This new lineage stems from populations of hunter-gatherers that split from western hunter-gatherers shortly after the 'out of Africa' expansion some 45,000 years ago and went on to settle in the Caucasus region, where southern Russia meets Georgia today.
The hunter-gatherers remained here for millennia, becoming isolated as the Ice Age culminated some 25,000 years ago.
Eventual thawing allowed movement and brought them into contact with other populations, likely from further east.
"This is a major new piece in the human ancestry jigsaw, the influence of which is now present within almost all populations from the European continent and many beyond," said Daniel Bradley, from Trinity College Dublin in UK.
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Previously, ancient Eurasian genomes had showed three ancestral populations that contributed to contemporary Europeans in varying degrees, said Andrea Manica, from Cambridge University in UK.
Finally, at the start of the Bronze Age around 5,000 years ago, there was a wave of Yamnaya migration from central Eurasia into Western Europe.
However, the sequencing of ancient DNA recovered from two separate burials in Western Georgia - one over 13,000 years old, the other almost 10,000 years old - has enabled scientists to show that the Yamnaya owed half their ancestry to previously unknown and genetically distinct hunter-gatherer sources - the fourth strand.
A similar population must have migrated into South Asia at some point, said Eppie Jones, a PhD student from Trinity College who is the first author of the research paper.
"India is a complete mix of Asian and European genetic components. The Caucasus hunter-gatherer ancestry is the best match we've found for the European genetic component found right across modern Indian populations," Jones said.
Researchers say this strand of ancestry may have flowed into the region with the bringers of Indo-Aryan languages.