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doi:10.1038/nindia.2014.75 Published online 30 May 2014

Software tools solve mysteries of human origins, crimes  

Biplab Das

Quintessential existential questions – “who am I” and “where do I come from” – might now have some answers, courtesy a set of unique software tools. These tools are capable of scanning the genomes of distinct global populations and can trace people down to their residential villages by analysing some signature marker genes1.

A large international team of scientists from India, USA, UK, Russia, Australia, France, Italy, Spain and Brazil have created these software tools. The tools have revealed how and when ancient people migrated and colonised remote islands of Southeast Asia and Oceania at the height of the last ice age when sea levels dropped to form land bridges between continents and islands.

The two software tools that the researchers used are called GenoChip, for genetic anthropology and population genetics, and AimsFinder, which identifies the smallest number of markers sufficient to differentiate a pair of genetically distinct populations. In addition, they applied an admixture-based Geographic Population Structure (GPS) method for predicting biogeographical origin of individuals worldwide.  
Pitchappan says the software can unravel vital clues to our cultural evolution.
CU, Chennai

Ramasamy Pitchappan from Chettinad University in Chennai is part of the global conglomerate of scientists using the tools. “This can help us understand the origins and spread of populations, unravelling vital clues to their cultural evolution,” he told Nature India. The tools can also be used for settling disputed claims of parents, identifying lost children, aiding crime investigations and discovering ancestry, he added.

GenoChip contains 130,000 ancestral informative markers, genetic markers from 98 global populations. These markers allow geneticists to trace our common evolutionary timeline back by many generations. 

Recent studies have shown a strong relationship between genes and geographic distances in global populations. These studies include computer-based models which are not good at tracking ancient migrations and origins of Europeans and non-Europeans. To overcome the limitations of previous studies, the scientists used a combination of these new tools.

In testing the precision of GPS and the other tools, the researchers assessed 243 Southeast Asians and Oceanians and 200 Sardinians from 10 villages lying 4 and 180 km apart using 40,000 and 65,000 GenoChip markers, respectively. They identified human expansions in Oceania regions that include Pacific Islands, Papua New Guinea and Australia about 50,000 years ago when Papua New Guinea and Australia formed the ancient landmass of Sahul. 

Co-researcher Arun Kumar prepares DNA sample from the mouthwash of tribal people.
CU, Chennai

This Oceanic pattern of human migration is also seen in Southeast Asian islands such as Nusa Tenggara and the Moluccas which indicates the route human colonizers followed to reach Sahul. However, the study revealed that the first wave of migrants arrived in remote Oceania such as the east of the Solomom Islands only about 3000 years ago and then spread to Fiji, Samoa and Tonga. 

Applied to Sardinian villagers, GPS correctly placed a quarter of the Sardinians in their village, as well as half within 15 km and 90% of individuals within 100 km of their homes. “We have shown that our approach can predict the geographical origin of worldwide individuals from single resident populations down to the level of island and home village and is more accurate than previous methods,” says Pitchappan.

The GPS which has successfully localised 83% of worldwide individuals to their country of origin could have other potential applications. In genealogical research, it could help adoptees find their home while in forensic research, it could improve the assignment of ethnic ancestry to DNA evidence.


References

1. Elhaik, E. et al. Geographic population structure analysis of worldwide human populations infers their biogeographical origins. Nat. Comm. (2014) doi: 10.1038/ncomms4513