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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 Hydra Manticore Yawclor
Hydra × 18 22
Manticore 18 × 8
Yawclor 22 8 ×

The table above represents a distance matrix for the following taxa: Hydra, Manticore, Yawclor. The values in the matrix correspond to the genetic distances between pairs of taxa.
For example, the distance between taxon Hydra and taxon Manticore is 18. Distances are symmetric, meaning that both the distance between taxon Manticore and taxon Yawclor is 8 and the distance between taxon Yawclor and taxon Manticore is 8.
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 Ashen Kraken Manticore Xeraph
Ashen × 16 32 16
Kraken 16 × 32 8
Manticore 32 32 × 38
Xeraph 16 8 38 ×

The table above represents a distance matrix for the following taxa: Ashen, Kraken, Manticore, Xeraph. The values in the matrix correspond to the genetic distances between pairs of taxa.
For example, the distance between taxon Ashen and taxon Kraken is 16. Distances are symmetric, meaning that both the distance between taxon Kraken and taxon Manticore is 32 and the distance between taxon Manticore and taxon Kraken 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 Faylen Narloc Phoenix Wyvern Yawclor
Faylen × 2 28 22 34
Narloc 2 × 26 18 36
Phoenix 28 26 × 30 38
Wyvern 22 18 30 × 36
Yawclor 34 36 38 36 ×

The table above represents a distance matrix for the following taxa: Faylen, Narloc, Phoenix, Wyvern, Yawclor. The values in the matrix correspond to the genetic distances between pairs of taxa.
For example, the distance between taxon Faylen and taxon Narloc is 2. Distances are symmetric, meaning that both the distance between taxon Narloc and taxon Phoenix is 26 and the distance between taxon Phoenix and taxon Narloc is 26.
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 Ashen Bellen Dibblet Elwet Kraken Xeraph
Ashen × 26 2 24 44 34
Bellen 26 × 20 14 42 32
Dibblet 2 20 × 26 46 34
Elwet 24 14 26 × 44 36
Kraken 44 42 46 44 × 44
Xeraph 34 32 34 36 44 ×

The table above represents a distance matrix for the following taxa: Ashen, Bellen, Dibblet, Elwet, Kraken, Xeraph. The values in the matrix correspond to the genetic distances between pairs of taxa.
For example, the distance between taxon Ashen and taxon Bellen is 26. Distances are symmetric, meaning that both the distance between taxon Bellen and taxon Dibblet is 20 and the distance between taxon Dibblet and taxon Bellen 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 5)

Click to show Gene Trees from Distance Matrices (Level 5) example problem
7 taxa × 7 taxa distance matrix
taxa Ashen Elwet Hydra Jackalope Kraken Manticore Rynoth
Ashen × 46 64 84 60 66 62
Elwet 46 × 68 80 60 68 64
Hydra 64 68 × 84 6 16 34
Jackalope 84 80 84 × 82 84 78
Kraken 60 60 6 82 × 20 36
Manticore 66 68 16 84 20 × 38
Rynoth 62 64 34 78 36 38 ×

The table above represents a distance matrix for the following taxa: Ashen, Elwet, Hydra, Jackalope, Kraken, Manticore, Rynoth. The values in the matrix correspond to the genetic distances between pairs of taxa.
For example, the distance between taxon Ashen and taxon Elwet is 46. Distances are symmetric, meaning that both the distance between taxon Elwet and taxon Hydra is 68 and the distance between taxon Hydra and taxon Elwet is 68.
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: "6balanced1".

tree code common name: 6balanced1
 Quokka 
 Chimera 
 Elwet 
 Xeraph 
 Bellen 
 Jackalope 


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: "None".

 Gorret 
 Faylen 
 Hydra 
 Unicorn 
 Narloc 
 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
 Elwet 
 Yawclor 
 Zypher 
 Jackalope 
 Wyvern 



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+pair2".

tree code common name: 4comb+pair2
 Gorret 
 Inktoad 
 Wyvern 
 Elwet 
 Bellen 
 Chimera 



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.