Archaeologists revisited the site in recent years because it was threatened by modern agricultural expansion.
The volume of undiscovered antiquities artifacts and new revelations came as a surprise.
The latest phase of work was funded by a grant from the National Geographic Society's Committee for Research and Exploration. (The National Geographic Society owns both National Geographic News and National Geographic magazine.)
"A Pretty Good Life"
Magnetic surveys followed by extensive excavations revealed approximately one meter's (one yard's) depth of undisturbed habitation layers—meaning different generations of the settlement are buried on top of one another.
Within those layers are numerous hearths containing carbonized grain, postholes and clay floors for structures, and the remains of domesticated animals.
Because the site is stratified, experts say, the find offers a rare opportunity to track changes in the settlement over time.
"Rather than seeing the Neolithic as one period [about 8500 B.C. to 4000 B.C.], we can begin to understand its time depth and discern different periods and developments," Wendrich said.
The discovered grains are mostly six-rowed barley and emmer wheat.
They match the cereals that Caton Thompson found in the storage pits and are the first evidence of how those crops were incorporated into the lives of Neolithic farmers.
"Now we have information from the [animal] bones and from the seeds, and you can produce a kind of [Neolithic era] diet, which was not possible before," said René Cappers, a professor of paleobotany at the University of Groningen in the Netherlands and co-director of the project with Wendrich.
The ancient structural foundations are the first discovered in Faiyum and also fill in a major piece of the Neolithic puzzle, according to Melinda Zeder, director of the Archaeobiology Program at the National Museum of Natural History in Washington, D.C.
"It was a big mystery where these people were actually living," said Zeder, a member of National Geographic's Committee for Research and Exploration.
"We knew they were doing a bunch of stuff there and storing grain, but households we just didn't have."
Further excavations could help experts determine whether the farmers lived at the site permanently, as in other ancient farming cultures, or only during the growing season.
So far, the newly discovered postholes have not fallen into a pattern, and the number of people who lived in the settlement remains undetermined.
Skeletal remains of sheep and goats were also strewn about the site, but the discovery of pig bones has intrigued the experts the most.
Pigs "are not an animal that is all that conducive to nomadic movement, so having a quantity of pigs may also speak to whether these people are moving in and out in the Faiyum or whether they are there year-round," Zeder said.
The excavators also uncovered beads made of ostrich shell, a bangle cut from a Red Sea shell, a finger ring, and a slew of pendants—all of which suggest personal adornment figured prominently in this Neolithic culture.
Large quantities of pottery, flint, grinding stones, and other tools were also discovered, along with an unfired clay vessel—the first known to have survived from the era.
The wealth of new evidence will finally bring into focus how Neolithic society fit into the larger mosaic of Egyptian history, according to Bruce Smith, an archaeobiologist and also a member of National Geographic's Committee for Research and Exploration.
"It's a missing link filling in a very important and poorly known phase of the development of agricultural systems, which led to the pyramids and later civilizations," Smith said.
Study co-author Wendrich agreed, adding that the discovery could alter the prevailing notion that the Neolithic period was primitive and disconnected from later and more sophisticated stages of ancient Egypt.
"The most important thing is that we don't look at this very early period of Egyptian history as something foreign to what happens later in the pharaonic period," she said.
"It's clear that this was not a bare existence that people had here. They made a pretty good life for themselves."
The discovery also adds to the narrative of Egypt's early contact with neighboring cultures.
The crops and animals—and techniques for raising them—were all introduced to Egypt from the ancient Middle East, where domestication of plants and animals is known to have existed as far back as 9000 B.C. It came together as a "package" around 7000 B.C., according to Zeder, an expert in Middle East domestication.
"An increasing area of study is looking at how this package diffused out of its homeland into other areas," Zeder said. We now have "really good prima facie evidence of some of the earliest movement of that technology into Egypt."
It's not clear whether the crops and animals were brought to Egypt by ancient mariners on the Mediterranean Sea or overland through the rugged Sinai desert or both. The presence of Red Sea shells at the site could indicate that the trading routes cut through the Sinai Peninsula.
As the new evidence is studied further, it could help experts iron out those details and also map the initial spread of farming across the African continent.
Faiyum "really is the beachhead front now in the movement of agriculture and the increase in trade into Africa," said Zeder, who added that the movement of agriculture may be the first example of globalization.
"It certainly is a major seismic shift in how cultures operated."
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