Much of the public is given the impression that Christianity became the official religion of the Roman Empire under the reign of Constantine. Though it is hard to deny that it was the favored religion, especially by the end of his rule, modern ideas of the “official” religion of a given state are somewhat anachronistic for this period and place. In The Last Pagans of Rome Alan Cameron argues that the true death-blow to non-Christian religions in the Roman Empire occurred during the reign of Gratian, 50 years after Constantine, with the cessation of subsidies to the traditional religion (a contrasting view is that elite paganism was vital as a public force up until Theodosius the Great’s conquest of the Western Empire).
In The Final Pagan Generation the author reviews the almost imperceptible change that occurred in the lives of the Roman elite, who looked back to a continuous cultural lineage that drew from the late republic. These elite men and women exhibited passivity and complacency, as the norms which had come before would presumably obtain until the end of time. What they did not understand is that there are periods when societies go through rapid changes, so that a rupture occurs between the past and the future in the span of a lifetime.
Whether you think elite public paganism lost its vitality in the last decades of the 4th century or sometime in the 5th, the reality is that it was a spent force by the time Justinian began his the marginalization of the last of the Neoplatonic philosophers around 500.
Of course, this does not mean that sub-pagan practices did not persist among the European peasantry for centuries. But the reality is that they were at least nominally Christian, and a coherent sense of traditional religious identity apart from that outward affiliation did not exist (at least after Christianization).
Which brings me to the people of the Mani peninsula, in the southern Peloponnese. This isolated region was reputed to retain the practices of Greek paganism as late as the year 1000 A.D. Let me quote Constantine VII, Byzantine emperor from 913 to 959:
Be it known that the inhabitants of Castle Maina are not from the race of aforesaid Slavs (Melingoi and Ezeritai dwelling on the Taygetus) but from the older Romaioi, who up to the present time are termed Hellenes by the local inhabitants on account of their being in olden times idolaters and worshippers of idols like the ancient Greeks, and who were baptized and became Christians in the reign of the glorious Basil. The place in which they live is waterless and inaccessible but has olives from which they gain some consolation.
The Basil in question reigned from 867 to 886.
Of course, we don’t know if Constantine and his contemporaries were correct in all the details of the people of Mani. It seems unlikely that he would have misidentified them as Greek as opposed to Slavs (whose paganism was more recent), but perhaps they practiced a debased form of folk Christianity mixed with old superstitions? But, if they did continue to practice the religion of ancient Greece it illustrates how persistent traditional beliefs than be in a world where the state and cultural elites have more limited purview than one might have thought. It seems unlikely that the people of Mani would have been unfamiliar with Christianity (there are ruins of churches going back to the 4th century in the area), but they may have been socially isolated enough that the incentives to convert to the new religion did not exist.
The Tengerrese people of East Java, who remain Hindu, maybe a modern analogy. The worshippers of the gods of the old Norse were by chance the Sami, who did not become fully Christian until after the Reformation. And up until the Islamic period, the city of Harran remained predominantly pagan (the Persians were close enough that the East Roman authorities respected the religious liberties of these people lest they defect).
When I was a kid “killer bees” were a major pop culture thing. There were movies about the bees, and we would get updates about their march northward in the news. They were a cautionary tale of our species’ hubris.
Today we have a little bit more perspective. These bees were actually just African honeybees, the ancestral population to European honeybees, which were introduced to the New World with Europeans centuries earlier than the African honeybees. African honeybees were not that different from European honeybees, but they were more aggressive and tended to outcompete European honeybee colonies. They are a major problem for the beekeeping industry, but not a major threat to human life.
Today the African and European populations in the United States seem to have stabilized in their ranges, with a hybrid zone between them. African bee’s migratory behavior makes them less competitive with European bees in colder climates.
