Course 24.3Lesson 3 of 3

Evolutionary trees and the numbers of human evolution

Two species look alike. Are they close relatives? A tree shows the answer, and numbers can build the tree. This lesson reads evolutionary trees, builds one from a table of differences and uses numbers to date a split.

about 30 min1 simulation1 practice question

Lesson 3 of 3Show all lessons

Try the code and the simulations beside the lesson.

What a tree shows

An evolutionary tree shows how species came from common ancestors. Each tip is a species. Each fork, called a node, is a common ancestor from which two lines split. The root is the oldest ancestor of all.

This part is not in the NEET syllabus, but A-Level and IB ask it. A tree is read by its forks and not by the order of the tips on the page.

Two species are more closely related if they share a more recent common ancestor.
A fork can be turned around, with the two branches swapped, and the tree still says the same.
A species that splits off first from the rest, and is a long way from all of them, is the outgroup.

Building a tree from numbers

In the first course, you compared a short piece of a gene in four species P, Q, R and S. The numbers of differences between the pairs of 20 bases were these.

Pair	Differences
P and Q	1
Q and R	2
P and R	3
R and S	3
Q and S	5
P and S	6

A simple method, called UPGMA, builds the tree in these steps.

Join the closest pair, P and Q, with 1 difference. Put the fork at half this distance, 0.5, since each species changed by half of the difference.
Treat P and Q as one group. The distance from the group to R is the average of 3 and 2, which is 2.5. The distance to S is the average of 6 and 5, which is 5.5.
The closest pair now is the group PQ and R, with 2.5. Join them at 1.25.
The distance from PQR to S is the average of 6, 5 and 3, which is 4.67. Join S at 2.33.

A tree drawn from left to right, with the root on the left at the height 2.33 and four species P, Q, R and S as the tips on the right. S is the top tip and its branch goes straight back to the root. The lower branch from the root, at 2.33, leads to a join at 1.25 that splits into R and a second join at 0.50. This last join splits into P and Q. The scale at the bottom is half the number of differences between two sequences.

The tree shows that P and Q share the most recent common ancestor, that R joins them next, and that S split off first.

The molecular clock

This part is not in the NEET syllabus, but A-Level and IB ask it. If a gene changes at a steady rate, the number of differences between two species grows with the time since they split. This is the molecular clock.

After the split, both lines change. So the difference grows at twice the rate of one line. If each line changes by $r$ per cent in each million years, the difference after $t$ million years is

\displaystyle d = 2rt \qquad\text{so}\qquad t = \frac{d}{2r}

A graph of the difference in a gene against the time since two species split, from 0 to 15 million years. Three straight lines rise from the origin: the steepest for 2 per cent per million years in each line, a middle one for 1 per cent and the lowest for 0.5 per cent. A dot on the lowest line marks a 6 per cent difference at 6 million years.

You should see that a faster rate gives an earlier-looking steeper line, and that the same difference means a younger split when the rate is faster.

A clock needs a rate that was measured on fossils of known age. No rate is exactly steady, so the answer is an estimate.

The numbers of human evolution

The tools of this lesson apply to the human line. With the middle of each NCERT range, the brain capacity rises as follows.

From Homo habilis (725 cc) to Homo erectus (900 cc): a rise of 24.1 per cent.
From Homo erectus to Neanderthal man (1400 cc): a rise of 55.6 per cent.

The two steps came about 0.5 million years and 1.4 million years after one another. Per million years, the rise is $175 \div 0.5 = 350$ cc and $500 \div 1.43 = 350$ cc. The two rates are almost the same. A rate computed from only three points cannot show a trend, so these numbers are for practice and not for a rule.

Try it in Python

The program builds the tree of the table above, step by step, and prints the height of each join.

Practise with new numbers

Common mistakes

Reading the tips as a ladder. The order of the tips on the page does not say that one species is older or more advanced.
Saying that two species are close because they look alike. Look at the common ancestor, not at the looks. Analogous features can mislead.
Using the rate of one line only in the clock. After the split, both lines change, so the difference grows at twice the rate.
Taking the molecular clock as exact. It is an estimate, and the rate must be checked on fossils.
Calling the distance of a join the height. The height is half of the distance, since each species changed by half.

Remember these

A tree shows common ancestors. More recent common ancestor means closer relatives.
UPGMA joins the closest pair, averages the distances, and repeats. Height is half the distance.
Molecular clock: $t = d \div (2r)$ , since both lines change.
Brain capacity (NCERT): Homo habilis 650 to 800 cc, Homo erectus about 900 cc, Neanderthal man about 1400 cc.

Check yourself

Try each one on your own first. If you are stuck, open a hint. Then check with Show the answer.

In a tree, species A and B share a common ancestor that is more recent than the ancestor that they share with C. Which two are the closest relatives?

Three species have these differences: X and Y 2, X and Z 8, Y and Z 8. Which two join first, and at what height?

Two species differ by 10 per cent in a gene. The gene changes by 1 per cent in each line in each million years. When did they split?

Why is the answer of a molecular clock only an estimate?

From Homo erectus (900 cc) to Neanderthal man (1400 cc), by how many cc did the brain capacity rise?

References

NCERT (2023). Biology, Textbook for Class XII, chapter 6.
Clark M. A., Douglas M. and Choi J. (2018). Biology 2e, OpenStax, chapter 20.2, Determining Evolutionary Relationships.