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A Rare Deep-Rooting D0 African Y-Chromosomal Haplogroup and Its Implications for the Expansion of Modern Humans out of Africa Marc Haber, Abigail L. Jones, Bruce A. Connell
Abstract "Present-day humans outside Africa descend mainly from a single expansion out ∼50,000-70,000 years ago, but many details of this expansion remain unclear, including the history of the male-specific Y chromosome at this time. Here, we re-investigate a rare deep-rooting African Y-chromosomal lineage by sequencing the whole genomes of three Nigerian men described in 2003 as carrying haplogroup DE* Y-chromosomes, and analyzing them in the context of a calibrated worldwide Y-chromosomal phylogeny. We confirm that these three chromosomes do represent a deep-rooting DE lineage, branching close to the DE bifurcation, but place them on the D branch as an outgroup to all other known D chromosomes, and designate the new lineage D0. We consider three models for the expansion of Y lineages out of Africa ∼50,000-100,000 years ago, incorporating migration back to Africa where necessary to explain present-day Y-lineage distributions. Considering both the Y-chromosomal phylogenetic structure incorporating the D0 lineage, and published evidence for modern humans outside Africa, the most favored model involves an origin of the DE lineage within Africa with D0 and E remaining there,[b] and migration out of the three lineages (C, D and FT) that now form the vast majority of non-African Y chromosomes. The exit took place 50,300-81,000 years ago (latest date for FT lineage expansion outside Africa - earliest date for the D/D0 lineage split inside Africa), and most likely [b]50,300-59,400 years ago (considering Neanderthal admixture). This work resolves a long-running debate about Y-chromosomal out-of-Africa/back-to-Africa migrations, and provides insights into the out-of-Africa expansion more generally.
quote:Originally posted by beyoku: Good find. There are have a few DE genetic relatives.
Do you think D0/DE in Africa was linked to MN/N*? Like a situation where they're both replaced or died out more or less together, or at the same time in Africa?
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quote:Originally posted by Elmaestro: [QB] A Rare Deep-Rooting D0 African Y-Chromosomal Haplogroup and Its Implications for the Expansion of Modern Humans out of Africa Marc Haber, Abigail L. Jones, Bruce A. Connell
in the phylogeny (Figure 1A), the DE lineage now contains three,rather than two early sub-lineages: one exclusively African (D0), one mainly African (E), and one exclusively non-African (D).We therefore consider the implications of this revised structure for interpreting the present-day Y phylogeography as the result of male movements at different times between 28,000 and 100,000 years ago (Figure 2). In order to do this, we need to calibrate the phylogeny, and for this use the ancient-DNA-based mutation rate (Fuet al.2014), which has been widely adopted (e.g. Pozniket al.2016); we consider in the Discussion the implications of alternative mutation rates and some of the other simplifying assumptions we make here.
Analysis of ancient African DNA from 50,000-100,000 years ago would provide conclusive information on Y haplogroup distributions at this time, but is not currently available.In the meantime, further focus of present-day Y-chromosomal lineages in central and western Africa in order to understand more about deep African lineage sseems warranted, and the current study illustrates the broad insights that can sometimes be revealed by very rare lineages.
quote:Originally posted by beyoku: Good find. There are have a few DE genetic relatives.
Do you think D0/DE in Africa was linked to MN/N*? Like a situation where they're both replaced or died out more or less together, or at the same time in Africa?
I thought about it but the lack of DE* in the East makes me not think so. I am still seeing it as an old L counterpart.
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posted
I am anxious about this. Like in most papers they give one thing and take four.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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posted
Here's one thing I find interesting about this study... Their lower bound dates are limited by the time of Neanderthal introgression.
Figure 2 Models for the early movements of Y-chromosomal haplogroups out of Africa and back.
Figure 3 Estimation of the time of the out-of-Africa migration incorporating information from Y-chromosomal lineages (green, this work), archaeological dates (brown, Fu et al. 2014) and ancient DNA (red, Fu et al. 2014) ________________________________________________________________________________________________
But they didn't have to be..
quote: We analyzed X chromosome diversity across the globe and discovered seventeen chromosomal regions, where haplotypes of several hundred kilobases have recently reached high frequencies in non-African populations only. The selective sweeps must have occurred more than 45,000 years ago because the ancient Ust’-Ishim male also carries its expected proportion of these haplotypes. Surprisingly, the swept haplotypes are entirely devoid of Neanderthal introgression, which implies that a population without Neanderthal admixture contributed the swept haplotypes. It also implies that the sweeps must have happened after the main interbreeding event with Neanderthals about 55,000 BP. These swept haplotypes may thus be the only genetic remnants of an earlier out-of-Africa event. Extreme selective sweeps displaced archaic admixture across the human X chromosome around 50,000 years ago L. Skov, M.C. Macià doi: https://doi.org/10.1101/503995
quote:Originally posted by Elmaestro: Here's one thing I find interesting about this study... Their lower bound dates are limited by the time of Neanderthal introgression.
