Being public on the internet means having to interact with many different sorts. Recently I’ve been having to deal with a heckler on Facebook. The heckler is actually of a particular type. I’m still trying to learn genetics at this point in my life, so I don’t propose to assert that my opinions are beyond dispute. But there is a variety of discussion which is not fruitful.

An interesting aspect of talking to people about genetics is that totally novice intelligent lay people are often very easy to communicate with. Genetics isn’t that hard, and when people want to learn new concepts and have the ability to it can be a great joy. Similarly, the numerous people who know much more genetics are easy to talk to, because they operate on a domain of fluency which makes conversation effortless (obviously this may not be reciprocated on their part in terms of their perception of your lack of knowledge!).

But there is a third sort of person, one who believes they know much more than a lay person, but does not know that they don’t know enough to really be able to talk about what they think they can talk about. Michael Scroggins, who has the temerity to assert that “a gene is more rhetorical topic than scientific fact”, is certainly in this category. But he is one of many. The standard way to identify this sort of person is that they often appeal to a particular touchstone or keyword, and then deploy them as if it were a sort of abracadabra magic. This generally works as a bluff among the ignorant, but it simply produces incredulous confusion when targeted against individuals who are moderately familiar with a particular discipline. For these people ideas like “evo-devo,” “epigenetics,” “development,” and “interaction” are positive buzzwords. “Reductionism” is a negative one. On occasion they are sophisticated Creationists, but much more often they’re Left-liberals from humanistic backgrounds angered by my “gene promotion” (frankly, I can often only get a flavor of their distaste, as I have a difficult time of parsing their gibberish in anything more than a superficial sense).

Below, submitted for your edification, are two screenshots which illustrate recent volley’s I’ve had to deal with. I have a difficult time parsing out the second comment as anything more than buzzwords meant to intimidate (yes, I am the person who “liked” the first comment).

To be clear, the comment below is responding to Human mutation unveiled (yes, I’m mystified by the causality in this case).

Readers should probably know that I regularly receive these sorts of comments, but never publish them (in fact, those individuals are always immediately banned). The reality of the uncanny valley of knowledgeable ignorance is particularly bittersweet for me, as I’m an dilettante. I always struggle with the possibility that I’m actually one of these people in the various fields in which I take an interest. A mode of operation that helps I suspect is that I try and not to leverage my thin knowledge set to any prior outside (e.g., political, social) commitments I might have in a vocal manner. Otherwise I might look the fool….

Credit: Albozagros

The genetics and history of Tibet are fascinating to many. To be honest the primary reason here is elevation. The Tibetan plateau has served as a fortress for populations who have adapted biologically and culturally to the extreme conditions. Naturally this means that there has been a fair amount of population genetics on Tibetans, as hypoxia is a side effect of high altitude living which dramatically impacts fitness. I have discussed papers on this topic before. And I will probably talk more about it in the future, considering rumblings at ASHG 2012.

But to understand the character of the effect of natural selection on a population it is often very important to keep in mind the phylogenetic context. By this, I mean that evolutionary processes occur over history, and those historical events shape the course of subsequent of phenomena. Concretely, to understand how the Tibetans came to be adapted to high altitudes one must understand who they are related to, and what their long term history is. There is a paper in Molecular Biology and Evolution which attempts to do just that, Genetic evidence of Paleolithic colonization and Neolithic expansion of modern humans on the Tibetan Plateau:

Tibetans live on the highest plateau in the world, their current population size is nearly 5 million, and most of them live at an altitude exceeding 3,500 meters. Therefore, the Tibetan Plateau is a remarkable area for cultural and biological studies of human population history. However, the chronological profile of the Tibetan Plateau’s colonization remains an unsolved question of human prehistory. To reconstruct the prehistoric colonization and demographic history of modern humans on the Tibetan Plateau, we systematically sampled 6,109 Tibetan individuals from 41 geographic populations across the entire region of the Tibetan Plateau and analyzed the phylogeographic patterns of both paternal (n = 2,354) and maternal (n = 6,109) lineages as well as genome-wide SNP markers (n = 50) in Tibetan populations. We found that there have been two distinct, major prehistoric migrations of modern humans into the Tibetan Plateau. The first migration was marked by ancient Tibetan genetic signatures dated to around 30,000 years ago, indicating that the initial peopling of the Tibetan Plateau by modern humans occurred during the Upper Paleolithic rather than Neolithic. We also found evidences for relatively young (only 7-10 thousand years old) shared Y chromosome and mitochondrial DNA haplotypes between Tibetans and Han Chinese, suggesting a second wave of migration during the early Neolithic. Collectively, the genetic data indicate that Tibetans have been adapted to a high altitude environment since initial colonization of the Tibetan Plateau in the early Upper Paleolithic, before the Last Glacial Maximum, followed by a rapid population expansion that coincided with the establishment of farming and yak pastoralism on the Plateau in the early Neolithic.

The two major salient points I think need emphasis are:

1) Massive sample sizes for mtDNA and lesser extent Y chromosomal linages

2) Tibetans are a compound of agriculturalists who arrived onto the plateau >10,000 years, and, hunter-gatherers who date back to the Paleolithic

Citation: Cai, Xiaoyun, et al. “Human migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum revealed by Y chromosomes.” PloS one 6.8 (2011): e24282.

There are many issues with this paper that bother me. The broadest interpretation of their thesis is one I find creditable, but in the details I’m left skeptical, confused, and more curious than when I began. Also, I need to add that I talked to the people who presented a poster on this paper at ASHG 2012, though I do not know if they were the authors. They seemed nice, but, also not necessarily totally focused on the questions they were exploring, as opposed to obtaining huge sample sizes and applying standard methods to them. Speak of which, the first thing that jumps out is that their sample is skewed toward what is today Tibet proper, the autonomous province. But Tibetan people have historically lived as far as Sichuan. Only 50% of ethnic Tibetans live in the autonomous region, but well over 90% of their samples are from this area. In terms of exploring adaptation to altitude this is fine, but if you are going to do phylogeography you need better geographical coverage I would think.

But that’s only a minor aside. The bulk of the paper consists of a laundry list of Y and mtDNA haplogroups, and coalescence times. Some of the results are very persuasive to me. There are some Y lineages which exhibit a “star shaped” phylogeny, which usually connotes a recent rapid population expansion. Using other methods the authors have inferred that there was indeed an expansion of population after the introduction of agriculture >10,000 years ago. There is no great reason on prior grounds to be skeptical of this finding. Nevertheless, drilling down produces great confusions, and I am not sure that the coalescence times and phylogenies actually mean what the authors assume they mean.

For example, here is a standard sort of analysis presented in this paper:

We identified a molecular signature of recent population expansion during the early Neolithic time in both paternal (Y-chromosomal D3a-P47 and O3a3c1-M117) and maternal (M9a1a and M9a1b1) lineages (10-7 kya) (table 1). The detailed analysis of haplotype sharing and time of divergence between Tibetans and Han Chinese suggests that the Neolithic population expansion on the Plateau was likely caused by the dispersal of the earliest Neolithic Han Chinese agriculturalists originating about 10 kya in what is now northwestern China….

