Of Sporks and Scorpions: Where Do Genes Come From? (Part 1)

Author: Bryan Moyers

Editors: Theresa Mau, Alex Taylor, and Kevin Boehnke

What exactly separates us from other animals?  For that matter, what makes any species or group of species special?  How is life so diverse?  How can cephalopods camouflage themselves so well, and how did platypuses become so bizarre?

Part of the answer is in genes.  Genes are sections of DNA that perform a specific function, usually after being translated into proteins by special cellular machinery.  Every species has genes that code for proteins, but different species have different numbers of genes. Humans have around 20,000, fruit flies have around 18,000, and the tiny water-flea has around 31,000 genes. Different sets of genes produce animals with different structures and functions.

Since these organisms have a common ancestor, at some point they all had the same number of genes.  Over the several millions of years since the species diverged, they must have somehow gained new genes*.  How did these new genes arise?  Of course, if a new gene shows up that helps a species survive and reproduce, that gene will stick around—that’s how evolution works!  But how exactly does a new gene show up in the first place?

Tried and True: Duplications

One way that a new gene can arise is through gene duplication.  Whenever a new baby is born (or otherwise shows up) in any species, a copy of the DNA is passed down to them.  Sometimes, there are errors in copying the DNA, and some gene gets copied twice – thus, a gene duplication.  

It turns out that duplications happen really frequently.  There are many pairs (or groups) of genes that look very similar to each other and perform similar jobs.  We call these pairs and groups gene families.  For quite a long time, it’s been thought that gene duplications account for most new genes and functional specializations within each species.  Extra genes can provide species with new tools, which can be used in a plethora of ways.

We have observed the consequences of gene duplication in real time.  Nylon was first invented in 1935—the world had never seen this molecule before.  Before long, it was being used to make clothing, ropes, and other gadgets for humans.  But by 1975, scientists found a strain of bacteria that was able to eat nylon.  Maybe that’s not so surprising, but other closely-related bacteria couldn’t eat nylon.  In less than 40 years, something had changed in this strain of bacteria that made it better at chomping through humans’ new favorite clothing material.

It turns out that the change was a gene duplication.  A gene that was already good at breaking down one type of molecule was duplicated, and after duplication, one of the copies gained a few random mutations that allowed it to break down nylon. We might ask: “How, exactly, do these two copies specialize?”  After a duplication, mutations can accrue on one of the copies.  Mutations can be harmful and make the gene non-functional. If there’s only one copy of a gene and it breaks, the organism might lose an essential function like processing its food.  But if there are two copies, one can change freely—if it breaks, that’s okay because there’s a backup.  While one of the duplicates is typically lost after duplication, some duplications can randomly benefit the organism.  This beneficial trait will often stick around and rapidly spread through the population.  

There are two general mechanisms for beneficial duplications, subfunctionalization and neofunctionalization, each acting in a different way.

Subfunctionalization:  Sporks Are Terrible

You’ve probably used a spork before.  It’s supposed to be this really great fusion between a fork and a spoon which allows both the stabbing prowess of a fork and the scooping skills of a spoon.  But in reality, it’s terrible at both of its jobs—it doesn’t stab as well as a fork does, and it doesn’t scoop as well as a spoon does.

This happens in biology, too.  For example, an enzyme that can modify two kinds of molecules is probably not equally efficient at modifying them both. Subfunctionalization can happen when an enzyme like this is duplicated.  Each of the two copies can specialize for modifying a different molecule.  In our spork example, if you have two sporks you can carve out longer teeth on one spork while using tape to finish the bowl shape on the other spork, making a spoon and a fork, each specialized for its job.

Neofunctionalization:  A New Twist on an Old Theme

Every few years, we see a new model of police cars.  But these cars aren’t designed from scratch.  Instead, these models are modified from existing models—sirens and lights are added and a special screen is installed to separate the police in the front seat from the criminals in the back seat.  In this case, the original car model wasn’t being used for both civilian and police purposes.  Instead, a car was taken and modified to do something different, which is analogous to what we’d call neofunctionalization of a gene.

In biology, this happens when a gene is duplicated, and one of the two copies gains mutations that grant the gene a new function.  Maybe the gene was originally used to determine where arms and legs sprout up as an organism is developing.  When there’s a duplication, one of the two copies might be modified to control what color different parts of the organism became, creating a striped pattern. Or, one of the two copies might cause a new segment to arise in the creature, as seems to have happened in scorpions.  

The Benefits of Imperfection

We’re still working to understand a lot about duplications—how frequently they benefit an organism, how much genes change after duplications, and what kinds of changes make them beneficial.  Duplications can help to explain not only how creatures are so diverse—from the terrifying body of scorpions to the tenacity of bacteria—but also how organisms become more complex over time by adding additional genes.  

Also, duplications emphasize that imperfections in biology can be a good thing!  A key aspect in gene duplication is the mutation that arises in the duplicated gene, and the duplications would never offer new benefits unless they gained mutations. Darwin’s “endless forms most beautiful” that fill the Earth are a result of the organisms’ genetic differences created through imperfections.

Teaser: In the next installment of this series, we will discuss another way that genes arise: when non-gene DNA is turned into a gene.  Come back for that in a week!

 

*Author’s note:  Of course, it’s possible that they all started with a ton of genes and they’ve just been losing genes, rather than gaining genes. That happens, too!  But for probabilistic reasons beyond the scope of this paper and known examples of gene gain, gene loss doesn’t account for all the differences.  

 

About the author

Our second co-founder, Bryan Moyers, is a recent alumnus of the Bioinformatics program at the University of Michigan. Bryan’s PhD research focused on methodological problems in molecular evolution, and correctly inferring information from data. In other words, his research sheds light on problems with the methods commonly used in the field of Evolutionary Biology so that improvements can be made. Bryan also holds degrees in Biology and Psychology from Purdue University. His interests are in science and education issues, philosophy of science, and the intersection of science and business. Outside of science, Bryan enjoys reading, running, hiking, and brewing/consuming beer.

Read more by Bryan here.

 

Image Credits:

1. https://commons.wikimedia.org/w/index.php?curid=18984516

2. https://commons.wikimedia.org/w/index.php?curid=2220101