Phylogeny & Evolutionary History

What is phylogenetic systematics?

Taxonomic classification based on evolutionary history of organisms

What does a phylogeny reflect?

Branching pattern of relatedness among populations over evolutionary time

What kinds of traits are used to study phylogeny?

DNA sequences, amino acid sequences, mating behaviors

What do interior nodes in a phylogenetic tree represent?

Common ancestors (branch points)

What does the root of a tree represent?

The lineage leading to the entire group (the origin)

Can rotating branches at nodes change relationships?

No, rotations do not change evolutionary relationships

Does the order of taxa at the tips show relatedness?

No, common ancestry depth determines relatedness

How can you tell which taxa are more closely related?

Taxa with a more recent common ancestor are more closely related

What is a monophyletic clade?

Group that includes an ancestor and all its descendants

What is a polyphyletic group?

Group with members that do not share a recent common ancestor

What is a paraphyletic group?

Group with an ancestor but missing some descendants

What is an outgroup in a phylogenetic analysis?

A taxon outside the group of interest that helps determine trait polarity (ancestral vs. derived)

What does a cladogram show?

Only evolutionary relationships, not change or time

What does a phylogram show?

Amount of character change along branches

What does a chronogram show?

Time-based divergence along branches

What is homology?

Trait similarity due to shared ancestry

What is analogy?

Trait similarity due to convergent evolution, not shared ancestry

What is divergent evolution?

Closely related species evolve different traits over time

What is convergent evolution?

Unrelated species evolve similar traits independently

What is aposematic coloration?

Bright colors warning predators of toxicity

What is cryptic coloration?

Camouflage that helps organisms blend into surroundings

What are vestigial traits?

Traits that no longer serve a function but are inherited from ancestors

What does the human plica semilunaris suggest?

Humans share ancestry with animals that have a nictitating membrane

What does phylogeny of snakes show?

Gradual loss of limbs from reptilian ancestors

Why are vestigial traits evidence for evolution?

They support Darwin’s theory of descent from a common ancestor

What is the generation-time hypothesis?

Shorter-lived species evolve faster due to quicker generations

Why do herbs have longer branches in phylogenies?

They evolve faster due to shorter generation times

What does phenetic mean in phylogenetics?

Classifying organisms based on similarity, not evolutionary relationships

What is parsimony in phylogenetics?

The principle that the best tree is the one with the fewest evolutionary changes

Why might parsimony fail?

It can be misled by homoplasies or unequal rates of evolution

What is homoplasy?

A trait shared due to convergence or reversal, not common ancestry

What is a character reversal?

The reappearance of an ancestral trait that had previously been lost

What is Dollo’s Law?

Once a complex trait is lost, it is unlikely to re-evolve in the exact same way

Why are autapomorphies uninformative for phylogeny?

Because they occur in only one lineage and don’t show relationships

What is a polytomy?

An unresolved node on a tree where more than two lineages emerge

How does a consensus tree help in tree building?

It summarizes relationships from multiple equally likely trees

What is a strict consensus tree?

A tree showing only relationships found in all candidate trees

What is a majority-rule consensus tree?

A tree showing relationships found in most candidate trees

What does sequence alignment do?

It lines up DNA or protein sequences to identify homologous positions

What is the neighbor joining method?

A distance-based method for constructing trees from pairwise distances

What is the Jukes-Cantor model?

A model assuming equal rates of all nucleotide substitutions

How is the Kimura two-parameter model different?

It distinguishes between transitions and transversions in nucleotide substitution

What are nuisance parameters?

Uninteresting variables (e.g., substitution rate) that must be estimated in likelihood methods

How does maximum likelihood work?

It finds the tree with the highest probability of producing the observed data

How does Bayesian phylogenetics differ?

It calculates the most probable tree given the data and prior assumptions

What is bootstrap resampling?

A technique for testing support by rebuilding trees from resampled data sets

What does a high bootstrap value (e.g. 100) mean?

Strong support for that particular branch across all resampled trees

What is the comparative method?

Tests for adaptation by comparing traits across species using phylogeny

What is an independent contrast?

A trait comparison between sister lineages that evolved separately

Why are independent contrasts used?

To control for shared ancestry in adaptive trait studies

How did Ebola virus phylogeny show rapid evolution?

By tracking mutations in viral genomes sampled over time

Why was Tiktaalik roseae an important fossil?

It links aquatic fish to terrestrial tetrapods—a key transitional species

What are synapomorphies?

Derived traits shared by multiple taxa indicating common ancestry

What are symplesiomorphies?

Shared ancestral traits not useful for recent evolutionary relationships

What is the order of trait evolution over time?

Autapomorphy → Synapomorphy → Symplesiomorphy

Why are outgroups used in phylogenetics?

To root trees and determine which traits are ancestral

What is a reversal in trait evolution?

A derived trait returns to resemble the ancestral state

What is parallel evolution?

Independent development of similar traits in closely related lineages

What does rooting a tree allow us to determine?

Directionality of trait evolution (ancestral vs. derived)

What did Bayesian analysis reveal about SARS-CoV-2?

It traced viral spread and origin across Europe with statistical modeling

How many unrooted trees exist for 6 species?

105 unrooted trees

How many rooted trees come from an unrooted tree with k species?

2k – 3 rooted trees per unrooted tree

What is the problem with distance-based methods?

They assume similarity equals relatedness, which may not hold with unequal evolutionary rates

What is a derived homology in a single lineage called?

Autapomorphy

What is the challenge in distinguishing homology vs. analogy?

They may produce the same trait appearance despite different evolutionary paths

How can allele frequencies be used in phylogeny?

To measure distance between populations of the same species

What is sequence alignment and why is it important?

Aligning DNA to detect homologous positions for tree construction

What happens when comparing distant species without adjusting for ancestry?

It may falsely suggest adaptation rather than shared ancestry

How did researchers show tail length correlated with arboreal habitat in snakes?

By using independent contrasts to control for phylogeny