Overview
Haplogroup DE is the pivotal branch of the Y-chromosome phylogeny that links early African CT-derived populations with some of the most geographically distinctive paternal lineages in both Africa and Asia. It is defined by a combination of SNPs and the well-known YAP (Y-chromosome Alu polymorphism) insertion, a mobile element that provides a convenient genetic marker for identifying DE and many of its descendants. From this lineage emerge two major clades: D and E. Haplogroup D is strongly associated with certain non-African populations in East and Southeast Asia, while haplogroup E dominates much of Africa and the African-derived paternal landscape in the Mediterranean and Middle East.
The existence of DE highlights that early modern human expansions did not follow a simple pattern of “Africa versus the rest of the world,” but instead involved complex branching within Africa that later contributed separately to African and non-African populations. One branch of DE (leading to E) remained strongly African, helping shape the paternal structure of North, East, and sub-Saharan Africa; another branch (leading to D) followed a distinct trajectory that eventually contributed to populations in Tibet, Japan, and the Andaman Islands. In this sense, DE embodies a bridge lineage: deeply African in origin but with descendants that span both continental Africa and distant parts of Asia.
Because of its age, DE likely arose during a period of significant climate-driven habitat shifts within Africa. Populations carrying early DE Y chromosomes may have occupied refugia where stable resources sustained small but persistent groups. As ecological opportunities opened—including along the Nile corridor, the Red Sea coastal routes, and interior savannah corridors—subgroups carrying early D or E lineages diverged and followed different demographic paths. This makes DE critically important for understanding how one ancestral population complex generated such different geographic outcomes.
Geographic distribution
Basal DE* is extremely rare and has been tentatively reported in only a handful of individuals, primarily in West Africa and Tibet in early studies, though subsequent high-resolution work has reinterpreted some of these as early D or E derivatives rather than stable DE* lineages. As a result, most of what we know about DE’s geography comes from its descendants rather than from DE* itself.
Haplogroup E, one of DE’s two principal branches, is overwhelmingly African. It dominates North Africa, the Horn of Africa, large portions of East Africa, and much of sub-Saharan Africa. E is also found at notable frequencies in North African–derived and Near Eastern populations, often associated with Afroasiatic language expansions, Saharan pastoralism, and later historical population movements.
Haplogroup D, in contrast, has a strikingly discontinuous distribution in modern populations. It is found at appreciable frequencies in Japan (among Ainu and some mainland Japanese lineages of D-M55), in Tibet and surrounding Himalayan regions (D-M174), and among the indigenous populations of the Andaman Islands (D-Andaman). This pattern suggests a very early dispersal of D-bearing populations into Asia, followed by intense geographic isolation and drift that shaped its modern distribution.
Taken together, these descendant clades show that DE’s legacy spans both Africa and Asia. While DE* is nearly absent today, the geography of its branches reveals an origin in Africa followed by at least one very early dispersal event into Asia carried by D ancestors, likely contemporaneous with or shortly following the main Out-of-Africa expansions.
Ancient DNA
- No securely assigned ancient individual has been placed at basal DE*, but numerous ancient males belong to D or E, confirming that DE-derived lineages were widely established by the Late Pleistocene and early Holocene.
- Ancient Tibetan and Himalayan genomes show clear evidence of D-M174 and its downstream branches, indicating a long-standing D presence in high-altitude East Asia.
- Holocene and Late Pleistocene African samples from North and East Africa frequently carry E-derived haplogroups, showing that the African branch of DE was tightly integrated into early pastoral and farming societies.
- The YAP insertion has been detected in both modern and historic samples, providing a stable marker for tracing DE and its descendant haplogroups across different time periods.
- Model-based estimates using present-day DE diversity suggest that the DE split into D and E may have occurred either within northeastern Africa or in a population closely linked to early migrations along northern corridors out of Africa.
Phylogeny & subclades
Within the CT clade, DE stands as one of two main branches (the other being CF). DE itself divides into two primary haplogroups: D and E. This DE → D/E split is one of the most important early events in the shaping of paternal structure, because it simultaneously produced lineages that would become core to Asia and Africa, respectively.
Haplogroup D encompasses several deeply structured sub-lineages such as D-M174, D-M15, and regionally restricted branches in Japan and the Andaman Islands. It shows evidence of long-term isolation in geographically extreme or insular contexts—Tibetan plateau highlands, Japanese archipelago, and remote islands in the Indian Ocean. These patterns suggest that early D populations were part of some of the earliest expansions into Asia, where they became geographically and demographically trapped in isolated refugia.
Haplogroup E, by contrast, underwent major expansions within Africa. It diversified into E1b1a, E1b1b, and other subclades that became central to the genetic structure of Afroasiatic-speaking populations, Bantu-scale expansions, Saharan and Nile Valley pastoralists, and North African–Mediterranean networks. The diversity within E today is vast and reflects multiple independent demographic events over the last 40,000 years.
DE’s placement above both of these lineages makes it an anchor point for reconstructing the early structure of CT-derived populations. It delineates the split between an African-dominant branch (E) and an Asia-focused branch (D), both of which ultimately derive from a common African ancestor under CT.
- DE* (basal, extremely rare and possibly under-characterised)
- D (East and Southeast Asian-focused, with isolated distributions)
- E (predominantly African, extremely diverse and widespread)
Notes & context
Haplogroup DE is often at the center of debates about the timing and routes of early human dispersals out of Africa. One key question is whether the D lineage exited Africa as part of an early CT-bearing wave that later diversified into DE and CF in Eurasia, or whether DE split within Africa first and then only its D lineages participated in the out-of-Africa process. Current evidence tends to favor an African origin for DE itself, followed by an early movement of D ancestors into Asia.
The presence of D in geographically isolated Asian populations points to an early and somewhat independent dispersal—separate from the later waves associated with F-derived haplogroups that dominate much of Eurasia and the Americas. Meanwhile, E’s overwhelming presence in Africa indicates that DE-based diversity remained strongly rooted on the continent as later cultural transitions—such as herding, agriculture, and state formation—unfolded.
From a phylogenetic standpoint, DE’s combination of the YAP insertion and defining SNPs makes it a robust anchor for tracing deep paternal histories. Many Y-phylogeny reconstructions rely on DE and its subclades to orient broader mutation patterns and calibrate molecular clock estimates. As whole-genome sequencing becomes more common in under-sampled African and Asian populations, additional deep-rooting DE or DE-like sub-branches may be discovered, refining our understanding of how this lineage connected early African and Asian demographic histories.
References & external links