A new short communication in Scientific Reports suggests that most demographic expansion as ascertained using mtDNA occurred before the Neolithic. MtDNA analysis of global populations support that major population expansions began before Neolithic Time:
Agriculture resulted in extensive population growths and human activities. However, whether major human expansions started after Neolithic Time still remained controversial. With the benefit of 1000 Genome Project, we were able to analyze a total of 910 samples from 11 populations in Africa, Europe and Americas. From these random samples, we identified the expansion lineages and reconstructed the historical demographic variations. In all the three continents, we found that most major lineage expansions (11 out of 15 star lineages in Africa, all autochthonous lineages in Europe and America) coalesced before the first appearance of agriculture. Furthermore, major population expansions were estimated after Last Glacial Maximum but before Neolithic Time, also corresponding to the result of major lineage expansions. Considering results in current and previous study, global mtDNA evidence showed that rising temperature after Last Glacial Maximum offered amiable environments and might be the most important factor for prehistorical human expansions.
I was a little sad when I heard my friend Steve Hsu had accepted a position at Michigan State some months back. My reasons were two-fold. First, I swing by Eugene now and then, and I wouldn’t have the opportunity to drop in on his office. Second, it seemed that Steve was becoming an Administrator. To some extent I feel like that’s going over to the dark side. But ultimately it’s his decision, and Steve has a lot of things going on at any given moment, and I’m hopeful he’ll continue to be involved in the production of scholarship in some form (he’s more of a scholar than most as it is).
Now apparently his move has resulted in submerged tensions coming to the fore. You can read the article in The Lansing Journal, New director’s experience a plus for MSU, but his controversial views concern some. Let’s qualify who these “some” are:
I’ve mentioned a few times that the Reich lab has been finding suggestive evidence for admixture between indigenous South Asians and a West Eurasian group on the order of ~3,000 years before the present. The modal explanation is probably an Indo-Aryan intrusion. Dienekes used rolloff in ADMIXTOOLS to repeat these general findings. Specifically, he found signal for an admixture event analogous to one between non-Brahmin South Indians and Northern Europeans. I say analogous because I do not mean to imply that the admixture was exactly of this form. Rather, there are general resemblances in the genetic profiles across the four groups (i.e., Orcadian & North Kannadi, and population X and Y which merged to form South Indian Brahmins).
When it comes to the human genetics of the Khoe-San there’s a little that’s stale and unoriginal for me in terms of presentation. The elements are always composed the same. The Bushmen are the “most ancient” humans, who can tell us something about “our past,” about “our evolution.” Tried & tested banalities just bubble forth unbidden. I have no idea why. There’s a new paper in Science on the genetics of the Khoe-San, which includes Bushmen, which brought to mind this issue for me because of the outrageous nature of the press releases.
The title of the paper itself is a testament to vanilla, Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History. This is absolutely not surprising. Are you shocked that the Khoe-San have adaptations? Or that African history is complex? The wonder of it all! This paper actually revisits much of the same ground as Pickrell et al.’s originally titled The genetic prehistory of southern Africa. Before Dr. Pickrell executes throw-down on me on Twitter let me concede that I have no creative ideas to offer in terms of an alternative title. Rather, I have an idea: perhaps in the future scientists could explore the evolutionary genetic basis for steatopygia? The trait is not limited just to Khoe-San, my distant cousins the Andaman Islanders also exhibit it. Perhaps this is the ancestral state of the human lineage? This is a situation where the titles just write themselves!
Over at Haldane’s Sieve there are more than preprints posted, there are commentaries from the authors as well. For example, for The genetic prehistory of southern Africa, the first author, Dr. Joseph K. Pickrell, has a extended comment up.
