Razib Khan One-stop-shopping for all of my content

January 4, 2013

Mitochondrial Eve: a de facto deception?

The above image, and the one to the left, are screenshots from my father’s 23andMe profile. Interestingly, his mtDNA haplogroup is not particularly common among ethnic Bengalis, who are more than ~80% on a branch of M. This reality is clear in the map above which illustrates the Central Asian distribution my father’s mtDNA lineage. In contrast, his whole genome is predominantly South Asianform, as is evident in the estimate that 23andMe provided via their ancestry composition feature, which utilizes the broader genome. The key takeaway here is that the mtDNA is informative, but it should not be considered to be representative, or anything like the last word on one’s ancestry in this day and age.


As a matter of historical record mtDNA looms large in human population genetics and phylogeography for understandable reasons. Mitchondria produce more genetic material than is found in the nucleus, and so were the lowest hanging fruit in the pre-PCR era. Additionally, because mtDNA lineages do not recombine they are well suited to a coalescent framework, where an idealized inverted treelike phylogeny converges upon a common ancestor. Finally, mtDNA was presumed to be neutral, so reflective of demographic events unperturbed by adaptation, and characterized by a high mutation rate, yielding a great amount of variation with which to differentiate the branches of the human family tree.

Many of these assumptions are are now disputable. But that’s not the point of this post. In the age of dense 1 million marker SNP-chips why are we still focusing on the history of one particular genetic region? In a word: myth. Eve, the primal woman. The “mother of us all,” who even makes cameos in science fiction finales!

In 1987 a paper was published which found that Africans harbored the greatest proportion of mtDNA variation among human populations. Additionally, these lineages coalesced back to a common ancestor on the order of 150,000 years ago. Since mtDNA is present in humans, there was a human alive 150,000 years ago who carried this ancestral lineage, from which all modern lineages derive. Mitochondrial DNA is passed from mothers to their offspring, so this individual must have been a woman. In the press she was labeled Eve, for obvious reasons. The scientific publicity resulted in a rather strange popular reaction, culminating in a Newsweek cover where Adam and Eve are depicted as naked extras from Eddie Murphy’s Coming to America film.

The problem is that people routinely believe that mtDNA Eve was the only ancestress of all modern humans from the period in which she lived. Why they believe this is common sense, and requires no great consideration. The reality is that the story being told by science is the story of mtDNA, with inferences about the populations which serve as hosts for mtDNA being incidental. These inferences need to be made cautiously and with care. It is basic logic that a phylogeny will coalesce back to a common ancestor at some point. Genetic lineages over time go extinct, and so most mtDNA lineages from the time of Eve went extinct. There were many woman who were alive during the same time as Eve, who contributed at least as much, perhaps more, to the genetic character of modern humans today. All we can say definitively is that their mtDNA lineage is no longer present. As mtDNA is passed from mother to daughter (males obviously have mtDNA, but we are dead ends, and pass it to no one), all one needs for a woman’s mtDNA lineage to go extinct is for her to have only sons. Though she leaves no imprint on the mtDNA phylogeny, obviously her sons may contribute genes to future generations.

Prior to ancient DNA and the proliferation of dense SNP data sets scholars were a bit too ambitious about what they believed they could infer from mtDNA and Y lineages (e.g., The Real Eve: Modern Man’s Journey Out of Africa). We are in a different time now, inferences made about the past rest on more than one leg. But the legend of Eve of the mtDNA persists, not because of its compelling scientific nature, but because this is a case where science piggy-backs upon prior conceptual furniture. This yields storytelling power, but a story which is based on a thin basis of fact becomes just another tall tale.

All this is on my mind because one of the scientists involved with Britain’s DNA, Jim Wilson, has penned a response to Vincent Plagnol’s Exaggerations and errors in the promotion of genetic ancestry testing (see here for more on this controversy). Overall I don’t find Wilson’s rebuttal too persuasive. It is well written, but it has the air of sophistry and lawyerly precision. I have appreciated Wilson’s science before, so I am not casting aspersions at his professional competence. Rather, some of the more enthusiastic and uninformed spokespersons for his firm have placed him in a delicate and indefensible situation, and he is gamely attempting to salvage the best of a bad hand. Importantly, he does not reassure me in the least that his firm did not use Britain’s atrocious libel laws as a threat to mute forceful criticism of their business model on scientific grounds. A more general issue here is that Wilson is in a situation where he must not damage the prospects of his firm, all the while maintaining his integrity as a scientist. From what I have seen once science becomes a business one must abandon the pretense of being a scientist first and foremost, no matter how profitable that aura of objectivity may be. The nature of marketing is such that the necessary caution and qualification essential for science becomes a major liability in the processing of communicating. It’s about selling, not convincing.

Going back to Eve, Wilson marshals a very strange argument:

“The claim that Adam and Eve really existed, as you suggest, refers to the most recent common ancestors of the mtDNA and non-recombining part of the Y chromosome. I don’t agree that there is nothing special about these individuals: there must have been a reason why mitochondrial Eve was on the front cover of Time magazine in the late 80s!….

A minor quibble, but I suspect he means the Newsweek cover. More seriously, this line of argumentation is bizarre on scientific grounds. Rather, it is a tack which is more rational when aiming toward a general audience which might purchase a kit which they believe might tell them of their relationship to “Eve.”

In the wake of the discussion at Genomes Unzipped I participated in further exchanges with Graham Coop and Aylwyn Scally on Twitter, and decided to spend 20 minutes this afternoon asking people what they thought about mitochondrial Eve. By “people,” I mean individuals who are pursuing graduate educations in fields such as genetics and forensics. My cursory “field research” left me very alarmed. Naturally these were individuals who did not make elementary mistakes in regards to the concept, but there was great confusion. I can only wonder what’s going through the minds of the public.

Analogies, allusions, and equivalences are useful when they leverage categories and concepts which we are solidly rooted in, and transpose them upon a foreign cognitive landscape. By pointing to similarities of structure and relation one can understand more fully the novel ground which one is exploring. Saying that the president of India is analogous to the queen of England is an informative analogy. These are both positions where the individual is a largely ceremonial head of state. In contrast, the president of the United States and the queen of England are very different figures, because the American executive is not ceremonial at all. This is not a useful analogy, even though superficially it sees no lexical shift.