Highly aggressive Africanized honeybees (AHB) invaded Puerto Rico (PR) in 1994, displacing gentle European honeybees (EHB) in many locations. Gentle AHB (gAHB), unknown anywhere else in the world, subsequently evolved on the island within a few generations. Here we sequence whole genomes from gAHB and EHB populations, as well as a North American AHB population, a likely source of the founder AHB on PR. We show that gAHB retains high levels of genetic diversity after evolution of gentle behaviour, despite selection on standing variation. We observe multiple genomic loci with significant signatures of selection. Rapid evolution during colonization of novel habitats can generate major changes to characteristics such as morphological or colouration traits, usually controlled by one or more major genetic loci. Here we describe a soft selective sweep, acting at multiple loci across the genome, that occurred during, and may have mediated, the rapid evolution of a behavioural trait.
Come for the bees, but stay for the soft selection! If you talk to anyone in evolutionary and population genomics you know that the future is in understanding patterns of soft selection and polygenic selection from standing variation. Though these are related phenomena which are associated with each other, all are all distinct.
Standing variation just refers to the diversity which is segregating in the population at any given time. At any given moment many loci exhibit polymorphism. This polymorphism can be a target of natural selection if it is correlated with heritable variation and differentials in fitness. Though soft selection can be quite wooly it’s inverse, hard selection, is clear: in genetic terms hard selection can be seen in allele frequency changes at a single variant in a locus, going from the point where it is a novel mutation to nearly fixed in the population. In Haldane’s original conception hard selection involved excess deaths, and imposed a limit on the rate of evolution as well as the amount variation you could expect within a given population. This model was convenient in the pre-genomic and early genomic era because empirical selection tests had to focus on large allele frequency changes around singular loci. Researchers didn’t have large numbers of whole-genome samples available (nor the computational ability to analyze them).
Today this is not a limitation. In the analysis above the authors had 30 individuals of the 3 populations sequenced at high quality (20x). They ended up with millions of genetic variants they could analyze.
The plot to the left shows that “gentle African honeybees” (gAHB) tend to be closer to the African honeybee populations (AHB) overall (though with some hybridization with European honeybees, EHB). This is not surprising.
But the key observation was that over 12 generations the African honeybees of Puerto Rico became progressively less aggressive, despite maintaining overall morphological similarities to the mainland Mexican African bees from which they likely derive. Though buried in the discussion, there is a rationale for why this morphological change may have occurred: the Puerto Rican bees are subject to a lot of negative selection against aggression because of the density of the island, as well as the reality that aside from humans there aren’t other many species where their aggressive tendencies are beneficial. Basically, if you are an aggressive colony, it’s harder to make a go in densely settled areas (the implication here then is that there are probably “gentle” African honeybee populations across Latin America, they just are never disaggregated from the broader meta-population).
It’s the genomics where the real evolutionary insight comes in: they found that there were multiple soft sweep events around genetic regions implicated in behavior. In their overall genome the gAHB of Puerto Rico resembled mainland AHB, but in this subset of genetic loci they resembled EHB. Many of these loci had also been known to be targets of selection when the original European bee population diverged from the ancestral African population. Basically this is a genomic illustration of convergent evolution.
Regular readers of this blog will recognize the ways they detected selection. They used a modified form of EHH, which is reasonable since the selection event was recent enough to have been associated with distinct haplotype blocks. Also, standard Fst analysis showed that these were outliers in relation to the broader genetic pattern of relatedness (these loci were more like EHB than AHB, while most loci were more like AHB than EHB).
So this a form of polygenic selection. Remember, natural selection only knows genes through the phenotype (with intra-genomic selection being an exception). A behavior like aggression is probably subject to the fourth law of behavior genetics. That is, variation won’t be defined around a single genetic locus. Rather, variation across the genome will be correlated with variation in the phenotype. As selection favors a particular value of the phenotype across the distribution the allele frequencies across many genetic loci will shift, but they will not necessarily fix. Polygenic selection operates on the dispersed standing genetic variation which explains much of the variation of the phenotype in question. Instead of total sweeps to fixation due to large fitness differences between a given allele and its alternative form, the selection impact is distributed and diffused across the genome.
