Macroevolution Exam 3

How can we place a fossil on the appropriate branch of the Tree of Life?

We must first assign the fossil to a clade (a group of related species). To do this, we look for shared, derived characters (distinguishing features) that define that clade. For instance, the 50-million-year-old fossil Pakicetus is placed on the cetacean branch because it possesses the involucrum, a feature of the middle ear that is a shared, derived character for living cetaceans. This requires examining the fossil's features and using comparative anatomy.

Describe at least two ways in which we can infer the biology (i.e., function, behavior, ecology) of a fossilized organism. Support your descriptions with examples.

Since many aspects of biology (like function, behavior, and ecology) do not fossilize, we reconstruct them based on living relatives.

1. Inferring Function and Behavior using Functional Morphology: We study how living organisms use their body structures (functional morphology) to create biomechanical models that can be applied to the extinct organism.

◦ Example (Function): Biomechanical models, inspired by living fishes, inferred that the extinct predatory fish Dunkleosteus was capable of rapid mouth closure and could generate forces high enough to break through bone

 ◦ Example (Behavior): It was hypothesized that the head crest of hadrosaurs acted as a resonance chamber to produce sound. This was supported by finding that the hadrosaur ear bone was sensitive to the frequencies predicted by sound models.

2. Inferring Ecology from Co-occurring Fossils: We examine other fossils found together in the same sedimentary layer to make inferences about ecological structure and interactions.

◦ Example (Community): Fossils from the Rhynie Chert reveal an early terrestrial community structure, including a vascular plant (Rhynia), a herbivorous insect (Rhyniognatha), and a spider-like arthropod (Trigonotarbid).

    ◦ Example (Interaction): Diet can sometimes be inferred directly from fossil material, such as coprolites (fossilized feces).

Describe three ways that a fossil can inform us about the history of the clade to which it belongs? Support your descriptions with examples.

Fossils inform us about the history of diversity in a group.

1. Estimating the Age of a Clade: Fossils are used to estimate the age of a clade. The oldest fossil that has the clade’s shared, derived characters provides a minimum age estimate. The lineage split must have occurred before the fossil was formed.

    ◦ Example: The 50-million-year-old Pakicetus fossil helps estimate the minimum age of the cetacean lineage.

2. Providing Evidence of Diversification: Fossils show diversification (the accumulation of species and morphological variety) through time. By tracing the fossil forms across different layers (strata), researchers estimate the number of species and morphological disparity present, inferring origination and extinction events.

    ◦ Example: Fossils trace the diversity through time of trilobites during the Paleozoic Era.

3. Informing Major Evolutionary Innovations (Transitional Fossils): Transitional fossils show intermediate forms and reveal the sequence of changes during the origin of a novel trait (innovation). These fossils possess only a subset of the derived characters defining the full clade.

    ◦ Example: Fossil lobe-finned fish (like Tiktaalik) reveal how the tetrapod limb evolved. These aquatic animals possessed some limb elements and used their appendages as paddles.

What do the branches of a phylogeny represent? What do the nodes represent?

• Branches: Represent ancestral lineages. Internal branches represent shared ancestors among taxa.

• Nodes: Represent where ancestral lineages split. Each internal node represents the most recent common ancestor (MRCA) of the lineages branching from it.

Explain what closeness of relationship means in terms of recency of ancestry. For a given phylogeny, be able to determine closeness of relationship between taxa.

Taxa are considered more closely related if they share a more recent common ancestor. In a phylogeny, taxa joined by a more recent node are more closely related.

What is a clade? How can you identify a clade on a phylogeny?

A clade is an evolutionary group that includes a common ancestor and all of its descendants. Clades contain species that are more closely related to each other than to any other species outside the group. Each node on a phylogeny represents a hypothesis about clade membership.

What do we mean by sister groups? How do we identify sister groups on a phylogeny?

Sister groups are the two descendant groups on either side of a node. For example, Mammals and Reptiles are considered sister groups on a specific tree structure.

How do we distinguish between monophyletic and paraphyletic groups on a phylogeny?

A monophyletic group (a clade) includes the common ancestor and all of its descendant species.

• A paraphyletic group excludes some of the descendants of the common ancestor.

In taxonomy, we accept only monophyletic groups as valid taxa. Why is that?

This is necessary because only monophyletic groups can be defined by synapomorphies. Synapomorphies are shared, derived characters that arose once in the common ancestor and were passed on to all group members, making them diagnostic features for the clade.

Give examples of morphological characters we could use in phylogenetic analysis. Give some examples of molecular characters we could use. What advantages do morphological characters provide over molecular characters? What advantages to molecular characters offer?

• Morphological Characters: These are observable phenotypic features. Examples of character states include dorsal fin morphology (e.g., notched or separated), the number of finlets, or quantitative measures like the length of the pectoral fin.

• Molecular Characters: Characters are typically base positions in a DNA sequence, where the character state is the nucleotide (A, C, G, or T) at that position.

What is an outgroup and why is it necessary to choose one for phylogeny estimation?

