By comparing genetic information from extant humans worldwide, researchers have painted a broadstrokes picture of human prehistory. However, these data reveal only the oldest and most recent chapters of the story of human evolution. On page 999 of this issue, Narasimhan et al. (1) capitalize on recent advances in high-throughput genome sequencing techniques and access to well-preserved ancient human remains to write a key middle chapter of this story.

Over the past 100,000 years or so, humans dispersed across Africa and then throughout the rest of the world, consequently adapting to a wide variety of lands, climates, and ecosystems (2). This basic narrative illuminates questions—about local adaptation, ecosystem disruption, linguistic evolution, and human prehistory—that genomic data from extant humans fails to answer. To address this deficiency, Narasimhan et al. built on previous large-scale studies of human migration history conducted with ancient DNA obtained from human remains across Eurasia (36) (see the figure). The authors sequenced more than 500 genomes of humans belonging to ancient cultures from archaeological sites across a large part of Asia. They then used an array of allele frequency–based statistics and algorithms to model human populations across time as mixtures of other, earlier populations and investigated outstanding questions about human dispersals in South and Central Asia. Although this effort does not rewrite the history of humans in South Asia, it does fill in several missing pieces.

Despite the archaeological and historical importance of the Copper Age Indus Valley Civilization in the northwest regions of South Asia, the genetic origins of the people of this culture remain uncharacterized. Narasimhan et al. identified 11 individuals who lived in regions adjacent to, but outside of, South Asia between 3300 and 2000 BCE and whose genetic signatures indicate that they were migrants from the south. Each of these migrant genomes was a mixture of one population comprising mostly early Iranian farmers and another resembling hunter-gatherers from the Andaman Islands south of India. These two groups mixed between 5400 and 3700 BCE, forming a genetic signature detectable in South Asian genomes today. Because these South Asian migrants were contemporaneous with the Indus Valley Civilization, Narasimhan et al. inferred that the migrants’ genetic profile was probably typical of members of the Indus Valley Civilization. Thus, their study provides evidence of the genomic origins of the Indus Valley Civilization despite not including any ancient genomes from the Indus Valley Civilization itself.

These new data also suggest that, after the fall of the Indus Valley Civilization, several migrations into South Asia led to the formation of two distinct populations therein, one more ancestral to modern North Indians and the other more ancestral to modern South Indians. The ancestry of most present-day Indians is probably composed of these two populations along with a handful of others (68). The ancestral South Indian population formed as individuals typical of the Indus Valley Civilization continued to mix with a population related to today’s Andaman Islanders; this genomic mixing likely persisted until as late as 1700 to 400 BCE.


Ancient human nuclear genomes published since 2010

Research articles returned in a PubMed search for “ancient genomes” were analyzed for newly published, genome-scale DNA sequencing data (single-nucleotide polymorphism or shotgun) from anatomically modern humans. Cited articles contributed the most ancient genomes in each year going back to 2014.




The ancestral North Indian population, by contrast, contains ancestry from migrants thought to have moved south from the Eurasian steppe—a flat, unforested grassland—but the source of this ancestry is controversial (68). During the Bronze Age, a culture of steppe pastoralists called the Yamnaya spread ancestry and probably technology and Indo-European languages as far west as Spain and as far east as the Altai Mountains in Siberia (45). Whereas some have suggested that the Yamnaya arrived in North India around 3000 to 2500 BCE (8), others argue that steppe ancestry in North India also contains a European Neolithic component, which implies that it came from a later eastward expansion around 2300 to 1200 BCE (6). Narasimhan et al. date the arrival of steppe ancestry to 1900 to 1500 BCE, which supports the latter hypothesis. Thus, steppe ancestry and the associated Indo-European languages arrived later in India than in Europe and likely arrived by way of Europe.

The amount of genome-wide data available from ancient humans has exploded in recent years, and the study by Narasimhan et al. is the largest contribution to date, with more than 500 ancient human genomes sequenced (see the figure). This scale of genomic data enabled the authors to compare genomes across a large number of locations and time points and to home in on increasingly specific questions that would have been unanswerable even a few years ago.


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Narasimhan et al. studied the DNA from more than 100 ancient humans unearthed from northernmost South Asia.




The human story revealed by Narasimhan et al. in South Asia is similar to those from elsewhere in Eurasia: Successive waves of migration altered the genetic makeup of, but did not completely replace, preexisting groups (46). Modern South Asians appear to be a mixture of Iranian-like hunter-gatherers, a population ancestral to the Andaman Islands, and Eurasian steppe herders who first settled in Europe. Some South Asian populations later received immigrants from other outside groups. As more genomes become available from previously unexamined historical cultures around the world, stories like this one will fill other middle chapters in the book of human history.




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