Genome-wide data substantiate Holocene gene flow from India to Australia

Richard Lewontin's Disappearing Act

The octogenarian bête noir of biological determinism reviews three new books about why we should be proud of our ancestry--or just be quiet about it. "There is a certain irony," he writes, "in claiming an undemonstrated biological superiority for a group, six million of whom were slaughtered for their claimed natural degeneracy." If your dynosaur feathers are not ruffled yet, read on. 

"Is There a Jewish Gene?"

by Richard Lewontin

December 6, 2012,

The New York Review of Books


Legacy:  A Genetic History of the Jewish People
by Harry Ostrer
Oxford University Press, 264 pp. $24.95


The Genealogical Science:  The Search for Jewish Origins and the Politics of Epistemology
by Nadia Abu El-Haj
University of Chicago Press, 311 pp., $35.00



Zionism and the Biology of the Jews (Zionut Vehabiologia Shel Hayehudim
by Raphael Falk
Resling, 2006 (not yet published in English)

The question of ancestry has been of human concern in virtually all cultures and over all times of which we have any knowledge. Whether it be a story about the origin of a particular tribe or nation and its subsequent mixture with other groups, or curiosity about a family history, there is always the implication that we understand ourselves better if we know our ancestors and that we, within ourselves, reflect properties that have come to us by an unbroken line from past generations. As treasurer of the Marlboro Historical Society in Vermont, I am the recipient of requests for printed copies of the Reverend Ephraim Newton’s mid-eighteenth-century history of our town, 70 percent of whose pages consist of “Genealogical and Biographical Notes” and a “Catalog of Literary Men.” Over and over our correspondents write of the “pride” they have in descending from these early settlers.

Surely pride or shame are appropriate sentiments for actions for which we ourselves are in some way responsible. Why, then, do we feel pride (or shame) for the actions of others over whom we can have had no influence? Do we, in this way, achieve a false modesty or relieve ourselves of the burdens of our own behavior? As a descendant of late-nineteenth-century Eastern European immigrants I cannot depend on Reverend Newton’s pages to explain my frequent contributions to The New York Review, but neither have the extensive “begats” in Genesis 10 or Matthew 1 been more enlightening.  Read More...

Were Neanderthals capable of creating art? The idea seems shocking to us. After all, we learned in school that these were brutish savages without higher thinking and symbolic thought or expression. The picture of a Neanderthal making hand prints in Spanish caves or making shell necklaces is odd indeed because art is largely “considered evidence of sophisticated symbolic thinking, [and] has traditionally been attributed to modern humans, who reached Europe some 40,000 years ago” according to the recent Wired Science article, “First Painters May Have Been Neanderthal Not Human.” (Left:  Panel of Hands in the El Castillo Cave, Spain, dated to 37,300 years old, photo by Pedro Saura.)

A recent Daily News and Analysis article, “Neanderthals Learned to Make Jewelry and Tools from Modern Humans, “ says an international team from the Max Planck Institute in Germany suggests there was a “cultural exchange” between the two species and there is evidence that Neanderthals “learned how to make jewelry and sophisticated tools” from the early ancestors of humans. The reasoning behind this is based on the fact that artistic relics were found near Neanderthal remains but the artwork was “clearly” indicative of human hands. So the conjecture is that it must have been learned.

Whether this is true or not, Neanderthals were creative.  According to Kate Wong, in her recent Scientific American article, “Oldest Cave Paintings May Be Creations of Neanderthals , Not Modern Humans,” according to archeological evidence, Neanderthals  not only wore feathers but “painted their skin” and “made jewelry from teeth and shells.”

