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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

Determining Gene Tree Structure from Distance Matrices

Click to show Determining Gene Tree Structure from Distance Matrices example problem
5 taxa × 5 taxa distance matrix
taxa Ashen Narloc Rynoth Thorret Xeraph
Ashen × 32 18 42 34
Narloc 32 × 34 48 8
Rynoth 18 34 × 40 36
Thorret 42 48 40 × 38
Xeraph 34 8 36 38 ×

The table above represents a distance matrix for the following taxa: Ashen, Narloc, Rynoth, Thorret, Xeraph. The values in the matrix correspond to the genetic distances between pairs of taxa.
For example, the distance between taxon Ashen and taxon Narloc is 32. Distances are symmetric, meaning that both the distance between taxon Narloc and taxon Rynoth is 34 and the distance between taxon Rynoth and taxon Narloc is 34.
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 Tree from Matrix (Level 1)

Click to show Gene Tree from Matrix (Level 1) example problem
3 taxa × 3 taxa distance matrix
taxa Elwet Kraken Wyvern
Elwet × 8 30
Kraken 8 × 22
Wyvern 30 22 ×

The table above represents a distance matrix for the following taxa: Elwet, Kraken, Wyvern. The values in the matrix correspond to the genetic distances between pairs of taxa.
For example, the distance between taxon Elwet and taxon Kraken is 8. Distances are symmetric, meaning that both the distance between taxon Kraken and taxon Wyvern is 22 and the distance between taxon Wyvern and taxon Kraken is 22.
Using this distance matrix, determine the most appropriate gene tree that accurately reflects the relationships and distances between these taxa.

 

Gene Tree from Matrix (Level 2)

Click to show Gene Tree from Matrix (Level 2) example problem
4 taxa × 4 taxa distance matrix
taxa Dibblet Hydra Narloc Wyvern
Dibblet × 26 34 22
Hydra 26 × 40 10
Narloc 34 40 × 40
Wyvern 22 10 40 ×

The table above represents a distance matrix for the following taxa: Dibblet, Hydra, Narloc, Wyvern. The values in the matrix correspond to the genetic distances between pairs of taxa.
For example, the distance between taxon Dibblet and taxon Hydra is 26. Distances are symmetric, meaning that both the distance between taxon Hydra and taxon Narloc is 40 and the distance between taxon Narloc and taxon Hydra is 40.
Using this distance matrix, determine the most appropriate gene tree that accurately reflects the relationships and distances between these taxa.

 

Gene Tree from Matrix (Level 3)

Click to show Gene Tree from Matrix (Level 3) example problem
5 taxa × 5 taxa distance matrix
taxa Bellen Elwet Faylen Kraken Wyvern
Bellen × 46 24 38 24
Elwet 46 × 46 54 46
Faylen 24 46 × 38 10
Kraken 38 54 38 × 38
Wyvern 24 46 10 38 ×

The table above represents a distance matrix for the following taxa: Bellen, Elwet, Faylen, Kraken, Wyvern. The values in the matrix correspond to the genetic distances between pairs of taxa.
For example, the distance between taxon Bellen and taxon Elwet is 46. Distances are symmetric, meaning that both the distance between taxon Elwet and taxon Faylen is 46 and the distance between taxon Faylen and taxon Elwet is 46.
Using this distance matrix, determine the most appropriate gene tree that accurately reflects the relationships and distances between these taxa.

 

Gene Tree from Matrix (Level 4)

Click to show Gene Tree from Matrix (Level 4) example problem
6 taxa × 6 taxa distance matrix
taxa Chimera Narloc Rynoth Thorret Wyvern Xeraph
Chimera × 66 38 44 12 64
Narloc 66 × 66 68 64 28
Rynoth 38 66 × 52 38 62
Thorret 44 68 52 × 48 72
Wyvern 12 64 38 48 × 66
Xeraph 64 28 62 72 66 ×

The table above represents a distance matrix for the following taxa: Chimera, Narloc, Rynoth, Thorret, Wyvern, Xeraph. The values in the matrix correspond to the genetic distances between pairs of taxa.
For example, the distance between taxon Chimera and taxon Narloc is 66. Distances are symmetric, meaning that both the distance between taxon Narloc and taxon Rynoth is 66 and the distance between taxon Rynoth and taxon Narloc is 66.
Using this distance matrix, determine the most appropriate gene tree that accurately reflects the relationships and distances between these taxa.

 

Gene Tree from Matrix (Level 5)

Click to show Gene Tree from Matrix (Level 5) example problem
7 taxa × 7 taxa distance matrix
taxa Ashen Faylen Hydra Jackalope Rynoth Thorret Yawclor
Ashen × 20 30 20 60 74 60
Faylen 20 × 28 4 66 64 58
Hydra 30 28 × 32 58 66 58
Jackalope 20 4 32 × 58 68 62
Rynoth 60 66 58 58 × 70 48
Thorret 74 64 66 68 70 × 66
Yawclor 60 58 58 62 48 66 ×

The table above represents a distance matrix for the following taxa: Ashen, Faylen, Hydra, Jackalope, Rynoth, Thorret, Yawclor. The values in the matrix correspond to the genetic distances between pairs of taxa.
For example, the distance between taxon Ashen and taxon Faylen is 20. Distances are symmetric, meaning that both the distance between taxon Faylen and taxon Hydra is 28 and the distance between taxon Hydra and taxon Faylen is 28.
Using this distance matrix, determine the most appropriate gene tree that accurately reflects the relationships and distances between these taxa.

 

Different Phylogenetic Trees (Easy)

Click to show Different Phylogenetic Trees (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: "4comb+pair4".

tree code common name: 4comb+pair4
 Quokka 
 Ashen 
 Chimera 
 Gorret 
 Faylen 
 Oclora 


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?

 

Different Phylogenetic Trees (Medium)

Click to show Different Phylogenetic Trees (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".

 Sphinx 
 Manticore 
 Hydra 
 Rynoth 
 Gorret 
 Jackalope 
 Chimera 


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?

 

Different Phylogenetic Trees (Rigorous)

Click to show Different Phylogenetic Trees (Rigorous) 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 8 leaves. This phylogenetic tree is affectionately named: "None".

 Kraken 
 Sphinx 
 Rynoth 
 Bellen 
 Jackalope 
 Zypher 
 Manticore 
 Phoenix 


Among the eight 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?

 

Same Phylogenetic Trees (Easy)

Click to show Same Phylogenetic Trees (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+pair1".

tree code common name: 3comb+pair1
 Phoenix 
 Xeraph 
 Unicorn 
 Gorret 
 Sphinx 



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?

 

Same Phylogenetic Trees (Medium)

Click to show Same Phylogenetic Trees (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: "6comb".

tree code common name: 6comb
 Chimera 
 Phoenix 
 Vyrax 
 Bellen 
 Inktoad 
 Dibblet 



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?

 

Same Phylogenetic Trees (Rigorous)

Click to show Same Phylogenetic Trees (Rigorous) 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 8 leaves. This phylogenetic tree is affectionately called: "None".

 Bellen 
 Kraken 
 Zypher 
 Lystra 
 Vyrax 
 Xeraph 
 Unicorn 
 Oclora 



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?

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