Introduction
A species’ genome, or its genetic material, is always evolving. New genetic mutations or genetic combinations can yield new traits in a species. These traits eventually lead to the development of new species from existing species. Random mutations, new combinations of genes, environmental changes, and population interactions all affect the evolution of the genome.
In this activity, you’ll create a model of a molecular clock to show how the genomes of related species can change over time.
Molecular Clocks
A gene is the sequence of DNA that codes for functional proteins. Mutations in genes can be both harmful and beneficial for the organism. Sometimes mutations don’t affect the organism’s survival at all. These mutations are called neutral mutations. Beneficial and harmful genes tend to be selected for or against during the process of natural selection. Neutral genes are usually not selected because they have no effect on the survival of the species.
Different theories provide evidence for evolution. The neutral theory of evolution states that most of the genetic variation of a species is actually due to the neutral mutations in the genome. Many scientists hypothesize that neutral mutations occur at a predictable rate. These genes may act like molecular clocks, which can be used to track the evolution of a species’ genome. Molecular clocks use mutation rates to determine evolution.
For example, researchers at the University of California, Berkeley, report that the gene that codes for specific hemoglobin protein experiences mutations in its nitrogen bases. The mutations occur at a rate of 0.56 base changes every 1 billion years. If this rate stays consistent, the mutation rate can be used to determine when different lineages of a particular species split. This model gives an example of how a gene can act like a molecular clock. It shows the lineage of two species that diverged from a common ancestor. As the two species diverged, they experienced different mutations in the DNA sequence, as shown in the image.
But how do scientists estimate the rate of mutation if they don’t have DNA evidence of the common ancestor? They can use the fossil record to estimate a date when the last known common ancestor between the species lived. By counting the differences in the nucleotide bases between the two species, scientists can find the estimated rate of genetic mutation over time.
Developing a Molecular Clock Model
In this activity, you will develop a model of a molecular clock to show the evolution of a species’ genome.
You will create a molecular clock model for an arthropod gene. Follow these guidelines to make your model:
Your timeline will span from 90 million years ago to the present. The common ancestor in your model is an arthropod that lived 90 million years ago. The gene that you’ll track codes for a protein in the species’ venom.
The DNA sequence you’ll track contains 10 nitrogen bases. You can choose the order of the bases and where the mutations occur.
This gene mutates at a rate of approximately 0.76 base pairs every 17.1 million years. To build your model, calculate the estimated time period it takes for 1 base pair to mutate.
The first time period will only show the common ancestor. At the beginning of the second time period, three lineages will diverge from the common ancestor, each with a different mutation in their gene sequences.
The first and third descendant species will survive for the rest of the timeline. The second descendant species was extinct 50 million years ago.
Calculate how long it will take for one full base pair mutation to occur. Explain your reasoning by constructing a mathematical equation.
Using this sample model as a guide, create a molecular clock model. Use the flowchart tools in your word processing program to make your model. Make sure the mutations are clearly visible in the strand. Consider using a different font color for the mutations. Use the Insert Image button to insert a screenshot of your model in the answer space provided.
Part C
Examine the differences between the common ancestor’s original gene and the genomes of the existing species. How can these changes affect the development of the protein in the descendant species?
Part D
The idea of molecular clock genes has been studied for decades, but the hypothesis remains a controversial topic in evolutionary biology. Why do you think that is the case? What are three questions you still have about the use of molecular clocks?
Part E
Your molecular clock model resembles another branching chart, the phylogenetic chart, which you’ve used in this unit. Review the sample phylogenetic chart. What types of data are used to build a phylogenetic chart? How do phylogenetic charts differ from molecular models, such as the molecular clock model?
Part F
Woolly mammoths became extinct around 4,000 years ago. A recent study conducted by scientists found that the last generations of woolly mammoths were plagued by harmful gene mutations. Some of the mutations caused them to have softer fur that didn’t protect them from the cold, a diminished sense of smell, and digestive problems.
A species potential for evolution is based on four factors:
the potential for a species to increase in number
the heritable genetic variation of individuals in a species due to mutation and sexual reproduction
organisms competing for limited resources such as food or water in their environment
the proliferation of those organisms that are better able to survive and reproduce in the environment
In two to three paragraphs, explain why the last generations of woolly mammoths couldn’t meet these factors to evolve in a changing environment. Also explain how data such as the fossil record and DNA evidence can identify the factors that can lead to the evolution of a species.