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But was their artistic expression learned? There are those that do not think so. According to Eric Wayner, in a recent Smithsonian article, “Do Feathers Reveal Neanderthal Brain Power?” Neanderthals wore feathers as personal adornments which showed them to be “capable of symbolic expression.”  And Wong says, there are Spanish and French caves thousands of years old with cave paintings long thought to be the artwork of early humans that are now thought to be the work of Neanderthals. Why? She says because of recently refined techniques of radiocarbon dating, that these paintings are “significantly older” than once thought. In fact, some may be older than the date when the first humans arrived in Europe around 41,500 years ago. When there were thought to be only Neanderthals.  “A large red disk” on one of the Spanish caves, El Castillo, is “at a minimum 40,800 years old, making it some 4,000 years older than the Chauvet paintings which were previously thought to be the oldest in the world.”  This and a “stretch of limestone wall with dozens of hands” in the same cave are both thought to possibly be the handiwork of Neanderthal painters because the “estimates” are considered to be at best a conservative “minimum.” According to Ker Than, in the recent National Geographic Daily News article, “The new dates raise the possibility that some of the paintings could have been made by Neanderthals who are thought to have lived in Europe some 30,000 or 40,000 years ago.” 

So if Neanderthals were painters where did they get their creative expression if not from humans? Wong says that both “modern humans and Neanderthals might have inherited their capacity for symbolic thinking from their common ancestor.”  And she says, if that is the case, “the roots of our symbolic culture go back half a million years.”

'Bigfoot' DNA Sequenced In Upcoming Genetics Study

PRWeb
Saturday, November 24th 2012

Five-Year Genome Study At DNA Diagnostics Yields Evidence of
Homo sapiens/Unknown Hominin Hybrid Species in North America

Dallas, TX (PRWEB) November 24, 2012

A team of scientists can verify that their 5-year long DNA study, currently under peer-review, confirms the existence of a novel hominin hybrid species, commonly called “Bigfoot” or “Sasquatch,” living in North America. Researchers’ extensive DNA sequencing suggests that the legendary Sasquatch is a human relative that arose approximately 15,000 years ago as a hybrid cross of modern Homo sapiens with an unknown primate species.

The study was conducted by a team of experts in genetics, forensics, imaging and pathology, led by Dr. Melba S. Ketchum of Nacogdoches, TX. In response to recent interest in the study, Dr. Ketchum can confirm that her team has sequenced 3 complete Sasquatch nuclear genomes and determined the species is a human hybrid: “Our study has sequenced 20 whole mitochondrial genomes and
utilized next generation sequencing to obtain 3 whole nuclear
genomes from purported Sasquatch samples . . .  Read article on PRWeb.  We note that there are also news reports that Sasquatch or Yeti sample analyses are about to be released in Russia, Australia, England and Idaho, and predict that this could be one of those breakthrough revelations in science where the news is broken simultaneously by independent sources.

Photo above:  Dr. Melba Ketchum of DNA Diagnostics. 

UPDATE FROM A CUSTOMER (11-25-12)

I have read that her FB page is now deleted. I don't know if that is correct or not, but I had it saved and copied what she said for you. She told her fans yesterday that she has to get this right to be accepted into a peer-reviewed  paper:

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Melba Ketchum's latest Facebook status regarding her DNA paper:

"For everyone that keeps asking for when the paper will be out, please understand that 1) I cannot talk about our data or it will never get published. Those are journal rules. 2) I cannot divulge which journal as that will kill our paper also so speculation is futile. 3) Peer review and publication can take 5 to 26 weeks and then there is the question of revision where they ask you to change or re-write or edit some of the paper. It is a rare paper that is accepted without some revision. I know this because I peer review for some well known scientific journals also. 4) Timing is very difficult to say the least because of #3 and once again, I am sure the journal would reject the paper if I told you exactly when I think the paper would be out. Soon is as much as I can say. I cannot afford to lose all of the exceptionally difficult work that my co-authors and I have put into this project. I am asking you to understand this! Please. 5) I also ask you to understand that I am not trying to be rude or disrespectful to anyone by my silence. I would love nothing better than to scream our results to the world. But, like everything else in the world of Sasquatch, it will NOT prove ANYTHING if the data doesn't undergo the rigors of peer review in the scientific community. It has to convince the skeptics (or at least skeptical scientists) or it is just another attempt to prove the existence of BF that cannot be substantiated even though we have overkilled the science on this project beyond all realms of reason. So, I guess the question is, do we rush and and fail, or do we play by the rules and prove something once and for all that will vindicate thousands who have had sightings. They are real and most if not all of the people on FB here are believers. Please, let's do this right so the world will know once and for all that there is a real and illusive creature that is alive and well right here in our own backyards. If I have any news I can share, I will share it here though, OK?"

