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Guide to Patagonia's Monsters & Mysterious beings

I have written a book on this intriguing subject which has just been published.
In this blog I will post excerpts and other interesting texts on this fascinating subject.

Austin Whittall


Friday, December 21, 2018

Atapuerca Sima de los Huesos remains were closer to the Neanderthals


Four and a half years ago I posted about a site in Spain, known as Atapuerca (What Science is all about), in it, I mentioned two studies that came to different conclusions: one stated that the human remains there resembled Neanderthals, the other that they were closer to the Denisovans than to the Neanderthals.


Today I read a paper that was published on Nov. 30, 2018 and which states that the teeth of remains from Atapuerca's Sima de los Huesos site shows that they had a close relationship to the later Neanderthal groups found in Europe.


The paywall protected abstract says:


"Enamel and dentin patterns have awakened a considerable interest in phylogenetic studies. However, almost nothing is known about the dental tissue proportions of European Pleistocene hominins, apart from Neanderthal populations. This study aims to assess the three-dimensional dental tissue proportions of permanent canines belonging to the extensive sample of hominin teeth at Sierra de Atapuerca (Spain) through the use of microtomographic techniques. Our results show that early and middle Pleistocene populations from Atapuerca exhibit large coronal and root dentine dimensions, as well as a thinly enamelled pattern, which has been traditionally considered an autapomorphic Neanderthal trait. Therefore, these results might support an early enamel thickness decrease which is already observed 800 kyr ago in Homo antecessor and maintained in later groups such as Sima de los Huesos and Neanderthal populations during the middle Pleistocene."


This is important because it shows that the Sima de los Huesos remains had a close relationship with the Homo neanderthalensis.



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

Wednesday, December 19, 2018

An ancient American origin of hepatitis B virus


Human hepatitis B viruses (HBV) are found in human populations all around the world. They can be grouped into ten genotypes named A to J (each with their own subgenotypes).


The genotypes have a distinct geographical distribution as you can see in the map below (Source):


Hepatitis B virus global distribution of genotyhpes.

A can be found in Africa, Asia, Europe and North America. B in Eastern and Southeastern Asia. C in the same region and Central Asia. D in India and western Eurasia. E a recent apparition, found exclusively in Africa (not taken to the Americas with slave trading and probably 200 years old only - read more).


F and H are exclusive to South and Central America.


And here is the unusual thing, thse F and H genotypes are distinct from all the other ones: they branch from the phylogenetic tree as a separate and earlier branch as can be seen in the following trees from different authors:


HBV phylogenetic tree.Credits

HBV, another phylogenetic tree Note location of chimps and gorillas.Credits

HBV, a phylogenetic tree. See the branch of the woolly monkeys by the American F and H genotypes.Credits

So where did HBV originate? And here is the difficult question which cannot be answered by the usual Out of Africa theory (originated in African apes and passed on to humans there, spreading out of Africa as our ancestors migrated across the globe, reaching America last).


This time the evidence does not point towards a clear African origin. It seems that the oldest and most distant branch is rooted in America.


Margaret Littlejohn, Stephen Locarnini, and Lilly Yuen describe the five theories about HBV's origin and their shortcomings:


  • New World origin (out of South America), and then reached the Old World after European discovery in 1492.
  • Cospeciation: evolved in parallel in certain primate species over the past tens of millions of years.
  • Coevolution as anatomically modern humans (AMH) migrated out of Africa. Caveat: "it does not fit with the close genetic relationships observed between primate and human HBV. Another inconsistency is that Native Americans predominantly have genotype F infections, whereas northeast-Asians, who are their closest relatives genetically, have genotypes B and C infections."
  • Cross-species transmission, between human and nonhuman primates.
  • Bat origin

The authors interestingly point out that "Given the arguments for and against each of these five theories, it is probable that HBV evolution cannot be explained by any single theory. The reality probably involves cospecies evolution within birds, rodents, and bats, followed by a series of cross-species transmission events to explain the close relationship between human and nonhuman primate HBVs observed today. Challenges for any unifying theory include the high level of genome divergence observed between HBV sequences of New World woolly monkeys and other nonhuman primates, w hich cannot be explained by the cross-species transmission theory, and also that HBV has only been detected in rodent species of the New World. If HBV coevolved with avian, rodent, and primate species, then why is it not found in all rodent and primate species? In addition, if HBV emerged out of Africa with AMH, then why are people from the New World, who are genetically most closely related to humans in the Far East, predominantly infected with HBV genotypes F and H rather than the genetically unrelated HBV genotypes B and C that are found in the Far East?"


As you can see, the American F variant and its presence in the New World woolly monkeys stand firmly against an Out of Africa origin.


Finally the paper mentions archaic hominins (Neanderthals, Denisovans and our admixing with them): "The influence of these various groups of archaic humans on the evolutionary history of HBV would be difficult to decipher. However, the possibility that human HBV may have originated, at least in part, from these archaic humans should not be discounted."


It is likely that it originated in the Americas in an Archaic (H. erectus) group and then moved into Asia and Africa (the most recent variant "E" is African after all!).


But Out of Africa is hard to beat. The author of a paper that studied HBV found in 7,000 year-old remains in Eurasia, is quoted here as follows:


"... it is still unclear how old HBV actually is. "It could be much older. It could even be coming out of Africa, which would explain why chimpanzees and gorillas fall together with the oldest HPV genomes" he adds. "That could be one explanation, but we also find it in the new world and new world monkeys and old world monkeys separated 60 million years ago, so it's very unlikely it's that old. There's lots of open question marks here."


But, he is mistaken, the gorillas and chimpanzees HBV does not align with the "oldest" groups (see second tree image further up), they lie closer to the more recent Eurasian variants..."


As usual, when an odd thing appears in the Americas which confronts the Out Of Africa theory, orthodox science finds it hard to explain them away and support the OOA theory.


Merry Christmas and Seasons Greetings to all our readers. And a Great 2019 for everyone!



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

Saturday, December 15, 2018

The "unsampled population" in America: archaic hominins?


I want to share an excellent article from "Ancient DNA Era", published on Nov. 27, 2018 by Alberto (Early human dispersals within the Americas – Moreno-Mayar et al. 2018).


In this article Alberto discusses a recent paper (Early human dispersals within the Americas, J. Victor Moreno-Mayar, Lasse Vinner, Peter de Barros Damgaard, Constanza de la Fuente et al, Science 08 Nov 2018 DOI: 10.1126/science.aav2621) which deals with "multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, and a later Mesoamerican-related expansion. These led to complex and dynamic population histories from North to South America."


Moreno-Mayar mentions:


"We sequenced 15 ancient human genomes spanning Alaska to Patagonia; six are ≥10,000 years old (up to ~18× coverage). All are most closely related to Native Americans (NA), including an Ancient Beringian individual, and two morphologically distinct "Paleoamericans." We find evidence of rapid dispersal and early diversification, including previously unknown groups, as people moved south. This resulted in multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, and a later Mesoamerican-related expansion."


Alberto focuses on the "previously unknown groups" and the "Australasian genetic signal" and he quotes the original paper:


"...further SFS-based modeling indicates that Mixe most likely carry gene flow from an unsampled outgroup […] Hereafter we refer to that outgroup as 'Unsampled population A' (UPopA), which is neither AB, NNA or SNA [Ancient Beringians, Northern Native Americans or Southern Native Americans], and which we infer split off from Native Americans ~24.7 ka, ranging from 30-22 ka (95% CI; this large range is a result of the analytical challenge of estimating divergence and admixture times in the absence of UPopA genome data).[…] Under a model with a pulse-like gene flow, we inferred a probability of ~11% gene flow from UPopA into Mixe ~8.7 ka (95% CI: 0.4-13.9 ka; the wide interval potentially reflects unmodeled continuous migration)"


Alberto then reasons as follows: (I quote him extensively below)


" When they say "unsampled", they mean unsampled. So no, we’re not talking about potentially "anyone", but quite specifically about a population that does not only seem to be an outgroup to NA, but also an outgroup to Eurasians.
If this is true, then who can be an outgroup to Eurasians? Basically there are 4 options:
– An African population (meaning a population that went Out of Africa after the main OoA event that gave birth to most Eurasians, and that somehow reached Central America some 9 kya). This one is the least likely, really.
– An early OoA population (meaning a population that went OoA before the main OoA event). We know from archaeology (and with some support from genetics) that such early events did occur but they hardly contributed to later Eurasian populations (maybe a tiny bit to some SE Asian/Australasian populations?). So this one would mean that such population made it to the Americas and survived somewhere around Central America until the second major wave arrived.
– Archaic hominins. Like Neandertals or Denisovans. A small admixture from such groups (on top of what other NA already have) would make the shared drift of Mixe with all other AMH be lower. So is it possible that some form of archaic hominin lived in America and survived until some 9 kya?
– A fourth option would be an early "generic" Eurasian population, something similar to Ust-Ishim samples from 45 kya, but not directly related to Ust-Ishim.
"


I favor option three "Archaic hominins" but Alberto believes option four is the most likely one.