But occasionally you get contributions & perspectives from non-authors which are very interesting. And it is to one of these I want to draw your attention, Thoughts on: The date of interbreeding between Neandertals and modern humans. It’s a comment on The date of interbreeding between Neandertals and modern humans. In the post Dr. Graham Coop contends:
At this point you are likely saying: well we know that Neandertals existed as a [somewhat] separate population/species who are these population X you keep talking about and where are their remains? Population X could easily be a subset of what we call Neandertals, in which case you’ve been reading this all for no reason [if you only want to know if we interbred with Neandertals]. However, my view is that in the next decade of ancient human population history things are going to get really interesting. We have already seen this from the Denisovian papers [1,2], and the work of ancient admixture in Africa (e.g. Hammer et al. 2011, Lachance et al. 2012). We will likely discover a bunch of cryptic somewhat distinct ancient populations, that we’ve previously [rightly] grouped into a relatively small number of labels based on their morphology and timing in the fossil record. We are not going to have names for many of these groups, but with large amounts of genomic data [ancient and modern] we are going to find all sorts of population structure. The question then becomes not an issue of naming these populations, but understanding the divergence and population genetic relationship among them.
This is a bold contention, and I suspect some physical anthropologists will take issue with it. But it’s a testable prediction. We’ll know if it’s panned out in 2020. I may still be blogging between now and then, and so I will now self-importantly label this “Coop’s Conjecture.” Is there anyone who wants to wager some money on Coop’s Conjecture? Any side of the bet you think is a sure thing?
The Pith: You’re Asian. Yes, you!
A conclusion to an important paper, Nick Patterson, Priya Moorjani, Yontao Luo, Swapan Mallick, Nadin Rohland, Yiping Zhan, Teri Genschoreck, Teresa Webster, and David Reich:
In particular, we have presented evidence suggesting that the genetic history of Europe from around 5000 B.C. includes:
1. The arrival of Neolithic farmers probably from the Middle East.
2. Nearly complete replacement of the indigenous Mesolithic southern European populations by Neolithic migrants, and admixture between the Neolithic farmers and the indigenous Europeans in the north.
3. Substantial population movement into Spain occurring around the same time as the archaeologically attested Bell-Beaker phenomenon (HARRISON, 1980).
4. Subsequent mating between peoples of neighboring regions, resulting in isolation-by-distance (LAO et al., 2008; NOVEMBRE et al., 2008). This tended to smooth out population structure that existed 4,000 years ago.
Further, the populations of Sardinia and the Basque country today have been substantially less influenced by these events.
It’s in Genetics, Ancient Admixture in Human History. Reading through it I can see why it wasn’t published in Nature or Science: methods are of the essence. The authors review five population genetic statistics of phylogenetic and evolutionary genetic import, before moving onto the novel results. These statistics, which measure the possibility of admixture, the extent of admixture, and the date of admixture, are often presented, but nested into supplements, in previous papers by the same group. On the one hand this removes from view the engines which are driving the science. On the other hand I have always appreciated that a benefit of this injustice to the methods which make insight possible is that those without academic access can actually bite into the meat of the researcher’s mode of thought.
I did read through the methods. Twice. I’ve encountered all the statistics before, and I’ve read how they were generated, but I’ll be honest and admit that I haven’t internalized them. That has to end now, because the authors have finally released a software package which implements the statistics, ADMIXTOOLS. I plan to use it in the near future, and it is generally best if you understand the underlying mechanisms of a software package if you are at the bleeding end of analytics. I will review the technical points in more detail in future posts, more for my own edification than yours. But for the moment I’ll be a bit more cursory. Four of the tests use comparisons of allele frequencies along explicit phylogenetic trees. That’s so general as to be uninformative as a description, but I think it’s accurate to the best of my knowledge. In the basics the tests are seeing if a model fits the data (as opposed to TreeMix, which finds the best model out of a range to fit the data). The last method, rolloff, infers the timing of an admixture event based upon the decay of linkage disequilibrium. In short, admixture between two very distinct populations has the concrete result of producing striking genomic correlations. Over time these correlations dissipate due to recombination. The magnitude of dissipation can allow one to gauge the time in the past when the original admixture occurred.
By now you have probably seen the new Denisovan paper in the media. John Hawks has an excellent overview, as you’d expect. The only thing I will add is to reiterate that I think population movements in near and far prehistory significantly obscure our comprehension of the patterns of past genetic variation. One reason that the Denisova hominin presents conundrums (e.g., how did Australians and Melanesians admix with a population whose only remains are found in Siberia) is that we’re viewing it through the lens of the present. What other lens can we view it through? We’re not time travelers. But we should be perhaps more conscious of the filter which that imposes upon our perception and model of the world. This is probably a time when it is best to have only a modest confidence in any given proposition about the prehistoric past.