I hope she does get this out. Fascinating story!








Yeti, or Abominable Snowman, seems
also close to being authenticated. 

As often happens in the annals of science, two research teams independently reached the same groundbreaking results, and publication to the scientific world occurred simultaneously. The breakthrough in the present case concerned the mutation rate of DNA and has profound implications for human evolution as well as for DNA Consultants' new offerings in autosomal DNA ancestry analysis, specifically our Rare Genes from History Panel.

The following two studies are already much cited by geneticists, though they have garnered little attention in the press. They appeared in online versions on the same day, August 23.

James X Sun et al., "A Direct Characterization of Human Mutation Based on Microsatellites," Nature Genetics 44/10 (October 2012): 1161-65.

A. Kong et al., "Rate of de novo Mutations and the importance of Father's Age to Disease Risk," Nature 488 (2012):471-75.  

 
A table summarizing their findings and older data is provided below for DNA testing customers' convenience.

 

DNA Mutation Rates

Study or Source	Type of DNA	Sample or Method	Rate per Generation	Time Depth in Years
Sun 2012	autosomal microsatellites	2,477 mutations in Icelanders	.001- .0001	25,000 to 250,000
Kong 2012	single nucleotide polymorphisms	4,933 mutations in Icelandic trios	63.2 or .000000012	Very great
Butler 2009	Core CoDIS STRs (microsatellites)	compiled from studies	.0028-.0001	9,000 to 25,000
Zhivotovsky 2004	Y chromosome STRs	Y haplogroup comparisons	.00069	36,000
Heyer 1997	Y chromosome tetranucleotides	42 males in forensic database	.002	12,500
FamilyTreeDNA 2004	Y chromosome STRs	Estimated from customer base	.004	6,250
Brinkmann 1998	STRs (CoDIS markers)	10,844 Father-son comparisons	0-.007	3,500 to Very Great
Parsons  1997	mitochondrial DNA	134 mtDNA lineages	.000029	862,000
DNA Consultants	Rare Genes from History	average estimate across loci	.001325	19,000

 
From this it can be seen that mutation rates vary from a low with SNPs to the high rate of Y chromsome STRs (as much as 0.4 % per generation). DNA keeps surprising us by proving to be more stable than we would tend to expect, dutifully transcribing its original values from generation to generation without many mistakes or changes. Only Y chromosome seems to be highly changeable, depending on the father's age (Kong 2012). Autosomal STRs mutate at a rate between SNPs and the Y chromosome, between every 19,000 or 25,000 and 250,000 years. 

For our new autosomal ancestry markers, that is confirmation that the alleles we are examining on a statistical basis are pretty much unchanged for the past 20,000 years. That's about twice the length of what we call world history, hence a meaningful enough time frame for valid inferences about population patterns and ancestry of individuals.

See also:  Rare Genes from History:  DNA Consultants’ Next-Generation Ancestry Markers

Rare Genes from History Panel Now Available for $289

Prelaunch of New Autosomal Products

Emerging Prehistory of Ethnic Groups

Technical Literature on Genotyping, including autosomal DNA and Forensic Literature

 

DEFINITION:  mutation   A change in a DNA sequence, either spontaneous within a generation or inherited, sometimes from a very distant ancestor. Mutations usually do not affect our health or cause any differences in our appearance. In other words, they are not genes proper and do not “code” for new proteins. Even though they are non-coding genes, though, they are useful in tracing lineages.             From A Glossary of Common DNA Terms

 

 

Were They Possibly Denisovan Hybrids?

The Cherokee called them the Moon People. The Utes and Paiutes spoke of a hideous race of cannibals ten feet tall living in caves. And the Choctaw also have an account of the race of giants that first colonized the Ohio Valley. 

From Old World Roots of the Cherokee, chapter 5, "America's Middle Ages," pp. 78-79, we read:

What kind of Indians lived in the territory the Choctaw and Chickasaw carved out for their new home? According to their traditions, reports Cushman, as confirmed by excavations of bones in Tennessee, it was a “race of white giants”:

[T]he tradition of the Choctaws . . . told of a race of giants that once inhabited the now State of Tennessee, and with whom their ancestors fought when they arrived in Mississippi in their migration from the west, doubtless Old Mexico. Their tradition states the Nahullo (race of giants [literally, wizards]) was of wonderful stature; but, as their tradition of the mastodon [which used to be found on the Great Plains], so this was also considered to be but a foolish fable, the creature of a wild imagination, when lo! Their exhumed bones again prove the truth of the Choctaws’ tradition (151).

