Monday, June 10, 2024

Two New Archaic Ancestry Papers

Neither of two new papers about archaic admixture, and in one case, more general issues in South Asian historical genetics, are paradigm changing. But both papers refine the story we already have with more fine detail and more certainty.
India has been underrepresented in whole genome sequencing studies. We generated 2,762 high coverage genomes from India––including individuals from most geographic regions, speakers of all major languages, and tribal and caste groups––providing a comprehensive survey of genetic variation in India. With these data, we reconstruct the evolutionary history of India through space and time at fine scales. 
We show that most Indians derive ancestry from three ancestral groups related to ancient Iranian farmers, Eurasian Steppe pastoralists and South Asian hunter-gatherers. We uncover a common source of Iranian-related ancestry from early Neolithic cultures of Central Asia into the ancestors of Ancestral South Indians (ASI), Ancestral North Indians (ANI), Austro-asiatic-related and East Asian-related groups in India. 
Following these admixtures, India experienced a major demographic shift towards endogamy, resulting in extensive homozygosity and identity-by-descent sharing among individuals. 
At deep time scales, Indians derive around 1-2% of their ancestry through gene flow from archaic hominins, Neanderthals and Denisovans. By assembling the surviving fragments of archaic ancestry in modern Indians, we recover ∼1.5 Gb (or 50%) of the introgressing Neanderthal and ∼0.6 Gb (or 20%) of the introgressing Denisovan genomes, more than any other previous archaic ancestry study. Moreover, Indians have the largest variation in Neanderthal ancestry, as well as the highest amount of population-specific Neanderthal segments among worldwide groups. 
Finally, we demonstrate that most of the genetic variation in Indians stems from a single major migration out of Africa that occurred around 50,000 years ago, with minimal contribution from earlier migration waves. 
Together, these analyses provide a detailed view of the population history of India and underscore the value of expanding genomic surveys to diverse groups outside Europe.
Gene flow from Neandertals has shaped the landscape of genetic and phenotypic variation in modern humans. We identify the location and size of introgressed Neandertal ancestry segments in more than 300 genomes spanning the last 50,000 years. We study how Neandertal ancestry is shared among individuals to infer the time and duration of the Neandertal gene flow. 
We find the correlation of Neandertal segment locations across individuals and their divergence to sequenced Neandertals, both support a model of single major Neandertal gene flow. Our catalog of introgressed segments through time confirms that most natural selection–positive and negative–on Neandertal ancestry variants occurred immediately after the gene flow, and provides new insights into how the contact with Neandertals shaped human origins and adaptation.

The best explanation for most Neanderthal DNA seen in the modern human genome was a single major period of interbreeding about 47,000 years ago that lasted about 6,800 years, the researchers found.


neo said...

what are the origin of the archaic hominins, Neanderthals and Denisovans?

andrew said...

Modern humans, Neanderthals, and Denisovans are sister clades that probably have a common ancestor post-Homo erectus, most likely H. heidelbergensis.

andrew said...

From the same link:

H. heidelbergensis is thought to have descended from African H. erectus — sometimes classified as Homo ergaster

neo said...

since they all mixing in multiple region it is multiregional origin

andrew said...

The original multiregional hypothesis is not an accurate description of human evolution. This hypothesis is described at

Modern humans evolved in Africa into many archaic hominin and pre-homo/post-great ape species, starting around 8-15 mya (all of them descend from a great ape species closest to chimpanzees and bonobos), with the first modern humans evolving ca. 300 kya in Africa. There were many archaic species of post-great ape hominins (including pre-homo species) all of which, except modern humans, went extinct at not very specifically determined times. Many of those archaic hominin species were dead ends not ancestral to modern humans.

All hominin species outside Africa derive from at least five significant Out of Africa waves of migration (probably (1) H. erectus, (2) a more archaic hominin ancestral to hobbits with timing unclear, (3) H. Heidelbergensis or a post-H. Heidelbergensis common ancestor of Neanderthals and Denisovans, and (4)-(5) at least two waves of modern humans one ca. 100-150kya and one ca. 70-50kya). Archaic hominins and first wave modern humans probably never made it to the Americas. Of course there has been migration of modern humans to and from Africa since then.