Also, I don’t know why, but I much like this tree:
The map to the right shows the frequencies of HGDP populations on SLC45A2, which is a locus that has been implicated in skin color variation in humans. It’s for the SNP rs16891982, and I yanked the figure from IrisPlex: A sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information. Brown represents the genotype CC, green CG, and blue, GG. Europeans who have olive skin often carry the minor allele, C. While SLC24A5 is really bad at distinguishing West Eurasians from each other, SLC45A2 is better. Though both are fixed in Northern Europe, the former stays operationally fixed in frequency outside of Europe, in the Near East. As I stated earlier the proportions of the ancestral SNP in the Middle Eastern populations in the HGDP seem to be easily explained by the Sub-Saharan admixture you can find in these groups.
In contrast major SNPs in SLC45A2 are closer to disjoint between Europeans and South Asians. For example I’m a homozygote for the C allele. And yet even here we need to be careful. I want in particular to draw your attention to the frequencies in the Middle Eastern populations, the Sardinians, and the Kalash of Pakistan.
The Kalash, and their Nuristani cousins, have often been observed to have “European” physical features. These populations even trade in legends of descent from the Macedonians of Alexander. And the genetics here shows why. Though the Kalash far are more closely related to other Northwest South Asians than to Europeans, on the subset of genes which are implicated in pigmentation many of them could actually “pass” for Europeans. In fact, it is interesting to me that by these measures the Sardinians are no more European than groups like the Kalash and the Druze (in contrast to the total genome, where Sardinians may be the best reference for Western Europeans). They have a lower frequency of the SNP strongly associated with blue eyes than either of these groups, for example.
In the above paper they also produced a chart which illustrated the relationships of HGDP populations as a measure only of the six SNPs they used in their prediction method. These are markers which distinguish blue and brown eye color in Europeans efficiently.
OK, perhaps I can help with that. Dr. Coop speaks of the collaboration between himself & Dr. Joseph Pickrell, Haldane’s Sieve, which I added to my RSS days ago (and you can see me pushing it to my Pinboard). From the “About”:
As described above, most posts to Haldane’s Sieve will be basic descriptions of relevant preprints, with little to no commentary. All posts will have comment sections where discussion of the papers will be welcome. A second type of post will be detailed comments on a preprint of particular interest to a contributor. These posts could take the style of a journal review, or may simply be some brief comments. We hope they will provide useful feedback to the authors of the preprint. Finally, there will be posts by authors of preprints in which they describe their work and place it in broader context.
We ask the commenters to remember that by submitting articles to preprint servers the authors (often biologists) are taking a somewhat unusual step. Therefore, comments should be phrased in a constructive manner to aid the authors.
It might be helpful if other evolution/genetics bloggers reblog this so we can push it up the Google search results. If you google “Haldane’s Sieve” some of the results are interesting…and not necessarily in a good way. I do feel guilt blogging on stuff my readers can’t get, so the more preprints become acceptable the more we (as in, the general public) can understand about evolution.
Interesting story in The New York Times, Genes Now Tell Doctors Secrets They Can’t Utter:
One of the first cases came a decade ago, just as the new age of genetics was beginning. A young woman with a strong family history of breast and ovarian cancer enrolled in a study trying to find cancer genes that, when mutated, greatly increase the risk of breast cancer. But the woman, terrified by her family history, also intended to have her breasts removed prophylactically.
Her consent form said she would not be contacted by the researchers. Consent forms are typically written this way because the purpose of such studies is not to provide medical care but to gain new insights. The researchers are not the patients’ doctors.
But in this case, the researchers happened to know about the woman’s plan, and they also knew that their study indicated that she did not have her family’s breast cancer gene. They were horrified.
“We couldn’t sit back and let this woman have her healthy breasts cut off,” said Barbara B. Biesecker, the director of the genetic counseling program at the National Human Genome Research Institute, part of the National Institutes of Health. After consulting the university’s lawyer and ethics committee, the researchers decided they had to breach the consent stipulations and offer the results to the young woman and anyone else in her family who wanted to know if they were likely to have the gene mutation discovered in the study. The entire family — about a dozen people — wanted to know. One by one, they went into a room to be told their result.
