All Y-chromosome haplogroups outside of Africa originated in East Asia

A paper published in December 2019 (Early replacement of West Eurasian male Y chromosomes from the east. Pille Hallast, Anastasia Agdzhoyan, Oleg Balanovsky, Yali Xue, Chris Tyler-Smith bioRxiv 867317; doi: https://doi.org/10.1101/867317) suggested that the Y chromosome of ALL non-Africans was replaced by lineages that originated in East Asia!

Published in bioRxiv it hasn't been peer reviewed and can be read in full. The summary of this idea is given in the abstract:

"phylogenetic analyses of haplogroup C, D and FT sequences, including very rare deep-rooting lineages, together with phylogeographic analyses of ancient and present-day non-African Y-chromosomes, all point to East/South-east Asia as the origin 50,000-55,000 years ago of all known non-African male lineages (apart from recent migrants). This implies that the initial Y lineages in populations between Africa and eastern Asia have been entirely replaced by lineages from the east, contrasting with the expectations of the serial-founder model."

So, this paper says that instead of splitting into different haplotypes close to Africa, say in the Middle East after leaving it, human Y-chromosomes began diversifying in Eastern Asia. Then these haplogroups replaced any others that may have appeared to the west of them.

Below is the map shown in this paper's Figure 3, mentioned in the following quote from the same paper.

"In a simple model of gradual human expansion from Africa to Asia and Oceania without subsequent continental-scale reshaping, we would expect the initial divergences in the Y-chromosomal phylogeny to have occurred in geographical locations close to Africa, and the present-day Y-chromosomal phylogeography to reflect this history by showing the presence of the early-diverging lineages within C, D and FT now being located geographically in Central/West Asia (Figure 3a). In stark contrast, the observed distributions of these lineages all lie further to the East, suggesting that their early divergences occurred in the East...
How then can the present-day Y-chromosomal phylogeography be reconciled with an out-of-Africa expansion? The simplest explanation is that initial western Y chromosomes have been entirely replaced by lineages from further east, perhaps on more than one occasion. "

Interesting version of an "Out of China" theory. Yet, it retains the original notion of H. sapiens leaving Africa and originating there.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2025 by Austin Whittall © 

Could Maludong remains belong to Denisovans?

A paper by Curnoe, Liu, Bao, Tacon and Ren published on Dec. 17, 2015, describes the unusal morphology of the remains found in Maludong (Yunnan), Southwest China.

They analyzed a femur found among other hominin remains and found that "...the Maludong femur has affinities to archaic hominins, especially Lower Pleistocene femora" but, this person lived only 14,000 years ago, so they were contemporaneous with modern Homo sapiens in that part of Asia. Something akin to the Flores hominin.

Are they Denisovan remains?

This is the best part (bold highlight is mine):

"It is intriguing that such a plesiomorphic hominin could have survived at Maludong until near the end of the Pleistocene. Yet, this finding applies also to H. floresiensis, with its apparent minimum geological age only slightly older than MLDG 1678. Homo floresiensis has only been found on the island of Flores in eastern Indonesia though, and its occurrence has been explained by island biogeography. Moreover, the Maludong femur is distinct from the highly unusual femora of this species, with its unique mosaic of traits including resemblances to Australopithecus taxa. One possible explanation is that the Maludong femur samples the population presently known only from Denisova Cave in the Altai region and dubbed the “Denisovans”. Another candidate is the presently unnamed taxon represented by the Xujiayao fossils. However, the absence of femora from both of these groups makes these scenarios impossible to test at present...
...the Maludong femur might represent a relic, tropically adapted, archaic population that survived relatively late in the biogeographically complex region of Southwest China. " [1]

Sources

[1] Curnoe D, Ji X, Liu W, Bao Z, Taçon PSC, Ren L (2015) A Hominin Femur with Archaic Affinities from the Late Pleistocene of Southwest China. PLoS ONE 10(12): e0143332. doi:10.1371/journal.pone.0143332

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2015 by Austin Whittall © 

Denisovans Amerindians and Austronesians

A paper by Pengfei Qin and Mark Stoneking (Denisovan Ancestry in East Eurasian and Native American Populations bioRxiv preprint first posted online April 3, 2015; doi: http://dx.doi.org/10.1101/017475), takes a look at the Denisovan content in modern Homo sapiens genes.

Below is one of the maps posted in the supporting information (from page 8) which shows (blue shades) the higher introgression of Denisovan DNA into humans in Australia, New Guinea and Melanesia, while the Neandertal content is given by the red shades (higher in Asia, America and Europe. Green tint is the neutral African area.

Neandertal and Denisovan DNA in modern humans. From Fig. S4 B in Pengfei and Stoneking.