Figure 2 Models for the early movements of Y-chromosomal haplogroups out of Africa and back.
Figure 3 Estimation of the time of the out-of-Africa migration incorporating information from Y-chromosomal lineages (green, this work), archaeological dates (brown, Fu et al. 2014) and ancient DNA (red, Fu et al. 2014) ________________________________________________________________________________________________
But they didn't have to be..
quote: We analyzed X chromosome diversity across the globe and discovered seventeen chromosomal regions, where haplotypes of several hundred kilobases have recently reached high frequencies in non-African populations only. The selective sweeps must have occurred more than 45,000 years ago because the ancient Ust’-Ishim male also carries its expected proportion of these haplotypes. Surprisingly, the swept haplotypes are entirely devoid of Neanderthal introgression, which implies that a population without Neanderthal admixture contributed the swept haplotypes. It also implies that the sweeps must have happened after the main interbreeding event with Neanderthals about 55,000 BP. These swept haplotypes may thus be the only genetic remnants of an earlier out-of-Africa event. Extreme selective sweeps displaced archaic admixture across the human X chromosome around 50,000 years ago L. Skov, M.C. Macià doi: https://doi.org/10.1101/503995
Case and point; CT D didn't necessarily have to leave Africa by 57,000 years ago. Ust-Ishim has addition African Ancestry. Or better yet...
African ancestry in OOA populations was bipartite
@Askia_The_Great @Beyoku @Tyrranhotep What you think??
Wait, wait, are you proposing that there were even more migrations out of Africa between the initial OOA and the Natufians? As in, Africa kept pumping people out throughout the late Pleistocene? That's a rather cool finding.
BTW, where did the last graph in your post come from? It doesn't seem to be in the OP paper.
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It's my graph.. lol. And I shouted you guys out because it was a hypothesis I had posted on FB almost a year ago. It's a fun Idea to play around with.
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posted
^ I too am convinced of that possibility from the old forum member Rasol who began posting data of African clades both paternal and maternal keeps popping up in Arabia.
But now you have some experts who are quickly trying to 'Eurasianize' these clades.
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Curiously of all the major populations in Eurasia who carry hg D (Tibetans, Andamanese, and Japanese) the Andamanese carry the highest at 100% in many samples.
This shows just how isolated these people are as Australasians. Even Sahulese populations i.e. Papuan-New Guineans, Australian Aboriginals, and Melanesians are more heterogeneous in terms of Y clades present. Take Australian Aborigines for instance whose oldest clade is C.
Deep Roots for Aboriginal Australian Y Chromosomes 144 self-identified Aboriginal Australian males who volunteered to participate in the Genographic Project were previously typed with Y SNPs to assign them to major haplogroups [6]. A large fraction (∼70%) of Aboriginal Australian males today carry Y chromosomes of Eurasian origin (∼59% European) due to admixture in the last ∼200 years after the European colonization of Australia [7]. Among the individuals with indigenous Y chromosomes, 44% belong to haplogroup C, with 42% being C-M347 and 2% the basal C-M130∗. Paragroup K∗ constitutes 56% of indigenous Y chromosomes, with 27% being S-P308, 2% being haplogroup M-M186, and 27% being the basal K-M526∗ [6]. Although we note that other nomenclatures with relevance to these haplogroups exist [8] or could be proposed, these labels suffice for the purposes of our present study, and for simplicity we hereafter refer to C-M347 and C-M130∗ as Aboriginal Australian C, to S-P308 and K-M526 as K∗, and to M-M186 as M. For distinguishing subclades of haplogroup C, we also make use of the haplogroup labels C1, C2, C3, C4, and C5 as they are used in [9]. 31 of the 144 typed individuals carried Y chromosomes belonging to one of the indigenous haplogroups.
Another thing to note is that even autosomally there is a huge gap between Andamanese and Sahulese populations.