O3a3c1-M117 is present at frequencies of nearly ~30%, and is connected with the Chinese as you can see above. This dovetails with other recent research which imply relatively recent common ancestors between Tibetans and Chinese. This result can be reconciled to the presence of Paleolithic roots via the fact that admixed populations will give you average results between the two extremes. The problem I have is that I am skeptical that Han Chinese existed 10,000 years ago, just as I am skeptical that Greeks existed 10,000 years ago.

Citation: Cai, Xiaoyun, et al. “Human migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum revealed by Y chromosomes.” PloS one 6.8 (2011): e24282.

A quick literature search yields the fact that M117 is modal in particular non-Han ethnic groups resident in southern China and northern Southeast Asia. I am not here proposing that the Hmong introduced M117 to the Tibetans. Rather, I am suggesting that we best be careful in assuming that we know the ethnic distribution of genetic haplogroups 6,500 years before there were any written records from a given region! To me the fact that there is a putative Sino-Tibetan group of languages is strongly indicative of diversification >10,000 years, not the existence of a Han ethnicity ~10,000 year ago. The historical records are clear that ~3,000 years ago the Yangzi river, now the informal dividing line between North China and South China, was the boundary of the zone where Han were demographically dominant. And even then there were clearly pockets of “barbarian” people on the North China plain itself! It simply does not stand up to the test of basic plausibility that the agricultural expansions ~10,000 years B.P. were Han as we would understand Han. The demographic and cultural dominance of the Han in Northeast Asia is a phenomenon of the last 3,000 years, perhaps 4,000 most generously (South China became Sinicized to some extent after the fall of the Latter Han Dynasty ~200 AD, and especially the Tang period ~600-950 AD).

Much of the argumentation is creaky because of these anachronistic assumptions and the casual inferences of contemporary haplogroup frequencies back toward ancient geographical demographic distributions. Ancient DNA has highlighted the danger of this in Europe, and that should update our priors as to the robustness of this sort of analysis. For example, the authors are curious as to the lack of structure of Y chromosomal lineages, combined with the fact of their deep coalescence times across Tibet. Why is this an issue? Because if these Y chromosomal lineages are Paleolithic, then the deep converges across the branches should also correspondent to geographic differences. But they don’t. To me the simplest explanation is that the last 10,000 years have seen a great deal of population movement, and sharply differentiated populations were brought together as agriculture opened up the Tibetan plateau. This presents a problem though with inferring ancient geographic connections from present distributions, since it opens up the possibility of migration, and radical genetic-demographic turnover.

Overall I would say that this paper is interesting and useful, but you should read it closely and not take the author’s inferences too much to heart. Those inferences are grounded in assumptions which may be built on false foundations.

Addendum: Also, a “gap” on a PCA plot does not necessarily mean long term isolation, as they say in the text. It might simply be a function of inadequate sampling. See above. There are many unsupported assertions such as that. But, I would like to add that the authors found a large number “exotic” haplogroups in Lhasa itself, which aligns with what we know about the cultural history of Tibet. Tibetan Buddhism actually is influenced more by extinct variants of South Asian (particularly, Bengali) Buddhism, rather than Chinese Buddhism. Though the demographic pump along the Himalayan border seems to go from the highlands to the lowlands, there were exceptions. And these exceptions tended to be found in Lhasa.

Citation: Cai, Xiaoyun, et al. “Human migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum revealed by Y chromosomes.” PloS one 6.8 (2011): e24282.

Byzantine Emperor Leo “the Khazar” with his son Constantine IV. Credit: Cplakidas

For the past year or so I’ve been getting queries about what I think about Eran Elhaik’s preprint on the genetic character of European Jews. I found some of the conclusions frankly a little weird, but I assumed that things would be cleaned up for publication. Well, it’s been out for a while now: The Missing Link of Jewish European Ancestry: Contrasting the Rhineland and the Khazarian Hypotheses. But some reporting in The Jewish Daily Forward has brought the author and his detractors a bit into the spotlight. The reason is that as you can tell from the title of the author takes a position on the Khazarian origin model of Ashkenazi Jews (in favor). Here is a non-genetic take over at GeoCurrents, the thrust of which I basically concur with.

In any case, many of the problems with the paper remain. Really it all begins and ends here:

Choice of Surrogate Populations

As the ancient Judeans and Khazars have been vanquished and their remains have yet to be sequenced, in accordance with previous studies (Levy-Coffman 2005; Kopelman et al. 2009; Atzmon et al. 2010; Behar et al. 2010), contemporary Middle Eastern and Caucasus populations were used as surrogates. Palestinians were considered proto-Judeans because they are assumed to share a similar linguistic, ethnic, and geographic background with the Judeans and were shown to share common ancestry with European Jews (Bonne´-Tamir and Adam 1992; Nebel et al. 2000; Atzmon et al. 2010; Behar et al. 2010). Similarly, Caucasus Georgians and Armenians were considered proto-Khazars because they are believed to have emerged from the same genetic cohort as the Khazars (Polak 1951; Dvornik 1962; Brook 2006).

Elhaik’s methods and data sets are all legitimate. But the outcome of this contest is already forgone by the nature of how he defined the rules of the game. There are reasonable arguments for thinking that modern Armenians may exhibit a closer genetic relationship to the Jews of Roman Antiquity, and perhaps even the Hebrews of the Persian years, than modern Palestinians. The two primary ones being that modern Palestinians have African ancestry, and, post-Islamic Arabian ancestry. Neither of which seem trivial.

For more, this old post, Ashkenazi Jews are probably not descended from the Khazars, will do.

Citation: Elhaik, Eran. “The Missing Link of Jewish European Ancestry: Contrasting the Rhineland and the Khazarian Hypotheses.” Genome biology and evolution 5.1 (2013): 61-74.

Credit: Kwamikagami

National Geographic has an interesting article up, unoriginally titled Australia’s Aboriginals. There are lots of great data in there, though not much novel for anyone who has tread this territory before. For example, Aboriginals tend to have much lower morbidity and mortality when they are living their “traditional” lifestyle. This isn’t a particular novel or surprising outcome. Rather, it seems like a supercharged version of the same problem which occurs when immigrants move from developing to developed societies, and shift toward massive portions and processed food. This modern regime is even impacting native born segments of America’s population in a negative manner. Interesting and true.

But what concerns me is the background assumption that Aboriginals are timeless and static, arriving ~50,000 years ago from Sundaland, and remaining in a stasis. My issue isn’t normative. And I’m fascinated by the inferences some archaeologists have made about the continuity of specific motifs in Aboriginal art. Additionally, from what I understand the material culture of Aboriginals is especially changeless in relation to other populations in the world. But one thing we know about H. sapiens is that cultural forms of expression are quite protean, especially symbolic aspects which might not preserve too well. Would the Aboriginals of Australia be immune from this? I doubt it.

