on characteristic traits suitable for species name.
- Biological species concept focuses on natural reproduction leading to fertile offspring.
Phylogenetic Systematics
- Natural entities in nature are species and monophyletic groups (taxa)
- Autapomorphies = derived traits unique to a taxon.
- Synapomorphies = shared derived traits revealing evolutionary relationships/sister groups (same parent/ancestor)
- Plesiomorphies = ancestral traits that evolved before the last common stem species.
- Linnean classification may result in paraphyletic or polyphyletic or monophyletic taxa
- Fossil taxa can be included in the system.
Homology and Observation Assessment
- Evolutionary evaluation includes identity (transition without modification) and similarity (transition with modification).
- Evolutionary novelty → homoplasy, convergent evolution.
Homology
- Homology is a rational term, applicable in contexts like anterior body parts of animals (e.g., bird and bat wings), but may conflict depending on other criteria
- Rationales for homology are position, identical substructures, and similar characteristics in evolutionary intermediates including fossil evidence.
- Detecting and identifying morphological structures involves morphological diagnostics (recognition and identification).
Ontologies
- Resource descriptions frameworks (RDF) use subject, property, and object, useful for complex structural concepts.
- RDF descriptions allow for complex structural analysis.
Cladistics
- Dendrograms are constructed using maximum parsimony from character/taxa datasets.
Optimal Trees
- Species must find a balance between function and historical constraints.
- Homologous assumptions (e.g., bird wings) are tested in cladistic analysis and are either supported or rejected based on their concordance with other characters.
Phylogenetic Tree Composition
- Trees are made of nodes and branches connecting them.
- Basic branches are often dichotomous. Base nodes are the root nodes, and terminal nodes are the leaves.
Rooted vs. Unrooted Trees
- Rooted trees depict an evolutionary lineage with a point of origin, whereas unrooted trees only show relationships, not a clear evolutionary direction.
- The number of possible trees increases exponentially as the number of organisms increases.
Tree Calculation
- Maximum parsimony finds optimal trees with the fewest steps needed to transform characters to their respective final states.
- Tree calculation is often done through algorithms like heuristic searches to find potential trees with the minimum steps.
Consensus Trees
- Consensus trees display nodes which appeared consistently across multiple trees to show general evolutionary relationships. Consensus trees are used when many trees are produced.
- Consensus trees may use the "majority rule" or the strict consensus, showing the most frequently observed evolutionary relationships among the trees.
Alignment Strategy
- Several alignment strategies exist such as those maximizing matches minimizing gaps (or similar).
- Scoring methods for alignments vary to weight matching positively (++) and gaps negatively (--) based on different costs for gap opening and gap extension.
Character Evolution
- Character states are transformations.
- Transitions (e.g., from present to absent) and transversions (e.g., from large to small) are changes. Ambiguity may occur if multiple states are likely.
Nucleotide Substitutions
- Various types of nucleotide substitutions exist, including single substitutions (A→G), multiple substitutions (A→G→T).
- Parallel or convergent substitutions occur in similar positions across lineages. Back substitution can also occur.
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Description
Test your understanding of cladistic methods and phylogenetic analysis with this quiz. It covers topics such as coding strategies, molecular versus morphological data, and human origins models. Explore the implications of these concepts in evolutionary biology.