“It was a heavy and intense experience,” Dr. Biesecker recalled.
Around the same time, Dr. Gail Jarvik, now a professor of medicine and genome science at the University of Washington, had a similar experience. But her story had a very different ending.
She was an investigator in a study of genes unrelated to breast cancer when the study researchers noticed that members of one family had a breast cancer gene. But because the consent form, which was not from the University of Washington, said no results would be returned, the investigators never told them, arguing that their hands were tied. The researchers said an ethics board — not they — made the rules.
Dr. Jarvik argued that they should have tried to persuade the ethics board. But, she said, “I did not hold sway.”
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 as one of the references. You don’t need to know the details, just that Northern European populations seem to exhibit an affinity to East Asians. Our favorite human genomicsts at Broad highlighted this tendency, and Dienekes went looking (if David Reich et al. were inclined toward mischief they should just posit some crazy scenario, and see if Dienekes assembles the requisite data set!). Which is all fine, and we’ll see more of this in the near future. It isn’t as if others aren’t using Sardinians.
ADMIXTURE and STRUCTURE tests aren’t formal mixture tests. Yes! In fact, in the “open science” community this issue is repeated over and over and over, because people routinely get confused (our audience does not consist of population geneticists and phylogeneticists by and large). So sometimes it is necessary to lay it out in detail as in the post above. The key point to always remember is that population genetic & phylogenetic statistics and visualizations are a reduction and summary of reality in human palatable form. They tell us something, but they do not tell us everything. A common issue is that for purposes of mental digestion it is useful to label ancestral elements “European,” or on PCA refer to a “European-Asian” cline, as if the population genetic abstractions themselves are the measure of what European or Asian is. But European and Asian are themselves human constructions, and subject to debate (e.g., do Turks count as Europeans? Indians as Asians?) The population genetic statistics are not themselves subjective, but the meanings we give them are.
As you may know the interminable Myriad genetics patents case has been making waves in the courts, most recently with mixed results as to whether their patents on several specific genetic diagnostics are valid. This aspect needs to be highlighted:
One of the three deciding judges, William Bryson, dissents in part from the majority opinion, arguing that Myriad’s claims to the BRCA gene and gene fragments are not valid. He writes that he feared that if the majority opinion stands, it “will likely have broad consequences, such as preempting methods for whole-genome sequencing.”
This is legalistic hyperbole. If “gene patents” become so ridiculous that whole-genome sequencing becomes unfeasible then the system of intellectual property is going to come crashing down. And whole-genome (and exome) sequencing is not that far off. The Myriad case feels so 2002 to me. It reminds me of another instance where the sluggishness of the legal process was such that the dispute became a moot point because of the march of technological history: the GIF. A particular company owned the rights to the GIF’s compression technique. But over the years the GIF became a marginal format, and the controversy just faded away.
Evaluating recent evolution, migration and Neandertal ancestry in the Tyrolean Iceman
Paleogenetic evidence from Neandertals, the Neolithic and other eras has the potential to transform our knowledge of human population dynamics. Previous work has established the level of contribution of Neandertals to living human populations. Here, I consider data from the Tyrolean Iceman. The genome of this Neolithic-era individual shows a substantially higher degree of Ne- andertal ancestry than living Europeans. This comparison suggests that early Upper Paleolithic Europeans may have mixed with Neandertals to a greater degree than other modern human populations. I also use this genome to evaluate the pattern of selection in post-Neolithic Europeans. In large part, the evidence of selection from living people’s genetic data is confirmed by this specimen, but in some cases selection may be disproved by the Iceman’s genotypes. Neolithic-living human comparisons provide information about migration and diffusion of genes into Europe. I compare these data to the situation within Neandertals, and the transition of Neandertals to Upper Paleolithic populations – three demographic transitions in Europe that generated strong genetic disequi- libria in successive populations.
Yesterday I pointed out that David Reich had a moderately dismissive attitude toward the new paper in PNAS, Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. Here’s what Reich said:
…But Reich believes that the discussion would have been different if it had happened in the open. The PNAS paper questioning the Neanderthal admixture addresses issues swirling around two years ago, but not Reich and Slatkin’s latest work. “It’s been an issue for several years. They were right to work on this,” says Reich. But now, “it’s kind of an obsolete paper,” he says.
