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11: Gene Trees

Students construct and compare phylogenetic trees, interpret evolutionary distances, and trace gene inheritance across species.

LibreTexts reference: Chapter 11: Gene Trees and Relationships LibreTexts

Gene Trees from Distance Matrices (Level 1)

Click to show Gene Trees from Distance Matrices (Level 1) example problem
3 taxa × 3 taxa distance matrix
taxa Bellen Jackalope Wyvern
Bellen × 12 20
Jackalope 12 × 20
Wyvern 20 20 ×

The table above represents a distance matrix for the following taxa: Bellen, Jackalope, Wyvern. The values in the matrix correspond to the genetic distances between pairs of taxa.
For example, the distance between taxon Bellen and taxon Jackalope is 12. Distances are symmetric, meaning that both the distance between taxon Jackalope and taxon Wyvern is 20 and the distance between taxon Wyvern and taxon Jackalope is 20.
Using this distance matrix, determine the most appropriate gene tree that accurately reflects the relationships and distances between these taxa.
Hint: taxa with smaller distances are more closely related. Look for clusters that best match the smallest distances.

 

Gene Trees from Distance Matrices (Level 2)

Click to show Gene Trees from Distance Matrices (Level 2) example problem
4 taxa × 4 taxa distance matrix
taxa Faylen Jackalope Narloc Phoenix
Faylen × 12 28 46
Jackalope 12 × 32 44
Narloc 28 32 × 42
Phoenix 46 44 42 ×

The table above represents a distance matrix for the following taxa: Faylen, Jackalope, Narloc, Phoenix. The values in the matrix correspond to the genetic distances between pairs of taxa.
For example, the distance between taxon Faylen and taxon Jackalope is 12. Distances are symmetric, meaning that both the distance between taxon Jackalope and taxon Narloc is 32 and the distance between taxon Narloc and taxon Jackalope is 32.
Using this distance matrix, determine the most appropriate gene tree that accurately reflects the relationships and distances between these taxa.
Hint: taxa with smaller distances are more closely related. Look for clusters that best match the smallest distances.

 

Gene Trees from Distance Matrices (Level 3)

Click to show Gene Trees from Distance Matrices (Level 3) example problem
5 taxa × 5 taxa distance matrix
taxa Chimera Dibblet Elwet Jackalope Narloc
Chimera × 36 8 38 42
Dibblet 36 × 38 28 16
Elwet 8 38 × 36 38
Jackalope 38 28 36 × 28
Narloc 42 16 38 28 ×

The table above represents a distance matrix for the following taxa: Chimera, Dibblet, Elwet, Jackalope, Narloc. The values in the matrix correspond to the genetic distances between pairs of taxa.
For example, the distance between taxon Chimera and taxon Dibblet is 36. Distances are symmetric, meaning that both the distance between taxon Dibblet and taxon Elwet is 38 and the distance between taxon Elwet and taxon Dibblet is 38.
Using this distance matrix, determine the most appropriate gene tree that accurately reflects the relationships and distances between these taxa.
Hint: taxa with smaller distances are more closely related. Look for clusters that best match the smallest distances.

 

Gene Trees from Distance Matrices (Level 4)

Click to show Gene Trees from Distance Matrices (Level 4) example problem
6 taxa × 6 taxa distance matrix
taxa Dibblet Elwet Jackalope Phoenix Wyvern Xeraph
Dibblet × 48 10 34 28 20
Elwet 48 × 44 48 52 48
Jackalope 10 44 × 28 34 20
Phoenix 34 48 28 × 2 28
Wyvern 28 52 34 2 × 28
Xeraph 20 48 20 28 28 ×

The table above represents a distance matrix for the following taxa: Dibblet, Elwet, Jackalope, Phoenix, Wyvern, Xeraph. The values in the matrix correspond to the genetic distances between pairs of taxa.
For example, the distance between taxon Dibblet and taxon Elwet is 48. Distances are symmetric, meaning that both the distance between taxon Elwet and taxon Jackalope is 44 and the distance between taxon Jackalope and taxon Elwet is 44.
Using this distance matrix, determine the most appropriate gene tree that accurately reflects the relationships and distances between these taxa.
Hint: taxa with smaller distances are more closely related. Look for clusters that best match the smallest distances.

 

Gene Trees from Distance Matrices (Level 5)

Click to show Gene Trees from Distance Matrices (Level 5) example problem
7 taxa × 7 taxa distance matrix
taxa Bellen Faylen Hydra Jackalope Manticore Phoenix Xeraph
Bellen × 26 40 4 54 56 16
Faylen 26 × 38 22 66 50 30
Hydra 40 38 × 36 58 54 38
Jackalope 4 22 36 × 64 50 16
Manticore 54 66 58 64 × 58 60
Phoenix 56 50 54 50 58 × 50
Xeraph 16 30 38 16 60 50 ×

The table above represents a distance matrix for the following taxa: Bellen, Faylen, Hydra, Jackalope, Manticore, Phoenix, Xeraph. The values in the matrix correspond to the genetic distances between pairs of taxa.
For example, the distance between taxon Bellen and taxon Faylen is 26. Distances are symmetric, meaning that both the distance between taxon Faylen and taxon Hydra is 38 and the distance between taxon Hydra and taxon Faylen is 38.
Using this distance matrix, determine the most appropriate gene tree that accurately reflects the relationships and distances between these taxa.
Hint: taxa with smaller distances are more closely related. Look for clusters that best match the smallest distances.

