How Mitochondrial DNA & Ribosomal RNA Provide Molecular Clocks

Instructor: Angela Hartsock

Angela has taught college microbiology and anatomy & physiology, has a doctoral degree in microbiology, and has worked as a post-doctoral research scholar for Pittsburgh’s National Energy Technology Laboratory.

In this lesson, we explore keeping time and dating evolution by tracking genetic mutations in our favorite molecular clocks: mitochondrial DNA and ribosomal RNA.

Keeping Time

I've got a few questions for you before we get started. What time is it right now? You can just look at the clock on your watch, phone, or computer screen to find that answer. What day of the week does Christmas fall on this year? You can easily find that information on a calendar. What famous event happened on June 15, 1215? Time to crack open your history book. How long ago did the last common ancestor of humans and chimpanzees live? I bet the Internet can answer that one, but where did your online source get the answer? Certainly not a watch, calendar, or history book. Believe it or not, that question can be answered with a clock, just not one you are probably familiar with.

DNA Mutations

Let's put the ancestor clock question aside for a minute and talk about genetic mutations. One of the key ideas in evolution is that the sequence of an organism's DNA can change through random mistakes during copying of the DNA. These mistakes are called mutations. Mutations can be positive or good for the organism, like antibiotic resistance mutations that help keep bacteria alive despite exposure to penicillin. Mutations can also be negative or bad for the organism, like the mutation in fruit flies that causes its wings to shrivel and become useless. Most mutations, though, are neutral. A neutral mutation is a change in the DNA sequence that is neither beneficial nor harmful to the survival of the organism. Since they aren't changing the odds of the organism's survival, these mutations can accumulate in the genome over time.

But if these mutations aren't changing the organism in significant ways (helping or hurting), why do we care about them? Well, it's almost time to revisit that clock.

The Rate of DNA Mutations

In the 1960s, three scientists proposed a theory that DNA sequences evolve at a relatively constant rate. Said another way: random, neutral mutations will accumulate in the DNA at a constant and predictable pace. So the differences in the DNA of two species is directly proportional to the length of time that has passed since they shared a common ancestor (the last point in evolutionary time when they were the 'same' species). The more similar the DNA of the two species, the more closely related they are and the more recently they shared a common ancestor.

But it's not very helpful to compare the complete sequences of two different species' entire genomes. There are way too many genes and not all organisms have all the same genes. To make things more complex, different genes can have different mutation rates. Some acquire mutations slowly while others change more frequently. So if we are going to pick genes to use to compare different organisms, which ones should we choose? It's best to select genes that are present in as many organisms as possible, have the same function, and accumulate mutations at a consistent rate.

Okay, you still probably don't see where we are heading with this, but let's go back to that clock.

Molecular Clocks

A piece of DNA in which random, neutral mutations accumulate at a consistent rate is called a molecular clock. Aha, here is that clock idea and now we have linked it to our gene/DNA mutation idea! So to calculate approximately how long ago the last common ancestor of humans and chimps lived, we need a molecular clock. But what DNA or genes should we use? We know they should be present in many organisms, have the same function in all organisms, and accumulate mutations at a constant pace. Using this criteria, scientists keyed in on the genes for ribosomal RNA and mitochondrial DNA.

All known living organisms contain genes for ribosomal RNA (rRNA). Ribosomes are machines built of rRNA and proteins that are used by cells to make all the proteins required for metabolism. Since all living organisms need proteins, they all must have ribosomes to make them. Comparing the DNA sequences of the rRNA genes of many different species shows slight variations. A slug, cheetah, and human will all have similar sequences. But the last common ancestor of the human and the slug existed much further back in evolutionary time than the last common ancestor of humans and cheetahs. So, the human and cheetah rRNA gene sequences will be more similar. We can use this information to estimate how long ago these last common ancestors lived.

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