Here’s what Nick Patterson, Reich’s colleague told me via email:
Ancient structure in Africa was considered when we wrote the Green et al. paper, and we were aware that this could explain D-statistics. But the hypothesis is no longer viable as the major explanation of Neandertal genetics in Eurasia. This was discussed in the recent paper of Yang et al. (MBE, 2012). (Not referenced by the PNAS paper).
A very simple argument, that convinces me, is that the allelic frequency spectrum of Neandertal alleles in Eurasia falls off very quickly. A bottleneck flattens out the spectrum, and it turns out that the Neandertal gene flow has to be placed after the out of Africa bottleneck or the spectrum is much too flat.
The paper on the arXiv from the Reich lab (Sankararaman et al.) is trying to do something much more subtle than this and date the flow. I personally am no longer interested in explaining the introgression as ancient structure. That ship has sailed.
Of course the question of what was the genetic structure of Ancient Africa is quite open, and remains very interesting.
If Nick’s explanation is a bit cryptic for you (he was a cryptographer!), figure 2 from the Yang et al. paper lays it out quite clearly:
In light of the previous post you know that I was going to post on the new paper in PNAS, North African Jewish and non-Jewish populations form distinctive, orthogonal clusters. Additionally, the press people at Albert Einstein did reach out to me. That doesn’t mean I’ll blog a paper, but it does mean that I’ll give it an extra look. If the authors or people associated with the paper care to have their work publicized, and reach out to humble bloggers, then that’s all good in my book. Also, I suppose over the past two years I’ve become a locus of “Jewnetics” commentary.
In some ways this is the Golden Age of Jewnetics, though we are approaching the epoch of silver. There has to be diminishing marginal returns at some point, and I think the 2010 papers which I reviewed earlier really established the broad outlines of the scientific genealogy of the Jewish people. But just because the broad outlines are established doesn’t mean that there isn’t something to say on specific aspects which haven’t been deeply explored. Some of the commentary on this weblog around the 2010 papers revolved in great deal on the origins of the Jews of North Africa.
The question is simple: how much of the ancestry of the Jews of North Africa derives from the original Jews of antiquity who settled this region, how much derives from indigenous peoples of North Africa, and now much derives from the Sephardic migration out of Iberia ~500 years ago? To recap, one of the major historical processes affecting the Mediterranean Jewry after 1500 was the expansion of a network of Spanish Jews who were expelled from their homeland (unless they converted to Christianity) to the southern and eastern shores of the Mediterranean (with some going to Italy and Western Europe). This resulted in the development of a “Sephardic international,” which was overlain upon an indigenous Jewish substrate which preceded the migrants. So, for example in Greece and Syria there are historically attested differences between the Sephardic Jews who arrived after 1500 and the Jewish communities which preceded them. The same was true of North Africa. But a major complication within this picture is that by and large culturally the Sephardic Jews won. The Sephardic identity superseded and absorbed that of most Jewish communities which had long standing roots in a particular region (e.g., Romaniotes).
In the case of North Africa there are myths which are promoted by some because of legends about Berber tribes which were Judaized. Though there is legitimate academic skepticism about the Jewish identity of Kahina, the Berber queen, it does stand to reason that if the Jewish communities of North Africa date back to Roman antiquity they would possibly have some indigenous ancestry (as well as Latin and Punic). The extent of this ancestry would be a function of the demographic, as opposed to cultural, influence of the Sephardic Jewry.
A few people have asked me about a new paper on arXiv, The Missing Link of Jewish European Ancestry: Contrasting the Rhineland and the Khazarian Hypotheses. Since it is on arXiv you can read the preprint yourself. And, since it is a preprint it is not quite polished, so keep that in mind when evaluating it. After a fashion we are part of the polishing process. So what do I think?