South Asians, particularly aboriginals of southern India seem to fill in this gap.
The Paniya are an aboriginal tribe of Kerala state south India.
Paniya men Posts: 26236 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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What is interesting about the Andamanese groups is also which genetic and historical relations they have to each other. I read that for example the Onge and the Jarawa mainly belong to the Y-DNA haplogroup D, but the Great Andamanese have haplogroups like K, L, O and P1. The great Andamanese have been subject to mixing with other groups though so their genetic composition may have looked differently in old times.
I don´t know about the Northern Sentinelese, it seems hard to be able to conduct any DNA tests on them. They will most certainly not agree to such a thing. Also I am not sure about the genetic profile of the Jangil who unfortunately have gone extinct.
There was once a very interesting book/site on the net with a lot of facts about the Andamanese, but unfortunately it is gone now.
But there are articles and studies, some of them referred to in this Wiki article
Survival International has also some material about the Andamanese and their present day situation:
quote:Originally posted by Archeopteryx: What is interesting about the Andamanese groups is also which genetic and historical relations they have to each other. I read that for example the Onge and the Jarawa mainly belong to the Y-DNA haplogroup D, but the Great Andamanese have haplogroups like K, L, O and P1. The great Andamanese have been subject to mixing with other groups though so their genetic composition may have looked differently in old times.
I don´t know about the Northern Sentinelese, it seems hard to be able to conduct any DNA tests on them. They will most certainly not agree to such a thing. Also I am not sure about the genetic profile of the Jangil who unfortunately have gone extinct.
There was once a very interesting book/site on the net with a lot of facts about the Andamanese, but unfortunately it is gone now.
But there are articles and studies, some of them referred to in this Wiki article
Survival International has also some material about the Andamanese and their present day situation:
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The morphological variation among early native Americans and also the population Y signal seems to somewhat confuse scientists and also artists like Cicero Moraes when it comes to their looks. Thus Moraes made reconstructions of ancient Mexicans like Eve of Naharon rather lightskinned. But a couple of Brazilians (Aipuna and Diarum) he made more dark skinned and with a bit curly hair. Then he made yet another Brasilian, ZuZu with straight hair. According to Moraes Zuzu shows morphological similarities with todays Malaysians and Vietnamese
Apiuna, one of the Brazilians made headlines in some News as a "cave man from Africa" due to his and some other ancient Brazilians morphology, which before DNA testing gave rise to different speculations.
Also the well known Luzia was reconstructed in ways that reminded of Africans, Melanesians and other foreign peoples. But other remains from the same place have still had "Native American" DNA. One individual had the Y-population signal.
Today Luzia is reconstructed as more like Native Americans like for example the Yanomami
The question of population Y is adressed in this thread:
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One interesting clue to were in Asia Native Americans originally came from is also to look at the percentage of Denisova ancestry in them. It seems the Denisova percentage are more in line with mainland Asians than with for example Papuans.
Proportion of the genome inferred to be Denisovan in ancestry in diverse non-Africans. The color scale is not linear to allow saturation of the high Denisova proportions in Oceania (bright red) and better visualization of the peak of Denisova proportion in South Asia.
The map copied from Svante Pääbos Nobel lecture, but originally from Sankararaman et al., 2016: `The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans´ Current Biology 26, 1–7, May 9, 2016
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quote:Originally posted by Archeopteryx: [QB] The morphological variation among early native Americans and also the population Y signal seems to somewhat confuse scientists and also artists like Cicero Moraes when it comes to their looks.
This is why I don't like many reconstructions that include skin color and hair type, it's often speculative (although some recent genetic testing purports to predict skin color >> but how can they prove it? ) I think often these reconstructions do not add to factual knowledge and are often used as a tool to sell articles in popular magazines/ online news "What_____________________Looked like Revealed for the First Time"
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quote:Originally posted by Archeopteryx: One interesting clue to were in Asia Native Americans originally came from is also to look at the percentage of Denisova ancestry in them. It seems the Denisova percentage are more in line with mainland Asians than with for example Papuans.
Proportion of the genome inferred to be Denisovan in ancestry in diverse non-Africans. The color scale is not linear to allow saturation of the high Denisova proportions in Oceania (bright red) and better visualization of the peak of Denisova proportion in South Asia.
The map copied from Svante Pääbos Nobel lecture, but originally from Sankararaman et al., 2016: `The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans´ Current Biology 26, 1–7, May 9, 2016
Either I'm confused or you got it backwards, you said "It seems the Denisova percentage are more in line with mainland Asians than with for example Papuans."
