Phylogeny & Evolutionary Relationships Notes

Fifty practice flashcards covering key concepts from phylogeny, systematics, classification methods, phylogenetic trees, and molecular data.

Phylogeny

evolutionary history of organisms, showing pattern of descent and ancestry, derived from morphological and molecular data.

Taxonomy

Linnaean binomial system and a rank-based classification (Domain to Species).

domain > kingdom > phylum > class > order > family > genus > species

What is the sequence of Linnaean ranks?

phenetics and phylogenetics (cladistics and phyletics)

What are the two main systems of classification?

Phenetics

Classification based on overall physical characteristics that yields phenograms; emphasizes similarity over ancestry.

Cladistics

A phylogenetic approach that groups organisms into clades based on common ancestry and shared derived traits; produces cladograms.

Phyletics

A distance-based method that emphasizes the amount of evolutionary change; yields phylograms.

Phylogenetic Tree

A visual hypothesis of relationships showing descent; includes clades, sister taxa, basal taxa; can be vertical/diagonal/horizontal.

Clade

A monophyletic group including a common ancestor and all its descendants.

Monophyletic Group

A group consisting of a common ancestor and all of its descendants.

Paraphyletic Group

A group that includes the common ancestor but not all descendants.

Polyphyletic Group

A group that does not include the most recent common ancestor; often based on convergent traits.

Sister Taxa

Taxa that share a common ancestor not shared by any other group.

Basal Taxon

A lineage that diverged early from the root and remains unbranched.

Root, branches/edges, branch points/nodes, leaves/tips.

Parts of a phylogenetic tree

Common ancestor

What is the root in a phylogenetic tree?

Lineages for taxa of interest; connections between nodes

What are branches/edges?

Speciation events where lineages diverge

What are branch points/nodes?

Species of interest or operational taxonomic units

What are leaves/tips?

vertical, diagonal, or horizontal

In what orientations can phylogenetic trees be drawn?

Monophyletic Clade

A clade that includes a common ancestor and all its descendants.

Paraphyletic Clade

A clade that includes the common ancestor but not all descendants.

Polyphyletic Group

A group that excludes the most recent common ancestor; often based on superficial similarity.

Homology

Phenotypic and genetic similarities due to shared ancestry; homologous structures.

Homoplasy

Shared character that evolved independently in different groups due to similar environments; analogous structures.

Plesiomorphy

An ancestral feature; not very useful in delineating groups.

Symplesiomorphy

A shared ancestral trait.

Apomorphy

A derived character.

Autapomorphy

A derived character unique to one taxon.

Ingroup

The species of interest in a phylogenetic study.

Outgroup

A species not closely related to the ingroup, used for rooting the tree.

Character Matrix

A table checking presence (1) and absence (0) of traits across taxa.

The outgroup with the smallest total (fewest 1s) across characters

How is the basal taxon identified in a character matrix?

To root the phylogenetic tree

What is the purpose of the outgroup in character matrices?

18S and 16S rRNA, COI, cytochrome-b, rbcL, and matK

What are sources of molecular data?

Highly conserved; used for eukaryotes

What is the 18S gene used for?

Used for prokaryotes

What is the 16S gene used for?

Animal DNA barcoding; a conserved gene important for electron transport

What is the COI gene used for?

Animal barcoding; useful for closely related taxa; resolution worsens with distance

What is cytochrome-b gene used for?

Plant barcoding; located in the chloroplast genome; universal to all plants

What is rbcL gene used for?

Plant barcoding; located in the chloroplast genome

What is matK gene used for?

distance-based methods

Methods using distance matrices to estimate relationships (e.g., UPGMA, Neighbor-Joining).

Unweighted Pair Group Method with Arithmetic Mean

UPGMA

Neighbor-Joining method

Joins pairs with smallest total branch length; builds the tree iteratively until one terminal remains.

Distance matrix

A matrix of pairwise differences or distances between sequences.

Align sequences; count differences to create the distance matrix; identify the smallest differences; rework matrix

What are the steps to construct a distance matrix?

Cladograms show branching order; phylograms show the amount of evolutionary change via branch lengths.

What is the difference between cladograms and phylograms?

Unrooted tree

A tree that does not have a root; shows relationships without indicating direction of descent.

Sister taxa relationship

Two taxa that share a most recent common ancestor not shared by other groups.

Monophyletic Clade

It includes the most recent common ancestor and all descendants, representing true evolutionary lineage.

Homology provides evidence of common ancestry used to infer relationships.

Why is homology important in phylogeny?

Independent evolution of similar traits can mislead analyses if not recognized.

Why is homoplasy problematic in phylogeny?

Derived Character

An apomorphy that provides information about relationships within a group.

Plesiomorphy or symplesiomorphy; often less informative for resolving recent divergences.

What is an ancestral character useful for?

To identify the most common characteristic and infer the base (basal) taxon.

What is a character matrix’s total used for?

Provides independent lines of evidence (DNA/RNA sequences) for inferring relationships.

What is the role of molecular data in phylogeny?

Phylogram

A phylogenetic tree where branch lengths reflect the amount of evolutionary change.

Cladogram

A tree showing only branching order without implying the amount of change.

Phylogenetic Hypothesis

A proposed explanation of evolutionary relationships based on available data.

An early-diverging lineage near the root of the tree

What is a basal lineage’s position in a tree?

Monophyletic clade

What is a clade composed of species that all share the same ancestor?

One or more descendants of the common ancestor

What does a paraphyletic group exclude?

The most recent common ancestor is not included in the group

What does a polyphyletic group imply about MRCA?

To indicate the amount of evolutionary change along that branch

What is the main function of branch lengths in a phylogram?

Two taxa that are each other's closest relatives

What characterizes a 'sister taxa' pair in a tree?

Selected genes that are conserved enough to align across taxa but variable enough to differentiate

How are molecular markers chosen for barcoding?

Provides a reference point to determine the direction of evolutionary change

What is the role of the outgroup in rooting a tree?

rbcL and matK

What are common plant barcode genes?

Phenograms are about character change and distances; cladograms emphasize branching order based on shared ancestry

What is the main difference between a phenogram and a cladogram?

It helps root the tree and anchor ancestral character states

What is the significance of a basal taxon being the outgroup with the smallest total in a matrix?