New AI study clarifies the origins of Papua New Guineans

Papua New Guineans are living proof of how isolation, ancient mixing, and survival in remote islands can preserve a unique piece of our shared human story.

A team of European researchers has shed new light on the genetic origins of Papua New Guineans. The team uses advanced Artificial Intelligence (AI) tools to demonstrate that Papua New Guineans are closely related to other Asian populations. They share a common ancestry from the same ‘Out of Africa’ event that also gave rise to other non-African groups.

Papua New Guineans look strikingly different from other Asian groups and share some features with Sub-Saharan African populations, which fueled theories that they might have descended separately from other non-African populations.

According to lead author Dr. Mayukh Mondal, the unique physical features of Papua New Guineans probably come from natural selection: “Perhaps adaptations to tropical climates that make them look more like Sub-Saharan African groups, even though their genetics clearly link them to other Asian populations. More studies are needed to uncover how evolution shaped this remarkable population.” 

The genetic origin remains unresolved

Scientists generally agree that modern humans left Africa about 50,000 to 70,000 years ago, spreading into Europe, Asia, and beyond. Early archaeological studies have suggested that the ancestors of Papua New Guineans came from a separate, earlier migration (also known as the ‘First Out of Africa’ hypothesis), taking a coastal route through India and Southeast Asia. Archaeological evidence confirms that some of the Papuan New Guineans' genetic ancestry could have come from this ‘First out of Africa’ event. This is because the earliest human site in Oceania dates back to around 50,000 - 60,000 years ago, older than Europe’s oldest sites.

In recent decades, advances in DNA sequencing have tested this ‘First out of Africa’ hypothesis. However, studies of maternal (mitochondrial) and paternal (Y-chromosome) DNA have found no clear evidence that the main ancestry of Papua New Guineans came from an earlier migration. Instead, analyses suggest that their lineages connect to other non-African populations. Still, we cannot rule out a trace number of ancient migrations from the ‘First out of Africa’ population.

Interestingly, the Papua New Guinean genome carries a significant percentage of Denisovan DNA — a ghostly relative of Neanderthals. This unique inheritance likely came from mixing with Denisovans in Southeast Asia or Oceania — another element that confirms the complexity of Papua New Guinean ancestry.

Despite these researches, the genetic origin of Papuan New Guineans remains unresolved. Did Papua New Guineans split off before Europeans and Asians? Or have similar populations contributed to their genome? Did they carry ancestry from the enigmatic ‘First out of Africa’ population? Or are they part of the same family tree as other Asians living in proximity?

Unique demographic history

In this study, scientists used high-quality genomic data and AI-powered models to compare different demographic scenarios for the origin of the Papuan New Guineans' genetic diversity. Their results suggest that Papua New Guineans are a sister group to other Asian populations. Contribution from a ‘First Out of Africa’ migration might not be needed to explain their origins.

The researchers found that the ancestors of Papuan New Guineans went through a dramatic population bottleneck — most likely their numbers dropped sharply after reaching Papua New Guinea and stayed low for thousands of years. Unlike other non-African groups, they did not experience the farming-driven population boom that reshaped Europe and Asia. This unique demographic history left genetic signatures that, if misunderstood, could look like evidence of a contribution from an unknown population.