Wouldn't the proper statement be
"It seems the Denisova percentage are more in line with, for example Papuans (5%) than with with mainland Asians (0.2%) "
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posted
In Svante Pääbos Linnaeus lecture 2022 he said that the amount of Denisova ancestry in Native Americans is similar to the percentage in people living in mainland Asia.
quote: 46:48 -Thank you. I would like to ask if indigenous Americans also carry DNA from Denisovans? 46:56 -Yes. They have similar levels on average, as people in mainland Asia. 47:03-So quite low, below one percent. 0.2-0.4 %.
The highest percentage Denisova ancestry seems to be among the Ayta people in the Philippines
quote: Multiple lines of evidence show that modern humans interbred with archaic Denisovans. Here, we report an account of shared demographic history between Australasians and Denisovans distinctively in Island Southeast Asia. Our analyses are based on 2.3 million genotypes from 118 ethnic groups of the Philippines, including 25 diverse self-identified Negrito populations, along with high-coverage genomes of Australopapuans and Ayta Magbukon Negritos. We show that Ayta Magbukon possess the highest level of Denisovan ancestry in the world c 30%–40% greater than that of Australians and Papuans—consistent with an independent admixture event into Negritos from Denisovans. Together with the recently described Homo luzonensis, we suggest that there were multiple archaic species that inhabited the Philippines prior to the arrival of modern humans and that these archaic groups may have been genetically related. Altogether, our findings unveil a complex intertwined history of modern and archaic humans in the Asia-Pacific region, where distinct Islander Denisovan populations differentially admixed with incoming Australasians across multiple locations and at various points in time.
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The aboriginal populations of Asia live on in the people you see in Asia today. "Negritoes" are just one example of the aboriginal populations of Asia and they are a group who practiced self isolation which is why they maintained their distinct genetic and physical characteristics for so long. This is unlike Australian Aborigines who were isolated because of geography and being cut off from the mainland after Sundaland sunk.
Also, Austronesians are not "aborigines" and they aren't a race, no matter how scholars keep trying to make them into one. Austronesians are a language group and not the only language group in South East Asia. AustroAsiatic is the other language group of South East Asia. But even then, both of these languages are only about 7,000 years old, which means most populations in South East Asia spoke some other languages prior to that. And it also means that both of these language families are associated with the spread of neolithic lifestyles, which is where the assumption of "new races" spreading across South East Asia comes from. The basal diversity of South East Asia long predates the spread of these language families and the more recent spread of Northern Asians into South East Asia is simply a layer on top of that ancient diversity. But all modern Asians are descendant of these aboriginal Asian groups with the most obvious proof being the dark brown hair most Asians have (Asian hair is not really black).
quote: Negritos in Southeast Asia have been described as the ‘First Sundaland People,’ implying that their direct ancestors had inhabited Southeast Asia ever since the Pleistocene, much earlier than the non-Negrito farmers who arrived here during the late Holocene (e.g. Bellwood Citation2017; Jinam et al. Citation2017). The Negrito Hypothesis proposes that the shared phenotype among various hunter-gatherer groups in Southeast Asia is due to common descent from a pre-Neolithic substrate of humanity, and the alternative view is that their distinctive phenotype results from convergent evolution (Endicott Citation2013). For instance, a half-century ago, Howells (Citation1973) suggested that the Negritos might be related to African Pygmies of similar phenotypes, and Coon (Citation1965) proposed a convergent evolution model in the natural environments of Africa and Southeast Asia. Today, the issue of the Negrito Hypothesis is still of great interest to many disciplines, which is related directly to human evolution, ecological adaption, the Out-of-Africa migration, and admixture with Denisovans, East Asian-related or other ancestries (Endicott Citation2013).
Currently, no archaeological sites in Taiwan have been dated in the range between 15,000 and 6600 cal. years BP, although nearly a hundred C14 dates collected from the Baxian Caves are between 30,000 and 15,000 cal. years BP.
In order to represent the later assemblages near the end of the preceramic period from Xiaoma and Chaoyin, some have postulated to name either the ‘Preceramic Culture’ (Huang Citation1991b) or ‘Chaoyin Culture’ (Tsang et al. Citation2018, 41–42).
