Traces of cacao have been found in pottery unearthed from an ancient ceremonial site in Ecuador, indicating our taste for chocolate began at least 5,300 years ago.

Key points: Chocolate was thought to have first been developed in Mexico and Central America

Chocolate was thought to have first been developed in Mexico and Central America The greatest diversity of chocolate trees was found in the Amazon rainforest

The greatest diversity of chocolate trees was found in the Amazon rainforest Scientists found evidence indicating ancient people were drinking cocoa in Ecuador at least 1,500 years earlier

The discovery, reported in the journal Nature Ecology and Evolution, suggests the chocolate tree was domesticated at least 1,500 years earlier and much further south than we previously thought.

Until now, there had been a long-held idea that chocolate was first developed in Mexico and Central America, said archaeologist Michael Blake.

"We knew, based on historical texts and archaeological evidence, that cacao and chocolate were tremendously important food and drink for people in that part of America," said Professor Blake, from the University of British Columbia.

An Aztec woman is depicted preparing chocolate in this 1553 image. (Getty Images: De Agostini Picture Library)

The word 'chocolate' is a European interpretation of a Mayan word for 'bitter water' — a description of the ritual drink prepared from fermented and roasted beans from the chocolate tree (Theobroma cacao).

Spanish conquistadors introduced the drink into Europe in the early 1500s after witnessing the Aztec king drinking cacao at the royal court in Tenochtitlan — what is now Mexico City.

Further south in Central America, pottery from Maya sites going back to 1300 BC was found to contain residues of theobromine — Latin for "the food of gods" — the active ingredient that gives cocoa its delicious flavour.

But botanists have long known that the Amazon basin is home to the greatest diversity of chocolate tree varieties and related species.

Sitting within that biodiversity hotspot is the ancient site of Santa Ana-La Florida on the eastern flanks of the Andes.

Since it was discovered in 2002, archaeologists have unearthed tombs and a range of ceramics and artefacts that suggest the site was used for religious rituals and funeral rites by the Mayo-Chinchipe people.

The Santa Ana-La Florida site is on the eastern slopes of the Andes in Ecuador. (Supplied: Francisco Valdez)

Some of the ceramics reminded Professor Blake of the spouted vessels used by the Maya for chocolate.

"Pouring the chocolate out of the spouts back and forth created a foam that was greatly prized by the Maya," Professor Blake said.

Three lines of detective work pin down cocoa

In 2010, Professor Blake asked anthropological archaeologist Sonia Zarrillo, who was studying starch remnants in the ceramics from the site, whether or not she had detected any signs of starch from cacao.

At first, Dr Zarillo — who studies the interaction between people and plants in the past — didn't think it would be possible to find the tiny grains.

Theobroma spp. starch grain (in box), among other particles in the residues. (Supplied: Sonia Zarrillo)

"Cacao seeds aren't starchy, like, say wheat or corn seeds," Dr Zarrillo explained.

But two years later, after collecting more grains from the pottery and comparing them to grains from a range of cacao varieties, she identified a shape that appeared to be unique to the Theobroma genus.

In the meantime, other members of the team detected chemical signatures of theobromine in residue in some of the artefacts, including one which was between 5,450 and 5,300 years old.

Then a team of geneticists led by Claire Lanaud analysed ancient DNA in the slurry of organic material that had seeped into the clay pots.

Chocolate residues were found in human effigy stirrup spout bottles. (Supplied: Francisco Valdez)

They found traces of ancient DNA from the T. cacao in about 35 per cent of artefacts, including a human effigy stirrup spout bottle, said Dr Lanaud, of the French Agricultural Research Centre for International Development (CIRAD).

Dr Lanaud said the ancient DNA also indicated cacao was continually used at the site until about 2,000 years ago.

She said the importance of chocolate is also reflected in a small cacao pod-shaped mortar found by locals at the site, which has been dated between 5,500 and 4,000 years old.

A mortar shaped like a cacao pod from the Santa Ana-La Florida site. (Supplied: Claire Lanaud/CIRAD)

"All these facts tend to demonstrate that cacao was really domesticated and used in the everyday life by Mayo-Chinchipe people, and not opportunistically used," Dr Lanaud said.

To find out what variety of cacao was used by the ancient people, the team compared ancient DNA fragments to the genetic material of modern varieties of the cacao tree.

Professor Blake said the ancient cacao was very similar to one of the varieties known as Purus that grows in southern Ecuador and northern Peru today.

"It's most similar to the varieties that wound up growing in Central America and Mexico," he said.

A variety of chocolate tree growing near the archaeological site in Ecuador (Supplied: Sonia Zarillo)

Artefacts and shells from the site indicate the Mayo-Chinchipe people had close trade ties with groups along the Pacific coast. It is possible, the researchers said, that they also traded important plants.

Professor Blake said future research will aim to analyse the origins of ancient cacao found in pottery in Mexico and Central America.

Domestication is a sticky issue

Today, the bulk of chocolate around the world is made from three varieties of cacao.

The most prized variety, which only lives in Central America, evolved from plants that originated in the Amazon, confirmed separate genetic research, published last week in Nature Communications Biology.

The variety known as Criollo was intensively domesticated about 3,600 years ago from no more than a couple of thousand trees, according to the analysis led by Omar Cornejo of Washington State University.

Dr Cornejo said the topic of just when and where people started to domesticate cacao is a sticky subject.

"I do think people were already using cocoa [in South America]. But they were using the plant, they were not intensively domesticating it for particular traits," he said.

Cacao … or cocoa? Cacao is the name given to a small evergreen tree, Theobroma cacao, native to tropical America, cultivated for its seeds. It is also the name given to the fruit and seeds of the tree.

is the name given to a small evergreen tree, Theobroma cacao, native to tropical America, cultivated for its seeds. It is also the name given to the fruit and seeds of the tree. Cocoa powder is the product of roasted fermented cacao/cocoa beans, used to make chocolate.

powder is the product of roasted fermented cacao/cocoa beans, used to make chocolate. However, the two words are at times used interchangeably. For example, the tree Theobroma cacao is often referred to as the 'cocoa tree'. Source: Macquarie Dictionary

"The only population — among the 10 major cocoa populations that have been described — that came across [in our study] as having a very strong signature of domestication, was the Criollo population."

What is clear though, is that the intensive selection of traits that give Criollo its delicate taste valued by boutique chocolate makers has taken its toll on productivity.

"With increasing ancestry of domesticated varieties, the amount of beans produced reduces significantly," Dr Cornejo said.

And that has chocolate companies, such as Mars who funded the research, looking back towards the Amazon.

"[We need to understand] how can we use some of these other varieties from South America that have very high productivity, but not as good a flavour, to increase productivity of delicious Criollo," Dr Cornejo said.