These giants could have been Rafinesque’s Atlans.

Cushman then recounts the discovery in 1880 at a burial mound site near Plano, Texas, of human bones “of enormous size . . . the femoral bones being five inches longer than the ordinary length, and the jaw bones . . . so large as to slip over the face of a man with ease.” Cushman goes on to identify them with the older occupants of North America called Allegewi or Taligewi (Talegans). Many historians, moreover, speculate they were the builders of the Adena mounds.

As for the Chickasaw, Cushman notes that they have no record of their history before the colonial period, although it is assuredly "the same as the Choctaws, being one tribe and people until the division made by their two chiefs Chikasah and Chahtah many years after their arrival and location east of the Mississippi River" (p 358). Of the Natchez, Cushman records that they, "if tradition may be believed, also came from Mexico where they had lived for centuries" (p 440).

A story was told by the Comanches in 1857: 

Innumerable moons ago, a race of white men, ten feet high, and far more rich and powerful than any white people now living, here inhabited a large range of country, extending from the rising to the setting sun. Their fortifications crowned the summits of the mountains, protecting their populous cities situated in the intervening valleys. They excelled every other nation which was flourished, either before or since, in all manner of cunning handicraft—were brave and warlike—ruling over the land they had wrested from its ancient possessors with a high and haughty hand. Compared with them the palefaces of the present day were pygmies, in both art and arms. They drove the Indians from their homes, putting them to the sword, and occupying the valleys in which their fathers had dwelt before them since the world began. At length, in the height of their power and glory, when they remembered justice and mercy no more and became proud and lifted up, the Great Spirit descended from above, sweeping them with fire and deluge from the face of the earth. The mounds we [i.e. the speaker Chief Rolling Thunder and his Spanish listener] had seen on the tablelands were the remnants of their fortresses, and the crumbling ruins that surrounded us all that remained of a mighty city.[i]

The word Nahoolo or Nahullo “is now emphatically applied to the white race and no other . . . The Nahullo were of white complexion, according to Choctaw tradition, and were still an existing people at the time of the advent of the Choctaws to Mississippi,” concludes Cushman (p 153) . In agreement, the Indian trader Adair often refers to the Nani Ishtahoolo as departed white ghosts vested with spiritual powers whose descendants were priests and magicians. Their cries and magic spells could still be heard in the mounds like those at Ocmulgee.[ii] These references contribute to the suspicion that the “Indians” who preceded Asiatic tribes from Mexico were, as we would say today, Caucasian.

About exactly a year ago on this blog, we published a post about "Neanderthals in America," mentioning also the peculiar archaic skeleton that is now a roadside attraction in Arizona, called The Thing. In the meantime, we acquired a copy of Fritz Zimmerman's book, The Nephilim Chronicles, which reproduces over 300 historical accounts of Giant skeletons. Many are associated with the earliest mound sites in America, but Zimmerman's survey of this worldwide phenomenon ranges from the Hunter-Fisher People of northeast Europe and Red Paint People whose movements were circumpolar to the giants of the Bible, noted by the Babylonian Talmud as having double rows of teeth, and "Giants' Remains in the British Isles" (pp. 157-65).

Navajo legends speak of the Starnake People, a regal race of white giants endowed with mining technology who dominated the West, enslaved lesser tribes and had strongholds all through the Americas. They were either extinguished or "went back to the heavens." The name may be a corruption of the Biblical race known as Anakim (Num. 13:33, Deut. 1:28). The name Og (Hebrew "chief") appears to be characteristic (see Zimmerman, pp. 188-91). The ogham alphabet is attributed to this cultural founder. 