Who was Eve? A plain reading is that she is the ancestor of all humans, and more importantly, the singular ancestress of all humans back to the dawn of time. This is a concept which the public grasps intuitively. Who is mtDNA Eve? A woman who flourished 150,000 years ago, who happened to carry the mtDNA lineage which would drift to fixation in the ancestors of modern humans. I think this is a very different thing indeed. For purposes of poetry and marketing the utilization of the name Eve is justifiable. But on scientific grounds all it does is confuse, obfuscate, and mislead.

The fiasco that Vincent Plagnol stumbled upon is just a symptom of a broader problem. Scientists need to engage in massive conceptual clean up, as catchy phrases such as “mitochondrial Eve” and “Y Adam” permeated the culture over the past generation, and mislead many sincere and engaged seekers of truth. This is of the essence because personal genomics, and the scientific understanding of genealogy, are now moving out of the ghetto of hobbyists, enthusiasts, and researchers. Though I doubt this industry will be massive, it will be ubiquitous, and a seamless part of our information portfolio. If people still have ideas like mitochondrial Eve in their head it is likely to cloud their perception of the utility of the tools at hand, and their broader significance.

December 1, 2012

Africa’s hidden people hold the keys to the past

I mentioned this in passing on my post on ASHG 2012, but it seems useful to make explicit. For the past few years there has been word of research pointing to connections between the Khoisan and the Cushitic people of Ethiopia. To a great extent in the paper which is forthcoming there is the likely answer to the question of who lived in East Africa before the Bantu, and before the most recent back-migration of West Eurasians. On one level I’m confused as to why this has to be something of a mystery, because the most recent genetic evidence suggests a admixture on the order of 2-3,000 years before the past.* If the admixture was so recent we should find many of the “first people,” no? As it is, we don’t. I think these groups, and perhaps the Sandawe, are the closest we’ll get.

Publication is imminent at this point (of this, I was assured), so I’m going to just state the likely candidate population (or at least one of them): the Sanye, who speak a Cushitic language with possible Khoisan influences. There really isn’t that much information on these people, which is why when I first heard about the preliminary results a few years back and looked around for Khoisan-like populations in Kenya I wasn’t sure I’d hit upon the right group. But at ASHG I saw some STRUCTURE plots with the correct populations, and the Sanye were one of them. I would have liked to see something like TreeMix, but the STRUCTURE results were of a quality that I could accept that these populations were not being well modeled by the variation which dominated their data set. Though Cushitic in language the Sanye had far less of the West Eurasian element present among other Cushitic speaking populations of the Horn of Africa. Neither were their African ancestral components quite like that of the Nilotic or Bantu populations. The clustering algorithm was having a “hard time” making sense of them (it seemed to wanted to model them as linear combinations of more familiar groups, but was doing a bad job of it).

Here is an interesting article on these groups: Little known tribe that census forgot. Like the Sandawe this is a population which seems to have been hunter-gatherers very recently, and to some extent still engage in this lifestyle. In this way I think they are fundamentally different from Indian tribal populations, who are often held up to be the “first people” of the subcontinent.  More and more it seems that the tribes of India are less the descendants of the original inhabitants of the subcontinent, at least when compared to the typical Indian peasant, and more simply those segments of the Indian population which were marginalized and pushed into less productive territory. Over time they naturally diverged culturally because of their isolation, but the difference was not primal. In contrast, groups like the Sanye and Sandawe may have mixed to a great extent with their neighbors (and lost their language like the Pygmies), but evidence of full featured hunting & gathering lifestyles implies a sort of direct cultural continuity with the landscape of eastern Africa before the arrival of farmers and pastoralists from the west and north.

* I understand some readers refuse to accept the likelihood of these results because of other lines of information. I am just relaying the results of the geneticists. I am not interested in re-litigating prior discussions on this. We’ll probably have a resolution soon enough.

November 20, 2012

San Francisco supported Proposition 37!

Filed under: Agriculture,Politics,Proposition 37 — Razib Khan @ 12:15 am

A few weeks ago I alluded to the controversy around proposition 37. This was the GMO labeling law proposal. Many life scientists in California opposed this law. One aspect of this issue is that it is an area where the Left may be stated to be “anti-science.” This is why this was highlighted in Science Left Behind. But there’s a problem with this narrative: the survey data for it is weak. There are broad suggestive patterns…but the reality is that the strongest predictor of skepticism of genetically modified organisms is lower socioeconomic status. The GSS has a variable, EATGM. Here are the results by ideology:

Liberal Moderate Conservative
Don’t care whether or not food has been genetically modified 15 16 17
Willing to eat but would prefer unmodified foods 55 53 52
Will not eat genetically modified food 30 30 31

 

I would caution that the sample size is small. But, if you dig deeper into the survey data you can find evidence that conservatives are more unalloyed in their support of biotech.

And yet with all this said, today I noticed that the California proposition 37 results are rather stark in their geographic distribution. The measure failed statewide, but 2/3 of the people in San Francisco and Santa Cruz counties supported it, as did 60% of the people in Marin (interestingly, only a little over 50% supported it in San Mateo and Santa Clara). I couldn’t find a tabular list with the results by county, but there are interactive maps. If someone was industrious (and had more time than I do) they would go and collect the data from the maps, and do a loess of “support proposition 37” vs. “support Obama.”

The main problem is that from what I can tell a lot of Left-liberals who support anti-GMO policies, explicit or implicit, do so because they believe that that is anti-corporate. My argument is that whatever issues one might have with agribusiness, one should litigate the question of scale in agriculture directly and forthrightly, rather than focus on sidelights like GMO.

August 21, 2012

The Sardinian meter

I cropped the image above from the paper Inference of Population Structure using Dense Haplotype Data. The main reason was emphasize the distinctiveness of the Sardinian cluster, on the bottom right. As you can see this population exhibits a lot of coancestry across individuals. This isn’t too surprising, Sardinia is an island, and islands are often genetically distinctive. Random genetic drift prevents populations from diverging through gene flow, but water is a major impediment to gradual isolation by distance dynamics. The original Sardinians are naturally going to diverge from mainlanders over time, and begin to share the same set of common ancestors in the recent past, because their space of reasonable mating possibilities is constrained. The other population which is similar in the heat map above are the residents of the Orkneys, off the north coast of Scotland (the Orkneys has a much smaller population than Sardinia, but, it is also much closer to the mainland).

This is on my mind because Dienekes has a long post where he explores the D-statistic results of various European populations, using Sardinians ...

June 28, 2012

Population replacement in Neolithic Spain?

