Macroevolution- Exam 3

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

• Fossils are used to estimate the age of a clade (ex. Fossils like Pakicetus help estimate the age of a clade by providing a minimum age for the evolutionary lineage and allowing scientists to correlate the age of the sedimentary rock layers in which they are found)

• Fossils provide direct evidence of diversification in a clade (ex. Diversity through time of trilobites during the Paleozoic era – shows diversification through adaptations such as changes in segment number, body shape for different lifestyles and development of protective features.)

• Transitional fossils inform about the progress of major transformations (ex. Fossil lobe-finned fish reveal evolutionary assembly of the tetrapod limb)

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

• Use characteristics of the fossil organism to determine its clade membership

• Assign the fossil to a clade if it exhibits shared, derived characters

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

• Branches are ancestral lineages (terminal branches lead to terminal descendants; internal branches represent shared ancestors among taxa)

• Nodes are the ends of the branches; Represent common ancestors ( Terminal nodes=tips; Internal nodes show splitting of ancestral lineages)

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 more closely related if they share a more recent common ancestor- taxa joined by a more recent node are more closely related

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

• Clade is a group of species that includes all descendants of their common ancestor

• Locate a node (branch point), follow the branches down, make a cut to remove the branches, confirm all it descendants

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

• Sister groups are the descendants on either side of a node

• Find two lineages that diverge from the same single branch point or node

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

• Monophyletic group includes all species descended from their common ancestor

• Paraphyletic group excludes some of the descendants of the common ancestor

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

• Only monophyletic groups can be defined by synapomorphies (shared, derived characters )

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

 

• Morphological example: skeletal structure (number of vertebrae), body shape, coloration, and other physical traits

• Morphological advantage: Can include fossil taxa and data collection is cheap

 

• Molecular example: DNA, RNA, protein sequences. Each nucleotide in DNA (A,C,G,T) can be treated as a character

• Molecular Advantage: Lots of data and can find homologous gene regions across all forms of life

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

• Outgroup is a taxon that is closely related to the ingroup but more distantly related than ingroups taxa are to each other

• Character states of the outgroup inform the ancestral state for ingroup

What is the optimization criterion for phylogeny estimation using parsimony?

• Minimize the total number of character state changes required to explain the observation data

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?

• Phylogenetic trees are hypotheses about evolutionary histories and not facts

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

• Create bootstrap data set with the same number of character as the original data set

• Re-run optimization to estimate phylogeny for bootstrapped data

• Repeat many times

• Compare the best tree from actual data to best tree obtained from bootstrapped replicates

What is polytomy? How do we interpret a polytomy?

• A polytomy shows more than two phylogenetic branches emerging from the same node

• Indicates that we cannot say which of these lineages are more closely related given the data

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

• Cladogram- No meaning

• Phylogram- shows topology and branch lengths in unit of evolutionary change

• Chronogram- Shows topology and branch lengths in unit of absolute time

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.

• To calibrate clade ages to the geologic time scale

• This information allows us to test hypotheses about the causes of diversification

• Example: What effect did the extinction of the dinosaurs have on the evolution of mammals?

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

• Morphological phylogeny

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

• The relatively constant rate of substitutions within DNA segments

• They allow some variability in substitution rates among lineages   

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. The fossil provides a minimum age constrain for what node on the phylogeny?

• Most recent common ancestor node

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

• Homology- shared character state that is inherited from a common ancestor

• Reconstruct a single origin of the character state

• Ex.  Similarity in anatomical organization and development ( forelimb of humans, bat dolphins, cat)

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

• Convergence: Shared character state that arose independently in separate lineages

• Reconstruct multiple origins of shared character state

• Usually occurs because similar selective factors favor a common form

• Ex.) Origin of birds- birds represent a major transformation; they differ from other living tetrapod’s in a suite of traits