Certainly, many of the mound sites uncovered in the nineteenth century tell a story of constant warfare by incoming Asiatic tribes  against the giants occupying the land. One grisly scene showed thousands of skeletons, male, female and young heaped in a mass grave, with warriors' skulls pierced by arrows. It would appear that as these aboriginal inhabitants of the Ohio Valley were gradually displaced, some members of their society went over into the ranks of the new conquerors, bequeathing a strain of great stature still noticeable, for instance, in the Mobilian chief Tuscaloosa and DeSoto's Indian queen Cofitachiqui, both of whom were said to be seven feet tall.

We are struck by the following traits of this giant race or ethnic group from human prehistory:

• Mother Goddess religion
• Copper (not bronze) axes 
• Polished slate tools including fishing plummets, which were apparently regarded as sacred
• Belief that the Grandmother Moon was the repository of souls
• Diet emphasizing shellfish (for which the double row of teeth probably was selected as an evolutionary advantage in their beachcomber origin out of Africa?)
• Building of fish weirs in North American rivers to trap migrating eels
• Certain vegetarian habits (wild rice, for instance)
• Inscriptions on artifacts, especially pipes, often buried with the dead
• Use of coal and petroleum
• Weaving and looms
• Knowledge of seafaring, mathematics and engineering, including canals and irrigation
• Burying of a dog with a child to guard the latter in the afterlife
• A language apparently Afro-Asiatic and close to Semitic tongues
• Kingcraft:  nobles were buried in seated positions on thrones surrounded by a coterie of their retainers

   

 
A new Cambridge University study claims that the 1-4% Neanderthal DNA in the average European is not the result of admixture or hybridization, as widely believed when the Neanderthal sequences were discovered in human DNA, but the signature of a remote split in hominid species in early Africa. The study is headlined "Humans, Neanderthals Did Not Have Babies" in Discovery News. According to the new model, Neanderthals died out 30,000 years ago in Europe and never had the opportunity to produce hybrid progeny with anatomically modern humans (Homo sapiens sapiens). 

But the new model is just that, a model, and proves nothing, say many critics of the explanation. Statistical programs can be set up to "prove" anything. The new model just proves that it could be a scenario that might have occurred in the dim human past. Not all possible scenarios are true, and in fact, many possible scenarios are unlikely . . . and well, not possible except in a statistical sense.

Essentially, the Cambridge study uses a conclusion to prove a hypothesis. It's supposed to work the other way around. And we thought Cambridge was the home of logicians!

Also, why are there no Neanderthals in Africa?

See our post "Most Humans Part Neanderthal"

Science, it seems, has been "the new religion" for a long time. And by the same token, it has always had its apostates and heretics, even its unremarkable and quotidian sinners. In an article titled "Disgrace," Charles Gross, a professor of psychology and neuroscience at Princeton University, reviews the whole subject of contemporary and historical scientific misconduct (The Nation, Jan. 9/16, 2012, pp. 25-32). He finds nothing new in the shocking case of Harvard's Marc Hauser, who was exposed two years ago for scientific misconduct, in of all fields, the biological basis of morality and genetic inheritance of doing evil.

Hauser apparently was guilty of the very venial sin of fudging facts. The three ways to do that, all frowned upon, are by fabrication (making data up), falsification (altering or selecting data, cherry picking) and sheer plagiarism (which all but entering Freshmen understand).

In 1830, computer science pioneer Charles Babbage published a book in which he distinguished "several species of impositions that have been practised in science...hoaxing, forging, trimming, and cooking."

Gross classifies the Piltdown man as an example of hoaxing. This fossil combining parts of an ape and human skull was discovered in 1911 and not discredited until the 1950s. Most hoaxes are intended to poke fun at the public's credulousness, but the Piltdown hoax was undertaken by well-meaning British imperialists who hoped their construction would fill an awkward gap in the record. Like God, if the missing link did not exist, we should have to invent one. Pip pip for the Royal Society!

Babbage believed that forging was uncommon. Rarely are results completely counterfeited and pulled out of thin air.

"Trimming" is probably a form of scientific misconduct that few scientists confess to their most exacting monitors such as the National Science Foundation but rather quietly cover up in bland hypocrisy. It consists of "eliminating outliers to make results look more accurate, while keeping the average the same." Who has not committed that little white sin? Let him who is without self-assurance cast the first chad.