Finally Alberto remarks: "Using qpGraph, this Australasian admixture is estimated to be around 3% in these samples (and modern Surui). How it got there (if it’s real, that it well could be) is unknown at this point, but it’s important to keep in mind that it was already present at least 10.4 kya, so it cannot be from any kind of Holocene migration of Australasians to South America. The possibility is that there was a small (?) population of Australasian origin at the arrival of the migrants of NE Siberian origin."


Skoglund already noticed the Australasian link in Native American DNA (See paper here and the other paper here) back in 2015.


In my book Monsters of Patagonia y point out the similarity between Australian and Patagonian native myths (read more), and conclude " Human remains discovered in Brazil show a very strong resemblance to modern South Pacific people, suggesting that America was first colonized by the generalized human (Homo sapiens) population that inhabited East Asia in the Late Pleistocene. These people arrived in America in very ancient times long before the Mongolid morphology of the forbearers of the Clovis had evolved."


We will have to wait for more evidence to learn about the unsampled population and the Australasian migrants.


Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

Wednesday, December 12, 2018

mtDNA can be inherited from both mother and father


A paper published in PNAS a few weeks ago -Nov. 26. 2018- (1), reports that mtDNA from both mother and father has been found in seventeen individuals.


This is a very important finding because until now, mtDNA in humans, was assumed to be inherited on a matrilineal basis: the mother's mtDNA was passed on to the nesxt generation.


This type of inheritance was the origin of the Out of Africa theory, by which all extant humans can trace their mtDNA to a woman living in Africa some 200,000 years ago.


And the splits between different human groups are all branches marked by different mutations of the original mtDNA lineage.


If the father's mtDNA can find its way into his offspring, this will alter the matrilineal inheritance and impact on the timescales used to estimate the origin of mankind.


This is what the paper says (abstract) -the rest is behind a paywall:


"Significance
The energy-producing organelle mitochondrion contains its own compact genome, which is separate from the nuclear genome. In nearly all mammals, this mitochondrial genome is inherited exclusively from the mother, and transmission of paternal mitochondria or mitochondrial DNA (mtDNA) has not been convincingly demonstrated in humans. In this paper, we have uncovered multiple instances of biparental inheritance of mtDNA spanning three unrelated multiple generation families, a result confirmed by independent sequencing across multiple unrelated laboratories with different methodologies. Surprisingly, this pattern of inheritance appears to be determined in an autosomal dominantlike manner. This paper profoundly alters a widespread belief about mitochondrial inheritance and potentially opens a novel field in mitochondrial medicine.
Abstract
Although there has been considerable debate about whether paternal mitochondrial DNA (mtDNA) transmission may coexist with maternal transmission of mtDNA, it is generally believed that mitochondria and mtDNA are exclusively maternally inherited in humans. Here, we identified three unrelated multigeneration families with a high level of mtDNA heteroplasmy (ranging from 24 to 76%) in a total of 17 individuals. Heteroplasmy of mtDNA was independently examined by high-depth whole mtDNA sequencing analysis in our research laboratory and in two Clinical Laboratory Improvement Amendments and College of American Pathologists-accredited laboratories using multiple approaches. A comprehensive exploration of mtDNA segregation in these families shows biparental mtDNA transmission with an autosomal dominantlike inheritance mode. Our results suggest that, although the central dogma of maternal inheritance of mtDNA remains valid, there are some exceptional cases where paternal mtDNA could be passed to the offspring. Elucidating the molecular mechanism for this unusual mode of inheritance will provide new insights into how mtDNA is passed on from parent to offspring and may even lead to the development of new avenues for the therapeutic treatment for pathogenic mtDNA transmission.
"


This had been reported back in 2002 (2) (see paper), this new study confirms the original finding.


Sources
(1) Biparental Inheritance of Mitochondrial DNA in Humans Shiyu Luo, C. Alexander Valencia, Jinglan Zhang, Ni-Chung Lee, Jesse Slone, Baoheng Gui, Xinjian Wang, Zhuo Li, Sarah Dell, Jenice Brown, Stella Maris hen, Yin-Hsiu Chien, Wuh-Liang Hwu, Pi-Chuan Fan, Lee-Jun Wong, Paldeep S. Atwal, Taosheng Huang Proceedings of the National Academy of Sciences Nov 2018, 201810946; DOI: 10.1073/pnas.1810946115

(2) Paternal inheritance of mitochondrial DNA, M Schwartz and J Vissing., N Engl J Med, Vol. 347, No. 8 pp. 576 August 22, 2002


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

Friday, November 23, 2018

Levallois tools: did this technology originate in Asia?


Earlier this year, a paper (Kumar Akhilesh et al., Early Middle Palaeolithic culture in India around 385–172 ka reframes Out of Africa models, Nature volume 554, pages 97-101, 01 February 2018) reported finding Levallois stone tools in a site called Attirampakam, in India. These tools were about 385,000 years old, which put the date of this stone knapping technology further back in time than had been previously expected.


These Indian tools are even older than the Levallois tools found in Africa, and they predate the currently accepted date of Homo sapiens expansion out of Africa.


Modern Brains


The Levallois tools represent a shift in stone knapping know-how. Until then the Acheulian (developed by Homo erectus) technique had been in use for over 1.4 million years.


It was named after the site where they were first discovered in the 1800s: Levallois-Perret, a suburb of Paris, in France.


It is distinctive of a more brainier hominid, who developed a new technique for knapping stones to obtain sharp flint tools.


But who made them? until recently it had been suggested that they were the result of archaic Homo sapiens migrating out of Africa.


But with the Indian tools dated around 385 kya and some found in Armenia (D.S. Adler et al., Early Levallois technology and the Lower to Middle Paleolithic transition in the Southern Caucasus, Science 26 Sep 2014: Vol. 345, Issue 6204, pp. 1609-1613 DOI: 10.1126/science.1256484) aged 325 kya, this explanation seems unfounded: there were no H. sapiens at that time.


Adler writes: "Our data from Nor Geghi, Armenia... are consistent with the hypothesis that this transition occurred independently within geographically dispersed, technologically precocious hominin populations with a shared technological ancestry."


Suggesting a pre-Homo sapiens origin.


The oldest remains of Homo sapiens and Levallois tools are from a site in Morocco and they are much more recent than the Armenian and Indian tools: 315,000 years old. (Read more).


We know that the Neanderthal made them in Europe, could they be the authors of these Eurasian tools?


A paper published four days ago: Yue Hu et al.Late Middle Pleistocene Levallois stone-tool technology in southwest China, https://doi.org/10.1038/s41586-018-0710-1 DO 10.1038/s41586-018-0710-1 ID Nature 19. Nov. 2018), reports finding Levallois tools in China:


"Here we present evidence of Levallois technology from the lithic assemblage of the Guanyindong Cave site in southwest China, dated to approximately 170,000-80,000 years ago. To our knowledge, this is the earliest evidence of Levallois technology in east Asia. Our findings thus challenge the existing model of the origin and spread of Levallois technologies in east Asia and its links toa Late Pleistocene dispersal of modern humans."


So once again who made them? This date is prior to any known H. sapiens presence in China. Were they Neanderthals? or perhaps Denisovans, who lived in Southern and Central Asia at that time?


Here we have a technological break-through that seems to have originated Out of Africa and not In Africa, our purported craddle of mankind. Did modern humans evolve outside of Africa?


Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

Saturday, November 3, 2018

HPV Neanderthals, Africans and the early peopling of America


Almost two years ago I posted about HPV16 and Humans, Neanderthals, Denisovans and the Out Of Africa theory, and asked an open question about some oddities in the global distribution of HPV lineages: "Why is "D" highest in the Americas if it is supposed to have originated in Africa (see further up)... slave trade by Europeans? We'd need to see Karitiana or Coya, Pima haplogroups...".

