Phylogenetic Trees and Evolutionary Relationships

What are branches in a phylogenetic tree called?

Taxonomic groups (or taxa)

Are phylogenetic tree models permanent or subject to change?

These models are always subjected to be updated or revised

What do phylogenetic trees show about ancestors and descendants?

The patterns in which ancestors gave rise to their descendants over time and show how various descendants are related to each other in present time

What is a lineage in phylogenetic terms?

A series of ancestor and descendant populations, shown as a line drawn on a time axis

What is a node in a phylogenetic tree?

A point in which a single lineage diverges and splits into separate lineages

What happens to lineages after they split at a node?

Each lineage continues to evolve independently as new traits arise

Where is the appearance of traits depicted on phylogenetic trees?

Along branches

Are ancestral groups usually still living today?

Ancestral groups are most often no longer living

What is the minimum number of tips any phylogenetic tree must have?

At least 2 tips

What do phylogenetic trees represent?

Models that represent currently supported evolutionary relationships

What direction does the time axis run on phylogenetic trees?

From the root towards the tips

What do nodes show on phylogenetic trees?

Points where ancestral populations split into independent lineages

What do the relative positions of nodes indicate?

Relative times of different taxa (relative times of divergence)

What do groups of different taxa have in common?

Many common ancestors, some more recent and some more distant

What do we focus on when studying common ancestry?

Most recent common ancestor (MRCA) of particular group of interest

What is a clade?

A group consisting of an ancestral species and all its descendants

What are the three types of taxonomic groups?

Monophyletic, paraphyletic, and polyphyletic

What are shared characters and traits derived from a common ancestor considered?

Homologous

What are synapomorphies?

Shared traits unique to a given clade

How do homologous traits differ from synapomorphies in scope?

Homologous traits are shared among different taxa and were derived from one of the groups' common ancestors; synapomorphies are clade-specific homologous traits

What makes synapomorphies special compared to other homologous traits?

Synapomorphies are uniquely derived from a clade's most recent common ancestor

What do phylogenies show?

The evolutionary history of relationships among organisms or their genes

What is a phylogenetic tree often called?

A cladogram

Can phylogenetic trees be drawn in different styles?

Yes, different ways of representing phylogenies exist

What is important when interpreting phylogenetic trees?

Correctly interpreting the time axis is important

How many branches does a single lineage typically split into?

As much as possible, single lineages will typically be shown splitting into two new branches but not more than two

Does rotation along a connecting branch change the meaning of a phylogenetic tree?

No, rotation along a connecting branch does not change the meaning of what is shown

Do distances between neighboring branches have meaning?

No, the distance between neighboring branches do not have any meaning, but are simply drawn to improve clarity

Where should tips always end in phylogenetic trees for this course?

Always draw tips to end at the same location

What does "extant" mean?

Still in existence

What assumption is made about groups labeled at the tips of trees?

Groups labeled at the tips of a tree are assumed to be extant

How are extinct species handled in tree diagrams for this course?

Extinct species will not be explicitly labeled in our tree diagrams

How are clades organized in phylogenetic trees?

Phylogenetic trees often consist of smaller clades nested within larger clades

What is the basis for determining evolutionary relatedness in phylogenetic trees?

Most recent common ancestry (not just common ancestry)

What does more recent common ancestor indicate?

More recent common ancestor = more closely related

What is a unifying concept about all life?

All life is connected through evolutionary history

What is the phylogenetic tree of life?

The complete evolutionary history of life

Define homologous traits in detail

Shared characters and traits derived from a common ancestor that are shared among different taxa and were derived from one of the groups' common ancestors

Define synapomorphies in detail

Clade-specific homologous traits that are shared traits unique to a given clade and uniquely derived from a clade's most recent common ancestor

Are all synapomorphies homologous traits?

Yes, synapomorphies are clade-specific homologous traits

Are all homologous traits synapomorphies?

No, homologous traits are broader - they include synapomorphies but also other shared traits from common ancestors

If a trait is found in multiple clades, can it be a synapomorphy?

No, synapomorphies are unique to a given clade

If two species share a trait from their common ancestor, is it homologous?

Yes, it is homologous because it's derived from a common ancestor

If two species in the same clade share a trait that no other clades have, what is it?

It is both homologous (shared from common ancestor) and a synapomorphy (unique to that clade)

What's the key difference between homologous traits and synapomorphies?

Homologous traits are ANY shared traits from common ancestors; synapomorphies are homologous traits that are UNIQUE to a specific clade

Can a trait be homologous but not a synapomorphy?

Yes, if the trait is shared among multiple clades (not unique to one clade)

Can a trait be a synapomorphy but not homologous?

No, all synapomorphies are by definition homologous traits

What makes a clade monophyletic?

Includes an ancestral species and ALL of its descendants

What makes a group paraphyletic?

Includes an ancestral species and SOME but not all of its descendants

What makes a group polyphyletic?

Includes species from different clades that do not share a recent common ancestor

Which type of taxonomic group is considered "natural" in evolutionary terms?

Monophyletic groups (clades) because they represent complete evolutionary units