Filed under: Agriculture,Anthroplogy,Neolithic,Paleolithic Europeans — Razib Khan @ 12:16 pm

There’s a new ancient DNA paper out which examines the maternal lineage and the autosomal background of two individuals extracted from a Spanish site dated to 7,000 years before the present. That is, during the European Mesolithic. In other words, these are the last wave of Iberian hunter-gatherers before agriculture. I have placed the PCA, with some informative labels, to illustrate the peculiarity of these samples. Here’s the abstract:

The genetic background of the European Mesolithic and the extent of population replacement during the Neolithic…is poorly understood, both due to the scarcity of human remains from that period…The mitochondria of both individuals are assigned to U5b2c1, a haplotype common among the small number of other previously studied Mesolithic individuals from Northern and Central Europe. This suggests a remarkable genetic uniformity and little phylogeographic structure over a large geographic area of the pre-Neolithic populations. Using Approximate Bayesian Computation, a model of genetic continuity from Mesolithic to Neolithic populations is poorly supported. Furthermore, analyses of 1.34% and 0.53% of their nuclear genomes, containing about 50,000 and 20,000 ancestry informative SNPs, respectively, show that these two Mesolithic individuals are ...

May 30, 2012

Cain, Where is Abel thy brother?

Filed under: Agriculture — Razib Khan @ 3:06 am

Community differentiation and kinship among Europe’s first farmers (via Dienekes):

Community differentiation is a fundamental topic of the social sciences, and its prehistoric origins in Europe are typically assumed to lie among the complex, densely populated societies that developed millennia after their Neolithic predecessors. Here we present the earliest, statistically significant evidence for such differentiation among the first farmers of Neolithic Europe. By using strontium isotopic data from more than 300 early Neolithic human skeletons, we find significantly less variance in geographic signatures among males than we find among females, and less variance among burials with ground stone adzes than burials without such adzes. From this, in context with other available evidence, we infer differential land use in early Neolithic central Europe within a patrilocal kinship system.

I have already stated on this weblog that we will probably begin to discern a rather strong pattern soon of an interleaved genetic pattern across Eurasia and Africa where we can infer that populations in an expansionary demographic phase absorbed a host of other groups (more, or less). The exact details are to be worked out, but I’m moderately confident in ...

April 28, 2012

Facing the ocean

Filed under: Agriculture,Anthroplogy,Human Genetics — Razib Khan @ 10:35 pm

Halford Mackinder’s conceptualization of the world

With the recent publication of the paper on the archaeogenetics of Neolithic Sweden I feel like we’re nearing a precipice. That precipice overlooks lands of great richness, filled with hope. It’s nothing to fear. It is in short a total re-ordering of our conception of the recent human past, at minimum. The “pots not people” paradigm arose in archaeology over the past few generations due to both scholarly and ideological factors. The scholarly ones being that intellectuals of the 19th and early 20th century made assumptions of extremely tight correspondence between material and cultural characteristics, and demographic dynamics, which seem to have been false. Therefore, the rise of an Anglo-Saxon England and the marginalization of Celtic Britain to the western fringes was not just a cultural reality, but also a fundamentally racial one, as Germans replaced Celts in totality. The ideological problem is that this particular framework was take as a given by the Nazis during World War II, lending a bad odor to the

hypotheses of migration which were once so ascendant.

No ...

April 26, 2012

The last days of Grendel

Filed under: Agriculture,Anthroplogy,Europe — Razib Khan @ 9:27 pm

A new paper in Science has just been published which in its broad outlines has been described in conference presentations. When examining the autosomal genetic variation of three individuals of the hunter-gatherer Pitted Ware Culture (PWC), and one of the agriculturalist Funnel Beaker Culture (TRB), the authors found that the two groups were sharply differentiated. The number of SNPs was on the order of 10,000 or so if I read the methods correctly. This is rather thin for studying contemporary within European population differences (~100,000 or more seems to be safe), in particular using hypothesis based clustering algorithms (it seems more manageable for PCA). But the findings are strong enough that I think we shouldn’t discount them. The most fascinating aspect of the results is that while the PWC seem to exhibit affinities with Northern and Northeastern Europeans, the TRB individual seems more similar to extant Southern Europeans!

Others have already commented extensively on the results. Keeping in mind the small sample sizes, limitation of comparisons, and the relatively thin marker set, I think the primary result we can take away from these findings is that old models ...

March 25, 2012

The agricultural “express train”

Filed under: Agriculture,Anthroplogy — Razib Khan @ 10:25 pm

One model for the spread of the agricultural way of life into Europe is of inexorable “demic diffusion” via a “wave of advance” of farming populations met by a land surplus. Conceptually and analytically it’s an elegant model. It’s also fundamentally methodologically individualistic, and so in keeping with the spirit of the age. There’s no need to appeal to higher order social structure or organization, farmers who have a specific cultural toolkit drive the dynamic through endogenous growth in pre-state cultures through the production of large families. This growth washes over the frontier of the advance, and the original locus of the demographic pulse synthesizes across a transect with the indigenous substrate. In the early aughts historical geneticists Bryan Sykes and L. L. Cavalli-Sforza sparred over whether demic diffusion was useful or not as a conceptual framework. Sykes reported chromosomal results which implied that 75 percent of the ancestry of Europeans derives from Pleistocene hunter-gatherers. Cavalli-Sforza’s riposte was that the original model did not specify a particular Paleolithic-Neolithic ratio, but rather characterized a dynamic which emphasized the necessity of migration as a mediator for cultural changes (the two perspectives are outlined in Seven Daughters of Eve and A Genetic and Cultural Odyssey).

 

In the end the debate did seem semantic quibbling. And today it also is likely outmoded and irrelevant. There is a high probability that the basic fundamental assumptions of the original diffusionist model, whether cultural or genetic, were pushed too far. It neglected the profound discontinuities introduced into the equation by the protean tendencies of human culture. Empirically there is evidence of this in works such as Lawrence Keeley’s War Before Civilization of this in the European context. As farmers impinged upon the territories of Mesolithic populations which utilized marine resources the advance of agriculture often stalled, and there are archaeological remains which are suggestive of violent conflict across Northern Europe’s maritime fringe. Additionally, when humans advance into “virgin” territory the landscape can often seem “patchy.” Instead of a spatially uniform wave of advance one almost certainly saw farmers race up favorable valleys and avoid zones of decreased fertility. In the United States the Far West was understood to be more amenable to agricultural techniques than the Great Plains in the 19th century, so one notes a “leap frog” to California and Oregon in the decades before the Civil War, leaving the intervening lands to native populations (at least temporarily).

