Domestic llamas and alpacas carry DNA from an extinct “ghost” population of their wild camelid relatives. Furthermore, their domestication may have involved interbreeding between two different species.

Domestic llamas (Lama glama) and alpacas (Vicugna pacos) were crucial for South American peoples like the Incas. But their origins are mysterious, says Paloma Fernández Diaz-Maroto at the University of Copenhagen in Denmark.

There are two wild South American camelids: guanacos (Lama guanicoe), which live in many habitats, and vicuñas (Vicugna vicugna), which only live high up in the mountains. Domestication was under way by 7000 years ago, but it isn’t clear which domestic species is descended from which wild species.

The question has also been confounded by more recent history. “At the time of the European conquest of the Americas, there was a massive slaughter of camelids,” says Pablo Orozco-terWengel at Cardiff University in the UK. “A lot of the animals themselves died, and a lot of the people who knew how to breed them died.”

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As a result, people allowed a lot of interbreeding. “Today we know about 36 per cent of the DNA of alpacas is not of alpaca origin,” says Orozco-terWengel.

To find out what happened, Diaz-Maroto, Orozco-terWengel and their colleagues obtained mitochondrial DNA from the remains of 61 ancient camelids from northern Chile, dated from 3500 to 2400 years ago. Mitochondrial DNA is only inherited from the mother, so it can reveal the female family line. They compared the ancient DNA with that from 66 modern South American camelids belonging to all four living lineages.

Llama and alpaca mitochondrial DNA was most similar to that of guanacos, while vicuñas were different to all the others. This suggests that llamas and alpacas were domesticated from ancient female guanacos. But the analysis also shows llamas and alpacas carry some ancient guanaco DNA that doesn’t match that seen in any present-day guanaco populations. That suggests it comes from a “ghost” guanaco population that has gone extinct in the past few thousand years.

The identity of the male ancestors of today’s llamas and alpacas is less clear. A 2020 study of present-day camelid nuclear DNA – which is inherited both paternally and maternally – found that alpacas have a lot of vicuña DNA. “That means vicuñas did contribute to the domestication,” says Orozco-terWengel, but it isn’t clear how to reconcile that with the mitochondrial DNA. “Female guanacos may have been used for domestication and crossed with male vicuñas,” suggests Orozco-terWengel.

Journal reference: eLife, DOI: 10.7554/eLife.63390