I also made a comment and aked a second question because it turned out that the American HPV was more diverse than the Old World variants... which is unusual, considering that Amerindians are always considered as the least diverse humans (the famous Beringian bottleneck!). My comment and question was:


"And the diversity again: "East Asian and Central American HPV16 isolates showed higher average number of pairwise differences compared with sub-Saharan African isolates, even after accounting for intralineage diversity.", what? something in America more diverse than in Sub-Saharan Africa... why?"


A paper published two days ago (Nov. 1, 2018) has revisited HPV and provided answers and more data on these issues. (Chen Z, DeSalle R, Schiffman M, Herrero R, Wood CE, Ruiz JC, et al. (2018) Niche adaptation and viral transmission of human papillomaviruses from archaic hominins to modern humans. PLoS Pathog 14(11): e1007352. https://doi.org/10.1371/journal.ppat.1007352).


The paper suggests that HPV originated in Africa and that some 618,000 years ago (roughly at the time that Neanderthals and our Homo sapiens ancestors were splitting apart) an ancient HPV variant "A" split from the variant that would become lineages "B", "C" and "D".

Neanderthals left Africa with HPV A, which over the next few hundreds of thousands of years evolved into sublineages A1, A2, A3 and A4, all found in Eurasia, and in America, but very very rare in Africa.

Modern H. sapiens then left Africa 120-60 Kya and had sex with Neanderthals, picking up the HPV virus in its A variant sublineages. The African "B" and "C" variants are preponderant in that continent, with very small proprotion in Eurasia (5.6% among Caucasians and 1.8% among Asians) and America (2.3%). And the American "D" variant, according to this paper, originated in Africa, passed through Eurasia where it is found in extremely small amounts among Caucasians (11%) and Asians (6.3%). It entered America where it represents 48.3% of the HPV lineages.


Surprisingly the A4 variant that is 29.9% prevalent in Asia and 0.4% among Eurasian Caucasians, does not appear among Americans.


The authors sampled 212 complete genomes and built a phylogenetic tree of the different HPV16 variants based on this data. This tree shows two separate clades which coincides with previous findings, which had identified an Eurasian and an African lineage. They identified four lineages and named them A, B, C and D. These in turn were subdivided into four sublineages (A1 to 4, B 1 to 4, etc.). The breakdown of lineages is the following, where the percentages indicate their proportion in each population:

  • A1 to A3: Eurasia (83% among Caucasians, 62% among Asians)and America (49.5%), only 2.4% prevalence in Africa.
  • A4: As mentioned above prevalent in Asia (29.9%) and very little of it found elsewhere (0.4% among Caucasians) and nill in America and Africa.
  • B: African (54.2%), 4% in European Caucasians, 0.2% in Asians and 0.5% among South and Central Americans.
  • C: African (36.1%), 1.6% among European Caucasians and 1.6% among Asians. 1.7% in South and Central Americans
  • D: America (48.3%), 7.2% in Africa, 11% in Europe, 6.3% in Asia.

Distribution of HPV16 lineages. From Schiffman M, Herrero R, Wood CE, Ruiz JC, et al.

The paper reports that there was more diversity in the African variants with an intragroup mean difference of 0.77% ± 0.04% compared to the Eurasian variants (0.32% ± 0.02%).

However the maximum divergence between sublineages was between the Eurasian A1 and the American D3 (2.23%) as can be seen in the Heatmap of pairwise diversity, which shows all of the 212 sequenced HPV16 genomes the maximum 2.23 difference is shown in red, and the minimum diferences are shown in blue. Amerindian D is therefore the most diverse.


So, summing up BCD and A split 618 thousand years ago, "indicative of an ancient divergence of HPV16 variants prior to the emergence of modern human ancestors".

The authors state: "The estimated divergence times between HPV16 A and BCD variants largely predated that of the out-of-Africa migration of modern human populations, consistent with a previously reported archaic hominin-host-switch scenario [19, 20]. One interpretation of the data implies that the present-day Eurasian HPV16 A variants were probably the products of multiple interactions between Neanderthals/Denisovans and modern Homo sapiens established during sexual contact after a long period of separation (e.g., 400–600 kya)"


The odd situation of the "D" variant (so diverse yet almost unique to America) is explained as follows (bold face is mine):


"Following a relatively recent out-of-Africa migration, the modern humans acquired the A variant from sex with archaic hominins and possibly carried D variants into Eurasia under conditions of a small population size. The ancestors of East Asian people crossed the Bering Strait and were early populators of the Americas (based on historical records and genetic relatedness). Surprisingly, the D lineage is phylogenetically rooted in the African clade, but we did not find a major reservoir of the D lineage in the present-day African populations. This interesting observation suggests either an advantage of niche ` colonization and expansion of HPV16 D variants in Native Americans or a bottleneck of HPV16 variants present in people populating the Americans. Alternatively, the lack of A4 and the high proportion of D lineages in the Americans could be the result of an early colonization of the Americas by an unknown group from Africa. More data is needed to sort out the evolutionary history of the HPV16 D lineage and might provide clues to new features of the populating of the Americas."


The idea of an "unknown group from Africa" colonizing America at an early date is very interesting. And the authors realize that this D lineage is special because in their closing comments they add: "Lastly, we provide new interpretations and questions on the HPV16 D lineage that is part of the African clade, but is highly prevalent in South/Central America.".



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

Friday, August 3, 2018

Windows of Opportunity for the early peopling of America over the last 800 Ky


Windows for the crossing of the Beringia landbridge into America from Asia have existed many times before the latest one (at the end of the last Ice Age) during which supposedly modern humans finally entered America around 16,000 years ago.


Animals have crossed to and fro between Asia and America (horses, black bears, caribou and camels went west into Asia while bison, mammoths, moose and elk moved east into America) during the last 8 million years. So why couldn't our more distant human relatives (H. habilis, H. erectus, Neanderthal or Denisovan) do the same thing?


The following chart from History of Earth's Climate 5. - Cenozoic II - Pleistocene at www.dandebat.dk, shows how the sea level rose and dropped over tha last 800,000 years. As you can see, during the interglacial periods -like the current one- ice melted and the sea levels rose (zero meter is the present sea level), but when the ice caps grew during the ice ages and glaciers advanced, water was moved from sea to continental ice sheets and therefore sea level dropped by over 120 meters or approx. 360 feet. More than enough to dry out Beringia and allow the land bridge to link America and Asia.


The red arrows show the dates these bridges formed: 140, 340, 630 and 720 thousand years ago. And the blue arrow shows the most recent event, the that is the "accepted" date for the entry of humans into America.


Actually the arrows point at the "lowest" sea levels but to cross Beringia only a drop of 60 meters is needed so there were plenty more "windows" and these lasted for quite a long time (see this map for an undersea level contour of Beringia).


sea level chart ice ages

Sea Level variations over the last 800 ky

The fact is that humans existed 140 kya, and perhaps even 340 kya. Neanderthals lived between 630 and 140 kya. Densiovans are a mystery but we may assume the same dates as those of the Neanderthals. Homo erectus on any date earlier than 340 kya.


So we should consider these dates as "windows of opportunity" for the first humans to reach America.



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

Short Stature evolved twice on Flores Island


A Report (Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia by Serena Tucci et al. Science 03 Aug 2018, Vol. 361, Issue 6401, pp. 511-516.DOI: 10.1126/science.aar8486) tells us that the pygmy-sized Hobbits of Flores island evolved their own short stature independently from the small-sized Homo sapiens that live nowadays in Flores (pygmies).


The background is (quote from the magazine):


"The genetics of human short stature
Flores Island in Indonesia has a long history of hominin occupation, including by the extinct Homo floresiensis and a more recent settlement by modern humans. Furthermore, Flores has an extant population of pygmy humans, and H. floresiensis exhibited a diminutive adult size relative to other hominins. Tucci et al. examined genetic variation among 32 individuals, including 10 sequenced genomes, from a population of pygmies living close to the cave where H. floresiensis remains were discovered. These individuals exhibit signatures of polygenic selection explaining the short stature and have genomic content from both Neanderthals and Denisovans, but no additional archaic lineages. Thus, restricted height is under selection at this location and has evolved independently at least twice in hominins.
"


Twice because it evolved once in Pygmies in Flores and again (or rather before) in the H. floresiensis.


