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Haplogroup H

H-M69

Macro-haplogroup

Parent clade

Formed (estimate)

c. 48,000–55,000 years before present

TMRCA (estimate)

c. 42,000–48,000 years before present

M69
M52 (upstream family)
L901
Z5857
other H-M69 backbone markers

Overview

Haplogroup H is one of the major Y lineages of South Asia and represents a deeply rooted paternal component within the subcontinent. Defined principally by the M69 mutation, it diverged early from other F derived lineages and is thought to have participated in the earliest expansions of modern humans into the Indian subcontinent. Its persistence at considerable frequencies across diverse linguistic, cultural and geographic environments highlights its long demographic continuity. H today has three principal radiations: H1 (M52), H2 (P96) and H3, which together cover a broad range of South Asian, Iranian, Central Asian and even early European contexts. H1 is the dominant branch in much of India, Pakistan and Sri Lanka, while H2 has significant archaeological relevance due to its presence in Neolithic Anatolia and Europe. H3 includes additional South Asian oriented branches. These subclades collectively reflect a complex demographic history involving early Holocene expansions, caste and clan structures, and multiple later dispersals including the migration of Romani populations into Europe.

Geographic distribution

H is most common in South Asia, especially among Indo Aryan, Dravidian and various tribal groups across India, Pakistan and Nepal. High frequencies are found among scheduled tribes, the Deccan plateau, northwestern India and the central Gangetic zone. Moderate levels appear in Iran, Afghanistan and parts of Central Asia due to ancient dispersals and continuous interactions between the Iranian plateau and the Indus region. Although primarily a South Asian lineage, subclades of H historically moved westward. The most prominent example is H1a1a, which forms the primary paternal lineage among Romani populations in Europe, reflecting an origin in northwest India and a medieval migration across the Middle East and Balkans. H2, while uncommon today, has been identified in Neolithic and early agricultural contexts in Anatolia, the Levant and southeastern Europe. This highlights an early westward movement of H derived lineages during the diffusion of farming.

Ancient DNA

H2 is archaeogenetically attested in Neolithic Anatolian and early European farming populations.
Low coverage H signatures appear in early Holocene and Neolithic South Asian individuals, suggesting long term continuity in the subcontinent.
Ancient samples from the Indus Valley cultural sphere may contain upstream H signals, although coverage is often insufficient for precise subclade assignment.

Phylogeny & subclades

Within the F framework, H branches deeply and independently alongside I, J and G. Its major internal split yields H1 (M52), H2 (P96) and H3. H1 is the overwhelmingly dominant modern branch and contains numerous downstream clusters associated with South Asia, Iran, Central Asia and the Romani diaspora. H2 is a distinct early branching lineage detected archaeologically outside South Asia, indicating ancient bidirectional movement. H3 captures an additional subset of South Asian oriented lineages that diverged early from the main H1 radiation.

H* basal
H1 (M52)
H2 (P96)
H3

Notes & context