In any case we know of likely changes in Aboriginal culture of relatively recent vintage. The map above shows the distribution of Australian Aboriginal language families, and you can see that one group, Pama-Nyungan is rather extensive. Just eyeballing this distribution and you can infer that it was probably the result of a recent expansion, and sure enough, linguists believe that it converges back to a common ancestor 3,000 to 5,000 years ago. A major language shift by necessity entails a major cultural shift, so one conclusion you can draw from this is that there has been a massive dynamic of ethnic sorting, extinction, and assimilation across much of Australia over the past 10,000 years. The dingo, that iconic quasi-companion of Aboriginals, is also a relatively new arrival (>10,000 years B.P.). Even the boomerang may be a Holocene aspect of Australian culture! I am not even commenting on the more recent genetic data, which draw some rather startling conclusions. The reality is that I won’t be totally comfortable accepting these conclusions if they are too strange unless I can play with the data myself, and for various political reasons there is a low probability of that. But the non-genetic data for change is compelling enough for me.

Why does any of this matter? Because implicitly and explicitly we often use Aboriginals as models of ur-humans, “hunter-gatherer” man. Unlike other non-agricultural populations the Aboriginals had the whole continent to themselves. I don’t think that drawing inferences from Aboriginals is illegitimate, but it is important to question the presupposition that they’re somehow trapped in cultural amber, perfect artifacts which are a window into the world of 50,000 B.C. I suspect they aren’t, so our conclusions have to appropriately modulated.

Credit: Tierrascott

In the 1980s I was fascinated by the pictorially oriented books on the wildlife of the world which dated to the 1960s and 1970s. One of the great conservation success stories of that era were the Saiga antelope of Eurasia. In 1920 there were only 1,000-2,0000 Saia left in the world. By the 1960s their numbers were in the millions. And so it was until the 1980s.

But the combination of the collapse of the Soviet Union, for which the Saiga was a notable conservation success, and the rise of the Chinese economy, have resulted in another crisis for the Saiga. Today their number is between 10,000-50,000, in a few fragmented regions. And yet this is still higher than their early 20th century bottleneck! The Saiga clearly have the capacity to recover from dramatic population crashes. The key, to be frank, is to keep the Saiga a viable population as China ascends up Maslow’s hierarchy of needs.

Cite: Wang, Guo-dong, et al. “The genomics of selection in dogs and the parallel evolution between dogs and humans.” Nature Communications 4 (2013): 1860.

To the left is a figure which illustrates the phylogenetic inferences from a new paper in Nature Communications, The genomics of selection in dogs and the parallel evolution between dogs and humans (see Carl Zimmer’s coverage in The New York Times). Why is this paper important? The first thing that jumped out at me is that because they’re using whole genomes (~10X coverage) of a selection of dogs and wolves the results aren’t as subject to the bias of using “chips” of polymorphisms discovered in dogs on wolves (see: Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication). The second aspect is that the coalescence of the dog vs. wolf lineage is pushed further back in time than earlier genetic work, by a factor of three. A standard model for the origin of dogs is that they arose in the Middle East ~10,000-15,000 years ago , possibly as part of the broad shift of lifestyles which culminated in the Neolithic Revolution.

This model is now in serious question. Though there have always been claims of fossils of older domestic canids (adduced as such in terms of morphology) than the ones discovered in the Middle East ~15,000 years ago, this year there has been publication of ancient mtDNA results from ~30,000 years before the present which imply the separation of putative domestic and wolf lineages at least to that date. Over the past few years I have wondered about the specific nature of the emergence of both modern humans and modern dogs, and their co-evolutionary trajectory, over the Pleistocene and into the Holocene, in light of these results.

So the preponderance of data (genomic and archaeological) leans me toward accepting the general shape and >15,000 year B.P. date for the divergence of dog and wolf lineages outlined by the authors. But there is a lot more in terms of the phylogenetics of the paper which I am not willing to agree with as so obvious and clear. In particular, the authors support a Chinese/Southeast Asian origin for the dog, rather than a Middle Eastern one. This position is backed up by the reality that the Southeast Asian dog lineages do seem quite genetically diverse, and basal to other dogs (i.e., they diverge first within the clade of domestic dogs). Additionally, in the paper itself they note that the PCA, which visualizes genetic distance, suggests that the East Asian lineages are somewhat shifted toward the wolf. Model based clustering also implies that East Asian lineages are “more wolf.”

The reason I don’t buy this conjecture is as they say in the paper itself modern distributions and relationships don’t always map onto ancient distributions and relationships. We’ve already gotten into trouble doing this for human populations of similar time depth as the new putative period of dog domestication. Ancient DNA has uncovered a great deal of discordance between the past and present. I don’t expect dogs to be any different. The authors have whole genomes of a dozen animals. When the data set is expanded to hundreds with reasonable geographic coverage let’s talk. They attempt to model some gene flow, but I suspect that this is a major problem when talking about regions of origin of a group of organisms whose divergence from the ancestral outgroup is not quite clear in its nature.

Human directed breeding. Credit: Galabwebdesign.

But, a bigger point which has less to do with the zone of origination of the dog is the mode of the origination “event.” In the paper the authors present a stark model of the classic origination event for dogs, where Ice Age hunter-gatherers adopt some puppies, and this population exhibits a sharp and punctuated divergence from the main line of the wolves.  These genetic data don’t indicate that at all. Rather, the “bottleneck” as very mild, if you could call it a bottleneck (see: Vulcans through the eye of the bottleneck). Certainly some inbred modern lineages have gone through bottlenecks, but this was long subsequent to the initial separation of dog and wolf. Rather, the authors put forward an alternative hypothesis where dogs were co-existent with early man, with a subset of wolves who were happy to scavenge on the margins of human settlements. There are variations and flavors of this sort of argument, but you can bracket them as the “self domestication” model. The reality here is that I think our explicit differentiation between forms of selection is wrongheaded, the primary issue isn’t whether dogs were self-domesticated or human-domesticated, but the rate of adaptation and demographic history. It may be that the best way to think about the origin of dogs and humans isn’t that the latter domesticated the former, but that both dogs and humans changed together as their lifestyles and interactions changed. With the rise of agriculture and increased specialization of human lifestyles there occurred a concomitant diversification of dogs.

And that is where I think the second part of the paper, focusing on parallel adaptations on the genomic level, is really interesting.

If you don’t want to click the image above, it seems that genes involved in neurological function, metabolism, and cancer are enriched in terms of signals of selection in domestic dogs. This is not surprising. Dogs exhibit great life history differences from wolves (they breed more, and are not pair bonded), and famously may be able to read human faces despite being less intelligent than wolves. And of course dogs have to eat what we eat, at least to some extent.

To understand this functional aspect of the evolutionary history of dogs though one does have to nail the phylogenetics down. So there will no doubt be more coming down the pipeline in this domain, and within the next few years the natural history of man’s best friend will be of deep interest. As ancient DNA has revolutionized the understanding of the human past, I suspect there will be attempts to analyze samples from dogs as well (though I assume that the data sets will always be thinner because scholars have always been preoccupied with human remains).

Citation: Wang, Guo-dong, et al. “The genomics of selection in dogs and the parallel evolution between dogs and humans.” Nature Communications 4 (2013): 1860.

Credit: Campbell, Catarina D., and Evan E. Eichler. “Properties and rates of germline mutations in humans.” Trends in Genetics (2013).

What a great age we live in. Until recently critical parameters in population genetics such as mutation rates had to be inferred and assumed, even though they served as bases for much more complex inferences. Now with humans (and humans are only the beginning!) much of what was inferred is being assessed in a more direct fashion. Caterina Campbell and Even Eichler have a review in Trends in Genetics which surveys the field as it stands now, Properties and rates of germline mutations in humans. Notice that there’s a rough convergence using pedigree analysis of a mutation rate in the low 10^-8 range. Additionally, it does seem that a disproportionate number of novel mutations come through the paternal lineage via sperm. This should increase our moderate worry about older fathers (something reiterated in the piece, with caveats). Finally, the authors suggest these results are a floor for the mutational rate, in part due to the long term conflict with the inferred ‘evolutionary rates,’ which are higher. This matters because to infer the last common ancestors between lineages the value of the mutation rate is obviously critical.

To me the obvious ‘killer app’ which derives from the understanding of mutations are analyses of pedigrees in terms of accretion of de novo mutations. With precise and accurate coverage of a whole pedigree you could theoretically perform a pre-implantation screening of a set of embryos and select exactly those you adduce to have received the lowest fraction of accrued mutations from the generation of the grandparents down. This isn’t rocket science, but simple comparison and counting. Spontaneous abortion rates on the order of ~50% set a floor on human many mutations viable offspring can carry (most aneuploidies are aborted), but it seems like we may be able to set the floor a bit higher.

Mozart, born that way, trained that way

A few years ago Malcolm Gladwell made the “10,000 hour rule” famous in his book Outliers. In practice (e.g., discussions with people day to day or on this blog) the rule gets translated into the inference “practice is what matters.” When talking about genetics this often implicitly also entails that “genes don’t matter.” I’m not saying that this is necessarily what Gladwell’s own exposition taken literally would suggest, but ideas have a way of evolving once they’re outside of the pages of a book.

My own response is that this sort of rhetorical device is silly. In domains of virtuosity the intersection of innate talent and conscientiousness are often critical. That’s because for outstanding excellence gains on the extreme margin of performance are critical. There are many born with talent, and those who hone and refine that talent will have an edge over those who do not exhibit the same work ethic. But the converse is that there are those born without talent for whom 10,000 hours of invested effort is lunacy.

A piece in Time reports on follow up research which seems to question the 10,000 hour rule. Reading the article one thing that I am struck by is the fact that scholar whom Gladwell originally relied upon to formulate the rule seems like a environmental maximalist. For example:

Ericsson doesn’t deny that genetic limitations, such as those on height and body size, can constrain expert performance in areas like athletics — and his research has shown this. However, he believes there is no good evidence so far that proves that genetic factors related to intelligence or other brain attributes matter when it comes to less physically-driven pursuits.

Update your priors appropriately when evaluating research. In any case the updated findings suggest that practice time can explain ~1/3 of the variance in outcomes for chess and music. This is obviously not trivial, and an important finding in and of itself. But, it does suggest that there is a lot more going on at these elite levels than simply perseverance.

Guess what, we’re related! Credit: Wapondaponda 

This is a public service announcement. If you are a user of direct-to-consumer personal genomics services, please do not pay any attention to your mtDNA and Y chromosomal haplogroups. Why? Because they hardly tell you anything about your individual ancestry. What do I mean by this? Your mtDNA comes down from your mother’s-mother’s-mother’s-mother… and similarly for your Y chromosomal lineage if you are a male. These few individuals are not any more likely to contribute to your ancestry than all those multitudes and multitudes who do not contribute to your mtDNA or Y lineages; also known as almost all your ancestors! What you should pay attention to are your autosomal results. Inferences made from most of your genome. These results may be more difficult to parse, but difficulty is no sin, and elegant ease is no virtue, in this case. That’s because you are interested in your ancestry, not a convenient interpretable story.

Of course I am not saying that mtDNA and Y chromosomal haplogroups are useless. They are useful for population scale phylogeography. But please don’t make inferences about yourself from one data point. At least in most cases.

The Black Death

I noticed during Peter Ralph and Graham Coop’s Ask Me Anything about their new paper, The Geography of Recent Genetic Ancestry across Europe, someone brought up the effects of plague. Recall that ~1/3 of Europe’s population died during the Black Death. And population size reductions on the order of ~50% due to epidemics are not unknown in human history. Surely this would have a major genetic effect? Well, in fact it would have a genetic effect due to possible adaptations to disease (see CCR5). But there would be little overall impact on genetic diversity, at least in the short term. That is because for bottlenecks to produce major change in the genetic character of a population they have to be rather extreme in magnitude.

This issue came to mind for me in 2009 when I watched Stark Trek. If you haven’t watched the J. J. Abrams reboot, and are a spoilerphobe, read no more! Now, with that out of the way you may recall that during this film the Vulcans suffered a genocidal attack. Out of billions of Vulcans only ~10,000 survived. Here’s some commentary on the possible consequences, New Star Trek Movie: A Vulcan Holocaust?:

Yes, there is a remnant of ten thousand Vulcans left. At the end of the movie, we are told that they have found a new planet to settle on. Still, we must ask: If we are now in a new timeline and all we have left are a few thousand survivors, will the Vulcans have any political influence at all? Or will they just become a relic on a museum planet? Spock even refers to his people as an endangered species.

…

It would seem the Vulcans will have no other choice but to accept “converts” if they want to survive, because 10,000 is not really a very big gene pool in the long haul. The Amish, who do not accept converts or newcomers, have become very inbred and are now facing problems with genetic diseases. European Jews, who lived in isolated communities for many centuries, also carry certain genetic diseases. However, the recent influx of Jews by Choice is bringing new DNA patterns into the community, so that Jews have fewer such problems than the Amish.

3.5% growth per year

First things first. Vulcans would have no problem reestablishing their population on a virgin planet. It’s simply the power of exponential growth. The nation of East Timor has a growth rate of 3.5% per year (total fertility rate ~6 per woman). This is not an outlandish value. The Puritans of New England maintained higher fertility for several generations. The key here is that humans (or humanoids) are like any organism when faced with a Malthusian surfeit: they breed. Though Vulcans live longer than humans, and have some life history quirks, I’m rather confident that Vulcans could reproduce at least as fast as humans. The reality is that they’re superior to humankind in almost every way possible (their lack of emotions is a testament to culture, not biology). Some quick computations tell me that it would take 400 years for Vulcans to get back to a population of 10 billion. Since some Vulcans can live longer than two centuries, this seems like a rather short window of time.

But what about the second clause? Vulcan genetic diversity. Vulcans are logical, so I’m rather confident that they would have sampled diverse populations when evacuating. And to my knowledge I am not aware of an ethnic skew of Vulcans who were resident across the Federation. So with concerns of representativeness addressed, what would such a crash in population entail?

First you need to become familiar with the concept of an effective population, Ne. Consider that in any given generation some individuals shall breed and some shall not. Though the count of population may be x, the count of those who contribute to the next generation is invariably (x – those who do not breed). And it is this inter-generational transfer which is relevant to population genetics. Also, for the purposes of genetics deep history matters a great deal. Bottlenecks have an inordinate impact on the long term effective population. Intuitively, consider the case of a large population which goes through an extreme bottleneck, and then expands again. The average census size over that time might be rather substantial. But for genetic purposes the lineages are likely to coalesce back to a few common ancestors at the bottleneck. The impact of the pre-bottleneck period is attenuated, because much of the population was simply not genetically sampled. It may as well have not existed!

To make it concrete, below is a toy example. Imagine an island with 10,000 individuals which undergoes population crashes. You see the results below.

The total number of individuals over the 30 generations across the three scenarios is about the same. But the long term effective population in the scenario where the size dropped to 10 is 30 times smaller than the case where the size was reduced to 10% of the prior value.

But what does this do to genetics? There are complicated ways to model this, because populations may be in mutation/drift/selection equilibrium, with the bottleneck being a temporary perturbation. But one way to think about the issue is that a bottleneck can drop heterozygosity by about a factor of 1-1/(2Ne). As Ne → ∞ there is no change. But 1-1/(2Ne), where Ne is 1,000 to 10,000 (assuming that Ne is smaller than the census size of 10,000), is not implying a great change in heterozygosity. Of course many rare alleles, or alleles private to families, will be lost. But so long as the Vulcan population was reasonably representative (not inbred), then I think they don’t have much to fret about in terms of genetic health.

The purpose of this post was not to answer a question of deep interest to Trekkies. Rather, it was to encourage people to establish some intuitions about these sorts of demographic processes and their effect upon genetics.

References:

Hartl, Daniel L., and Andrew G. Clark. Principles of population genetics. Vol. 116. Sunderland: Sinauer associates, 1997.

Nei, Masatoshi, Takeo Maruyama, and Ranajit Chakraborty. “The bottleneck effect and genetic variability in populations.” Evolution (1975): 1-10.

Credit: Characterizing the admixed African ancestry of African Americans

My own inclination has been to not get bogged down in the latest race and IQ controversy because I don’t have that much time, and the core readership here is probably not going to get any new information from me, since this is not an area of hot novel research. But that doesn’t mean the rest of the world isn’t talking, and I think perhaps it might be useful for people if I stepped a bit into this discussion between Andrew Sullivan and Ta-Nehisi Coates specifically. My primary concern is that here we have two literary intellectuals arguing about a complex topic which spans the humanities and the sciences. Ta-Nehisi, as one who studies history, feels confident that he can dismiss the utility of racial population structure categorization because as he says, “no coherent, fixed definition of race actually exists.” I am actually more of a history guy than a math guy, not because I love history more than math, but because I am not very good at math. And I’ve even read books such as The Rise and Fall of the Caucasian Race and The History of White People (as well as biographies of older racial theorists, such as Madison Grant). So I am not entirely ignorant of Ta-Nehisi’s bailiwick, but, I think it would be prudent for the hoarders of old texts to become a touch more familiar with the crisp formalities of the natural sciences.

In his posts on this topic Ta-Nehisi repeatedly points to the real diversity in physical type and ancestry among African Americans, despite acknowledging implicitly the shared preponderant history. But today with genomic methods we have a rather better idea of the distribution of ancestry among African Americans. The above plot is from Characterizing the admixed African ancestry of African Americans, a 2009 paper with 94 Africans of diverse geographic origins, 136 African Americans, and 38 European Americans. They looked at 450,000 genetic variants (SNPs) per person (there are somewhat more than 10 million SNPs in the human genome). Obviously individuals and populations exhibit genetic relationships to each other contingent upon the patterns of the variation of base pairs (A, C, G, and T) across the genomes of individuals, but there’s no reasonable way to comprehend this “by eye” when you’re talking about hundreds of thousands of markers. The authors used two simple methods to infer clustering within the data set.

First, you see a PCA plot. This method is one where the independent dimensions of variation within the data set of the markers are pulled out. They are rank ordered in terms of how much variation they can explain (dimension 1 by convention explains the most, dimension 2 explains the second most, and so forth). Each dimension can be thought of has having a value proportional to its explanatory power. Each individual then has a value position on the dimension, dependent on how that individual relates to the others. When you take multiple dimensions and transpose the data geometrically you quickly see population structure fall out of the data set. Notice above that the first dimension of variation (PC1) separates the Europeans from all the African populations. The second dimension of variation (PC2) separates the hunter-gatherer populations of Africa from the agriculturalists. While the Mandenka are from Senegal, the Yoruba are from Nigeria, at opposite ends of what is traditionally termed West Africa. This was the presumed source of most of the African slaves who arrived in the United States. Once these slaves came to the United States some of then had children with white Americans.  It turns out that the average African ancestral contribution to to African Americans is ~80%, with the balance being mostly European (there is some Native American, but not much). In fact this is very close to the estimates which were produced by genealogists. The concordance of these methods is reassuring, since the underlying phenomena is the same.

Notice that on the PCA plot no African American falls in the Mandenka-Yoruba cluster. That is because almost no African American whose ancestors are not recent immigrants from Africa lack white ancestry. This is entirely reasonable when you consider that the vast majority of their ancestors were resident in the colonies before the Revolutionary War. Admixture events would have percolated throughout the genealogical tree in subsequent generations. The African Americans are distributed almost perfectly along a line between the West African populations and the European Americans. Observe that the density seems to decrease as you approach the European American cluster.

Now we can move to the second visualization technique. While the PCA does not posit any hypothesis of population structure (it just “fell out” of the genetic variation due to the shared history of some individuals via their common ancestors), the second method is “model based,” in that the authors posited seven ancestral populations to match the seven populations which African Americans may be derived from. In a way this is rigging the game; if you force the method to squeeze out particular numbers of populations it may act strangely. But in this case we have prior expectations, so this number of populations is not unreasonable. Above each bar plot represents an African American individual, with each fraction of shading an ancestral element. The results from the PCA are reproduced nearly perfectly by this differing method. The average ancestral quantum of African heritage in this sample is ~80%. And, you see more cleanly the variation in European ancestry among African Americans. Less than 10% of African Americans are like Barack Obama, at least 50% (or more) of European ancestry. The African ancestry excludes the hunter-gatherer populations which is reasonable since the slaves were from the Congo in the east (where some were Bantu) as far as Senegal in the west.

The first black head of the NAACP

Ta-Nehisi has used an imagine of Walter White, the first African American head of the NAACP, to illustrate the pliability of the black identity. It certainly shows that there are no fixed definitions of race which are particularly useful. But that is a misconception of biological science, which is rife with exceptions and boundary conditions, and characterized by an instrumental perspective. The data above suggests that self-identified African Americans are characterized by some African ancestry, but over 90% are more than 50% African in ancestry. Walter White, who had five black great great great grandparents and 27 white ones, was almost certainly less than 20% African in ancestry. There are such people even today, but they are not typical, and do not disprove the reality that African Americans are predominantly of African ancestry.

From a scientific perspective in biology there are not ultimate and fundamental taxonomic facts. There are simply useful ideas and concepts to illustrate and explore the objective phenomena of the natural world. The Species Concepts debate shows us this reality well, as even species can be tendentious. But the debate often shakes out along disciplinary lines. Many more ecological scientists seem to be taken by the ecological species concept, while evolutionary geneticists are more keen on the biological species concept. That is because they are choosing the framework most useful for their ends. There is nothing “Post Modern” in this in that it denies reality. Rather, we are disputing the ideas which we use to capture the essence of real phenomena in compact semantic relations suitable for symbolic representation (whether with math or language).

Prior to the modern systematic era of biology humans did attempt to classify themselves. Generally they looked at a few informative features. For example the Chinese referred to both South and Southeast Asians as “black,” not because they thought they were African, but because they had brown or dark brown skins. Similarly, Arab ethnographers differentiated between ruddy peoples to the north, black ones to the south, and black ones to the east (Indians). And so on. This is almost certainly an elaboration of our innate cognitive ‘folk biology.’ By this, I mean that we as humans tend to classify organisms. Why this is adaptive is trivially obvious. When humans meet new organisms which resemble those which they have familiarity with prior, they simply reformulate the novel creatures as variants of the familiar ones. For example the Tasmanian Tiger was no tiger. It was not even a placental mammal. But through convergent evolution it resembled placental carnivores. Analogously, when Europeans first met the straight haired brown skinned native peoples of the New World they termed them “Indians,” a straight haired brown skinned population of the Old World. When they met the very dark and kinky haired peoples of the western Pacific they assumed they were some relation to Africans, and these became “Melanesians” (which means “black islanders”).

A second component of human nature which Coates alludes to is our tendency to cohere into groups with narratives of internal identity set apart from the Other. In the pre-modern world these inter-group cleavages would be marked by accent, dress, and tattoos. In the early modern world they would be correlated with religion or nationality. The dynamic at issue here is that extremely genetically close populations which would be indistinguishable naked had to generate salient cultural markers. In the case of the ancient Hebrews one could argue that circumcision was exactly the sort of marker which would persist even when naked!* This does not mean that there were no detectable genetic differences between adjacent small scale societies; there are after all detectable genetic differences across European villages today. But for particular technical evolutionary reasons (far more within group variance than between group variance in regards to genetics) it is likely that for inter-group competition cultural forces reigned supreme over biology, and were determinative of identity.

Both of these parameters are from our deep history as a species characterized by life as hunter-gatherers in bands. The next force is more recent, and historically contingent. As I suggested above non-European and pre-modern peoples had a vague conception of race on the continental scale. The Classical Greeks even distinguished he various brown peoples, the Egyptians and the Indians of the north, and black peoples, the Ethiopians and the Indians of the south. The fact that the initial explorers who arrived in the New World labeled the indigenous people Indians, and not Chinese or Africans, shows an awareness of global diversity (in contrast, the British referred to the Australian Aboriginals as blacks). When the British first arrived in India as supplicants to the Great Mughal they differentiated between the diverse races of the subcontinent. The black and brown natives, and a portion of the elites who were white (West Asian Persians and Turks).

This changed over the centuries, and after 1800 the age of European supremacy and the rise of systematic science produced the sort of racial nationalism which serves as the backdrop to our understanding of race more generally. Whereas the pre-modern folk biological taxonomies were coarse, but generally accurate up to a point, the age of white supremacy produced a somewhat schizophrenic science of precision and exaggeration. By this, I mean that the attempt to be formally scientific resulted in a plethora of categorizations and grades of hierarchy. But, the reality of white supremacy generated a taxonomy of dominion, where all the races of color were aggregated into an amorphous whole. Perhaps these two countervailing tendencies explains the juxtaposition of quasi-fixed racial characters with a bizarrely elastic definition of the Other, the non-white. Few moderns agree with Lothrop Stoddard’s The Rising Tide of Color Against White World-Supremacy, but many implicitly accept the framework of whites and a coalition of “people of color.”

So there you have it. An underlying biological reality which is a reflection of deep history. It may not be real or factual, but it is consistent and coherent. Then there are innate faculties which lead us toward categorization of humans into various kinds, for deeply adaptive purposes. Finally, there are historically contingent events which warp our perception of categories so as to fit into power relations in a straightforward sense. But wait, there’s more!

Diabetes risk higher in African Americans with more African ancestry, link

The biological aspect above focused on ancestry and history. But this is not academic detail. The history of a population affects it genome, and its genome effects the nature of its traits and diseases.  Because of differences across populations statistical geneticists with medical aims routinely restrict their data set to individuals of one population. And, within groups like African Americans which are admixed there is variation in disease risk by genomic fraction. Though an individual with 60 percent African ancestry may feel and say they are no more or no less African American than someone who is 80 percent African in ancestry, there are differences in disease susceptibilities.

There is no Platonic sense where there are perfect categories with ideal uses. Rather, we muddle on, making usage of heuristics and frameworks which are serviceable for the moment. We lose our way when we ignore the multi-textured nature of the issues.

* Though many of the neighboring peoples practiced circumcision, so this is more of an apocryphal illustration than a real instance of functional traits on a cultural level in societies.

I went to the talks about the Myriad case at ASHG, and I have to say it was all law, and no science. The science was confused and laughable. The panelists themselves rolled their eyes and expressed resignation as to the garbled ratiocinations of the judges who reviewed the case. There is a classic “two cultures” problem.

Credit: cavorite

A few years ago I predicted to some friends that ancient DNA would transform our understanding of the human past. The reason being that inferences of population movements via material remains were imprecise at best. We are beginning to see my prediction come to fruit (mind you, the prediction was not a bold or courageous one). A new short communication in Nature Communications, A European population in Minoan Bronze Age Crete, addresses an old and frankly somewhat outdated question: whether the first European literate civilization derived from a transplantation from Egypt, or was autochthonous.

I say that this is a somewhat outdated test because the modern proponent of this theory, Arthur Evans, lived a century ago, when our understanding of pre-Classical antiquity (i.e., the world before 600 BC and literate alphabetic Greek civilization) was sketchy at best. The reality is that ancient Crete, like the ancient Levant, does seem to have been in the greater Egyptian culture sphere of influence, just as ancient Elam (southwest Iran) was a de facto part of the Mesopotamian world. But we know the language of the Elamites, and it was not related to Mesopotamian languages. Just as the Finns have been influenced by their Nordic neighbors, so were the Elamites influenced by their Sumerian neighbors. But their linguistic difference points to fundamentally distinct origins. And so it is with the Minoans. It was already likely from the peculiar nature of Minoan writing, Linear A, that this civilization was not a simple derivation of Egypt. These genetic data just add more evidence.

Over at Nature Ewen Callaway has naturally written up an excellent summation of the relevant points of the paper. First, they used mtDNA. The maternal lineage (mtDNA is copious, so excellent for ancient DNA extraction). They compared their several dozen Minoan era (Bronze Age) samples to other various ancient and modern populations. Even with the modest sample sizes and the mtDNA as the sole line of inference it seems that the authors do a reasonable job of rebutting a North African origin for Minoans. Plenty of modern data imply that for whatever reason the Mediterranean is a formidable barrier, and that populations seem to have hugged the northern and southern coasts as they pushed from the East. The exceptions in later times, for example the migration of the Sea Peoples in the Bronze Age, seem not to have perturbed the underlying genetic substrate. More importantly, as I note above we know far more about the Bronze Age Aegean than Sir Arthur Evans. For example, we know that the mainland populations who seem to have displaced Minoan civlization >1500 BC were Greek speakers! Evans did not know this, and this fact was somewhat of a surprise when Michael Ventris stumbled upon this reality.

Credit: Rosemania

To understand why, one must grasp that we are arguably more culturally conscious of the Athens of the 5th century BC than those Athenians were of the Athens of the 12th century BC. At the end of the Bronze Age there was a great cataclysm in terms of the breakdown of the social and political order. Aegean civilization as it was properly understood was erased, and Greece descended into barbarism. Egypt itself barely managed to hold onto its sense of self in the face of barbarian attacks. While Egypt retrenched the mysterious Hittite Empire of Anatolia collapsed in totality. The only recollection of the Hittites persisting down to the modern era can be found in the Hebrew Bible, where there are references toward satellite Levantine Hittite principalities which limped onward after the fall of the center.

After the collapse of the Myceanean citadel culture which succeeded the Minoans Aegean Greek civilization was rebuilt on fundamentally different foundations. The Greeks forgot the art of writing, and invented their own alphabet after being stimulated by the Phoenicians. The legends of the Trojan War and the broader mythological backdrop of Classical Greek society recalled fragments of the memories of the Bronze Age, but only just fragments. The tales of Agamemnon reflect barbaric Dark Age Greece (1200-800 BC), not the bureaucratized world of the Mycenaeans.

In light of all this it is no surprise that early 20th century scholars posited an exotic origin for the peculiar Minoan-Myceanean civilizations whose material remains they stumbled upon. Many of these were gentlemen who were classically educated, and the coarse and brutal world of Bronze Age Greece was utterly alien to them. Not only that, these scholars would have been surprised that Crete and to a lesser extent the Myceaneans were part of the broader Near Eastern world system, despite being of fundamentally different cultural origin. The reality is that it is somewhat deceptive to label Cretan civilization as European, because Europe is an anachronism.

Over the next few years more and more DNA samples will come to light. I will predict that the Mediterranean islands were come to viewed as very specific reservoirs for ancient genetic variation. The mainland seems to have been  subject to folk migrations, but islands were spared (because barbarians from the hinterland lack native skill on the sea?) As more Greek samples come in I suspect that Slavic admixture will be obvious, meaning Create and Cyprus (along with Sardinia)  represent more ‘authentic’ ancient Greek populations.

Note: I highly recommend Michael Wood’s In Search of the Trojan War.

I will state though Kevin’s argument seems to be predicated on the implicit assumption that his interlocutors hold to some sort of Platonic ideal of the most-perfect-human. There’s no such thing obviously, and even those who sympathized with eugenic policies such as W. D. Hamilton rejected this notion at the end of the day. Rather, human traits are evaluated in terms of how they serve the flourishing of individuals and society according to understood values. Intelligence is generally assumed to benefit individuals, and, I believe that it benefits society as well through innovation. Innovation drives the productivity growth which is the foundation of our post-Malthusian age.

And the reality is that this isn’t all about talk. As I’ve mentioned multiple times the frequency of individuals with Down syndrome is reduced by selective abortion. Screens to detect this condition in utero are getting better and better. The sketchy empirical results we do have implies that ~90 percent of couples who receive a “positive” result chose to abort. Should this be against the law? If you take the anti-eugenic argument to its logical conclusion perhaps, because you are making a value judgement on the “quality” of an individual.

Taking an argument to a logical conclusion may give some insight, but generally it is not too useful in practice. We should be careful about taking things their logical conclusion because human affairs aren’t often dictated by logic. The reality is that eugenics in the 21st century will be driven from the “bottom-up,” through individual choice. Market forces and revealed preferences. There will be no ministry of procreation, or social engineering to sculpt the Übermensch. In fact there may be rational reasons to regulate and curtail choice so as to minimize positional bidding on the margin.

On a broader normative note, I am fine with the idea that there are beautiful people and ugly people, smart people and stupid people, nice people and mean people. Some of this is socially constructed, but some of this is not. Kevin makes the accusation of elitism against those academics, such as Steve, who support selection for intelligence. Let me suggest something here: Steve has much to lose in a selfish zero sum sense because he’s already rather assured of intelligent offspring. He’s smart. His wife is smart. Standard quantitative genetics implies that even if they regress to the mean his offspring will be quite bright. There may not be much more juice to squeeze out of that genetic background. It may be very different for a couple with more average endowments. So sorry to turn this upside down, but personal eugenics may in fact be a boon for the ugly, stupid, and psychologically unstable, because it gives them a opportunity to close much of the gap with those who were lucky in the genetic lottery. Some of you may object to terms such as “ugly,” “stupid,” or “psychological unstable.” But people with these issues have to deal with them in their day to day. One can make all the platitudes one wants to make about “inner beauty,” but very few people live by this ideal.

The biggest issue I have with Kevin’s post is that it’s general and over-broad, with a focus on 20th century industrial scale eugenics and genocide. What we’re really going to confront are a myriad of specific cases, and market-driven personal eugenics which has a service sector tinge.

Addendum: It makes sense to be skeptical of the scientific possibilities in the near to medium term.

* Someone attempted to post the following comment:

“I don’t have a great deal of time to engage Kevin right now.” is not the best way to begin an article in which you proceed to do exactly that. It’s disrespectful to both your readers and Kevin: either engage properly or not at all.

1) If you attempt to be my editor I’m going to ban you without warning. Readers don’t make demands of me. If you do so, I’ll ban you.

2) This post was nothing of the kind in terms of being a real response to Kevin’s very wide ranging elucidation of opinions. It took 30 minutes of my time to quickly reiterate some rather simple positions I’ve long stated. That being said, I think it was still useful for someone to outline this position concisely, which is all I could do with my current constraint of marginal time.

I haven’t been able to blog much because of various other responsibilities, but I definitely do feel pent up posting energy. So when I come back I assume that I’ll have a lot of stuff to say. Meanwhile I’m chortling a bit about this bizarre attack on my friend Steve Hsu. Here’s the issue that I always have with this: Steve managed to get tenure as a theoretical physicist. When you’re talking to someone who is an academic theoretical physicist it is generally optimal to not assume a priori that they’re ignorant dullards. Unless that is you want to just engage in empty signalling rhetoric.

Though despite not having concerted time to write, I am tweeting a lot since that requires only minimal lengths of attention. Mostly it’s just repeating the functionality of my Pinboard, though I do comment and what not.

Finally, I keep hearing that the Big Five personality typology is much more scientific than Myers Briggs. So I took a bunch of tests which purport to analyze the Big Five categories.

