Sequencing entire genomes
from ancient tissues helps researchers reveal the evolutionary
and domestication histories of species. (Thomas Harper, The
Pennsylvania State University)
In the early 2000s, archeologists began excavating a rock shelter
in the highlands of southwestern Honduras that stored thousands
of maize cobs and other plant remains from up to 11,000 years ago.
Scientists use these dried plants to learn about the diets, land-use
and trading patterns of ancient communities.
After years of excavations, radiocarbon dating and more traditional
archaeological studies, researchers are now turning to ancient
DNA to provide more detail to their insights than has ever before
In a paper
published today in the Proceedings of the National Academy of Sciences,
scientists used DNA from 2,000-year-old corn cobs to reveal that
people reintroduced improved varieties of domesticated maize into
Central America from South America thousands of years ago. Archeologists
knew that domesticated maize traveled south, but these genomes provide
the first evidence of the trade moving both directions.
Researchers at the Smithsonian and around the world are just beginning
to tap into the potential of ancient DNA. This study shows how the
relatively recent ability to extract whole genomes from ancient
material opens the door for new types of research questions and
breathes new life into old samples, whether from fieldwork or forgotten
corners of museum collections.
Cobbling together DNA
DNA, packed tightly into each of our cells, holds the code
for life. The complex molecule is shaped like a twisting ladder.
Each rung is made up of two complementary molecules, called a base
pair. As humans, we have around three billion base pairs that make
up our DNA. The order of these base pairs determines our genes,
and the DNA sequence in its entirety, with all the molecules in
the correct position, is called a genome. Whole genomes provide
scientists with detailed data about organisms, but the process of
acquiring that information is time sensitive.
"In every cell, DNA is always being bombarded with chemical and
physical damage," said lead author Logan
Kistler, curator of archeobotany and acheogenomics at the Smithsonian's
National Museum of Natural History. "In live cells, it's easily
repaired. But after an organism dies, those processes that patch
things up stop functioning." As a result, DNA begins breaking down
into smaller and smaller fragments until it disappears entirely.
This decomposition poses the greatest challenge for scientists trying
to sequence entire genomes from old or poorly-preserved tissue.
Researchers wear protective
suits and work in sterile conditions in the ancient DNA lab
to prevent contamination. (James DiLoreto, Smithsonian)
"You have to take these really, really small pieces of DNA
the length of the alphabet in some cases and try to stitch
them back together to make even a 1000 piece long fragment," said
Hawkins, a curator of mammals at the Smithsonian who works with
DNA. "It's like trying to put a book back together by having
five words at a time and trying to find where those words overlap."
This laborious process prevented researchers from sequencing whole
genomes from ancient DNA until around 2008, when a new way to sequence
DNA became available. Since then, the technology and the ability
to reconstruct ancient DNA sequences has grown rapidly.
Ancient DNA still proves challenging to work with, however. Kistler
and colleagues collected 30 maize cobs from the thousands in the
El Gigante rock shelter in Honduras. The material ranged in age
from around 2,000 to around 4,000 years old. Of the 30 cobs that
the researchers tried to extract DNA from, only three of the 2,000-year-old
samples provided enough to stitch together whole genomes. A few
others provided shorter snippets of DNA, but most of the cobs didn't
have any usable genetic material left after thousands of years.
The second biggest problem researchers face when working with ancient
DNA is contamination. "Everything living is a DNA factory," said
Kistler. When working with samples that are thousands of years old,
the researchers take extra precautions to avoid mixing modern DNA
into their samples. They don sterilized suits and work
in an air-tight, positive-pressure lab designed specifically
for working with ancient DNA.
The ability to sequence whole genomes from thousands of years ago
has allowed researchers to ask questions they couldn't think of
answering using individual genes or smaller DNA fragments.
"A whole genome is comprised of several hundred ancestral genomes,
so it's sort of a time capsule of the entire population," said Kistler.
For important staple crops like maize, this means researchers can
study the genes associated with domestication and determine when
and how people changed it over time. And knowing what
communities were doing with crops provides insight into other
parts of life, such as land-use and trading.
"Whole genome sequencing of ancient materials is revolutionizing
our understanding of the past," said co-lead author Douglas
Kennett from the University of California, Santa Barbara. The
authors dug into the whole genome for information about how maize
domestication occurred and where it spread.
The cobs from 4,000 years
ago and before did not have enough genetic material left for
researchers to produce genomes. (Thomas Harper, The Pennsylvania
Before their results, it was widely assumed that maize was mostly
flowing southward. They were surprised to learn that improved maize
varieties were also reintroduced northward from South America. "We
could only know this through whole genome sequencing," said Kennett.
Next, the scientists plan to pinpoint more specific dates for the
movement of maize and connect its history to broader societal changes
in the pre-colonial Americas.
The same technological advances that made Kistler and Kennett's
maize study possible have also created new uses for museum specimens.
Scientists use ancient genomes to study how humans influenced plant
and animal population sizes over time, species diversity and how
closely related organisms are to each other. They even expect to
discover new species hiding in plain sight.
"Sometimes, species are really hard to tell apart just by looking
at them," said Hawkins. "There is so much more that we don't know."
To make extracting and sequencing DNA from older museum specimens
easier, the Smithsonian is in the process of building a historic
DNA lab. This space, separate from the ancient DNA lab, will allow
researchers to focus on older collections with tissue quality that
falls between ancient samples from archeological sites and freshly
The ancient DNA lab at
the Smithsonian takes several precautions to preserve existing
DNA and prevent contamination. (James DiLoreto, Smithsonian)
"It's really amazing that we have the opportunity to learn from
samples that have already been here for 100 years," said Hawkins.
"We've unlocked all these museum collections, and we can do so many
more things with them now than anyone had a clue was possible even
15 years ago."
Erin Malsbury is an intern in the Smithsonian National Museum of
Natural History's Office of Communications and Public Affairs. Her
writing has appeared in Science, Eos, Mongabay and the Mercury News,
among others. Erin recently graduated from the University of California,
Santa Cruz with an MS in science communication. She also holds a
BS in ecology and a BA in anthropology from the University of Georgia.
You can find her at erinmalsbury.com.