The Abstract tells us the following:


"Flores Island, Indonesia, was inhabited by the small-bodied hominin species Homo floresiensis, which has an unknown evolutionary relationship to modern humans. This island is also home to an extant human pygmy population. Here we describe genome-scale single-nucleotide polymorphism data and whole-genome sequences from a contemporary human pygmy population living on Flores near the cave where H. floresiensis was found. The genomes of Flores pygmies reveal a complex history of admixture with Denisovans and Neanderthals but no evidence for gene flow with other archaic hominins. Modern individuals bear the signatures of recent positive selection encompassing the FADS (fatty acid desaturase) gene cluster, likely related to diet, and polygenic selection acting on standing variation that contributed to their short-stature phenotype. Thus, multiple independent instances of hominin insular dwarfism occurred on Flores."


So the pygmy population that is now living on the island has Denisovan and Neanderthal admixture -but no additional archaic lineages. The latter is interesting. Maybe this has been concluded as the only genetic components are that of Denisovans, H. sapiens and Neanderthals.


But, as a BBC News article points out today: "Unfortunately, the wet and tropical conditions on Flores mean that all efforts to isolate hobbit DNA have so far failed. Dr Serena Tucci told the BBC: "Like many other scientists, it is my dream to find ancient DNA from the Hobbit. No DNA was recovered in the original Hobbit fossils, but DNA methods have improved markedly in the last few years.".


So no genetic comparison was made between both short statured groups.



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

Wednesday, August 1, 2018

45 KY old African teeth from Magubike with Neanderthal and H. erectus traits...


This paper Middle Stone Age human teeth from Magubike rockshelter, Iringa Region, Tanzania, by Pamela R. Willoughby, Tim Compton, Silvia M. Bello, Pastory M. Bushozi, Anne R. Skinner and Chris B. Stringer. Published: July 31, 2018https://doi.org/10.1371/journal.pone.0200530, discusses human teeth found in Africa:


They are significant because they come from Tanzania (the Magubike rockshelter) and are apparently fom Middle Stone Age (MSA) deposits dated and a "conservative estimate of their minimum age is 45,000 years" according to the paper.


As we all know, finding human remains in this part of Africa, especially those from the Middle Stone Age (which took place between 320,000 and 30,000 years ago) is a very rare event.


The authors try to find similarities between these ancient teeth and the San people (the San are always mentioned because they are assumed to be a "relict" of the original Homo sapiens that left Africa, the "oldest" extant humans, the "most diversified" members of our species.


And they say so, albeit cautiously, in this paper: "... a number of characteristics in the Magubike teeth suggest possible San affinities.".


But as we go into the details, it seems that these teeth are indeed quite unique, and, in my opinion, not at all like those of the San people:


Quoting the authors: (bold is mine)


"In summary, the Magubike teeth have the characteristics typical of African sub-Saharan Homo sapiens Holocene teeth, but aspects of the morphology of the upper canine and third premolar are atypical for the African mid/late Pleistocene sample. However, this may be at least partly due to its North African bias. Certain traits present ― e.g. the root shape of the lateral incisor and canine, and the presence of a cingulum pit on the lateral incisor ― are rare or absent in the comparative samples. Traits specific to Homo heidelbergensis / archaic Homo sapiens and Aterian teeth are not present. Despite their large size, there is some suggestion of San affinities, though this interpretation must be very tentative, being based on a single individual."


The interesting part is the similarity with Neanderthal and Homo erectus features: (again bold is mine)


"... The pronounced buccal vertical curvature of the canine root found at Magubike is seen in early teeth, Homo erectus and Neanderthal [22, 47], but not in samples of early modern Homo sapiens (Skhūl and Qafzeh) or European Upper Palaeolithic Homo sapiens[48].
In recent teeth, the buccal surface is usually straight or has a mild curvature [49]. The few canine roots that could be observed in the Kenyan early Holocene sample, and the two in the Gwisho sample, are straight, and in the mid/late Pleistocene sample only the Broken Hill canine has similar curvature to that of the Magubike canine.
"


In other words it is not found among early modern Homo sapiens, only in Neanderthals and H. erectus. The authors continue, finding some examples of curvature in recent African samples (7% of them - a low figure) which may have come from out of African migrants in more recent times...:


"However, four instances were found in the recent sub-Saharan East/South African sample (7%). Similarly, the incomplete root of the Magubike lateral incisor has pronounced buccal vertical curvature in contrast to the more evenly tapered form of recent teeth [50]. A lateral incisor of this form occurs at the Klasies River Main site [51] and in one of four in the Gwisho sample, but in just one out of seventy-five in the recent East/South African sample."


As we see in the preceden paragraph, there are yet more morphological traits that are not at all related to modern African samples.


And the authors admit the teeth's unusual uniqueness very clearly:


"The six Magubike teeth are differentiated from African archaic Homo sapiens / Homo heidelbergensis and Aterian teeth in terms of size and the lack of morphological traits that could be associated with these groups. They are also differentiated from the Kenyan early Holocene and Gwisho samples and more recent teeth in terms of the relative size of the incisors, the incisor crown heights, the relative crown heights of the two premolars, and the long premolar roots. However, the morphological evidence is contradictory, principally in relation to the canine having traits that are rare or absent in the African mid/late Pleistocene sample, though this may be partly due to the small size of this sample and its North African bias."


They attribute this to the small sample size and its "North African bias"


But why try to find them similar to San teeth? Well, orthodoxy requires it: oldest African remains of a Homo sapiens and "oldest" extant humans (SAN) "must" be related:


"Small bodied individuals recovered from East African LSA sites have often been described as having “Khoisanoid affinities”, implying an assumed connection with the small bodied people of South Africa, including the San [75]. There are also still people in northern Tanzania today whose languages are often related to Khoisan (the Hadzabe and Sandawe), implying some possible past connections with southern African peoples [78]."


But what if... the teeth resemble Homo erectus and Neanderthal teeth because these migrated INTO AFRICA? As we can see they don't resemble the African teeth of that time or those of early Modern Homo Sapiens...



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

Wednesday, July 18, 2018

More on the Fuegian "dog" (actually a fox)


Following a recent paper that more or less says that American dogs were wiped out when Europeans arrived post-1492 AD, I came across this paper on the Fuegian Dog, which ratifies what I posted (Fuegian Dog: that they were domesticated foxes!)


This paper Molecular identification of a Fuegian dog belonging to the Fagnano Regional Museum ethnographic collection Tierra del Fuego by Romina S.Petrigh, Martín H.Fugassa, https://doi.org/10.1016/j.quaint.2013.07.030, Quaternary International, Volume 317, 13 December 2013, Pages 14-18, tells us the following:


"Abstract
Native-European contact in Tierra del Fuego was a rapid process, for which little ethnographic information has been produced. Although the Fuegian dog seemed to have been important to Selk'nam people's life, the taxonomic status of this extinct animal is still uncertain. The aim of the present work was to determine the zoological identity of a taxidermized canid belonging to a Fagnano Regional Museum collection, Río Grande, Tierra del Fuego. For this purpose, DNA from Fuegian dog and patagonian wild canids (Lycalopex culpaeus, Lycalopex griseus and Lycalopex gymnocercus) hairs was extracted. An mtDNA Region Control fragment was amplified by PCR and sequenced. Sequence alignment was performed among the sequences that were obtained in this research and the Canis lupus familiaris sequence from GenBank. Pairwise analysis showed a higher identity between the Fuegian dog and the culpeo fox (97.57%), with greater divergence with the current domestic dog (88.93%). These results were supported by the molecular phylogenetic analysis, suggesting atypical fox domestication by hunter-gatherers.
"


Above is the tree from the cited paper


This is another reference on Fuegian dogs (The Natural History of Dogs: Canidae Or Genus Canis of Authors ; Including Also the Genera Hyaena and Proteles, Volume 2) from 1840, by Charles Hamilton Smith.