First wave modern humans probably never made it further than India, but it is possible that some Asian Negritos, Papuans, and Australian Aboriginal peoples have non-negligible first wave modern human ancestry. Second wave modern humans also expanded within Africa, and mostly replaced older clades of modern humans there like the pygmies and the Khoisan peoples (and other early modern human clades that are lost as distinct populations, including one that is a source of some ancestry in most people ancestrally native to Mozambique and the vicinity).

Ultimately all hominin species except modern humans went extinct, probably not later than about 25 kya, with a possible few small relict populations that held on a bit later (and possibly even a few hundred or so relict archaic hominins existing in remote places like deep in Indonesian jungles today).

Neanderthals and Denisovans probably diverged from either H. Heidelbergensis or a post-H. Heidelbergensis common ancestor not shared to modern humans in Eurasia. Neanderthals evolved from this common ancestor in West Eurasia (and eventually expanded as far east as India and the Denisovan cave which was roughly the east-west boundary in central Asia), while Denisovans evolved in Eastern Eurasia (north and south of the mountain ranges to the east of India and up to about the Denisovan cave).

Neanderthals and Denisovans (and conceivably ghost populations of archaic hominins in Africa and possibly another archaic hominin species that might have encountered modern humans in SE Asia) introgressed in minority percentages into modern human populations that replaced them.

All non-African modern humans have Neanderthal admixture. The main Neanderthal admixtures (probably distinct waves of it with first wave and second wave Out of African modern humans) would have been in the Middle East (i.e. SW Asia and West Asia) with smaller secondary admixtures in Europe and South Asia.

Denisovan admixture probably occurred mostly in SE Asia and East Asia, with minor secondary admixture near Tibet. Some archaic hominin population (probably H. Erectus) introgressed into Denisovans before their admixture with modern humans.

Modern humans probably contributed to the extinction of Neanderthals and Denisovans.

H. Erectus was probably not capable of forming hybrid individuals with modern humans, unlike Neanderthals and Denisovans. But probably was capable of doing so with Denisovans.

andrew said...

H. Erectus can be lumped in with H. antecessor and H. ergaster with are sometimes viewed as proto-H. Erectus and evolved ca. 2 mya. H. heidelbergensis evolved from H. Erectus ca. 500-800 kya, with Neanderthals and Denisovans evolving after that but before modern humans evolved in Africa.

H. Erectus evolved from H. habilis ("Lucy") which arguably included H. rudolfensis and evolved ca. 2.6-3.0 mya.

Archaic hominin offshoots not directly ancestral to us include H. Naledi which existed contemporaneously with early modern humans in Southern Africa.

H. habilis probably evolved from genus Australopithecus (including species sediba, garhi, africanus, afarensis and anamensis) which evolved ca. 4 mya from Ardipithecus (including species ramidus and kadabba) ca. 5.8 mya.

No archaic hominin species more basal than H. habilis (that was not actually a true great ape) left Africa, and the migration of H. habilis out of Africa is only a strongly suggested hypothesis with an uncertain timing.

Ardipithecus probably evolved from genus Orroin (including species praegens and tugenensis) which evolved ca. 7 mya.

Intermediate between our chimpanzee/bonobo-like ancestor and Orroin (the earliest bipedal primate in our lineage) were from most recent to oldest at the genus level, Sahelanthropus, Graecopithecus, Oreopithecus, Chororapithecus, and Sivapithecus, which evolved respectively in the time periods from ca. 8.5 mya to 7 mya.

The order in which the various species evolved is more reliable than the absolute dates, which could have systemic errors up to maybe 60% longer or maybe 20% shorter.

andrew said...

It is more useful to specify what precisely happened as we understand it from the available facts and observations, than it is to assign a particular label to it.

We have a much more detailed understanding of what happened now than we did when the Out of Africa v. Multiregional debate was flourishing, and that modern detailed understanding has a wide consensus in its general outlines although some fine details are uncertain or the subject of ongoing debate.

neo said...

but Multiregional is valid by DNA that other Homo species were mixed with other over deep time

neo said...

there are other species of Homo,
DNA for just 3, Sapiens Neanderthals and Denisovans all show Multiregional admixture

NeilB said...

Wow Andrew, that is a pretty comprehensive run-through of hominid evolution and dispersal - impressive! I guess we must put the tools in the Sawaliks (2.3Myold) down to Homo habilis then? NeilB