It is with this in mind that we must take in results being published more recently which suggest a more confused and irregular shift of peoples and cultures in Neolithic Europe. For example, at the symposium on Modern Human Genetic Variation Mattias Jakobsson is reporting on results of ancient DNA from ~5,000 year old samples from Scandinavia. The individual who was a farmer resembles Southern Europeans, while the two hunter-gatherers resemble modern Northern Europeans. Jakobsson observes that most modern European populations span the gamut between the two extremes. A few years ago a paper came out which reported that the mtDNA lineages of LBK individuals from Central Europe (the earliest farming culture) resembled Near Easterners more than modern Europeans. A similar discontinuity seems evident in France. At this point I think there are enough data to force us to move past an simple Neolithic demic diffusion wave of advance, and any model which posits pure cultural diffusion or total replacement of the indigenous populations. We should be careful about making grand pronouncements for the next few years, because the outlines will be clear and pegged down within 5 years due to the impending surfeit of ancient DNA studies.

Rather, let’s switch back to the question of clines and gradual shifts. The problem here may be the granularity of the archaeological data. It seems likely that the expansion of agriculture was more spatially patchy, and exhibited more starts and stops, then the samples we have allow us to infer with any confidence. The arrival of startlingly distinctive populations genetically and culturally across which likely rapidly traversed territory in a point-to-point fashion, and their subsequent extinction or assimilation into local substrate, is less surprising when we keep in mind the discontinuous nature of much of cultural change.

February 25, 2012

Basque maternal heritage & continuity

Filed under: Agriculture,Anthroplogy,Basque — Razib Khan @ 3:02 pm

There’s a new paper in AJHG which caught my eye, The Basque Paradigm: Genetic Evidence of a Maternal Continuity in the Franco-Cantabrian Region since Pre-Neolithic Times (ungated). The first thing you need to know about this paper is that it focuses on only the direct maternal lineage of Basques via the mtDNA. In some ways this is weak tea, since it doesn’t give us a total genome estimate. But there are major upsides to mtDNA and Y. First, because of the lack of recombination it is relatively easy to generate a nice phylogenetic tree using a coalescent model. And second, for mtDNA the molecular clock is considered relatively reliable.

In this specific paper they also expanded the scope of their analysis to the whole mtDNA sequence, instead of just the hypervariable region. Not only did they look at whole sequences, but they also had an enormous sample size. They sequenced over 400 mtDNA genomes from the Basque country and neighboring regions. Haplogroup H peaks in frequency among Basques, and drops off among their neighbors (Gascons, Spaniards, etc.). Because the Basque speak a non-Indo-European language they are usually presumed to be indigenous in relation to their neighbors (or at least more indigenous). Until recently there was a strong presupposition that the Basque were ideal representatives of the pre-Neolithic populations of Western Europe. One common method of analysis would be to use the Basque as a pre-Neolithic “reference,” and simply estimate the impact of a Neolithic demographic wave of advance by using a eastern Mediterranean population as a second “reference” within an admixture framework. But more recent work has muddled the idea that the Basque are the descendants of Paleolithic Europeans. Finally, I suspect we’ll also have to acknowledge complexity in demographic histories. To say that the Basque exhibit continuity with Mesolithic Iberians may not contradict a substantial Neolithic contribution. South Asians for example are one numerous modern group which exhibits sharply divergent affinities if you use Y chromosomes (West Eurasian) or mtDNA (not West Eurasian). Why? The details are prehistorical.


The major takeaway from this paper is that the Basque mtDNA exhibit a pattern of demographic expansion ~4,000 years BP, and ~8,000 years BP. But I think it is important to look at the range of outcomes over their confidence intervals, so I’ve reproduced their second table below:


Table 2. Time Estimates of the Six Autochthonous Haplogroups

Haplogroup N Percentage Rho Standard Error Age (in Years) 95% Confidence Interval
Coalescence Age
H1j1 52 12.4% 1.86 0.49 4845 2324 − 7408
H1t1 34 8.1% 1.94 0.97 5057 99 – 10176
H2a5a1 22 5.2% 1.33 0.65 3422 118 – 6800
H1av1 17 4.0% 1.24 0.52 3213 567 – 5906
H3c2a 14 3.3% 1.27 0.37 3291 1403 – 5204
H1e1a1 12 2.9% 1.23 0.72 3187 −464 – 6927
Splitting Age
H1j1 52 12.4% 2.86 1.11 7514 1764 – 13470
H1t1 34 8.1% 2.94 1.39 7730 554 – 15227
H2a5a1 22 5.2% 2.33 1.19 6094 −6 – 12434
H1av1 17 4.0% 2.24 1.13 5854 65 – 11860
H3c2a 14 3.3% 2.27 1.07 5934 443 – 11619
H1e1a1 12 2.9% 5.23 2.13 14011 2729 – 26000
 

For our purposes the splitting age is important, because it shows when the Basque specific H lineages diverged from other European H lineages. Some of the intervals are huge (look at H1e1a1), so I don’t know what to make of it. I’ll leave further comments to those more well versed in the mtDNA literature, but I would like to say that it is important to remember that we don’t know where the demographic events inferred occurred. It may not have been in the trans-Pyrenees region at all.

More later.

January 14, 2012

The old Amazon

Filed under: Agriculture,Amazon,Anthroplogy,Charles C. Mann,Environment — Razib Khan @ 2:49 pm

Once Hidden by Forest, Carvings in Land Attest to Amazon’s Lost World:

For some scholars of human history in Amazonia, the geoglyphs in the Brazilian state of Acre and other archaeological sites suggest that the forests of the western Amazon, previously considered uninhabitable for sophisticated societies partly because of the quality of their soils, may not have been as “Edenic” as some environmentalists contend.

Instead of being pristine forests, barely inhabited by people, parts of the Amazon may have been home for centuries to large populations numbering well into the thousands and living in dozens of towns connected by road networks, explains the American writer Charles C. Mann. In fact, according to Mr. Mann, the British explorer Percy Fawcett vanished on his 1925 quest to find the lost “City of Z” in the Xingu, one area with such urban settlements.

In addition to parts of the Amazon being “much more thickly populated than previously thought,” Mr. Mann, the author of “1491,” a groundbreaking book about the Americas before the arrival of Columbus, said, “these people purposefully modified their environment in long-lasting ways.”

If one wants to recreate pre-Columbian Amazonia, most of the forest needs to be removed, with many people and a managed, highly productive landscape replacing it,” said William Woods, a geographer at the University of Kansas who is part of a team studying the Acre geoglyphs.

“I know that this will not sit well with ardent environmentalists,” Mr. Woods said, “but what else can one say?”


There are two descriptive models which have to be interpreted in different normative frames. First, there is the model whereby before the arrival of the Europeans the New World was lightly populated by indigenous groups which had a minimal impact upon the environment. This is the description. Before the 1960s this was viewed by the mainstream culture as a rationale for the justified conquest of the New World by Europeans, who put the land to productive economic usage, whereas before it had been fallow and under-untilized. After the 1960s many, especially in the environmental movement, inverted the moral valence of the description. Instead of being primitive savages, the native peoples were at balance with the environment. Rather than an outmoded way of life to be superseded, they were a potential model for the future.

The second descriptive model is the one that Charles C. Mann outlines in 1491: New Revelations of the Americas Before Columbus. It posits that in fact the New World was much more heavily populated and its environment more impacted by humanity than we had thought previously. Rather, it suggests that the introduction of Old World diseases resulted in massive population crashes, subsequent to which there was a “re-wilding” of much of the Americas. Mann focuses more on the period before the arrival of Europeans, but if you read the scholarship on the arrival of Paleo-Indians there is a fair amount of evidence that even their appearance resulted in a massive change in the suite of fauna which characterized the New World (e.g., the gray wolf and American bison are also Holocene newcomers, just like man).

Some have argued tat Mann has taken a maximalist position (in fact, some readers have lied and stated that Mann argued that the Amazon was as populated as Bangladesh!). But even granting that Mann may be sampling from the more revisionist tail of the scholarship, I think it is creditable that we need to move away from the extreme position of the first descriptive model. There is a fair amount of circumstantial evidence that New World civilizations had not attained the same level of sophistication and complexity as Old World civilizations (see Guns, Germs, and Steel for some of the reasons why). But it is also likely that the Aztecs and Incas were not sui generis aberrations, but rather one point along the spectrum of social complexity which characterized the New World.

This is a subtle point though, because the new model also has normative ramifications. I state above that New World civilizations were not as complex or developed as Old World ones, and that is not a position that many are comfortable with. Rather, they may want to assert that the New World societies were just as complex and sophisticated as the Old World civilizations, that fundamentally all civilizations have equal value and similar character. Therefore, these partisans are particularly enthusiastic about the model which Charles C. Mann popularizes in 1491, as it reverses the narrative of noble simple savages, projecting the indigenous as highly cultured, and only brought down by the biological weapons which Europeans brought.

Where does that put those who wish to construct a plausible model of reality, rather than a mythic history for purposes of ideology? It is lazy to simply pick the position in the middle, but in this case that’s probably the most prudent unless you want to dive into the primary literature yourself. I don’t accept the old model anymore for a variety of reasons, not just having to do with the natural history of the New World. But, I can’t personally assess in detail the magnitude of the numbers that some of the scholars Mann relies upon to revise upward population estimates. So I take the revision with a grain of salt and some caution.

I would conclude that there is one reason I can think of why the Amazon basin might have been more suitable for human habitation that some other wet tropical zones in the Old World: the relative lack of disease. Many wet lowland zones which would otherwise be suitable farmland are lightly populated due to malaria, but this was not an issue in the New World before 1492.

January 7, 2012

Human behavior over the ages

Filed under: Agriculture,Anthroplogy,Human Evolution,Neolithic Revolution — Razib Khan @ 2:49 pm

Over at Scientific American Eric Michael Johnson has a very long post up, The Case of the Missing Polygamists. It is a re-post of something he already published at Psychology Today a few years ago. Though provisionally a review of Sex at Dawn, Johnson covers a lot of ground, and also has extensive quotations from Sarah Blaffer Hrdy.

I’m reflecting upon the post for a second time because it is very rich in ideas, and lays out may different general concepts and specific propositions. The bottom line from what I can gather is that Johnson agrees with those thinkers who believe that agriculture and the Neolithic revolution to a great extent reshaped social relations, and give us a skewed perception of “normal” human societies. I’m not going to rehash all of the points in the piece, but will focus on just a few which I think I can extend upon fruitfully.


Long time readers of this weblog know that I tend to accept that something radical shifted during the Neolithic revolution. I’m of the opinion that like most animals humanity’s state was Malthusian during the age of hunter-gatherers, and of farmers. That is, gains in population eventually absorbed productivity increases due to technology (e.g., bow and arrow) or surplus land (e.g., settlement of the New World by humans). But different forms of Malthusianism can obtain different stable states. The rhythm of life of a Chinese peasant and a Bushmen are very different, despite the fact that both may operate on the Malthusian subsistence margin. Malthusianism is a end point, it does not specify the dynamic by which one proceeds toward it.

Johnson relays the idea that prior to agriculture humanity had a matrifocal and de facto polyamorous bias. For the purposes of my thought here we need to separate the social and biological. In the social sense matrifocality simply means that males move between focal groups, while females remain in their natal groups. Polyamory implies that males and females may have multiple sexual relationships. In a genetic sense matrifocality should imply that Y chromosomes flow between groups (lower Fst), and mitochondrial lineages exhibit greater geographical constraint (higher Fst). In the longer term equitable pure polyamory would not be genetically distinguishable from pure equitable momogamy (because of more combinations in the former case there may be more diverse autosomal haplotypes, but I’m not sure this is very relevant for this discussion).

It isn’t innovative or surprising for someone to assert that agriculture was a major rupture in human history. Major public intellectuals routinely take a shot at characterizing what made it so special, and it’s a lively area of scholarship. Rather, I will reiterate here what I have held for many years: the “traditional” and normative social systems common among civilized societies since the rise of agriculture and the emergence of mass society are cultural adaptations which serve to constrain impulses which are deeply hard-wired within our species. Elite lineages the world over arranged the pair bonds of their offspring for many generations, and yet this often meets resistance, or at least resignation. The tales of adulterous lovers subject to a tragic fate are common literary motifs. This is I suspect an aspect of evoked culture, the inevitable tension between our deep impulses driven by individual preferences, and the social obligations which many have to had fulfill as part of extended kinship networks which had accrued prestige and capital. Both of these are human universals, as are the consequences. The high culture literature records this tension, and elaborates upon it so as to model proper and correct behavior for elites so as to avoid tragedy.

I have no doubt that hunter-gatherer societies had lineages which accrued prestige and capital. The modern hunter-gatherer societies which Eric Michael Johnson highlights are not representative of the human past. They have been relegated to marginal land. In the past hunter-gatherer societies drew upon lands with greater primary productivity, so the chasm between themselves and their farming successors in terms of physical capital and social stratification was often less than we may expect using the modern relics as references. But, agriculture clearly signaled a shift in scale and quantity. Super-male lineages, such as that of Genghis Khan, are possible only due to the contingent conditions of civilization, in particular all the elements necessary for globalism. Agriculture was likely an amplification of a “winner take all” dynamic in the game of social positioning. And not surprisingly these societies also developed complex belief systems and institutions to moderate and dampen these tendencies, likely due to their innate instabilities, as well as a human bias toward egalitarianism (i.e., land redistribution and opposition to inequality is a tendency in many societies at the commanding heights, while world religions all exhibit an anti-Nietzschean bent, for lack of a better term).

The reason that “Western culture” with its individualist ethos is so attractive, and threatening, is that in many ways it is a purer reflection of the impulses which were operative in the ancestral environment. I am not here talking about the most extreme manifestations of Western liberality in sexual mores, such as gay marriage or formal polyamory (most people do not crave homosexual relations). Rather, a modicum of personal choice and sexual egalitarianism, are out of keeping with the norms which were necessary to maintain social order in the period between small-scale hunter-gatherer societies and the rise of the mass consumer society. On the margins of subsistence in a world of farmers individual action may redound very negatively upon the broader kinship group, so personal norms of honor and propriety may be highly developed.

And yet if these cultural norms were so strong why did humans not evolve their way out of their hunter-gatherer ethos? There are two primary reasons for this. First, for much of human history the norms outlined in high culture texts and religions were applicable only to elite lineages. This is history recorded in the texts, but it may not be most of lived human history. For example, religious marriages in much of medieval Europe were obligate for noble families, but may not have been for peasants, who made recourse to common law relationships. Bastardy is less of a concern in scenarios where property divisions are of no consequence. There’s no property to inherit. But, this phenomenon is probably moderated by the fact that over much of history elite lineages may have been more fecund than the masses. Lived history may be more ephemeral than we realize in a genetic sense.

A second explanation though is that the very tendencies which make adherence to traditional norms somewhat discomforting on an individual level are necessary in other contexts. Love is an inconvenience when it comes to arranging marriages for your offspring optimally on a social dimension, but it may be necessary for men and women to invest in their offspring due to the love they feel for them so that they live and flourish. In other words, psychological impulses which were inconvenient in one domain were necessary and adaptive on others. Phenotypically I’m implying that there was functional constraint, and genetically it would manifest as pleiotropy. I suspect that a strong tendency toward developing loving bonds with children is a much more important characteristic in these elite lineages than dampening the initial discomfort that may occur when one is paired off with someone with whom one is not particularly enamoured. In a social and biological evolutionary sense romantic love is less important than we might think in our individualist age. But, romantic love remains hard-wired within us because it is biologically impossible to suppress its manifestation so long as we need the emotion of love more importantly to bind us together with children.

Finally, let’s go back to Johnson’s treatment of the disjunction between idealized polyamory and realized polygyny in the ancient environment (at least to a mild extent). By this, he points to the reality that some of the Y chromosomal data point to a reproductive skew, where a few males tend to give rise to a disproportionate number in the next generation. In extreme polygyny you have a Genghis Khan situation, where males of one narrow lineage have an enormous reproductive advantage. The scenario sketched out in Johnson’s post is that females may have had relationships with several males (and the inverse), but there was a tendency toward favoring reproduction with one focal male or female. This does not seem to negate the reality of jealousy and drama. We see this among common chimpanzees, who have a classic mating system in the extreme sense outlined by Johnson (this species has huge testicles to generate viscous sperm the competition is so extreme). And modern polygamorists who have formal relationships all tell tales of enormous time investments necessary to maintain proper relationship equilibrium. This is I think the reason that elite lineages in mass agricultural societies turned toward simpler relationship networks. The older model was simply not sufficiently stable for the purposes of maintaining the social and cultural systems necessary for the proper functioning of the older Malthusian civilizations. This is evident when conflicts within elite lineages are often rooted in questions of paternity and maternity (half siblings; Charles Martel was the bastard son of his father, who superseded the legitimate line), or accusations of false paternity (the first Chinese Emperor was subject to this rumors due to his bad reputation in later generations).

Where does this lead us? I think it’s complicated. Many social conservatives would argue that you can’t just dispense with the whole cultural toolkit which has organically evolved over the last 10,000 years, and revert back to the more primal state of affairs before agriculture. Social liberals point out that the forms of the past are no longer necessary in the present. But though affluence has removed many necessary social constraints, we have not warped ourselves back to the Paleolithic either. The balance between our instincts, which evolved in small groups thousands of years ago, and our notional cultural mores, which crystallized during the Axial Age, is still a work in progress. I believe that the world religions were version 1.0 in regards to formalizing workable compromises between our basic natures and the realities of the aristocratic world. What we need is a version 2.0, where we balance the needs of the common person on the street, with their basic impulses. The great compromise between our biology and our current social complexity will continue. But it is a dynamic parameter, not a static element.

December 12, 2011

Out of the agricultural hearths

Filed under: Agriculture,Anthroplogy,anthropology,Genetics,Genomics — Razib Khan @ 2:34 pm

Dienekes has an important post up, The womb of nations: how West Eurasians came to be. He outlines a scenario where a rapid expansion of a farming population has overlain much of Western Eurasia, atop aboriginal substrata. A few years ago you’d have laughed at such a model, mostly due to the authority of archaeologists and phylogeographers relying on mtDNA lineage distributions. No longer. This is not necessarily an orthodoxy, and the details of the model vary, but here is my verbal rendering of the simplest scenario:

1) ~50 thousand years hybridization between Eurasian hominins and “Out of Africa”

2) ~40-10 thousand years before the present, crystallization of the Paleolithic order of human population structure, derived from groups seeded in the original migration

3) ~10 thousand to a few thousand years before the present, the Paleolithic order is replaced and assimilated by farmers expanding from a few hearths

Below the fold is a stylized tree representation of what I have in mind.


November 1, 2011

Men on the move, part n

Filed under: Agriculture,Genetics,Genomics,Human Genetics — Razib Khan @ 2:28 am

Ancient DNA suggests the leading role played by men in the Neolithic dissemination:

The impact of the Neolithic dispersal on the western European populations is subject to continuing debate. To trace and date genetic lineages potentially brought during this transition and so understand the origin of the gene pool of current populations, we studied DNA extracted from human remains excavated in a Spanish funeral cave dating from the beginning of the fifth millennium B.C. Thanks to a “multimarkers” approach based on the analysis of mitochondrial and nuclear DNA (autosomes and Y-chromosome), we obtained information on the early Neolithic funeral practices and on the biogeographical origin of the inhumed individuals. No close kinship was detected. Maternal haplogroups found are consistent with pre-Neolithic settlement, whereas the Y-chromosomal analyses permitted confirmation of the existence in Spain approximately 7,000 y ago of two haplogroups previously associated with the Neolithic transition: G2a and E1b1b1a1b. These results are highly consistent with those previously found in Neolithic individuals from French Late Neolithic individuals, indicating a surprising temporal genetic homogeneity in these groups. The high frequency of G2a in Neolithic samples in western Europe could suggest, furthermore, that the role of men during Neolithic dispersal could be greater than currently estimated.

Some notes:


- Otzi the Iceman is G2a.

- A continuity of local maternal lineages would not be so surprising. Recall that ~50% of Argentine mtDNA seems to be indigenous, even though they’re ~80% European in total ancestry, and ~95% European in the paternal line.

- This is not limited to Latin America. In South Asia the majority of the maternal lineages are non-West Eurasian, while the majority of paternal lineages are West Eurasian. Autosomal ancestry seems to be about half West Eurasian.

- There are now several instances of Neolithic settlements yielding relatively rare paternal lineages, which are almost certainly intrusive, but left little impact. The authors step forward with the most plausible, and frankly suprising, rationale:

The high frequency of G2a haplogroup in Neolithic specimens, whereas this haplogroup is very rare in current populations, also suggests that men could have played a particularly important role in the Neolithic dissemination that is no longer visible today. This would imply that intra-European migrations related to the metal ages may have strongly affected the modern
gene pool.

In other words, the European paternal lineage landscape may not be determined primarily by the hunter-gatherers or first farmers, but subsequent groups. The relative lack of the two dominant European haplogroups, R1a and R1b, is particularly notable. What’s going on? Perhaps male lineages were “winner-take-all,” and have a tendency to rise to near fixation and then shift toward extinction, more than female lineages? The Genghis Khan haplotype story may be less exceptional than we think. If this is right then we need to be very careful about the historical lessons we draw from mtDNA and Y chromosomes, because they may give us a skewed and unrepresentative picture of the demographics of the past.

October 29, 2011

Unfrying the egg

Dienekes has a long post, the pith of which is expressed in the following:

If I had to guess, I would propose that most extant Europeans will be discovered to be a 2-way West Asian/Ancestral European mix, just as most South Asians are a simple West Asian/Ancestral South Indian mix. In both cases, the indigenous component is no longer in existence and the South Asian/Atlantic_Baltic components that emerge in ADMIXTURE analyses represent a composite of the aboriginal component with the introduced West Asian one. And, like in India, some populations will be discovered to be “off-cline” by admixture with different elements: in Europe these will be Paleo-Mediterraneans like the Iceman, an element maximally preserved in modern Sardinians, as well as the East Eurasian-influenced populations at the North-Eastern side of the continent.

This does not seem to be totally implausible on the face of it. But it seems likely that any “West Asian” component is going to be much closer genetically to an “Ancestral European” mix than they were to “Ancestral South Indians,” because the two former elements are probably part of a broader West Eurasian diversification which post-dates the separation of those groups from Southern and Eastern Eurasians. In other words, pulling out the distinct elements in Europeans is likely a more difficult task because the constituents of the mixture resemble each other quite a bit when compared to “Ancestral North Indians” vs. “Ancestral South Indians.”


The bigger issue which this highlights though is that the reality that many of these clustering methods are temporally sensitive. Given enough time a “hybrid” population is no longer a hybrid, but rather a new distinctive population which itself can be a “parent.” Recombination breaks apart the long range genetic physical associations which are the hallmarks of distinctive admixed ancestry on the genomic scale. That is why clustering methods easily generate a pure “South Asian” component. After at least ~3-4,000 years of continuous admixture the synthesis is now far less coarse, and the elements much more de facto miscible. And yet via other clustering techniques, such as principle components analysis, you get different results. The peculiar position of the “South Asian” individuals between Europeans and East Asians in direct proportion to their caste and regional origins becomes highly indicative of some sort of admixture event in different proportions as a function of geography and social context. The technique in Reconstructing Indian population history allowed for a resolution of this paradox by sifting through the variation and extracting out the ancestral components. The recent papers which came out on Australian Aboriginal genetics do something similar, in terms of making sense of somewhat puzzling results which are found when generating inferences from aggregate genomic variation.

Imagine how much more difficult the task would have been if the ancestral components were much closer! I suspect that’s what’s going on in Europe. I’m not privy to any big secrets, but I have heard of whispers of research groups using Sardinians as a “pure” outgroup to model the changing demographics of Europe since the arrival of agriculture. What David Reich stated at the conference was not particularly surprising to me in light of that possibility. Sardinia regularly pops out as a weird outlier in many analyses. One simple possibility here is that that’s simply a function of the fact that it’s an island, and therefore has diverged from mainland populations due to isolation from conventional village-to-village mate exchange. Another possibility, mooted by Dienekes, is that it may be a repository of European genetic variation from earlier periods, relatively unaffected by later perturbations due to demographic changes. The main reason that I can give some credit to Dienekes’ thesis has less to do with Sardinians than Basques. The French Basques in the HGDP are less atypical than the Sardinians, but in some runs they do lack a component which is most obviously classed as “West Asian,” and which other French have. In Dienekes’ own runs with a diverse array of Iberian populations this same distinction emerges.

All of this reminds us that clustering methods give us great insights into how populations are related to each other, but they don’t tell us about the details of how that relatedness came to be. It makes a great difference if an element is the outcome of relatively recent (<10,000 years) hybridization events, as opposed to having deeper roots. For example, admixture between Polynesians and Melanesians brings together two components, whatever their own prior origins, diverged on the order of 50,000 years before the present. And yet if the two groups mentioned earlier are correct than the Melanesian component itself must be decomposed into two fractions, one of which is much closer to the Polynesians than the other, our understanding of the past changes.

As I implied earlier today I think the era of wild hypothesis generation in the area of the settling of Europe over the last 10,000 years is coming to the end. The combination of more powerful analytic techniques and the emergence of ancient DNA samples with which to calibrate, peg, and check, inferences from those techniques, will probably clarify our understanding of the past to a great extent.

Image credit: yomi955

September 25, 2011

The last 100,000 years in human history

Filed under: Agriculture,Anthroplogy,Human Evolution,Human Genomics — Razib Khan @ 7:02 pm

In light of the recent results in human evolutionary history some readers have appealed to me to create some sort of clearer infographic. There’s a lot to juggle in your head when it comes to the new models and the errors and uncertainties in estimates derived from statistical inference. Words are not always optimal, and there’s often something left out.

So I spent a few hours creating a series of maps which distill my own best guess as to what occurred over the past 100,000 years. I want to emphasize that this purely my own interpretation, based on what I know. This is naturally going to be biased (I don’t know as much about uniparental lineages as some of my readers, and have a weak grasp of a lot of morphological changes, etc.). But it is a place to start. I’ve put the maps into a slideshow. Please observe that in brackets I’ve put qualifies such as “high”, “medium” and “low” in regards to my assertions. That shows you how confident I am about a given assertion. I’m 100% sure that I’m wrong in a lot of the details here, but this is my best guess as to the shape of things over the past 100,000 years. Feel free to ask more in the comments. Also, take the dates with a little fudge room. If I used exact precise dates for everything there would be too many slides.

Note: You can’t see the slideshow in the RSS browser.

September 18, 2011

The words of the father

Over at A Replicated Typo they are talking about a short paper in Science, Mother Tongue and Y Chromosomes. In it Peter Forster and Colin Renfrew observe that “A correlation is emerging that suggests language change in an already-populated region may require a minimum proportion of immigrant males, as reflected in Y-chromosome DNA types.” But there’s a catch: they don’t calculate a correlation in the paper. Rather, they’re making a descriptive verbal observation. This observation seems plausible on the face of it. In addition to the examples offered, one can add the Latin American case, where mestizo populations tend to have European Y chromosomal profiles and indigenous mtDNA.


In one of the more nuanced instances cited by Renfrew and Forster they note that though there is a fair penetration of both Austronesian mtDNA and Y chromosomes amongst Austronesian speaking inhabitants of New Guinea, Austronesian Y chromosomes are nearly absent from those populations which speak Papuan. In other words, the inference is that the native indigenous male elite perpetuated the Papuan language! I think the key issue here is social dominance, and the role of male cultural units. This is clear when you have a group like African Americans. Though mostly West African in ancestry this ethnic group clearly has ~20% European ancestry, mostly mediated through European males. This is simply a function of the social dominance of European males in relation to African males. And, it may be telling that African Americans are an English speaking Christian population, albeit with their own distinctive accent.

In the paper the authors note:

…It may be that during colonization episodes by emigrating agriculturalists, men generally outnumbered women in the pioneer colonizing groups and took wives from the local community. When the parents have different linguistic backgrounds, it may often be the language of the father that is dominant within the family group….

There is certainly some truth to this. But what I think that this narrative misses are the coarser and larger scale social units which expansive male cultural communities operate through. The spread of European males in Latin America was not uncoordinated. Often small groups of males decapitated indigenous male power elites, sometimes literally! Long distance travel, such as what the Austronesians engaged in, almost certainly must have entailed a minimal level of political and ideological commitment. They cite the example of the Genghis Khan haplotype, but that wasn’t perpetuated through a process of gradual demic expansion.

July 30, 2011

A world full of children

Filed under: Agriculture,Culture,Environment,Neolithic,Neolithic Revolution — Razib Khan @ 11:07 pm

The figure to the left is from a new paper in Science, When the World’s Population Took Off: The Springboard of the Neolithic Demographic Transition. It reports the findings from 133 cemeteries in the northern hemisphere in regards to the proportion of 5-19 year old individuals. When calibrated to period when agriculture was introduced into a specific region there seems to be a clear alignment in terms of a demographic transition toward a “youth bulge.” Why? A standard model of land surplus explains part of it surely. When farmers settle “virgin land” there is often a rapid “catch up” phase toward the Malthusian limit, the carrying capacity. Another possibility though is that sedentary populations did not need to space their offspring nearly as much as mobile hunter-gatherers. Whatever the details, the facts remain that the data do point to a shift in the age pyramid during this period. The author wonders as to the possible cultural implications of this. There is an a priori assumption that a young vs. old age profile in a society constrains its choices and channels its energies (e.g., think the “baby boom” generation in ...

July 7, 2011

The biocultural frog and tortoise

As many of you know when you have two adjacent demes, breeding populations, they often rapidly equilibrate in gene frequencies if they were originally distinct. There are plenty of good concrete examples of this. The Hui of China are Muslims who speak local Chinese dialects. The most probable root of this community goes back to the enormous population of Central Asia Muslims brought by the Mongol Yuan dynasty that ruled ruled China for over a century from the late 1200s to 1300s. Genetic studies of this group that I’ve seen indicate that a high bound estimate for West Eurasian ancestry is ~10%. The other ~90% is interchangeable with the Han Chinese. So let’s assume that the Hui are ~10% West Asian. If you assume that in the year 1400 the Hui were “pure,” you have 24 generations (25 years per generation). The original population of “Central Asian Muslims” were heterogeneous, including Iranians and Turks. But let’s take it granted that they were 50% East Eurasian and 50% West Eurasian in ancestry at the time of their arrival. What would the intermarriage rate per generation have to be so ...

June 28, 2011

“What if you’re wrong” – haplogroup J

Back when this sort of thing was cutting edge mtDNA haplogroup J was a pretty big deal. This was the haplogroup often associated with the demic diffusion of Middle Eastern farmers into Europe. This was the “Jasmine” clade in Seven Daughters of Eve. A new paper in PLoS ONE makes an audacious claim: that J is not a lineage which underwent recent demographic expansion, but rather one which has been subject to a specific set of evolutionary dynamics which have skewed the interpretations due to a false “molecular clock” assumption. By this assumption, I mean that mtDNA, which is passed down in an unbroken chain from mother to daughter, is by and large neutral to forces like natural selection and subject to a constant mutational rate which can serve as a calibration clock to the last common ancestor between two different lineages. Additionally, mtDNA has a high mutational rate, so it accumulates lots of variation to sample, and, it is copious, so easy to extract. What’s not to like?

First, the paper, Mutation Rate Switch inside Eurasian Mitochondrial Haplogroups: Impact of Selection and Consequences for Dating Settlement in Europe:

R-lineage mitochondrial DNA represents over 90% of the European ...

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