They put forward two possible ways for the admixture of Denisovan and Homo sapiens genes. Allow me to quote them:

"However, there are (at least) two potential alternate scenarios that could explain these results. First, Denisovan admixture could have occurred in a population that was ancestral to both EE/NA (East Asia and Native American) and Oceanian populations; second, admixture could have occurred in a population that was ancestral specifically to Mamanwa, Australians, and New Guineans (as suggested previously (2)), followed by a back-migration from New Guinea to mainland East Asia. This putative back-migration would then have spread both New Guinea and Denisovan ancestry throughout East Asia and Siberia, and ultimately to the Americas."

The first option (admixture in Siberia near Denisova), would be followed by additional dilution in East Asia of Denisovan genes when more modern humans migrated into East Asia and admixed with the population that had originally received the Denisovan input. While this did not take place in Oceanian peoples.

In my opinion the back-migration out of Australia is unlikely. But what if... there was a sizeable populations of Denisovans in South East Asia and Sahul. Humans arrived and mixed with them. The higher the density of Denisovans or ratio of Denisovans to H. sapiens, the higher their "input" of genes into the mixed offspring of human - Denisovan matings. So PNG, Australia had a higher ratio of Denisovans than East Asia... or America (why must we always assume that the introgression took place once in one place?). Because admixture could have taken place in several locations: America, Asia and Austronesia.

Who are these Denisovans? The most likely candidate is an ancestor that lived in Asia and had left Africa before Humans and before Neandertals... that spells Homo erectus. They did live in Sahul and China (maybe America but that is not considered by mainstream science).

The interesting thing is that Neanderthal (see the red hues in the map above) genes are very strong in America among Native Americans too, suggesting (a) Modern Humans mixed with them in Asia and brought the Neandertal genes with them into America or (b) Admixture took place in America: modern humans met and mated with Neandertals in the New World.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Very odd teeth found in China

First of all, my best wishes for 2015!.

Today I read an article that led me to a paper (Hominin teeth from the early Late Pleistocene site of Xujiayao, Northern China, by Song Xing, María Martinón-Torres, Jose María Bermúdez de Castro, Xiujie Wu1 and Wu Liu. Article first published online: 20 OCT 2014. DOI: 10.1002/ajpa.22641) which is very interesting.

The Abstract (paper is behind a paywall) is:

ABSTRACT
It is generally accepted that from the late Middle to the early Late Pleistocene (∼340–90 ka BP), Neanderthals were occupying Europe and Western Asia, whereas anatomically modern humans were present in the African continent. In contrast, the paucity of hominin fossil evidence from East Asia from this period impedes a complete evolutionary picture of the genus Homo, as well as assessment of the possible contribution of or interaction with Asian hominins in the evolution of Homo sapiens and Homo neanderthalensis. Here we present a comparative study of a hominin dental sample recovered from the Xujiayao site, in Northern China, attributed to the early Late Pleistocene (MIS 5 to 4). Our dental study reveals a mosaic of primitive and derived dental features for the Xujiayao hominins that can be summarized as follows: i) they are different from archaic and recent modern humans, ii) they present some features that are common but not exclusive to the Neanderthal lineage, and iii) they retain some primitive conformations classically found in East Asian Early and Middle Pleistocene hominins despite their young geological age. Thus, our study evinces the existence in China of a population of unclear taxonomic status with regard to other contemporary populations such as H. sapiens and H. neanderthalensis. The morphological and metric studies of the Xujiayao teeth expand the variability known for early Late Pleistocene hominin fossils and suggest the possibility that a primitive hominin lineage may have survived late into the Late Pleistocene in China.

In other words they compared some teeth from the Xujiayao site in Northern China and found that it combines modern and archaic traits, some are also found among the Neanderthals and even some older traits found among earlier Asian hominins (maybe H. erectus).

The clean cut theory of a recent Out Of Africa into a world free of more primitive relatives has changed considerably over the last few years. I am glad to see that Neanderthals are found furhter and further east from their purported European Homeland, and that Homo erectus may not have vanished into nothingness before H. sapiens evolved.

It is likely that H. erectus mixed with Neanderthals and moder Humans, as recent findings have shown, they were intelligent beings, with symbolic representations (i.e. the engreaved sea shell found recently). They had everything that is necessary to survive in Asia until modern times, and who knows, perhaps moved north and east, into America.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

The oldest sequenced Human genome

A Russian artist, Nikolay Peistov uncovered the remains of a human being (H. sapiens) in Western Siberia in 2008 while he was looking for mammoth tusks as a source of ivory for his work (he carves ivory).

The find took place along the shores of Irtysh River at Ust-Ishim. Among his hoard of ivory was a bonew which turned out to be a human tighbone 45,000 years old.