 

Non-Equivalent Phylogenetic Tree Structures (EASY)

Click to show Non-Equivalent Phylogenetic Tree Structures (EASY) example problem

Find the DIFFERENT tree

Phylogenetic trees are fundamental tools in genetics research, enabling scientists to visualize evolutionary relationships among species, gene sequences, or populations. By tracing shared ancestry, these trees can provide valuable insights into genetic biodiversity. Applications of phylogenetic trees include tracking disease evolution, identifying conserved genetic sequences, and understanding speciation processes. Phylogenetic trees are indispensable for both theoretical and applied genetics.
The tree diagram below is a phylogenetic tree with 6 leaves. This phylogenetic tree is affectionately named: "3comb+pair2+1".

tree code common name: 3comb+pair2+1
 Faylen 
 Jackalope 
 Dibblet 
 Elwet 
 Phoenix 
 Rynoth 


Among the five phylogenetic trees displayed below, all but one have the same structure and represent the same evolutionary relationships as the tree above.
Your task is to identify the single different phylogenetic tree that does NOT share the same structure or relationships as the reference tree above.

Which one of the following phylogenetic trees represents a DIFFERENT phylogenetic tree?
Hint: trees can be rotated at internal nodes without changing their meaning. Focus on branching order, not left/right orientation.

 

Non-Equivalent Phylogenetic Tree Structures (MEDIUM)

Click to show Non-Equivalent Phylogenetic Tree Structures (MEDIUM) example problem

Find the DIFFERENT tree

Phylogenetic trees are fundamental tools in genetics research, enabling scientists to visualize evolutionary relationships among species, gene sequences, or populations. By tracing shared ancestry, these trees can provide valuable insights into genetic biodiversity. Applications of phylogenetic trees include tracking disease evolution, identifying conserved genetic sequences, and understanding speciation processes. Phylogenetic trees are indispensable for both theoretical and applied genetics.
The tree diagram below is a phylogenetic tree with 7 leaves. This phylogenetic tree is affectionately named: "5comb+pair".

tree code common name: 5comb+pair
 Ashen 
 Gorret 
 Inktoad 
 Quokka 
 Phoenix 
 Wyvern 
 Yawclor 


Among the six phylogenetic trees displayed below, all but one have the same structure and represent the same evolutionary relationships as the tree above.
Your task is to identify the single different phylogenetic tree that does NOT share the same structure or relationships as the reference tree above.

Which one of the following phylogenetic trees represents a DIFFERENT phylogenetic tree?
Hint: trees can be rotated at internal nodes without changing their meaning. Focus on branching order, not left/right orientation.

 

Equivalent Phylogenetic Tree Structures (EASY)

Click to show Equivalent Phylogenetic Tree Structures (EASY) example problem

Find the SAME tree

Phylogenetic trees are fundamental tools in genetics research, enabling scientists to visualize evolutionary relationships among species, gene sequences, or populations. By tracing shared ancestry, these trees can provide valuable insights into genetic biodiversity. Applications of phylogenetic trees include tracking disease evolution, identifying conserved genetic sequences, and understanding speciation processes. Phylogenetic trees are indispensable for both theoretical and applied genetics.
The tree diagram below is a phylogenetic tree with 5 leaves. This phylogenetic tree is affectionately called: "3comb+pair3".

tree code common name: 3comb+pair3
 Inktoad 
 Kraken 
 Bellen 
 Chimera 
 Lystra 



Several phylogenetic trees are shown below, but only one has the SAME structure and represents the same relationships as the phylogenetic tree above.
Your task is to identify the single same phylogenetic tree that shares the same structure and relationships as the reference tree above.

Which one of the following phylogenetic trees represents the SAME tree relationships or is equivalent to the phylogenetic tree above?
Hint: trees are equivalent if internal nodes can be rotated to match. Ignore the exact left/right placement of taxa.

 

Equivalent Phylogenetic Tree Structures (MEDIUM)

Click to show Equivalent Phylogenetic Tree Structures (MEDIUM) example problem

Find the SAME tree

Phylogenetic trees are fundamental tools in genetics research, enabling scientists to visualize evolutionary relationships among species, gene sequences, or populations. By tracing shared ancestry, these trees can provide valuable insights into genetic biodiversity. Applications of phylogenetic trees include tracking disease evolution, identifying conserved genetic sequences, and understanding speciation processes. Phylogenetic trees are indispensable for both theoretical and applied genetics.
The tree diagram below is a phylogenetic tree with 6 leaves. This phylogenetic tree is affectionately called: "4comb+pair3".

tree code common name: 4comb+pair3
 Dibblet 
 Vyrax 
 Xeraph 
 Faylen 
 Jackalope 
 Rynoth 



Several phylogenetic trees are shown below, but only one has the SAME structure and represents the same relationships as the phylogenetic tree above.
Your task is to identify the single same phylogenetic tree that shares the same structure and relationships as the reference tree above.

Which one of the following phylogenetic trees represents the SAME tree relationships or is equivalent to the phylogenetic tree above?
Hint: trees are equivalent if internal nodes can be rotated to match. Ignore the exact left/right placement of taxa.