Nav: Home

How much are we learning? Natural selection is science's best critic

December 17, 2018

Cold Spring Harbor, NY -- In 2003, the Human Genome Project revealed to the world the three billion chemical units within human DNA. Since that time, scientists have designed many ways to organize and assess this overwhelmingly large amount of information. Now, scientists at Cold Spring Harbor Laboratory (CSHL) have determined that evolution can help guide these efforts.

Researchers have already concluded that a mere one percent of the human genome is made up of the genes that make the proteins our bodies need to grow and function. However, they've also learned that roughly five percent of the human genome has remained the same, or been conserved, over countless generations of mutation and evolution.

"That suggests that an extra four percent of the genome is doing something that's really important, even though we don't know exactly what that is," explained Adam Siepel, a computational biologist and professor at CSHL.

To solve the mystery of the four percent, scientists have spent more than a decade developing powerful methods to look for distinct functions among various bits of the genome. And, to understand what influences the genome has upon an organism, they've had to look to evidence from the epigenome. The epigenome is a universe of chemical compounds that attach themselves to DNA, influencing how and when parts of the genome are used by cells.

Searching for patterns among epigenomic factors has allowed scientists to guess where important parts of the genome may be and if they share biological function. However, this is no more certain than trying to determine the significance of a scene in a play by seeing only the props and costumes involved.

"This uncertainty about the true biological significance of many epigenomic measurements is a critical barrier not only for interpretation of the available data, but also for prospective decisions about how much new data to collect, of what type, and in what combinations," Siepel and his colleague Brad Gulko explained in the latest publication of Nature Genetics.

The Siepel lab has found a way around this barrier.

"So my lab and I decided to come at this from a different angle," added Siepel. "We asked, 'What if we let evolution do the work of telling us how much of the genome is important?' and, 'How much do we learn from each epigenomic data set?'"

The researchers used data from modern human populations to find evidence of recent natural selection. Then, they compared the genomes of humans and chimpanzees to get information that goes back five to seven million years to the divergence of humans from our great ape cousins.

"This allowed us to sort of chart how strong natural selection was during that whole period of time," Siepel explained.

The result was a way to guide future research. Siepel and his colleagues clustered sites within the genome based upon epigenomic features and how consequential each site has been for the survival of our species, according to evolutionary history. The resulting scores for each feature were then aggregated to create "fitness consequence maps," or FitCons maps.

If natural selection has been a powerful influence on a site in the genome--preserving it for countless generations despite mutation and evolution--this part of the genome should be important for survival. Moreover, if an epigenomic analysis identifies more of these conserved sites than not, then it will prove to be an informative study.

Siepel hopes that his fellow researchers will be able to reference FitCons to help determine which epigenetic markers or combinations of markers can prove the most informative for further investigation.

"This is an effort to try to see what we can learn by considering evolutionary information alongside what we already know," he said.
-end-
About Cold Spring Harbor Laboratory

Founded in 1890, Cold Spring Harbor Laboratory has shaped contemporary biomedical research and education with programs in cancer, neuroscience, plant biology and quantitative biology. Home to eight Nobel Prize winners, the private, not-for-profit Laboratory employs 1,100 people including 600 scientists, students and technicians. The Meetings & Courses Program annually hosts more than 12,000 scientists. The Laboratory's education arm also includes an academic publishing house, a graduate school and the DNA Learning Center with programs for middle and high school students and teachers. For more information, visit http://www.cshl.edu

Cold Spring Harbor Laboratory

Related Evolution Articles:

A window into evolution
The C4 cycle supercharges photosynthesis and evolved independently more than 62 times.
Is evolution predictable?
An international team of scientists working with Heliconius butterflies at the Smithsonian Tropical Research Institute (STRI) in Panama was faced with a mystery: how do pairs of unrelated butterflies from Peru to Costa Rica evolve nearly the same wing-color patterns over and over again?
Predicting evolution
A new method of 're-barcoding' DNA allows scientists to track rapid evolution in yeast.
Insect evolution: Insect evolution
Scientists at Ludwig-Maximilians-Universitaet (LMU) in Munich have shown that the incidence of midge and fly larvae in amber is far higher than previously thought.
Evolution of aesthetic dentistry
One of the main goals of dental treatment is to mimic teeth and design smiles in the most natural and aesthetic manner, based on the individual and specific needs of the patient.
An evolution in the understanding of evolution
In an open-source research paper, a UVA Engineering professor and her former Ph.D. student share a new, more accurate method for modeling evolutionary change.
Chemical evolution -- One-pot wonder
Before life, there was RNA: Scientists at Ludwig-Maximilians-Universitaet (LMU) in Munich show how the four different letters of this genetic alphabet could be created from simple precursor molecules on early Earth -- under the same environmental conditions.
Catching evolution in the act
Researchers have produced some of the first evidence that shows that artificial selection and natural selection act on the same genes, a hypothesis predicted by Charles Darwin in 1859.
Guppies teach us why evolution happens
New study on guppies shows that animals evolve in response the the environment they create in the absence of predators, rather than in response to the risk of being eaten.
Undercover evolution
Our individuality is encrypted in our DNA, but it is deeper than expected.
More Evolution News and Evolution Current Events

Top Science Podcasts

We have hand picked the top science podcasts of 2019.
Now Playing: TED Radio Hour

In & Out Of Love
We think of love as a mysterious, unknowable force. Something that happens to us. But what if we could control it? This hour, TED speakers on whether we can decide to fall in — and out of — love. Guests include writer Mandy Len Catron, biological anthropologist Helen Fisher, musician Dessa, One Love CEO Katie Hood, and psychologist Guy Winch.
Now Playing: Science for the People

#543 Give a Nerd a Gift
Yup, you guessed it... it's Science for the People's annual holiday episode that helps you figure out what sciency books and gifts to get that special nerd on your list. Or maybe you're looking to build up your reading list for the holiday break and a geeky Christmas sweater to wear to an upcoming party. Returning are pop-science power-readers John Dupuis and Joanne Manaster to dish on the best science books they read this past year. And Rachelle Saunders and Bethany Brookshire squee in delight over some truly delightful science-themed non-book objects for those whose bookshelves are already full. Since...
Now Playing: Radiolab

An Announcement from Radiolab