Origin of R1a Haplogroup among Indo-Aryans

Table of Contents

• Introduction
• The R1a-Z93 Phylogenetic Tree
• Ancient DNA Evidence
  • Sample Analysis
    • DS21 (Devitsa V)
    • DS92 (Semiluk settlement)
    • DS32 (Semiluk settlement)
  • Genetic Interpretation
• Synthesis and Implications
• Conclusion
• References

Introduction

The origin of the R1a haplogroup among Indo-Aryans has long been debated in population genetics and South Asian history. R1a-Z93 and its subclades are carried by 15–30% of Indo-Aryan males today, with frequencies reaching 60–70% in certain groups, including specific Brahmin communities (Sequeira et al. 2025). This distribution has fueled competing hypotheses about the demographic processes behind Indo-Aryan language and culture formation.

Earlier studies lacked direct evidence of how steppe-derived lineages became integrated into South Asia. Recent ancient DNA work by Andreeva et al. (2025) helps bridge this evidentiary gap. The discovery of R1a-Y2 lineages in Scythian-era burials from the Middle Don region provides a clearer picture of how steppe populations carried distinct paternal branches that later spread southward.

The R1a-Z93 Phylogenetic Tree

Understanding the structure of R1a-Z93 is central to tracing Indo-Aryan origins. The following tree shows major subclades, with ancient individuals placed on their respective branches:

R1a-Z93
└─ R-Z94
   ├─ R-Y3 [F2597]  ← Nepluyevsky b8-2 (1877–1642 BCE)
   │   ├─ R-Y2 [M732/AM00479, R1a1a1b2a1]
   │   │   ├─ DS21 (Middle Don Scythian, Devitsa V, Mound 6, 4th c. BCE)
   │   │   └─ DS92 (Semiluk child, Burial 13, 4th-3rd c. BCE)
   │   └─ R-Y27 ← (Sarmatian DA136, 350 BCE) & (Roopkund I6942, 774–885 CE)
   │       └─ R-L657  ← major Indo-Aryan subclade
   │           ├─ R-BY101830*
   │           │   └─ DS32 (Semiluk child, Burial 14, 4th-3rd c. BCE)
   │           ├─ R-Y7
   │           └─ R-Y29 (~1500 BCE)
   │                 ├─ R-FTF40903 (Sohi Jatt Sikh line)
   │                 └─ R-FTD76230 (Iyer Tamil Brahmin line)
   └─ R-Z2124
       ├─ R-Z2122
       │   └─ R-Y2631 (Middle Don Scythian line)
       └─ R-Z2125
           └─ R-Y934 (Late Bronze Age Srubnaya, Middle Don)
  

Plain-language summary:

• R1a-Z93 splits into two broad paths under Z94.
• Middle Don samples fall on both sides: R-Y2 under Y3, and R-Y2631 under Z2122.
• R-Y2 (DS21, DS92) connects to the Y27 → L657 pathway, while DS32 carries R-BY101830*, an actual sub-branch of L657—the dominant Indo-Aryan lineage today.
• DS32 represents the first ancient steppe individual found with a lineage that directly exists in modern Indo-Aryan populations, not just an ancestral branch.
• This demonstrates genetic continuity between Iron Age steppe populations and South Asian paternal ancestry.

Ancient DNA Evidence

The Middle Don region offers a unique window into demographic change. Andreeva et al. (2025) assigned Y-chromosome haplogroups to 35 males spanning the Late Bronze Age and Iron Age. Their results reveal stark contrasts:

• Late Bronze Age Srubnaya: homogeneous R-Y934 (Z2125).
• Iron Age Scythians: more diverse, carrying R-Y2631 (Z2122) and R-Y2 (Y3).

Sample Analysis

DS21 (Devitsa V)

This 30-40 year old male was buried in an elaborate wooden frame-pillar tomb with six companions, oriented north-northwest to south-southeast. The burial contained three individuals: DS21 (male, 30-40 years), a woman (20-29 years), and another male (40-50 years). Their scattered bones suggest post-burial disturbance. Grave goods included iron spearheads with shaft attachments, iron arrowheads, two iron knives, two iron browbands, and bone and iron belt mountings—typical elite Scythian warrior equipment. The skeleton showed signs of a hard life: arthrosis in the extremity joints and sclerotization of ligaments, indicating significant physical stress.

Genetic Profile: Y-chromosome haplogroup R-Y2 connects DS21 directly to the Y27→L657 pathway that dominates modern Indo-Aryan populations. Phenotype predictions based on genetic markers suggest DS21 had pale skin, predominantly blond hair with some brown tones, and predominantly blue eyes—the most "northern" appearance among the three samples.

DS92 (Semiluk settlement)

This 3-year-old child was found in burial 13, a repurposed pear-shaped household pit beneath the hillfort's cultural layers. The pit contained remains of 12 individuals total, with DS92's skull labeled as "skull 9." This mass burial context, using a former storage pit, reflects the distinct burial practices of the non-Scythian Semiluk population, possibly the Budini mentioned by Herodotus as living north of the Scythians.

Genetic Profile: DS92 carries 68% Sintashta_MLBA ancestry with 32% West_Siberian_HG component. Like DS21, his Y-chromosome haplogroup R-Y2 places him on the ancestral path to modern Indo-Aryan lineages. Phenotype predictions indicate pale to intermediate skin tone, mostly brown hair with some blond, and mixed eye colors (blue, intermediate, and brown)—showing more pigmentation variation than DS21.