"Cooking," on the other hand, the purposive selection and distortion of data, might be a real concern for all of us.

Gross goes on to inspect the career of Harvard's "war crimes professor" Richard Herrnstein, who became a co-author after his death of the book The Bell Curve about racial differences in intelligence. It is not a very pretty kettle of fish.

Charles Darwin essentially stole the idea of natural selection from Alfred Russel Wallace, the father of biogeography, did he not, and if he didn't, certainly failed to credit some of his predecessors in his rush to fame and self-glorification.

In genetics, we are reminded that the saintly Gregor Mendel probably falsified the suspiciously exact 1:3 ratio he "observed" in comparing pure dominant with hybrid peas (p. 26).

Alarmingly, we learn that "the modal scientific miscreant is a bright and ambitious young man at an elite institution," just the sort of role model worshiped by the popular press.

Maybe our society should be examining a few of science's feet of clay rather than pompously setting more laurels on the heads of its exalted heroes.

Gene surfing is a process in population expansion whereby certain variations become prominent and dominant in a short time, appearing to skip the slow, steady, uniform accumulation of variegation and diversification. According to a study of the population structure and genealogies of Saguenay Lac-Saint-Jean in Quebec, this type of drastic change accompanied the immigrant wave front that spread over the area in the 17th century. "Deep Human Genealogies Reveal a Selective Advantage to Be on an Expanding Wave Front" in Science magazine describes the resulting demographics.

Abstract
Since their origin, human populations have colonized the whole planet, but the demographic processes governing range expansions are mostly unknown. We analyzed the genealogy of more than one million individuals resulting from a range expansion in Quebec between 1686 and 1960 and reconstructed the spatial dynamics of the expansion. We find that a majority of the present Saguenay Lac-Saint-Jean population can be traced back to ancestors having lived directly on or close to the wave front. Ancestors located on the front contributed significantly more to the current gene pool than those from the range core, likely due to a 20% larger effective fertility of women on the wave front. This fitness component is heritable on the wave front and not in the core, implying that this life-history trait evolves during range expansions.

So gene surfing in an expanding colonization phase can produce a genetic revolution whose effects will be felt for hundreds or thousands of years downstream in history.

We wonder if the same wave front demographics might explain some of the following population phenomena:

• Large scale triumph of Norman male lineages following the conquest of England in 1066.
• Selective expansion of Middle Eastern genes in Tennessee (including Cherokee families, Jewish male and female lines and Melungeons)
• Relatedness among Jews and "Jewish diseases"
• Diversity-within-uniformity of Polynesians
• Population replacement of Old European (U, N) by Middle Eastern genes (T, J)  in Europe as a result of the Neolithic Agricultural Revolution

Many students of history are puzzled why old populations have the allele frequencies and heterozygosity clines they have. Genetic drift is only part of the answer. Gene surfing and selection in deep history are the rest of it.

More information about Melungeons
Toward a Genetic Profile of Melungeons in Southern Appalachia
Melungeon Studies
Melungeon Match

A mental foramen is a small hole in the mandible whose purpose is to allow passage of nerves and vessels to the brain and probably also to relieve tension during chewing and gnawing. It has been identified as a sign of archaic humans, including Neanderthals. Do you have one?

I asked my dentist to look at my X rays on file and he confirmed I have a mental foramen. He has often told me I have "powerful" jaws. It is unclear whether there are normally two of them and what their typical positions are.

In a previous blog post, "Neanderthals in America," we discussed mental foramina (the plural of foramen), occipital bulges or bumps and other archaic skeletal traits. Melungeons seem to have many of these ancestral marks.

Do you? You might want to check with your dentist.

Studies show that Europeans have, on average, between 1 and 4 percent Neanderthal genes from an early out-of-Africa interbreeding period in the Middle East. Science has not decided to consider Neanderthals a separate species or sub-species in relation to H. sapiens sapiens (humans).

DNA Consultants offers an estimate of Neanderthal ancestry based on matches with other archaic humans called Neanderthal Index.

Line drawing of Neanderthal male ©DNA Consultants.



More information about Melungeons
Toward a Genetic Profile of Melungeons in Southern Appalachia
Melungeon Studies
Melungeon Match