how to draw a phylogenetic tree from a table

Practise they just look for similarities between the whole genomes? Or just specific genes? Or RNA? Or what exactly?

- A high schoolhouse educatee from Egypt

June iv, 2022

A phylogenetic tree is a diagram used to prove how organisms are related to ane some other.

There are actually a lot of dissimilar ways to make these copse! As long equally you have something you tin compare beyond different species, you tin make a phylogenetic tree.

A phylogenetic tree tin be congenital using concrete information like trunk shape, bone structure, or behavior. Or it tin be built from molecular information, like genetic sequences.

In general, the more information y'all're able to compare, the more authentic the tree will be. So you'd get a more accurate tree by comparing unabridged skeletons, instead of just a unmarried bone. Or past comparison entire genomes, instead of just a single gene.

Any DNA, RNA, or poly peptide sequence can be used to generate a phylogenetic tree. But Dna sequences are near commonly used in generating trees today.

What's in a phylogenetic tree?

In a phylogenetic tree, each line is called a branch. The stop of each branch is called a tip– this is where you put a species!

Each signal where the two branches separate is called a node. A node is the most contempo common antecedent of all species on those branches.

And if y'all go all the way down to the bottom of the tree, the concluding node is called the root. This is the common ancestor all the species in the tree!

You can draw phylogenetic trees in many different shapes. It doesn't matter whether it'southward rectangular or circular. The import office is how it is branched. The branching represents the differences in the relationship of species.

These copse all show exactly the same information! Just in different shapes.

How to construct a phylogenetic tree?

Any DNA, RNA, or protein sequences tin can be used to describe a phylogenetic tree. Just Deoxyribonucleic acid sequences are the most widely used. Information technology's pretty cheap and easy now to get Deoxyribonucleic acid sequences. Plus Dna contains more data, which can make more accurate trees. For example, some changes in DNA sequences do not lead to changes in proteins.

To construct a tree, we'll compare the DNA sequences of different species.

Evolutionarily related species have a mutual ancestor. Earlier they carve up into separate species, they had exactly the aforementioned Deoxyribonucleic acid. But as species evolve and diverge, they will accumulate changes in the DNA sequences.

We can use these changes in the DNA to tell how closely related two species are. If there aren't very many differences, they're probably closely related. If there are a lot of changes, they might be more afar relatives.

The get-go matter to do is align the 2 DNA sequences together that you're going to compare. Make sure you're comparing the same gene! (Or other sequence.) Otherwise you are comparing apples to oranges.

This sequence alignment is often done with the help of computer programs. The strategy is to find the alignment that has the most matches and the least mismatches.

You can align and compare as many sequences as yous desire. Recollect, the more information you consider, the more than accurate your tree will be!

Convert sequence alignment to a relatedness

Ok, so you've got your Deoxyribonucleic acid aligned. Now what? How exercise you lot convert that into a tree?

Next you compare the sequences, to meet how like they are to each other.

Nosotros can meet that Sequence #ane vs #2 accept one difference. Sequence #2 vs #3 accept 2 differences. Sequences #3 vs #4 has 5 differences. And then on.

But by looking at them, we can see that Sequences i and 2 are pretty similar. We would group them together in a tree.

Just nosotros tin can do better than only looking at them. You lot tin really calculate how like any two sequences are, and make a table to compare all the differences. This peculiarly helps when you're comparison a lot of data!

Sequences 1 and 2 differ by 1 nucleotide, out of the 20 full. And so the difference betwixt Sequence ane and 2 is:

1/20= 0.05

Nosotros can summate the difference between each pair of sequences. If we put the calculated differences in a matrix, it would look like this:

Now if you await at the matrix, the pairs that have the lowest values are the nigh similar. Equally before, we can meet that sequences 1 and 2 are very like. So nosotros tin can put one and two together.

After nosotros put 1 and ii together, we will take to recalculate the difference betwixt sequences. Now that nosotros've 1-ii together in the tree, nosotros're going to consider them as a single group. We'll summate the differences with other sequences past taking an average.

For example, the difference between 1&two vs 3 would exist:

Average of (1 vs 3) and (2 vs 3) = 1-2 vs iii
½ * (0.1+0.1)= 0.1

Similarly, we could summate the differences with other sequences. We would have a table like below:

Looking at the tabular array, we can come across 3 is virtually like with 1-2. And so we can group 3 together with 1-2.

Now, we will repeat the above steps. We will treat 1, 2, and 3 as one species every bit we go on edifice the tree. We'll use the average of 1-2 vs other and three vs otherto do this.

For example, the divergence betwixt 1-3 and 4 would be:

Boilerplate of (ane-ii vs 4) and (iii vs 4) = 1-2-3 vs four
½ * (0.two+0.25) = 0.225

We can calculate the rest with the same method. Now we have a tabular array equally below:

We tin encounter that i-3 and four are most like. And so nosotros can put 4 and ane-3 together.

Now we can add in sequence 5 and get our tree!

Yous can use this method to build all sorts of trees! Not all copse will look like this one, but the same bones principles will use.

By Allison Zhang, Stanford University

Source: https://genetics.thetech.org/ask-a-geneticist/how-build-phylogenetic-tree

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