This study clarifies that female hunter-gatherer specimens from Xiaoma and comparative pre-farming sites in southern China, Vietnam, and the Jomon site in Japan, all belonged to the ‘first layer’ population within the previously reconstructed two-layer model. In this respect, the findings demonstrate a close cranial affinity between the study specimens and the Australo-Melanesian samples (including Papuan). A comparison of the samples encompassing west Eurasia and Africa produces a more comprehensive interpretation. In this regard, the examined early hunter-gatherer skulls and Australo-Melanesian (including Papuan) samples exhibit a closer resemblance to African samples than the present-day Eurasian series, which includes northeastern, southeastern, and/or western Asians. This finding supports the hypothesis that the first layer was of close African origin, for instance in the cases of archeologically excavated skulls without significant morphological alteration in accordance with a particular climate. The majority of present-day Eurasian people (‘the second layer’) possess a different cranial shape, generally attributed to dry and/or cold climate adaptation. The assumption is that many Palaeolithic or Mesolithic pre-farming populations in East/Southeast Asia and Europe originally had shared common features with tropical African, but these features later were replaced by (or admixed into) Neolithic farming migrants whose close common ancestors already adapted to the extremely dry climate in West Eurasia or to extremely cold weather in northern East Eurasia during the Last Glacial Maximum (see discussion in Matsumura et al. Citation2019).
Previous genetic studies have shown that the modern-day Negritos of the Andaman Islands, Malay Peninsula, and Philippine Islands represent one of the earliest branches of AMH to have reached Southeast Asia (Jinam et al. Citation2017). A recent genetic study on the Mani (Maniq) Negritos of southern Thailand concludes that they are closely related genetically to the Semang in the Malay Peninsula (Malay Negritos), who altogether carry an Andamanese-related ancestry linked to the ancient Hoabinhian hunter-gatherers of Mainland Southeast Asia (Göllner et al. Citation2022). Interestingly, while Ayta Magbukon in the Philippines possesses a high level of Denisovan ancestry (Larena et al. Citation2021), the Denisovan ancestry of the Mani is undatable. The result is consistent with several other studies, indicating that the ancestors of Australo-Papuans and Philippine Negritos likely encountered a Denisovan introgression event east of the Wallace line (Göllner et al. Citation2022). Still, the origin of the small stature of Negritos has not yet been identified conclusively as possibly inherited from a common ancestry in ancient time or else developed later within different areas convergently.
The Xiaoma skeleton from the preceramic burial feature has revealed new insights into the ancient population structure of Taiwan and the larger regional picture in Southeast Asia. The apparent Negrito affiliation at Xiaoma nearly 6000 years ago conceivably could represent a direct descendance from the original Palaeolithic Changbinian population who had settled at the Baxian Caves of eastern Taiwan about 30,000 years ago, but equally the Negrito affiliation could represent a second or later wave of migration, still within the general ‘first layer’ of hunter-gatherer occupation of East/Southeast Asia.
Previous studies (e.g. Matsumura et al. Citation2008, Citation2017, Citation2019, Citation2021) of more than 1000 individuals excavated from sites in southern China and Southeast Asia demonstrate that the pre-Neolithic populations were quite varied in stature, although their cranial morphologies all clearly connected to the ‘first layer’ population. Currently, the most similar archaeological example for Xiaoma is from the Niah Caves in Sarawak of Borneo, although the site dating is much older. In the West Mouth of the Niah Caves, a partial femur recovered with the famous Deep Skull by the Harrissons in 1958 was examined. This specimen dated to about 30,000 to 39,000 cal. years BP, ranking among the oldest long bones from an AMH in Southeast Asia. The size and shape of this femur are very similar to that of the Aeta Negritos from the Philippines, noting a small stature of roughly 145 to 146 cm and a weight around 35 kg (Curnoe et al. Citation2019).
These papers keep promoting this myth that the only populations in South East Asia prior to the Neolithic were "negritoes" which is simply false. And the only reason why Negrito groups are important is to understand how and why they chose to stay culturally and socially isolated from surrounding groups for so long (over 30,000 years). Because we know other aboriginal populations from South India and into Australia have always been present in South East Asia with straight hair and taller physiques, along with taller curly haired people like Papuans.
The bigger problem with these studies is a lack of remains from between 20,000 BC and the Neolithic era which would be able to show the diversity of the populations prior to, during and after the Neolithic. This particular paper simply has 1 6,000 year old skeleton that they try to use as "repesentative" of the entire island at the time or all of South East Asia, which makes no sense.
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