Phylogeny

Phylogeny is the evolutionary history of a species or group of related species.
Systematics is a discipline focused on classifying organisms and determining their evolutionary relationships.

Given a phylogenetic tree, students should be able to:
1. Label the root, nodes, branches, and tips.
2. Identify the type of taxon at the tips (e.g., species or larger group).
3. Circle and label several monophyletic groups, at least two of which are nested.
4. State at least one synapomorphy that identifies each of the circled monophyletic groups.
5. Find the most recent common ancestor of any two given taxa.
Given a phylogeny and information about a trait in species included, students are to mark the tree to indicate where changes in the trait occurred.

Compare phylogenies built with:
1. Synapomorphies.
2. DNA sequences.
Construct a tree showing the relationships among the three domains and label it with synapomorphies.
Explain how a molecular clock attempts to calculate an absolute date using incomplete data.

A phylogenetic tree is a visual representation of the relationships between different organisms, displaying the evolutionary path from a common ancestor to different descendants.
Trees can represent relationships from the entire history of life on Earth to specific individuals in a population.
Branch points in the tree are referred to as nodes.

Vertical lines in a phylogenetic tree, referred to as branches, represent a lineage.
Nodes (or branch points) represent speciation events from a common ancestor.
The trunk at the base of the tree is called the root, representing the most recent common ancestor of all taxa in the tree.
An operational taxonomic unit (OTU) is a singular taxon if DNA sequences are used.

Sister taxa: Groups that share a common ancestor not shared by any other group.
Outgroup: A taxon closely related to, but not part of the group of species being studied (the ingroup).
Relationship interpretation:
- Taxa A & B are more closely related to each other than either is to taxa C.

A group containing a common ancestor and all its descendants is called a clade (also referred to as monophyletic).
Clades can range in size from thousands of species to just a few.
Clades form a nested hierarchy where smaller clades exist within larger clades.
- Example: Imagine clipping a single branch off the phylogeny; all organisms on that pruned branch constitute a clade.

Members of a monophyletic group share traits that evolved along an ancestral branch; such traits are termed synapomorphies.
Example: Feathers evolved after lineage A branched off from the clade containing taxa B, C, and D, hence B, C, and D are expected to have feathers.

Monophyletic groups: Consist of an ancestor and all its descendants (valid clades).
Paraphyletic group: Consists of an ancestral species and some, but not all, descendants.
Polyphyletic group: Includes distantly related species but excludes their most recent common ancestor.

Maximum parsimony assumes that the most likely tree is the one requiring the fewest evolutionary events.
Example: Tree A, which states that primates are more closely related to birds than rodents, is less parsimonious than Tree B, because Tree B indicates that the trait of hair only needed to evolve once.
In DNA-based phylogenies, the most parsimonious tree has the fewest base changes.

Definition: A molecular clock is a method used to estimate the absolute time of evolutionary change based on the observation that genes evolve at a constant rate over time.
Molecular clocks are calibrated by graphing the number of mutations against known branch point dates from the fossil record.
- Linear Regression equation: Y = a + bX, where:
- X: independent variable on the X-axis
- Y: dependent variable on the Y-axis
- b: slope of the regression line.

Some genes may evolve in bursts rather than at a steady rate, resulting in irregular clock-like behavior.
Natural selection can influence mutation rates, causing deviations from the average.
Different taxa may exhibit varying rates of molecular evolution; clock-like genes can evolve at dramatically different rates.

The nature of mutations can be selective (neutral or significantly harmful).
Critical amino acid sequences that impact survival will result in slower evolution.
Less critical sequences may permit faster change due to more neutral mutations.
Selection pressures may fluctuate, leading to a general averaging over time, enhancing clock-like characteristics.

HIV originated from viruses that infected primates but not humans, with the zoonotic mutation occurring more than once (estimated >1).
The most common strain in humans is HIV-1 M.
Molecular clock analysis indicates HIV spread to humans around the year 1930.

What is phylogeny and how does it relate to systematics?
Given a phylogenetic tree, label the root, nodes, branches, and tips.
Identify a monophyletic group on a provided phylogenetic tree and state one synapomorphy characterizing it.
Explain the difference between synapomorphies and operational taxonomic units (OTUs).
How can sister taxa be defined within the context of a phylogenetic tree?
Describe the characteristics of monophyletic, paraphyletic, and polyphyletic groups with examples.
What is maximum parsimony in phylogenetics? Provide an example of two trees for comparison regarding parsimony.
Define a molecular clock and explain how it is calibrated using known branch point dates.
Discuss the limitations of using molecular clocks in estimating evolutionary time.
Analyze the factors that can affect the speed of a molecular clock in various taxa.
In the case of HIV's origin, summarize how molecular clock analysis has contributed to our understanding of its spread to humans.