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

Wednesday, July 11, 2018

Hominins in China 2.1 Million years ago... pushing back the dates in Asia


The paper Hominin occupation of the Chinese Loess Plateau since about 2.1 million years ago by Zhaoyu Zhu et al, published today in Nature, is very interesting as it pushes back the date of an early hominin migration into Asia well beyond the Dmanisi hominins found in Georgia:


The abstract states:


"Considerable attention has been paid to dating the earliest appearance of hominins outside Africa. The earliest skeletal and artefactual evidence for the genus Homo in Asia currently comes from Dmanisi, Georgia, and is dated to approximately 1.77–1.85 million years ago (Ma). Two incisors that may belong to Homo erectus come from Yuanmou, south China, and are dated to 1.7 Ma; the next-oldest evidence is an H. erectus cranium from Lantian (Gongwangling)—which has recently been dated to 1.63 Ma—and the earliest hominin fossils from the Sangiran dome in Java, which are dated to about 1.5–1.6 Ma. Artefacts from Majuangou III5 and Shangshazui6 in the Nihewan basin, north China, have also been dated to 1.6–1.7 Ma. Here we report an Early Pleistocene and largely continuous artefact sequence from Shangchen, which is a newly discovered Palaeolithic locality of the southern Chinese Loess Plateau, near Gongwangling in Lantian county. The site contains 17 artefact layers that extend from palaeosol S15—dated to approximately 1.26 Ma—to loess L28, which we date to about 2.12 Ma. This discovery implies that hominins left Africa earlier than indicated by the evidence from Dmanisi."


And this is in China, surely the hominins who made those tools reached western Eurasia far earlier than the 2.12 My age assigned to those tools. Which may imply that they were not Homo erectus, maybe Homo habilis or even an australopithecine species! (maybe the ancestors of the primitive Flores island "Hobbit").


Maybe there are older tools at the site. The ones found are cobbles similar to those found in Africa with a similar age.


Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

Monday, May 21, 2018

First Asians were not Homo erectus revisited


Back in 2011 I posted The first Asians were not Homo erectus, and proposed some migration routes including one (shown in green in the map included in the post) leading to Flores Island, home of the Hobbit.


Today after reading the article on the 709,000 year-old evidence of hominins in the Philippines (see my previous post), I checked some recent papers on the Flores Island "pigmy" hominin, and found a paper suggesting that they descended from Homo habilis: The affinities of Homo floresiensis based on phylogenetic analyses of cranial, dental, and postcranial characters by Debbie Arguea, Colin P.Groves, Michael S.Y.Lee, William L.Jungersde. Journal of Human Evolution Volume 107, June 2017, Pages 107-133 Journal of Human Evolution. https://doi.org/10.1016/j.jhevol.2017.02.006. Below I quote from the abstract (paper behind a pay wall): note, I highlighted the bold text.


"Although the diminutive Homo floresiensis has been known for a decade, its phylogenetic status remains highly contentious. A broad range of potential explanations for the evolution of this species has been explored. One view is that H. floresiensis is derived from Asian Homo erectus that arrived on Flores and subsequently evolved a smaller body size, perhaps to survive the constrained resources they faced in a new island environment. Fossil remains of H. erectus, well known from Java, have not yet been discovered on Flores. The second hypothesis is that H. floresiensis is directly descended from an early Homo lineage with roots in Africa, such as Homo habilis; the third is that it is Homo sapiens with pathology. We use parsimony and Bayesian phylogenetic methods to test these hypotheses. Our phylogenetic data build upon those characters previously presented in support of these hypotheses by broadening the range of traits to include the crania, mandibles, dentition, and postcrania of Homo and Australopithecus. The new data and analyses support the hypothesis that H. floresiensis is an early Homo lineage: H. floresiensis is sister either to H. habilis alone or to a clade consisting of at least H. habilis, H. erectus, Homo ergaster, and H. sapiens. A close phylogenetic relationship between H. floresiensis and H. erectus or H. sapiens can be rejected; furthermore, most of the traits separating H. floresiensis from H. sapiens are not readily attributable to pathology (e.g., Down syndrome). The results suggest H. floresiensis is a long-surviving relict of an early (>1.75 Ma) hominin lineage and a hitherto unknown migration out of Africa, and not a recent derivative of either H. erectus or H. sapiens."


So, the Flores hominin was not afflicted with Down syndrome, instead it was a relict of an ancient (1,750,000 year old) migration out of Africa, which as you can see above is most likely Homo habilis.


Could these "primitive" relatives have moved across the sea into the Philippines... or across Asia and into America, long before Homo erectus appeared on the face of Earth?.


Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

Hominins in the Philippines 709,000 years ago: watercraft?


This paper published in Nature a few weeks ago: Earliest known hominin activity in the Philippines by 709 thousand years ago, by T. Ingicco et al. (Nature volume 557, pages 233–237 (2018) doi:10.1038/s41586-018-0072-8) is amazing: the authors find stone tools and the remains of butchered megafauna several hundreds of thousands of years older than expected. These hominins were not Homo sapiens, and the Philippines was separated from the rest of Sundaland by open sea. So how did they get there? Did they use boats?


The paper says the folowing:


  • The remains are between 631 and 777 Ky old. So this is +600 ky older than the alleged Out of Africa event of modern humans.
  • They found dozens of stone tools, rather primitive, lacking retouching.
  • They also found rhinoceros bones with cut marks and percussion marks (to break the bones), a clear indication of hominin activities.

The authors write: "Our excavations at Kalinga and the numeric dating results clearly provide securely dated evidence for human colonization of the Philippines by the early Middle Pleistocene epoch, and long before the appearance of modern humans in both the local context and wider Island South East Asia region. Although the identity of these archaic toolmakers remains unknown, it is likely that they dispersed over at least one sea barrier to reach Luzon Island. The most likely points of origin are Borneo through Palawan to the west, or China through Taiwan to the north, this latter island was connected to mainland Asia during periods with low sea levels..."


Then they wonder if these hominins are related to more recent remains found at Callao Cave, those of a small adult human:


"...a question clearly linked to our discovery is the origin of the Callao Cave hominin that has been dated to 66.7 ± 1 ka. This diminutive Callao hominin may represent a direct descendent from a Pleistocene migration stock related to these early Kalinga toolmakers—similar to what happened on Flores Island—or may be derived from a more recent migration wave of anatomically modern humans..."


The Callao Cave hominin was reported (New evidence for a 67,000-year-old human presence at Callao Cave, Luzon, Philippines,Armand Salvador Mijares et al. Journal of Human Evolution Volume 59, Issue 1, July 2010, Pages 123-132 https://doi.org/10.1016/j.jhevol.2010.04.008) after the discovery of a metatarsal bone (foot bone) of a diminutive hominin, which may have been or not a modern human:


"[The] metatarsal definitely belongs to the genus Homo. Morphometric analysis of the Callao metatarsal indicates that it has a gracile structure, close to that observed in other small-bodied Homo sapiens. Interestingly, the Callao metatarsal also falls within the morphological and size ranges of Homo habilis and H. floresiensis. Identifying whether the metatarsal represents the earliest record of H. sapiens so far recorded anywhere east of Wallace’s Line".


So it may have been a Homo habilis or even a Flores hominin! or, as the authors of the most recent find suggest, a migration of Homo erectus (see below) that became tinier due to insular dwarfism, see what Ingicco et al say about the rhino slayers:


"Despite the current evidence, it still seems too farfetched to suggest that H. erectus, or another unknown Pleistocene ancestral candidate for the Kalinga toolmakers (for example, Denisovans), were able to construct some sort of simple watercraft and deliberately cross sea barriers to reach these islands. However, considering evidence of overseas dispersal during the Middle Pleistocene stage is increasing in number, such a hypothesis cannot currently be rejected."


For me the important thing is precisely that: they crossed open sea to reach the Philippines. This means they dominated the art of building and sailing watercraft long before humans appeared, at the time that Neanderthals were splitting from the ancestors of H. sapiens (if the Out of Africa theory is correct). But do note how hesitant the authors are, to admit this (they write "too farfetched" instead of admitting that they did build a boat...)



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

Wednesday, May 16, 2018

Sub Saharan Africans admixed with archaic hominins and that gave them more diverse genes


And yes, another post on archaic hominin introgression into modern humans in Africa: Yorubans have admixed with an unknown hominin and this gave them archaic genes. So much for the "diversity" of Sub Saharan Africans as proof of them being ancestral to the rest of human beings.


This paper: Recovering signals of ghost archaic admixture in the genomes of present-day Africans, by Arun Durvasula and Sriram Sankararaman - doi: https://doi.org/10.1101/285734 - says that:


"Yoruban individuals trace about 7.9% of their genomes to an as yet unidentified archaic population."


