Archaic Adaptive Introgression

Certainty Style Key
Hover over keys for definitions:
True   Likely   Speculative
Human Uniqueness Compared to "Great Apes": 
Likely Difference
Human Universality: 
Individual Universal (All Individuals Everywhere)
MOCA Domain: 
MOCA Topic Authors: 

     An interesting emerging feature of human evolution is the presence and persistence of DNA with non-modern human origins. Prior to the dispersal of the first modern humans from Africa, the precursors to other archaic human groups, namely Neanderthals and Denisovans, migrated and settled across Eurasia. Preceding modern humans by at least a few hundred thousand years, these groups diverged genetically and phenotypically from out last common ancestor, in part due to natural selection imposed by their novel environments. As modern humans emerged from Africa, they overlapped spatially and temporally with these divergent archaic groups. Modern DNA sequencing has revealed a number of regions of the modern human genome that appear to have been introgressed from limited number of human-archaic (i.e., Neanderthal) matings. Although much of the introgressed DNA appears to have undergone negative selection, a few notable regions appear to have been positively selected. These regions include gene involved in immunity, hair and skin pigmentation, freckling, metabolism and high altitude resistance. The positive selection of some introgressed regions suggest that as modern humans migrated from Africa and eventually replaced the archaic groups, sporadic interspecific breeding events may have allowed modern humans to take advantage of the evolutionary history of these groups and more rapidly adapt to their new environments. There is considerable debate about how formative these events were for the emergence of our species, but for at least some human populations they may have been essential for survival.
     At current it is unclear how prevalent instances of archaic adaptive introgression are across great apes as the genetic and demographic studies have not been performed. It may be reasonable to presuppose that, among great apes, this evolutionary process is a uniquely human feature stemming from the unusual successive global migrations to diverse environments made by modern humans and their archaic sister species. The construction of the hybrid zones and successive backcrossing required to support archaic adaptive introgression appears to be generally rare in ecology, although it is also an understudied phenomenon.


Timing of appearance of the difference in the Hominin Lineage as a defined date or a lineage separation event. The point in time associated with lineage separation events may change in the future as the scientific community agrees upon better time estimates. Lineage separation events are defined in 2017 as:

  • the Last Common Ancestor (LCA) of humans and old world monkeys was 25,000 - 30,000 thousand (25 - 30 million) years ago
  • the Last Common Ancestor (LCA) of humans and chimpanzees was 6,000 - 8,000 thousand (6 - 8 million) years ago
  • the emergence of the genus Homo was 2,000 thousand (2 million) years ago
  • the Last Common Ancestor (LCA) of humans and neanderthals was 500 thousand years ago
  • the common ancestor of modern humans was 100 - 300 thousand years ago

Possible Appearance: 
600,000 thousand years ago
Probable Appearance: 
300 thousand years ago
Definite Appearance: 
100 thousand years ago
Background Information: 

Adaptive Introgressed Regions

Gene/Region containing            Function                          Likely Source              Presence in                      Evidence         Citations
Introgressed haplotype                                                                                          Modern Populations                                               

HLA-A, HLA-B, HLA-C              Immune Response          Neanderthal                Europeans, East               Likely               1
                                                                                           and Denisovan            Asians, Melanesians

HLA-DPB1                                 Immune Response          Neanderthal                 Europeans                       Mixed                2,3

STAT2 (Haplotype N)                 Pathogen Defense          Neanderthal                 Non-Africans                    Likely                4

STAT2 (Haplotype D)                 Pathogen Defense          Denisovan                    Melanesians                    Speculative       4

OAS1                                         Viral Immune Response  Denisovan (or               Melanesians                    Mixed                5,6,7
                                                                                          unknown group)

OAS gene cluster                      Viral Immune Response  Neanderthal                 Non-Africans                   Speculative        6,7

HYAL2                                       Cellular Response to       Neanderthal                 East Asians                     Strong                8,9,10,11
                                                  UV Radiation

BNC2                                        Skin Pigmentation and    Neanderthal                  Europeans                      Strong                5,12,13,14

POU2F3                                    Keratinocyte                    Neanderthal                  East Asians                    Strong                 5,12

TMEM136                                 Unknown                         Neanderthal                   East Asians                   Strong                  5,12

MC1R                                       Melanocyte Function;      Neanderthal                   Non-Africans                 Mixed                  8,15
                                                 Red-hair, freckles and
                                                 fair skin

SLC16A11                               Lipid Metabolism              Neanderthal                  Native Americans          Likely                   16

SLC16A13                               Lipid Metabolism              Neanderthal                  Native Americans          Likely                   16

DMD                                        Skeletal Muscle                Neanderthal                  Non-Africans                 Speculative          17,18

EPAS1                                     Response to High             Denisovan                     East Asians                   Strong                  19,20
                                                Altitude Hypoxia                                                     (perhaps Tibetans only)
Multiple regions                      Multiple genes                   Neanderthal                  Europeans                     Likely                    21
identified by a                         involved in
genome-wide scan                 integumentary system

Multiple regions                      Multiple genes                   Neanderthal                   Europeans and             Likely                    12
identified by a                         involved in lipid                                                        East Asians
genome-wide scan                 catabolism

Multiple regions                      Multiple genes                   Neanderthal                   Europeans and             Likely                     5
identified by a                         involvedin keratin                                                     East Asians
genome-wide scan                 filament, sugar metabolism,
                                                musclecontraction and

Multiple regions                      Not characterized              Neanderthal                   Europeans, East           Speculative            22, 23
identified by a                                                                    and Denisovan              Asians, Melanesians
genome-wide scan

Table adapted from Racimo et al 2015.

Strong Evidence = Multiple published reports supporting AAI
Likely Evidence = A single published report supporting AAI
Speculative Evidence = Proposed AAI but no published statistical test
Mixed Evidence = Inconsistent published support for AAI

The Human Difference: 

 Because of the unique way in which humans and their archaic sister species successively spread across the globe at time intervals that allowed local adaptation, they may be the only great ape to have receive adaptive introgressed DNA. It is unclear if the dispersion and migration of other great apes could have allowed for such a process.

Universality in Human Populations: 

 Adaptive Introgression is likely present in most to all human populations, although any one introgressive event may be present in only a subset of populations.

Possible Selection Processes Responsible for the Difference: 

 The introgressed DNA was selected via natural selection. Only a few beneficial segments were retained while as a majority of introgressed DNA was selected against.

Occurrence in Other Animals: 

 This type of DNA transfer among sister species appears generally rare in ecology, although it is understudied. There are numerous hybrid zones and interbredding between sister species, but the type of long separation and replacement with introgression has only been observed in a few distant species, namely, salamanders and mice. Archaic adaptive introgression has also been observed in some plant species.

Related MOCA Topics
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  1. Neanderthal introgression reintroduced thousands of ancestral alleles lost in the out of Africa bottleneck, Capra, John A., and Simonti Corinne N. , American Society of Human Genetics, (2017)
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  27. Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico., Williams, Amy L., Jacobs Suzanne B. R., Moreno-Macías Hortensia, Huerta-Chagoya Alicia, Churchhouse Claire, Márquez-Luna Carla, García-Ortíz Humberto, Gómez-Vázquez María José, Burtt Noël P., Aguilar-Salinas Carlos A., et al. , Nature, 2014 Feb 6, Volume 506, Issue 7486, p.97-101, (2014)
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