First, it seems to me that the author has a sense of humor about this, and I don’t know how seriously to take some of his assertions. Consider this passage: Such an unnatural growth rate (1.7-2% annually) over half a millennia, affecting only Jews residing in Eastern Europe is commonly explained by a miracle (Atzmon et al. 2010). Unfortunately, this divine intervention explanation poses a new kind of problem – it is not science. Taken literally this seems rather bizarre. In the paper referenced the author refers to the “so-called demographic miracle of population expansion,” alluding to another scholar’s observation. It seems obvious that miracle in this context simply means an inexplicable phenomenon, not a genuine supernatural intervention. There are also plain factual problems which I assume will get cleared up in the final draft. Romania and Hungary are referred to as Slavic nations which were targets of migration by Khazars fleeing the collapse of their polity. Neither of these nations were then, or are now, Slavic. In general I have to say that the historical framework of the paper is very skeletal, verging on incoherent (at least to me).
Dienekes points to a David Reich video where he shows his hand as to future possible results to come out of his lab. The short of it is that it seems likely that most agricultural populations exhibit the same dynamic outlined in Reconstructing Indian History. At the least you have an intrusive group admixing with indigenes. At the extreme you have total replacement. The pattern is confirmed for India, Ethiopia, and Southeast Asia. It seems highly likely in Europe. There are other rumored results in East Asia which might shake things up.
On a minor note, I do want to add that I think many archaeologists aren’t going to be totally surprised that modern Europeans don’t derive by and large from Aurignacians. But, the relatively recent nature of the map of genetic variation which we take for granted probably will shock, and result in a high degree of skepticism. Yet if I had to bet I would bet on the model being sketched out by David Reich. These admixtures and replacements are likely to resolve some confusions of our understanding of the settlement of the world using simple tree models with branching points tens of thousands of years in the past (e.g., you already know that Oceanians will have a longer branch because of archaic admixture).
In many ways the image of Africa in the minds of Westerners has become a trope. The “Dark Continent,” eternal, and primal. Like many tropes the realized existence of this Africa is only within the imagination. The real Africa is far different. For there is no real Africa, there Africas. This truth is on my mind this week as two papers of great importance in understanding African genetic history finally saw the light of day. First, Dr. Joseph Pickrell et al. posted their preprint, The genetic prehistory of southern Africa, to arXiv. Second, out of the Tishkoff lab came Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers. Let me step aside here and observe a secondary, but non-trivial, detail. The former is an open access preprint. The second is a complete paper published in a relatively high impact journal, Cell, for which the paper itself does not seem typical or appropriate. This is fair enough, most people do not read journals front to back in this day. But unlike Dr. Joseph Pickrell’s paper the paper in Cell is paywalled, and from what I can tell you can not obtain the supporting information without getting beyond the gate! So if you need that paper, email me and I will send it onward (I would just post it on a server, but I’ve gotten nasty emails from the legal departments of publishers, so I am wary of doing that).
Jews, and Ashkenazi Jews in particular, are very genetically distinctive. A short and sweet way to think about this population is that they’re a moderately recent admixture between a Middle Eastern population, and Western Europeans, which has been relatively isolated due to sociocultural forces. As far as their inbreeding, well, here’s one recent paper, Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population: To explore the amount of genetic variation within the AJ and European populations, we first measured the mean heterozygosity. Surprisingly, we found a higher level of heterozygosity among AJ individuals compared with Europeans…confirming speculation made in one recent report and a trend seen in another…Although this difference may appear small, it is highly statistically significant because of the large number of individuals and markers analyzed, even after pruning SNPs that are in high LD. The higher diversity in the AJ population was paralleled by a lower inbreeding coefficient, F, indicating the AJ population is more outbred than Europeans, not inbred, as has long been assumed…The greater genetic variation among the AJ population was further confirmed using a pairwise identity-by-state (IBS) permutation test, which showed that average pairs of AJ individuals have significantly less genome-wide IBS sharing than pairs of EA or Euro individuals…Thus, our results show that the AJ population is more genetically diverse than Europeans. How could Ashkenazi Jews be more diverse? Look at what I wrote above, and what most people intuitively assume: Ashkenazi Jews are an admixed population, so they likely carry the alleles unique to both Western Europeans and Middle Eastern peoples! On the other hand, Ashkenazi Jews do have a lot of the genome identical by descent, as befits a population which has long been endogamous, and entered into a recent population expansion from a more modest base.
Image credit: Georges Beard.