An eight percent of their genes are archaic far more than the Neanderthal admixture in Eurasians or the Denisovan introgression into non-Africans... This is really a "Big" introgression and that explains why they, the Africans are so different and "diverse" from non-Africans. They mixed with diverse ancient genes of some unknown hominin. So they aren't older than us, they simply "admixed" with archaic hominins.


The authors add:


"suggesting that there was a rich diversity of hominin species within Africa and that introgression was commonplace. Using our inferred segments of archaic ancestry in the Yoruba, we find that there are regions of the genome that are under higher selective constraint have reduced archaic ancestry on average indicating that the archaic alleles were deleterious in the hybrid population. More data is needed for a complete picture of these ghost populations. For example, it is unclear whether the archaic signatures found here are from the same as those found in other African populations"
....
"...Taken together, these results suggest that introgression from one or more deeply diverged populations 278 has shaped the genomes of a modern human population in Africa."


And no, these ancient genes didn't come from mixing with Pygmies. The authors found evidence "...suggesting that the Biaka are not the source of admixture"



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

Archaic hominins admixed with Pygmies in Africa


Continuing with the theme of "archaic hominins admixed with modern humans in Africa leading to their current genetic diversity", I read this paper: Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies, by PingHsun Hsieh, August E. Woerner, Jeffrey D. Wall, Joseph Lachance, Sarah A. Tishkoff, Ryan N. Gutenkunst and Michael F. Hammer. February 17, 2016, doi: 10.1101/gr.196634.115 Genome Res. 2016. 26: 291-300.


Spoiler alert: the Pygmies, often touted as being diverse, isolated from the rest of H. sapiens, according to this paper, are part of the "...complex human evolutionary history in Africa, which involves at least a single admixture event from an unknown archaic population into the ancestors of AMH, likely within the last 30,000 yr.".


An admixture 30 Kya, after the alleged Out of Africa event means that some archaic group with very diverged genes mixed with modern Humans in Africa and gave them "old" and "diverse" genes, which would, in my opinion, make them seem "more diverse" than the rest of non-African Homo sapiens.


Below I quote from this paper:


" Plagnol and Wall (2006) and Wall et al. (2009) inferred a 5% genetic contribution from a now-extinct taxon to the Niger-Kordofanian Yoruba farmers or their ancestors. Hammer et al. (2011) analyzed DNA sequence data from 61 noncoding loci in three contemporary sub-Saharan African populations. They found that hunter-gatherer African populations, including the Biaka Pygmy, Mbuti Pygmy, and San, contain ∼2% genetic material likely introgressed ∼35 kya from an archaic population that split from the ancestors of modern humans ∼700 kya." (This last citation, Hammer et al, is what I mentioned in my previous post).


"...our inferences suggest recurrent archaic admixture in AMH evolution in Africa, with evidence that at least one such event occurred as recently as ∼9000 yr ago."


"...our results imply that frequent but low-level interbreeding between archaic and modern humans or their ancestors might have occurred in the past in Africa."


Of course the dates are uncertain: "... we found evidence of at least one African archaic admixture event within the last ∼150,000 yr. From our simulation study, this inferred admixture date of ∼9000 (95% C.I.: 1305–28,275) yr ago should be treated as a lower bound".


"However, it is important to point out that archaic introgression need not have been directly into the ancestors of modern Pygmies; rather, it may have resulted from recent gene flow from one or more modern human populations that themselves were recently admixed or that shared recent common ancestry with some unknown archaic hominin(s). The date of the inferred admixture is coincident with the development of agriculture in Africa ∼5–10 kya (Phillipson 2005) and the estimated time of agriculture expansion for Niger-Kodorfanian-speaking farmers ∼7 kya (95% C.I.: 5.7–9.6 kya) (Li et al. 2014). African Pygmies have undergone extensive gene flow with neighboring farmers (Patin et al. 2009; Tishkoff et al. 2009; Jarvis et al. 2012; Hsieh et al. 2016), and recent studies suggest that some Western African populations, including the Niger-Kodorfanian Yoruba farmers from Nigeria, show strong signals of ancient admixture (Plagnol and Wall 2006; Wall et al. 2009). Thus, it is plausible that archaic lineages associated with this inferred admixture event introgressed recently into one or more non-Pygmy African populations, such as the ancestors of African farmers, and subsequently entered the Pygmy population through recent gene flow from these non-Pygmy neighboring groups."


So much for the ancient roots of Pygmies and their archaic Y chromosome and mtDNA... could these have been an introgression from these "ghost" archaic hominins?


Interested in archaic introgression within Africa? Check this post: Archaic MUC7 Haplotype introgression in Africa.



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

More on archaic introgression into H. sapiens in Africa: the source of African's genetic diversity


In a recent post titled African diversity is the result of admixture with archaic hominids I once again supported the notion that African genetic "diversity" is probably due to admixture between modern humans and archaic hominids in Africa and not the result of Homo sapiens having originated in Africa long ago, and all the rest of non-Africans having less "diversity" due to founder effects & bottle-necks.


Today I came across this paper: Genetic evidence for archaic admixture in Africa by Michael F. Hammer, August E. Woerner, Fernando L. Mendez, Joseph C. Watkins, and Jeffrey D. Wall. PNAS September 6, 2011. 201109300; published ahead of print September 6, 2011. https://doi.org/10.1073/pnas.1109300108.


The paper puts forth proof of an archaic hominin admixing with Homo sapiens during a "recent interbreeding event". The abstract says (I highlighted relevant parts in bold font):


"A long-debated question concerns the fate of archaic forms of the genus Homo: did they go extinct without interbreeding with anatomically modern humans, or are their genes present in contemporary populations? This question is typically focused on the genetic contribution of archaic forms outside of Africa. Here we use DNA sequence data gathered from 61 noncoding autosomal regions in a sample of three sub-Saharan African populations (Mandenka, Biaka, and San) to test models of African archaic admixture. We use two complementary approximate-likelihood approaches and a model of human evolution that involves recent population structure, with and without gene flow from an archaic population. Extensive simulation results reject the null model of no admixture and allow us to infer that contemporary African populations contain a small proportion of genetic material (≈2%) that introgressed ≈35 kya from an archaic population that split from the ancestors of anatomically modern humans ≈700 kya. Three candidate regions showing deep haplotype divergence, unusual patterns of linkage disequilibrium, and small basal clade size are identified and the distributions of introgressive haplotypes surveyed in a sample of populations from across sub-Saharan Africa. One candidate locus with an unusual segment of DNA that extends for >31 kb on chromosome 4 seems to have introgressed into modern Africans from a now-extinct taxon that may have lived in central Africa. Taken together our results suggest that polymorphisms present in extant populations introgressed via relatively recent interbreeding with hominin forms that diverged from the ancestors of modern humans in the Lower-Middle Pleistocene.


The authors add "... central Africa may have been the homeland of a now extinct archaic form that hybridized with modern humans".


This is an extremely interesting step in the right direction!



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

Friday, May 11, 2018

On the genes that regulate teeth, archaic hominins and Africans


A paragraph in this paper: Neanderthal and Denisova tooth protein variants in present-day humans) by Clément Zanolli , Mathilde Hourset, Rémi Esclassan, Catherine Mollereau (Published: September 13, 2017https://doi.org/10.1371/journal.pone.0183802) caught my eye. It pointed out an anomaly: Africans sharing a trait with Neanderthals and Denisovans!


This is what it says:


"The finding in living Africans of rare derived polymorphisms that were present in Neanderthals (Fig 2: ENAM G389S, 5%) or Denisova (Fig 3: CEMP1 R80H, 0.5%) is difficult to reconcile with the fact that interbreeding of AMH with Neanderthals occurred out of Africa [75, 76]. However, as mentioned above, this could be explained by the inside Africa admixture between the ancestors of AMH and archaic hominins, or by the possible back migration of Neanderthal gene flux. Further genome analysis of the Neanderthal and Denisova polymorphisms in AMBN, ENAM, and CEMP1 certainly deserves attention as they could trace back an African ancestor common to Neanderthals, Denisova and early anatomically modern humans."


Well, it is not "difficult to reconcile" if the fact is wrong and AMH interbred with Neanderthals inside Africa...