An outgroup is a taxon used in phylogeny estimation (e.g., Squaretail was used in the fish activity). It serves as a crucial reference point for understanding the evolutionary relationships within the ingroup

What is the optimization criterion for phylogeny estimation using parsimony? Be able to map one or more characters onto alternative phylogenies and choose the best tree using the principle of parsimony.

The optimization criterion for parsimony is choosing the phylogeny that minimizes inferred evolutionary changes. To find the best tree, you reconstruct the changes for all characters on each alternative phylogeny, then count the total number of evolutionary changes across all characters. The tree with the fewest total changes is the most parsimonious.

Why is it so important to evaluate uncertainty in a phylogeny? In other words, why do we want to evaluate the level of support for particular nodes on a phylogeny

A phylogenetic tree is only a hypothesis of evolutionary relationships, and these relationships are inherently uncertain because the true ancestry is unknown. We must evaluate the degree of uncertainty by looking at the support for the nodes in the tree. Since each node represents a hypothesis about clade membership, evaluating its support tells us how much confidence we should have in that hypothesized relationship.

Describe the procedure involved in bootstrapping analysis? Be able to interpret bootstrap support for nodes on a phylogeny.

Bootstrapping is a statistical method used to estimate confidence in the nodes of a phylogeny.

Procedure:

1. Resample: Create many new data sets by randomly resampling the original character data with replacement. Each new set must have the same number of characters as the original.

2. Re-estimate: The phylogenetic method is re-run to estimate a new phylogeny for each resampled data set.

3. Evaluate: The analysis checks how often each node from the best tree is recovered across all these bootstrap replicates (at least 100 are typical).

Interpretation of Support: Bootstrap support is expressed as a percentage:

• Strongly supported if >95%40.

• Marginally supported if <95% but >70%40.

• Unsupported if <50%40.

What is a polytomy? How do we interpret a polytomy?

A polytomy is a node on a phylogeny from which more than two phylogenetic branches emerge. Polytomies are usually formed when nodes with insufficient bootstrap support (e.g., <50%) are collapsed. We interpret a polytomy as meaning that we cannot determine which of the emerging lineages are more closely related given the current data.

What information is contained in the branch lengths of a cladogram, phylogram, and chronogram?

All methods estimate topology (the branching pattern of ancestry).

• Cladogram (Parsimony): Branch lengths are uninformative.

• Phylogram (ML/Bayesian): Branch lengths reflect the amount of divergence between lineages, measured in units of substitutions per site.

• Chronogram: Branch lengths represent absolute time, measured in millions of years.

Why do we want to estimate the ages of nodes on a phylogeny? Give an example of a question we could address with divergence time estimates.

We estimate divergence times (node ages) primarily to calibrate clade ages to the Geologic Time Scale. This information helps us test hypotheses about the causes of diversification.

• Example Question: We can test the hypothesis that the extinction of the dinosaurs affected the evolution of mammals. Divergence time estimates can date the splits (nodes) of the mammal phylogeny to see if a burst of diversification occurred shortly after the End-Cretaceous (KPg) Extinction event.

What information do we need to estimate absolute ages for nodes on a phylogeny?

We need two types of information:

1. A Phylogram, which is a phylogeny where branch lengths are represented by the number of substitutions. This gives us the relative ages of the nodes.

2. Calibrations (absolute age estimates), typically provided by fossils, used to calibrate the relative node ages to absolute time.

What is the molecular clock, and why is it significant in divergence time estimation?

The molecular clock refers to the relatively constant rate of nucleotide substitutions (replacement of one nucleotide with another) within DNA segments during evolution. It is significant because, by assuming the clock runs constantly, the number of inferred substitutions is proportional to divergence time. This relationship allows us to use the number of substitutions to estimate the relative timing of divergence events.

True or False. Living lineages have evolved for equal amounts of time since they split from their common ancestor.

True

Consider a fossil placed on a branch of a phylogenetic tree. This fossil provides a minimum age constraint for what node on the phylogeny?

The fossil provides a minimum age constraint on the node below it. Since the fossil represents the first evidence of that descendant lineage, the divergence event (the node) must have happened earlier

What is homology? How can you use a character history to infer homology? Give an example of a homologous character.

Homology: A shared character state that was inherited from a common ancestor.

• Inference: A character history shows homology if it reconstructs a single origin of the character state. Although the character may diverge in function among descendants, it retains similarities (like anatomical organization) that show shared ancestry.

• Example: The forelimbs of different mammals (like humans, cats, whales, and bats) are homologous because they share the same underlying anatomical organization (e.g., Humerus, Radius, Ulna, etc.).

What is convergence? Describe the character history that indicates convergence. Give an example of convergence.

• Convergence (Homoplasy): A shared character state that arose independently in different lineages. This often happens because similar environmental pressures favor a common form.

• Character History: A history that indicates convergence must reconstruct multiple independent origins of the shared character state.

• Example: Wings for flight: As mentioned above, bats, birds, and insects all evolved wings independently to achieve flight, but the underlying bone structure is different.