DS32 (Semiluk settlement)

This 4-5 year old child was one of seven individuals in a sub-oval household pit converted for burial use. DS32 (individual 2) was carefully positioned: laid on his back with arms bent at the elbows and pressed to the body, right leg bent at the knee and laid aside, left leg extended, skull turned left. This deliberate positioning in undercuts carved into the pit walls shows the care taken with these burials. Genetic analysis revealed DS32 was a second-degree relative of another child (DS31) in the same burial, and both carried a rare pathogenic variant (p.Tyr1584Cys) in the VWF gene associated with von Willebrand disease—a bleeding disorder that would have been particularly dangerous in ancient times.

Genetic Profile: DS32 shows 85% Sintashta_MLBA ancestry with 15% West_Siberian_HG component, the highest Siberian proportion among the three samples. DS32's R-BY101830* placement directly under L657 confirms this connection. Phenotype predictions suggest pale to intermediate skin, mostly brown hair with some blond, and predominantly brown eyes with some blue—showing the most pigmentation among the three samples despite high Sintashta ancestry.

These findings demonstrate that R-Y2 was distributed across both elite Scythian burials and local Middle Don settlements, indicating integration across social and cultural boundaries. All three individuals show predominantly Sintashta-like Middle/Late Bronze Age ancestry (65-72%), characteristic of Indo-Iranian steppe populations, with West Siberian hunter-gatherer admixture (28-35%) but lacking significant local Middle Don Neolithic ancestry. The phenotype predictions—ranging from DS21's blue-eyed, blond appearance to DS32's darker features—align with their genetic profiles and reflect the northern European components (Latvia_BA-like ancestry) present in steppe populations of this period.

Genetic Interpretation

The reappearance of R-Y2 (previously seen in Abashevo Bronze Age sample R-AM00479 from Verkhniy Olgashi) within Scythian contexts highlights continuity of this branch across a millennium. This lineage was later found in Sarmatians (DA136, 350 BCE) and medieval India (I6942, 774-885 CE). Modern carriers of R-Y2 are predominantly from South Asia (India, Pakistan) and the Arabian Peninsula, with only rare carriers in Eastern Europe.

The phylogenetic structure suggests multiple scenarios for these Middle Don samples:

Parallel survival hypothesis: The Y2 lineage may have split around 1500 BCE, with some branches (Y29 carriers) participating in southward migrations that contributed to Indo-Aryan populations, while others remained in the steppe. Under this model, DS21, DS92, and DS32 represent descendants of the northern branch that persisted in the Pontic-Caspian region through the Iron Age.

Crucially, neither the R-Y2 lineage nor the more common Scythian R-Y2631 lineage descends from the R-Y934 haplogroup that dominated the Late Bronze Age Srubnaya culture in the same Middle Don region. This represents a complete paternal lineage replacement between the Bronze and Iron Ages. The R1a haplogroup appears in Central and South Asian ancient DNA only after ~2000 BCE, arriving with steppe migrants—a pattern that aligns with the Indo-Aryan expansion timeline.

Alternative explanations include back-migration from South/Central Asia or continuous gene flow between steppe and settled regions. The limited sample size prevents definitive conclusions, but the presence of Y2 lineages in both Iron Age steppe contexts and modern Indo-Aryan populations (via Y27→L657) demonstrates genetic continuity between these groups, regardless of the specific demographic scenario.

Synthesis and Implications

The Middle Don evidence reshapes our understanding of R1a dispersal:

1. Multiple steppe sources: Both R-Y2 and R-Y2631 operated in the same microregion, showing Indo-Iranian expansions were not the product of a single lineage.
2. Bronze to Iron Age transition: The replacement of homogeneous R-Y934 with diverse lineages suggests population turnover, likely tied to broader cultural shifts in the steppe.
3. South Asian significance: The path from Y3 → Y2 → Y27 → L657 provides a direct paternal connection between Iron Age steppe populations and modern Indo-Aryans. DS32's R-BY101830* subclade survives unchanged in modern South Asian populations.
4. Historical context: These findings support models where steppe migrations played a major role in shaping South Asian demography, language spread, and elite male ancestry, while highlighting the demographic complexity of these processes.

Conclusion

The Middle Don Scythian burials, particularly DS32, mark a pivotal discovery: the first ancient steppe DNA belonging to a direct subclade of R-L657, the haplogroup defining most Indo-Aryan paternal lineages. This discovery moves beyond identifying broadly ancestral lines, providing a concrete temporal and geographic anchor for a key Indo-Aryan lineage squarely within the Iron Age steppe.

This finding powerfully reinforces the model of a Bronze Age steppe origin for Indo-Aryan paternal ancestry. The high degree of Sintashta-related ancestry (65-87%) in these individuals demonstrates a clear connection to earlier steppe cultures, while the presence of the R-Y2 and R-L657 subclades illustrates the persistence and evolution of these specific paternal lines. The Middle Don samples serve as a crucial waypoint, confirming that populations carrying these haplogroups were positioned in the western steppe corridor long after the Bronze Age collapse.

References

• Sequeira, J. J., Shastri, S., Shrivastava, P., et al. (2025). "Exploring the genetic footprints of the gotra system in the Koṅkaṇī Sārasvata Brahmins." Molecular Genetics and Genomics, 300, 76. https://doi.org/10.1007/s00438-025-02280-4
• Andreeva, T. V., et al. (2025). "Genetic history of Scythia." Science Advances, 11, eads8179. https://doi.org/10.1126/sciadv.ads8179
• Gulyaev, V. I., Volodin, S. A., & Shevchenko, A. A. (2020). "Элитный курган скифского времени на Среднем Дону (по материалам раскопок могильника Девица V)" [Elite mound of Scythian time in the Middle Don (based on excavations of the Devitsa V cemetery)]. Российская археология [Russian Archaeology], (4), 21-39. https://doi.org/10.31857/S086960630009046-9