The ENAM G389S variant is found not only in Africa at 5% but also at very low frequencies in the Americas 0.3% (maybe imported by African slaves or perhaps a genuine Amerindian-Neanderthal admixture). Its global prevalence is only 1.3% and is virtually absent in Asia and Europe. Denisovans carried the ancestral "G" type, found in chimps and gorillas. Neanderthals and modern humans carry the derived "S" type.


They also found a some proteins in Denisovans (K55 E variant) that appear at 26% frequency among Africans and 7% globally (the highest outside of Africa being in America at 2% and far lower elsewhere). This is the ancestral type, found in Denisovans, chimpanzees and modern humans, but it was not found in Neanderthals.


The paper also hints at an admixture in Africa between H. Sapiens and some archaic homo 35,000 years ago:


"Most of the amino acid changes are found in the dentin and enamel proteins that are encoded by genes located in two close clusters on the chromosome 4 (Fig 4) and supposed to derive from an ancestral gene encoding a secretory calcium-binding protein [68]. These clusters fall apart from known haplotypes on chromosome 4 and do not correspond to candidate Neanderthal or Denisovan gene flow regions in non-African living humans [69, 70]. However, a signal of archaic introgression in the locus 4qMB179 on chromosome 4 has been evidenced in Central African populations, and is supposed to result from admixture with an archaic Homo some 35 kya [71]."


Admixture with archaic hominins in Africa would "enrich" the diversity of African DNA and therefore contradict the prevailing theory that Africans are more diverse and therefore they are the "original" source of humanity.



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

Haplogroups of Humans and Neanderthals and Denisovans: mtDNA and Y chromosomes)


I have just read a paper that refutes my closing comments of this 2014 post: A shared Y chromosome lineage Neanderthals and Modern Humans but it does support the image I posted in it, pictured below:


Neanderthal and human Y chromosome tree
Hypothetical Y chromosome phylogenetic tree for humans and Neanderthal. Copyright © 2014 by Austin Whittall

I explained the image as follows: "the ancestral population of both humans and Neanderthals, split into two groups: one that would later evolve into modern humans, and another that would evolve into Neanderthals. Each would carry, in the beginning, the "original" archaic Y chromosome of the ancestral population, which, as each lineage accumulated mutations due to chance and positive selection would begin to grow in different directions, forming two distinct branches, which then in turn would continue branching as more mutations appeared."


And that is what the paper states (Reconstructing the genetic history of late Neanderthals by Mateja Hajdinjak et al., 652 NATURE VOL 555 29 march 2018, doi:10.1038/nature26151.) Figure 2 in the article is shown below, and it agrees with the Y chromosome tree that I proposed back in 2014:


Phylogenetic trees for mtDNA, autosomal DNA and Y-chromosome of humans, Neanderthals, Denisovans and Sima de los Huesos hominin. From Hajdinjak et al.

The Human haplogroups are on distinct branches, well away from those of the older hominins.



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

On human and Neanderthal - Denisovan mtDNA


There is no evidence at all of extant Neanderthal mtDNA in modern humans. This seems quite surprising, and many explanations have been offered. But the most simple and clear cut one is, in my opinion, the lack of enough samples of Neanderthal mtDNA tested to date. And this is precisely what this paper says: No Evidence of Neandertal mtDNA Contribution to Early Modern Humans, by David Serre, Andre Langaney, Mario Chech, Maria Teschler-Nicola, Maja Paunovic, Philippe Mennecier, Michael Hofreiter, Göran Possnert, Svante Pääbo (Published: March 16, 2004https://doi.org/10.1371/journal.pbio.0020057)


They clearly state the following:


"..Under the model of a constant human effective population size (Tavare 1984; Nordborg 1998) of 10,000 over time (Figure 4A), any contribution of Neandertal mtDNA to modern humans 30,000 years ago larger than 25% can be excluded at the 5% level (Figure S3). A more realistic scenario may be that the spread of modern humans was accompanied by an increase in population size before and during their migration out of Africa and subsequent colonization of western Eurasia (see Figure 4B). In that case, the Neandertal contribution that can be excluded is smaller (i.e., less gene flow could have taken place)...
It is noteworthy that under the model of constant population size, about 50 early modern human remains would need to be studied to exclude a Neandertal mtDNA contribution of 10%. To exclude a 5% contribution, one would need to study more early modern human remains than have been discovered to date. Thus, definitive knowledge of the extent of a putative contribution of Neandertals to the modern human gene pool will not be possible...
."


The authors indicate that the Neandertal fossil remains carry "closely related mtDNAs that are not found among current humans", in fact all reads are very similar to each other and, different to the standard modern human reference.


They mention the possible causes for this lack of Neanderthal mtDNA in H sapiens: "...such a contribution might have been erased by genetic drift or by the continuous influx of modern human DNA into the Neandertal gene pool. A further concern is that if some Neandertals carried mtDNA sequences similar to contemporaneous humans, such sequences may be erroneously regarded as modern contaminations when retrieved from fossils.".


Both causes seem very reasonable and the authors fin that this "... excludes any large genetic contribution by Neandertals to early modern humans, but does not rule out the possibility of a smaller contribution."


So, after all, there may have been a small introgression of Neanderthal mtDNA into us.


An intersting point to ponder is that "Although mitochondria retain their own genome, the vast majority of the >1000 proteins that function in mitochondria are encoded in the nucleus" (from The Mitonuclear Dimension of Neanderthal and Denisovan Ancestry in Modern Human Genomes. Joel Sharbrough Justin C. Havird Gregory R. Noe Jessica M. Warren Daniel B. Sloan. Genome Biology and Evolution, Volume 9, Issue 6, 1 June 2017, Pages 1567–1581, https://doi.org/10.1093/gbe/evx114).


This means that the mitochondrial genes and the nuclear genes that encode these proteins (known as N-mt genes), proteins used by the mitochondria, have to adapt to each other during episodes of introgression in order to function correctly and not cause the death of the hybrid individual.


Sharbrough et al then apply this concept to Neanderthal ⁄ Denisovan admixture with H. sapiens:


"The potential for mitonuclear interactions among hominins is of interest because, unlike in the nuclear genome, there has not been any detectable mtDNA introgression from Neanderthals or Denisovans into modern human populations (Krings et al. 1997; Serre et al. 2004). Regardless of what has caused this lack of mtDNA introgression, one consequence is that all introgressed Neanderthal and Denisovan nuclear alleles must function on a modern-human mitochondrial background..."


In other words if there is no Neanderthal or Denisovan mtDNA in humans, our modern mtDNA however must have had to adapt to the N-mt genes that did introgress from our older relatives (Neanderthals and Denisovans). And their paper looks into this.


They concluded that "... genes involved in mitochondrial function may have been subject to distinct selection pressures during the history of introgression from archaic hominins but that mitonuclear incompatibilities have had, at most, a small role in shaping genome-wide introgression patterns, perhaps because of limited functional divergence in mtDNA and interacting nuclear genes."


In other words there wasn't much incompatibility between the mtDNA and the N-mt genes after all! And this was because our and their mtDNA and nuclear genes were, or are, very similar. Which is what you'd expect anyway, we all branched off from the same tree not that long ago (say 750 Ky).


I do look forward to mtDNA sequences more complete in nature, from more individuals (archaic H. sapiens and Neanderthal & Denisovans), who knows, we may actually find one with a shared mtDNA Haplogroup...



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

Neanderthal and Denisovans split around 750 Kya


This paper: Early history of Neanderthals and Denisovans, by Alan R. Rogers, Ryan J. Bohlender, and Chad D. Huff (PNAS September 12, 2017. 114 (37) 9859-9863; published ahead of print August 7, 2017. https://doi.org/10.1073/pnas.1706426114), has some interesting insights into Neanderthal diversity and population size. Below we quote from this paper


"Discussion
These results contradict current views about Neanderthal population history. For example, Prüfer et al. estimate that the Neanderthal population was very small—declining toward extinction. This view receives additional support from research showing elevated frequencies of nonsynonymous (and presumably deleterious) mutations among Neanderthals. This abundance of deleterious alleles implies that drift was strong and thus that population size was small. Yet our estimate of Neanderthal population size is large—in the tens of thousands."