The bone's genome was sequenced by a team led by Svante Pääbo, of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and their findings are interesting:

Oldest human genome sequenced

This is the oldest human genome that has been sequenced (45,000 years old), and the team found that this person: had more Neanderthal DNA than modern Asians or Europeans have, and that this Neander genetic material was unevenly distributed, being found in longer sequences than those found in modern humans.

This "integrity" of the archaic sequences means that Neander - Human admixture had taken place quite recently. This is because each passing generation breaks up the DNA segments due to crossover and exchange of DNA between parents, so a more intact sequence means a more recent introgression.

The information is scarce because these findings have not been published yet in a scientific journal, they were only mentioned in an article in Science magazine [1].

Other human remains close by

Interestingly the "Denisovans" are not mentioned as part of this man's genome.

Denisova Cave is also located in Southern Siberia and it is a site that displays cultural sequences dating from 282.0 ± 56.0 Kya to roughly 9.8 Kya, including not only modern humans but also Neanderthals and the mysterious Denisovans. Denisovan ancestry has been found in Papuans suggesting human - Denisovan admixture, but Pääbo does not mention them in relation to the Ust-Ishim genome.

We should point out that there is evidence of Mid Paleolithic occupations within the 45 kya period, in the region surrounding Denisova: [2]

• Kara-Bom. Located about 60 km (38 mi.) south of Denisova Cave. With an earliest occupation date of 43,300 and 44,000 BP.
• Ust-Karakol 1, right beside Denisova Cave, to the south has Mousterian layesrs with dates ranging from 50,000 +- 12,000 to 35,100 BP.
• Okladnikov, about 30 km north of Denisova Cave, along the same Amui River. has dates of 43,000 to 28,500 BP.

Any of these people could have been contemporaries of the Ust-Ishim man.

Sites in Siberia mentioned in the text. Copyright © 20143 by Austin Whittall

Long before him, Hominids have inhabited these parts of Siberia for several hundreds of thousands of years [2]:

"According to Arkhipov (1999), the earliest human occupation of eastern and northeastern Siberia (for example, Berezhekovo site in the Yenisei River basin) could have occurred during the Tobolian Interglacial [...] about 380,000 - 260,000 years ago, though only a few sites may correspond to this time interval (such as Berezhekovo and Diring Yuriakh). [...]
At Berezhekovo, thermoluminescence (TL) dates of 130,000+ -10,000 years above the cultural layer, and 540,000 + -12,000 years below the cultural layer were obtained (Arkhipov 1999) [...] At Diring Yuriakh, an open air site in central Yakutia, the 370,000 - 270,000 year determinations by TL dating (Waters et al. 1999; Carlson 2001)..." [2]

Mal'ta boy

Younger than those ancient remains, and even younger than the Ust-Ishim remains are those from Mal'ta:

• The specimen (MA-1) from Mal'ta in South-Central Siberia, is a modern H. Sapiens 24,000 years old.
• American Indians share between 14 and 38% of their autosomal ancestry with him.
• Genetically, MA-1 is closer to contemporary Native Americans than to Northeast Asians.
• However he is different from Amerindians: he lacks shoveled incisors and his nuclear and mtDNA haplogroups (hg) are different from those found in America:
  
  • His Y chromosome is hg R; common in India and Western Eurasia yet much younger than the hg Q found in very high frequencies in the Americas (and a small region in Northern Central Siberia.
  • His mtDNA is hg U, which is not found in America or East and South Asia and is very frequent in Western Eurasia, India and North Africa.

Considering that 20,000 years separate Mal'ta and Ust-Ishim yet Mal'ta appears to be closer to Europeans than to East Asians, it will be interesting to find out the Y and mtDNA hg of Ust-Ishim. Will they be ancestral to Mal'ta's? Since American Natives have a higher proportion of Neanderthal genes than other groups from this region, could they be closer to the Ust-Ishim people than Eastern Asians? Did the Ust-Ishim move on, into America 45 ky ago?

We will have to be patient and wait for the final paper.

Sources

[1] Ann Gibbons, (2014), News & Analysis. Human Evolution. Oldest Homo sapiens Genome Pinpoints Neandertal Input. Science 28 March 2014: Vol. 343 no. 6178 p. 1417. DOI: 10.1126/science.343.6178.1417
[2] Anatoly P. Derevianko, Alexander V. Postnov, Eugeny P. Rybin, Yaroslav V. Kuzmin and Susan G. Keates, (2005). The Pleistocene peopling of Siberia: A review of environmental and behavioural aspectsIndo-Pacific Prehistory Association Bulletin 25, 2005 (Taipei Papers, Vol 3). pp. +57

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall ©