Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Pastby Published 27 Mar 2018
|Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past.pdf|
A groundbreaking book about how technological advances in genomics and the extraction of ancient DNA have profoundly changed our understanding of human prehistory while resolving many long-standing controversies.
Massive technological innovations now allow scientists to extract and analyze ancient DNA as never before, and it has become clear--in part from David Reich's own contributions to the field--that genomics is as important a means of understanding the human past as archeology, linguistics, and the written word. Now, in The New Science of the Human Past, Reich describes with unprecedented clarity just how the human genome provides not only all the information that a fertilized human egg needs to develop but also contains within it the history of our species. He delineates how the Genomic Revolution and ancient DNA are transforming our understanding of our own lineage as modern humans; how genomics deconstructs the idea that there are no biologically meaningful differences among human populations (though without adherence to pernicious racist hierarchies); and how DNA studies reveal the deep history of human inequality--among different populations, between the sexes, and among individuals within a population.
"Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past" Reviews
This was a fantastic condensation of modern research on genomics and it's effect on our understanding of anthropology and history. Really, what is it with biologists that they are able to write these books understandable to a relatively lay audience without hiding entire detail about how the scientists go about doing their research and draw conclusions:
We scientists are conditioned by the system of research funding to justify what we do in terms of practical application to health or technology. But shouldn’t intrinsic curiosity be valued for itself? Shouldn’t fundamental inquiry into who we are be the pinnacle of what we as a species hope to achieve? Isn’t an attribute of an enlightened society that it values intellectual activity that may not have immediate economic or other practical impact? The study of the human past—as of art, music, literature, or cosmology—is vital because it makes us aware of aspects of our common condition that are profoundly important and that we heretofore never imagined.
Not that some details are hidden. Like use of Principal Component Analysis and other statistical techniques and how they get around problems with these techniques is mostly elided. Still it was fun learning about things Four Population Tests to identify likely common ancestors and how they group current and past populations of people.
The weakest parts of the book are when Reich is trying to walk the tight rope of modern connections between race, behavior and genetics. Which is understandable, because it is a difficult topic. But his bad arguments don't do well for the values he wants to espouse. There is a lot of is vs. ought confusion, with no consistency. This is especially egregious in Chapter 11. Why do I need to be reminded of treating individuals as individuals, just because we find something about group averages. There's something to be said about Nietzsche, that he was correct to claim that trying to derive all our values from objective truth is not ideal, to say the least. But an interesting quote:
I have deep sympathy for the concern that genetic discoveries about differences among populations may be misused to justify racism. But it is precisely because of this sympathy that I am worried that people who deny the possibility of substantial biological differences among populations across a range of traits are digging themselves into an indefensible position, one that will not survive the onslaught of science. In the last couple of decades, most population geneticists have sought to avoid contradicting the orthodoxy. When asked about the possibility of biological differences among human populations, we have tended to obfuscate, making mathematical statements in the spirit of Richard Lewontin about the average difference between individuals from within any one population being around six times greater than the average difference between populations. We point out that the mutations that underlie some traits that differ dramatically across populations—the classic example is skin color—are unusual, and that when we look across the genome it is clear that the typical differences in frequencies of mutations across populations are far less. But this carefully worded formulation is deliberately masking the possibility of substantial average differences in biological traits across populations.
Anyway the book is a lot of fun. One of the funniest parts was about them finding proof for West Eurasian ancestry of large parts of South Asian population:
They did not want to be part of a study that suggested a major West Eurasian incursion into India without being absolutely certain as to how the whole-genome data could be reconciled with their mitochondrial DNA findings. They also implied that the suggestion of a migration from West Eurasia would be politically explosive. They did not explicitly say this, but it had obvious overtones of the idea that migration from outside India had a transformative effect on the subcontinent.
So to get around this:
We wrote that the people of India today are the outcome of mixtures between two highly differentiated populations, “Ancestral North Indians” (ANI) and “Ancestral South Indians” (ASI), who before their mixture were as different from each other as Europeans and East Asians are today. The ANI are related to Europeans, central Asians, Near Easterners, and people of the Caucasus, but we made no claim about the location of their homeland or any migrations. The ASI descend from a population not related to any present-day populations outside India. We showed that the ANI and ASI had mixed dramatically in India. The result is that everyone in mainland India today is a mix, albeit in different proportions, of ancestry related to West Eurasians, and ancestry more closely related to diverse East Asian and South Asian populations. No group in India can claim genetic purity.
And for the rest of the chapter, he deadpan goes on using the ANI-ASI terminology.
Finally, no one comes out looking good when you go far back in time. And we are mixes all the way down.
Traces the general history of humanity from its origins in Africa and the subsequent lineages that went to Europe, South Asia, East Asia, Australasia, The Americas and subsequent African lineages as they changed in the genetic record up to the present. Also covers the detective story behind the discoveries in DNA research which has given us a way more complete history than the archeological record. Tells the varied stories of humanity.
The author, David Reich, is a eminent population geneticist whose work is shedding light on questions of archeology and history. This book is primarily about the origins and movements of the ancestors of persons today. When it sticks to that topic, the book is excellent, except for the occasional awkward sentence.
Unfortunately, the author finds it necessary to make disparaging, and in my opinion misleading, remarks about Nicholas Wade, Henry Harpending, and James Watson. He also repeatedly attacks a straw man in regards to "racial purity."
I recommend the book to those interested in population genetics, human biodiversity, archaeology, anthropology, and ancient history.
"Who We Are and How We Got Here" is great book with some flaws. As a one-stop guide for catching up with the ancient DNA revolution, it is unequaled. It is also a refreshingly honest look into the life of a practicing prominent scientist in the age of large research labs and giant research consortiums.
Coming along for the ride are some lucid explanations of many of the statistical tests used in ancestry mapping, like the Four Populations Test, and methods used to estimate the dates of admixture events. For any outsider to the field who wants to be able to read the flood of research on ancient genomics with more comprehension, this is a valuable introduction.
An incomplete list of some prominent themes with illustrative quotes:
1. The most central theme of the book is probably the immense power of ancient DNA as a way to understand the past. Reich views it as more powerful than radiocarbon dating, the most important scientific advance in archeology:
* "These advances mean that whole-genome study of ancient DNA no longer requires screening large numbers of skeletal remains before it is possible to find a few individuals whose DNA can be analyzed. Instead, a substantial fraction of screened samples dating to the last ten thousand years can now be converted to working genome-wide data. The new methods have made it possible to analyze hundreds of samples in a single study. With such data, it is possible to reconstruct population changes in exquisite detail, transforming our understanding of the past."
* "These days, human genome variation has surpassed the traditional toolkit of archaeology—the study of the artifacts left behind by past societies—in what it can reveal of changes in human populations in the deep"
2. There has been Neanderthal, Denisovan, and other Archaic Human admixture into many extant human populations, with proportions and sources varying for different populations.
* It seems very likely that some genes in those admixture events were advantageous and have subsequently been selected for, while others have experienced have strong selection against them:
* "One of the most striking genomic discoveries of the past few years is a mutation in a gene that is active in red blood cells and that allows people who live in high-altitude Tibet to thrive in their oxygen-poor environment. Rasmus Nielsen and colleagues have shown that the segment of DNA on which this mutation occurs matches much more closely to the Siberian Denisovan genome than to DNA from Neanderthals or present-day Africans.21 This suggests that some Denisovan relatives in mainland Asia may have harbored an adaptation to high altitude, which the ancestors of Tibetans inherited through Denisovan interbreeding. Archaeological evidence shows that the first inhabitants of the Tibetan high plateau began living there seasonally after eleven thousand years ago, and that permanent occupation based on agriculture began around thirty-six hundred years ago.22 It is likely that the mutation increased rapidly in frequency only after these dates, a prediction that will be possible to test directly through DNA studies of ancient Tibetans."
* "at genes associated with the biology of keratin proteins, present-day Europeans and East Asians have inherited much more Neanderthal ancestry on average than is the case for most other groups of genes.23 This suggests that versions of keratin biology genes carried by Neanderthals were preserved in non-Africans by the pressures of natural selection, perhaps because keratin is an essential ingredient of skin and hair, which are important for providing protection from the elements in cold environments such as the ones that modern humans were moving into and to which Neanderthals were already adapted."
3. Currently extant human populations roughly match folk notions of race but in a deep sense are themselves the result of many admixture events in the distant past. That is, while Europeans are quite distinct from East Asians, who are themselves quite distinct from Native Americans/Amerindians, these continental groups are themselves the results of admixture events from previously distinct populations, who were themselves the result of mixture events. In other words, we [humans] are a mix all the way down.
* "Today, the peoples of West Eurasia—the vast region spanning Europe, the Near East, and much of central Asia—are genetically highly similar. The physical similarity of West Eurasian populations was recognized in the eighteenth century by scholars who classified the people of West Eurasia as “Caucasoids” to differentiate them from East Asian “Mongoloids,” sub-Saharan African “Negroids,” and “Australoids” of Australia and New Guinea. In the 2000s, whole-genome data emerged as a more powerful way to cluster present-day human populations than physical features."
* "Measured in this way, populations within West Eurasia are typically around seven times more similar to one another than West Eurasians are to East Asians. When frequencies of mutations are plotted on a map, West Eurasia appears homogeneous, from the Atlantic façade of Europe to the steppes of central Asia. There is a sharp gradient of change in central Asia before another region of homogeneity is reached in East Asia."
* "What we had found was evidence that people in northern Europe, such as the French, are descended from a mixture of populations, one of which shared more ancestry with present-day Native Americans than with any other population living today."
* "Instead of a tree, a better metaphor may be a trellis, branching and remixing far back into the past. " (7)
4. Contrary to post WWII anthropology's consensus, at least some of the great cultural transitions that occurred in the archaeological record were the result of population replacement, not just the cultural propagation of new ideas and technologies. This partially validates the predictions of some old-school (and often racist) anthropologists who thought genocide and conquering (ala Conan the Barbarian's line [https://www.youtube.com/watch?v=6PQ63...] ) was the most common cause of drastic change in the archaeological record but the deep origins of human populations as fundamentally mixed kind of pushes back against many of their other claims.
* " The discovery that the Corded Ware culture reflected a mass migration of people into central Europe from the steppe was not just a sterile academic finding. It had political and historical resonance. At the beginning of the twentieth century, the German archaeologist Gustaf Kossinna was among the first to articulate the idea that cultures of the past that were spread across large geographic regions could be recognized through similarities in style of the artifacts they left behind. He also went further in viewing archaeologically identified cultures as synonymous with peoples, and he originated the idea that the spread of material culture could be used to trace ancient migrations, an approach he called the siedlungsarchäologische Methode, or “Settlement Archaeology.” ... Kossinna suggested that the cultural roots of the Germans and of Germanic languages today lay in the Corded Ware culture. In his essay “The Borderland of Eastern Germany: Home Territory of the Germans,” he argued that because the Corded Ware culture included the territories of Poland, Czechoslovakia, and western Russia of his day, it gave Germans the moral birthright to claim those regions as their own. "
* "migrating farmers whose ancestors originated in the Near East spread over Europe with little mixture with the hunter-gatherers they encountered along the way, a sharp contrast to Luca Cavalli-Sforza’s model for the farming expansion into Europe that had been popular until this time and that emphasized extensive mixture and interaction with the local hunter-gatherers during the expansion. ."
* "The extraordinary fact that emerges from ancient DNA is that just five thousand years ago, the people who are now the primary ancestors of all extant northern Europeans had not yet arrived"
* "Prior to the explosion of ancient DNA data in 2015, most archaeologists found it inconceivable that the genetic changes associated with the spread of the Yamnaya culture could be as dramatic as the archaeological changes. "
5. In an understandable but misguided (in Reich's view)) effort to push back against racism, many population geneticists and anthropologists have been mealy-mouthed/deceptive about what DNA actually reveals about population structure by saying mathematically true but deceptive statements, using unfamiliar words like ancestry or population structure to refer to traditional notions of race, and avoiding the issue entirely. He views Lewontin, Gould and others as falling in this camp of 'deceptive with good intentions', and thinks that scientists should discuss the issue more head-on, as doing otherwise will concede the issue to scientists or informed bloggers who are less averse to speaking openly and speculatively on race.
* Examples of political considerations impacting science:
* "While we were in the final stages of preparing a paper for submission in 2015, one of the German archaeologists who contributed skeletal samples wrote a letter to all coauthors: “We must(!) avoid…being compared with the so called ‘siedlungsarchäologische Methode’ from Gustaf Kossinna!” He and several contributors then resigned as authors"
* "At the time I felt that we were being prevented by political considerations from revealing what we had found."
* "At a workshop on genetic studies of Native Americans that I attended in 2013, multiple researchers stood up from the audience to say that the response of the Karitiana, Havasupai, Navajo, and others had made them too wary to do any research Native Americans (including disease research)....the withdrawal of Navajo samples from out study was distressing, since they were among those with the very best documentation of informed consent..these individuals personals decisions to participate in the study were overruled by the tribal council's moratorium nine years later. "
*"I have deep sympathy for the concern that genetic discoveries about differences among populations may be misused to justify racism. But it is precisely because of this sympathy that I am worried that people who deny the possibility of substantial biological differences among populations across a range of traits are digging themselves into an indefensible position, one that will not survive the onslaught of science. In the last couple of decades, most populations geneticists have sought to avoid contradicting the orthodoxy. When asked about the possibility of biological differences among human populations, we have tended to obfuscate.."
* "To understand why it is no longer an option for geneticists to lock arms with anthropologists and imply that any differences among human populations are so modest that they can be ignored, go no further than the 'genome bloggers'...take pleasure in pointing out contradictions between the politically correct messages academics often give about the indistinguishability of traits across populations and their papers showing that this is not the way the science is heading. "
6. One of the most interesting findings from ancient genomics is using ancient DNA to infer social inequality in admixture events by seeing relative diversity in mitochondrial (maternally transmitted only) DNA versus more homogenity in Y chromosomes (paternally transmitted only). Lots of mt-DNA in conjunction with only a few Y chromosomes implies a few men with many corresponding females, a marker of sexual inequality (via polygamy) and social inequality (the ability of a few men to monopolize the available women). This pattern is seen in many population replacements or admixture events:
* "mixtures of highly divergent groups have happened time and again, homogenizing populations just as divergent from one another as Europeans, Africans, and Naive Americans. And in many of these great admixtures, a central theme has been the coupling of men with social power in one population and women from the other. "
* "Comparison of Y-chromosome and mitochondrial DNA types that are highly different in frequency between African-Americans and Europeans also shows that by far the majority of the European ancestry in these populations comes from males, the result of social inequality in which mixed-race couplings were primarily between free males and females slaves...contribution of European American men to the genetic makeup of the present-day African American population is about 4 times that of the European American women....sociologist Orlando Patterson, he pointed out that fraction of the European ancestry in African Americans that came from males-- which if different from half is called ''sex bias"-- must have been far greater during the time of slavery. Since the civil rights movement in the USA in the mid-20th century, cultural changes have caused the sex bias to reverse, with more coupling between black men and white women. If we carried out DNA studies of African American skeletons from a hundred years ago, there is every reason to expect an even greater sex bias. "
* "sex bias has been central to the history of our species. "
* "great variability among males in the number of offspring produced means that by searching for genomic signatures of past variability in the number of children men have had, we can obtain genetic insights into the degree of social inequality in society as a whole, and not just between males and females. "
* "Star Cluster analysis provides objective information about the importance of extreme inequalities in power at different points in the past. "
* "on the Y chromosome, the studies found a pattern that was strikingly different. IN East Asians, Europeans, Near Easterners, and North Africans, the authors found many Star Clusters with common male ancestors living roughly 5 thousand years ago...powerful males in this period left an extraordinary impact on the populations that followed them-- more than in any previous period-- with some bequeathing DNA to more descendants today than Ghengis Khan. "
Miscellaneous notes I took on themes
1. Neanderthal and out-of-Africa humans mixed and male offspring had reduced fertility
2. We're mixes all the way down
3. There can be REALLY strong endogamy for thousands of years: Ari ethnic group in Ethiopia, caste system in India,
4. Inequality between sexes and within societies has a genetic proxy: inbalance between male and female ancestry-- find this with Star Cluster Analysis
* Yamnayo are BIG in this.
5. Ancient DNA is revealing TONS of surprises...
6. Reich consistently points out places where he got stuff wrong or changed his mind
* used to be strong proponent of Mitochondrial Eve hypothesis and Out of Africa Hypothesis
* didn't believe Excoffier on lower fertility of Neanderthal-Human hybrids
Highly recommended book!
Some flaws that I'm not qualified to speculate overmuch on:
Mainly, Reich is very dismissive of research outside genetics on the question of average phenotypic differences between groups as any kind of evidence for or against average genetic differences. I'm obviously not an expert on this, but head to Twitter to see smarter people duking it out on this or wait for more reviews from actual scientists...
He also has a few throwaway suggestions on the moral imperative to treat individuals as individuals, and not let any conclusions we come to in the future on groups impact individual treatment. His suggestions are so uncontroversial and obvious (like his suggestion to measure phenotype instead of using genotype to predict phenotype) that I'm unsure if he meant them as serious suggestions as opposed to platitudes. For one, Stephen Pinker has made the same argument with the same reasoning in 'The Blank Slate' at least a decade before Reich, as have serious thinkers from all political sides for the last 50 years. So that's not exactly something we needed genetic evidence to remind us of. So don't expect political radicalism from this book-- which is a good thing, IMO.
Having read earlier books on this topic by Svante Paabo, Spencer Wells and others I was anxious to read something current. I wasn't disappointed. This, as others have said, is an excellent summary of the state of genetic research using ancient DNA to determine how we all got to where we are today. The only downside is that the rate of advancement in the field--as the author states--is so high at the moment that unless you read this within two to three years of publication it may well be out of date.
The author emphasizes the importance of "whole genome" research, pointing out that the companies providing genetic information to the public today are primarily using only mitochondrial and Y-chromosome DNA, which only tell the story of two lineages out of thousands.
Some key points for me were that the history of humankind is not like a tree with branches that separate and never rejoin. Ancient DNA has revealed that it is more like a trellis or a braided stream where lineages branch off but then often merge at some later point, Homo sapiens and Neanderthals being just one example of many.
Another interesting point was that Northern Europeans are more closely related to Native Americans than they are to East Asians. This is due to an ancient population of north Eurasians that no longer exist, but when they did they spread west and east across Europe and Siberia and thus contributed ancestry to the people that left northeast Asia to cross Beringia as well as modern north Europeans. Similar stories are recounted for other modern day groups such as those from India and Oceania.
One final story of personal interest is that ancient DNA research has revealed that the sub-Saharan tribe that is most closely related to all non-African people today are the Hadza hunter-gatherers of Tanzania. Coincidentally I was in Tanzania a little over a year ago and had the pleasure of going on a hunt with a small band of Hadza men. They are rapidly being squeezed out of their ancestral hunting territories and number less than 1500 individuals today, so it was very special to spend a day with them.
This is a very worthwhile read, but don't leave it your bookshelf unread for too long.