So the authors find that the neanderthal population was large!. They then try to find common ground with other authors, adding:


"To reconcile these views, we suggest that the Neanderthal population consisted of many small subpopulations, which exchanged mates only rarely. In such a population, the effective size of the global population can be large, even if each local population is small. A sample from a single subpopulation would show a misleading signal of gradual population decline, even if the true population were constant. Furthermore, there is direct evidence of large genetic differences among Neanderthal populations. Finally, the rich and widespread fossil record of Neanderthals is hard to reconcile with the view that their global population was tiny. We suggest that previous research has documented the small size of local Neanderthal populations, whereas our own findings document the large effective size of the metapopulation that contributed genes to modern humans."


All of which makes perfect sense. They then address the timing of Neanderthal-Denisovan split:


"...As discussed above, our results also disagree with previous estimates of the Neanderthal–Denisovan separation time. On the other hand, Meyer et al. show that 430 ky-old fossils from Sima de los Huesos, Spain are more closely related to Neanderthals than to Denisovans. This implies an early separation of the two archaic lineages. Our own estimate—25,660 generations, or 744 ky—is earlier still. It is consistent with the results of Meyer et al. but not with those of Prüfer et al., as discussed above. The cause of this discrepancy is unclear. Prüfer et al. use the pairwise sequentially Markovian coalescent (PSMC) method, which may give biased estimates of separation times in subdivided populations..."


So they find a rather old (almost 750,000 years ago) split between Neanderthals and Denisovans.


In their introductory comments they mentioned some competing theories


"Around 600 kya, Europe was invaded by large-brained hominins using Acheulean stone tools. They were probably African immigrants, because similar fossils and tools occur earlier in Africa. They have been called archaic Homo sapiens, Homo heidelbergensis, and early Neanderthals, yet they remain mysterious. They may have been ancestors of Neanderthals and modern humans, or ancestors of Neanderthals only, or an evolutionary dead end. According to this last hypothesis, they were replaced later in the Middle Pleistocene by a wave of African immigrants that separated Neanderthals from modern humans and introduced the Levallois stone tool tradition to Europe."


Regarding the above, the authors write:


"Our results shed light on the large-brained hominins who appear in Europe early in the Middle Pleistocene. Various authors have suggested that these were African immigrants. This story is consistent with genetic estimates of the separation time of archaics and moderns. Our own results imply that, by the time these hominins show up in European archaeological sites, they had already separated from Denisovans. This agrees with Meyer et al., who show that the hominins at Sima de los Huesos were genetically more similar to Neanderthals than to Denisovans. It also agrees with Hublin, who argues that Neanderthal features emerged gradually in Europe, over an interval that began 500–600 kya."


And, they conclude:


"It appears that Neanderthals and Denisovans separated only a few hundred generations after their ancestors left the modern lineage. During the intervening interval, the Neanderthal–Denisovan lineage was small. After separating from Denisovans, the Neanderthal population grew large and fragmented into largely isolated local groups. The Neanderthal metapopulation that contributed genes to modern humans was much larger than the local population of the Altai Neanderthal fossil."


Denisovans admixed with Africans


Among their findings is corroboration of what we already know: "...yn is more common than xn —Neanderthals share more derived alleles with Europeans than with Africans. This suggests gene flow from Neanderthals into Europeans", and then, a startling finding: "More surprisingly, xd is more common than yd. The same pattern appears in all four combinations (YRI.CEU, YRI.CHB, LWK.CEU, and LWK.CHB) of African and Eurasian populations in our analysis. This pattern suggests gene flow from Denisovans into Africans..." (bold mine). This is unexpected: Denisovan admixture into Africans! Maybe it reflects an Out of Asia episode into Africa...


The fact that the Neanderthals were a large population split into sub-groups is very interesting because it is the opposite to what has been widely proclaimed until now: that they were a small, inbred group on the verge of vanishing when they mingled with modern humans...



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

Monday, April 30, 2018

Asian backflow into Africa


Asians returned to Africa or, at least that is what this paper says: Brief communication: mtDNA variation in North Cameroon: Lack of asian lineages and implications for back migration from Asia to sub‐Saharan Africa, by Valentina Coia Giovanni Destro‐Bisol Fabio Verginelli Cinzia Battaggia Ilaria Boschi Fulvio Cruciani Gabriella Spedini David Comas Francesc Calafell, first published: 13 May 2005, https://doi.org/10.1002/ajpa.20138.


The abstract is very clear:


"The hypervariable region‐1 and four nucleotide positions (10400, 10873, 12308, and 12705) of the coding region of mitochondrial DNA (mtDNA) were analyzed in 441 individuals belonging to eight populations (Daba, Fali, Fulbe, Mandara, Uldeme, Podokwo, Tali, and Tupuri) from North Cameroon and four populations (Bakaka, Bassa, Bamileke, and Ewondo) from South Cameroon. All mtDNAs were assigned to five haplogroups: three sub‐Saharan (L1, L2, and L3), one northern African (U6), and one European (U5). Our results contrast with the observed high frequencies of a Y‐chromosome haplogroup of probable Asian origin (R1*‐M173) in North Cameroon. As a first step toward a better understanding of the evident discrepancy between mtDNA and Y‐chromosome data, we propose two contrasting scenarios. The first one, here termed “migration and asymmetric admixture,” implies a back migration from Asia to North Cameroon of a population group carrying the haplotype R1*‐M173 at high frequency, and an admixture process restricted to migrant males. The second scenario, on the other hand, temed “divergent drift,” implies that modern populations of North Cameroon originated from a small population group which migrated from Asia to Africa and in which, through genetic drift, Y‐chromosome haplotype R1*‐M173 became predominant, whereas the Asian mtDNA haplogroups were lost."


In plain English, there is an Asian Y-chromosome haplogroup in North Cameroon, in equatorial Africa and the authors can't quite fit it into the Out of Africa theory because it is a male lineage and there are no Asian mtDNA groups in the region...


Did a band of men from Asia move across Africa to Cameroon without women? leaving their Y-chromosome DNA but no mtDNA... Or did genetic drift erase the invading group's women's mtDNA?. Why would this happen?


I think that the U haplogroup mtDNA is the key here... see the map below:



The map shows mtDNA haplo U distribution. Clearly an "into Africa" move.


This surely introgressed Neandertal DNA into Africans.



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

On some misconceptions regarding mutations and "antiquity"


This website in an attempt to explain DNA diversity that allows us to identify "older" genomes from more "recent" ones, says the following:


"There are parts of your (our) genome where random mutations won’t generally kill you. Random mutations tend, therefore, to accumulate there. Since have some pretty decent estimates for how often random mutations occur, comparing the mutations in two different populations lets us estimate how long ago they split. For example, let’s suppose you get one random mutation per hundred years, and we’re comparing two populations that split 300 years ago and haven’t seen each other since. Population A should have gotten 3 mutations during that 300 years, and Population B should have gotten 3 mutations. So if we look at a third population, C, and find that they have 5 mutations that they don’t share with A or B, then we conclude that C split off from some ancestral population 500 years ago. We can reconstruct this as: 600 years ago, there was a group called ABC, but 500 years ago, it split into Group AB and Group C. 300 years ago, Group AB split into Group A and Group B."


Sounds great, so clear, so logical... but... This is a typical explanation for diversity in Africa vs. out of Africa and to put it bluntly, it is Wrong!!. And this is why:


It says there was an ancestral group, ABC which split 500 years ago into AB and C. Since the split, group C accumulated 5 mutations. And group AB split 300 years ago. Each sub group, A and B, accumulated 3 mutations each, which made them different. So as C has 5 mutations but A and B only 3 each, C is "older" than A or B. Did you see the mistake in this logical explanation?


The error is that although they postulate a random mutation every 100 years, the group AB which split from ABC 500 years ago did not accumulate any mutations from then until the split of A and B 300 years ago.


AB group did not accumulate a single mutation over 200 years, but C did, it added 2.


Then, A split from B, and both of them kept on mutating at 1 mutation every hundred years. Final score: C = 5 mutations and A & B only 3.


Actualy AB would have accumulated mutations over those 200 years, different mjtations from those of C. In fact all groups A, B and C would have accumulated 5 mutations over those 500 years.


All humans are equally ancient, we all carry the original DNA, and after we split into separate groups, our random mutations led us to split apart a bit more, but we all have roughly the same amount of mutations, unless, of course these mutations are not random, but are mobilized by selection, but that will be discussed in another post.



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 
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