Extraverted: Very high. Consistent. I was 90-99% on all tests.
Agreeableness: Low. Consistent. Generally in the 15-0% range.
Openness: Medium. This was not very consistent. 40-60% range.
Neuroticism: Erratic. For whatever reason I varied from 20-80% here.
Conscientiousness: Medium. But there was some variation.

Oh, and here’s a list of books I’ve rated for Good Reads.

(via The Festival of Patience)

Cite: :10.1080/00224499.2011.628132

The above figure displays results from males in the General Social Survey who answer yes to the proposition that they’ve watched a pornographic film over the past year. This fact was cited in my post Porn, rape, and a ‘natural experiment’, to disabuse people of the notion that porn consumption has increased radically the past generation. I was aware of this finding, and so generally am careful to focus on the quantity of porn consumed, rather than the social penetration of porn consumption. No matter what the “survey says,” the IT sector is quite aware of the fact that pornographic material is a very high fraction of internet traffic (e.g., more people check Pornhub than BBC).

But I am not sure sure we should trust the GSS results any more at this point. I did some cursory poking around and last month there was a large sample size survey of Dutch youth to investigate the effects of porn consumption, Does Viewing Explain Doing? Assessing the Association Between Sexually Explicit Materials Use and Sexual Behaviors in a Large Sample of Dutch Adolescents and Young Adults:

The study found that 88% of men and 45% of women had consumed SEM ["sexually explicit material"] in the past 12 months. Using hierarchical multiple regression analyses to control for other factors, the association between SEM consumption and a variety of sexual behaviors was found to be significant, accounting for between 0.3% and 4% of the total explained variance in investigated sexual behaviors.

How the sample was collected is important for generalization, so I want to reproduce that part of the method in case you don’t have access:

Data were collected as part of the “Speak up now!” survey, a comprehensive online sexuality study among a large and diverse, self-referred sample of adolescents and young adults in The Netherlands…To be eligible for participation, individuals had to be between 15 and 25 years of age and have had any sexual experience as self-defined, with sex indicated to encompass a broad range of behaviors other than sexual intercourse, including having kissed someone or having engaged in any other type of sexual behavior. Participants were recruited between November 2008 and June 2009 through advertisements in various online and offline youth media and on electronic blackboards at schools. Ads were strategically published to promote the inclusion of lower educated, ethnic minority, and same-sex-attracted young people. The ads invited young people to express their views about sexuality and share their sexual experiences by completing a series of online questionnaires and routed them to the study website that also provided further participant information research details, and referral information for participants wanting to seek counseling.

I’ll put the study’s demographics below. The key for me is that 30% of young male Dutch nationals looked at porn less than once a month, or never. Feel free to find other citations and drop them in the comments. If you don’t have access I’ll check out the descriptive results.

 SEXUALLY EXPLICIT MATERIAL CONSUMPTION OF DUTCH YOUTH

Don’t forget the deep structure in Italy!
Credit: Rita Molnar

Standard apologies that I have had not the marginal time to blog much, but I thought it was important that I least note that Dr. Peter Ralph and Dr. Graham Coop’s paper on identity-by-descent segments and European populations and history is out in its final form in PLoS Biology, The Geography of Recent Genetic Ancestry across Europe. I’ve been familiar with the outlines of these results for about a year now, and to be frank I am still digesting them. The media hype will come and go, with true but to some extent trivial headlines that “all Europeans are related,” but the consequences of these sorts of genetic inquiries into the relatedness of populations are going to be long lasting. At least they should be.

But before I go on about that, if you find the paper itself a bit daunting (though the main body of the text strikes me as eminently readable for a piece of statistical genetics), see Carl Zimmer’s condensation. With this sort of result there is liable to be confusion, so note that Graham Coop has been posting comments on Carl’s blog (and elsewhere, and you can always send him a note on Twitter). Additionally he has a very readable FAQ out. Dr. Coop told me on Twitter that there would even be updates tomorrow as well! In particular one aspect of the paper which I noticed is that most relatively short, but detectable segments (~10 cM), between any two individuals in many nationalities is not going to be evidence of recent genealogical affinities, but deeper historical process.

As for my earlier allusion about this paper: every historian of the Roman Empire interested in demographic and social questions needs to read this sort of work. The reason is the specific result from Italy, which seems to exhibit a lot of deep local population structure. This is in contrast to other European nations, which are relatively homogenized, to the point of being international in the case of Slavic peoples. Despite decades of genetic work on Italians (thanks to L. L. Cavalli-Sforza) this is the first work which highlights this particularity in relation to other Europeans. That is because as Ralph & Coop note other measures of genetic differentiation (e.g., PCA utilizing thick density SNP-chips) tend to pick up deeper time historical and prehistorical events. In contrast Ralph & Coop are focusing upon segments of the genome inherited as a unit from a common ancestor, whose detectable integrity decays rapidly over the generations via recombination. Though this technique of focusing on inherited segments is powerful, it also has a shallow time depth.

I shall quote the authors from their discussion on Italy:

In addition to the very few genetic common ancestors that Italians share both with each other and with other Europeans, we have seen significant modern substructure within Italy (i.e., Figure 2) that predates most of this common ancestry, and estimate that most of the common ancestry shared between Italy and other populations is older than about 2,300 years (Figure S16). Also recall that most populations show no substructure with regards to the number of blocks shared with Italians, implying that the common ancestors other populations share with Italy predate divisions within these other populations. This suggests significant old substructure and large population sizes within Italy, strong enough that different groups within Italy share as little recent common ancestry as other distinct, modern-day countries, substructure that was not homogenized during the migration period. These patterns could also reflect in part geographic isolation within Italy as well as a long history of settlement of Italy from diverse sources.

The latter idea is the classic one the native Italian people were replaced by migrants during the Roman period, especially from the Eastern Mediterranean. Epigraphic and textual evidence as to the proliferation of Greek names in places such as Rome are proffered to support this case. I am skeptical of these data because slaves and the urban proletariat often had low fertility in antiquity, and cities may have been population sinks anyhow. Rather, I suspect that the primary eastern influence on the genetics of modern Italians comes from the era of Greek colonization during Magna Graecia, because despite the urban focus of their civilization the Hellenes did engage in agriculture.

Rather, I lean toward the proposition that Italy was sui generis in continental Europe after the fall of Rome in that despite its regress it maintained local regional identities due to high population densities. The widespread coalescence of genealogies across vast swaths of the other post-Roman domains (Iberia, France, and Britain) may reflect the shattering of the societies and demographic collapse and localized disturbances. The true test of this hypothesis is when these methods expand out to other regions of the world, especially the southern Mediterranean. Egypt and the Levant should exhibit a more Italian pattern, because there was no deep rupture with antiquity in these areas.

There is much more to say about this paper. But I feel that this result from Italy the sore thumb that sticks out and warrants out attention. Ralph & Coop suggest that collaboration with anthropologists and historians is needed. True indeed.

Citation: Ralph P, Coop G (2013) The Geography of Recent Genetic Ancestry across Europe. PLoS Biol 11(5): e1001555. doi:10.1371/journal.pbio.1001555