Though most of the genetic variants seem to recapitulate the evolution of the less aggressive phenotype that occurred with the original migration north of African honeybees, some of the selection signatures were novel. This points to the reality that when you have soft selection on standing variation you may have similar phenotypes which evolve via different means. Additionally, the authors noted that these results were in contrast to controlled breeding experiments in mammals where selection for gentility (“domestication”) often targeted a few loci and exhibited strong pleiotropic effects (due to the genetic correlation). These results point to the limitations of inferences made from human-directed selection.
Soft selection is probably ubiquitous. Consider the evolution of skin color in humans. There are lots of variants and lots of variation, and most of the variation seems to be ancestral. Only at the locus SLC24A5 do you have a perfect illustration of a hard selective sweep, probably from a de novo mutation that emerged around the Last Glacial Maximum.
From a geneticists’ perspective evolution is basically conceived of as changes in allele frequencies over time. Much of this is due to natural selection. Now that the world of soft selection is opening up, I suspect that we’ll understand a lot more of what we see around us, at least in the generality.
Because of what I have been provided by my employers over the last few years I’ve been working on a Macbook Pro. These are fine machines, but they have not converted me to being a convert to all things Apple. I have two machines with Ubuntu at home that I have no problem with using (one of them has a dual-boot where I have a copy of Windows which I use every six months or so to make sure that security updates are installed).
In any case, my current phone has been acting erratically over the past few weeks. Up until now I had been resisting getting a new phone because it wasn’t as if I really needed one…but when there is a jeopardy that your phone will decide to not boot up, one has to act.
So I was agonizing over the Samsung 8 or iPhone 8. I’ve had multiple Samsung’s before. And the Samsung 8 seemed fine. The flip side is that everyone in my office uses an iPhone 8, and I get crap for staying with Android. This is not a major issue…but I can’t lie, I’m curious about the iPhone.
In the end, I probably stayed with Android for one primary reason: people in the Apple ecosystem seem totally hostage to Apple. Upgrades are a total pain, and there are minor things I need to get fixed in regards to my Macbook Pro‘s OS which is going to require a “Genius.” The whole situation strikes me as farcical and not futuristic. I’d rather tinker with my Ubuntu distribution than wait in line at a crowded Mac store.
The customers who have already purchased Neanderthal and Metabolism will probably get their results first, because remember that Helix apps reuse the original data sequenced and typed. Those who have already gotten previous results on any Helix app will be able to get results almost immediately when the app is live (the constraint here is compute time).
Currently, we are projecting the appl to be live starting January 8th, 2018 (being conservative).
Also, at $19.99 this is a great way to get into the Helix ecosystem.
(note the current ancestry product is autosomal analysis. no Y and mtDNA)
We live in a time of transitions when it comes to Neanderthals. Since the 2010 discovery of strong genomic evidence for Neanderthal ancestry in most humans they’ve been…humanized. This was pretty much inevitable, but, I also think it was right. Neanderthals were a big-brained human species which dominated much of Eurasia for hundreds of thousands of years. Their culture did exhibit a certain stasis, but then so did that of our modern African ancestors ~200,000 years ago.
There has been a recent debate about how far back the divergence between Neanderthals and modern humans goes back. My own views is that it’s probably further back than 500,000 years, perhaps closer to 750,000 years, but that there may have been ancient gene flow between lineages as well.
A new paper is now out which suggests that Neanderthals persisted in southern Spain for 3,000 years after they disappeared elsewhere, Precise dating of the Middle-to-Upper Paleolithic transition in Murcia (Spain) supports late Neandertal persistence in Iberia. Obviously, I can’t evaluate the taphonomy and all that. There have long been debates by paleoanthropologists about this region and its Neanderthal habitation (some earlier dates suggested Neanderthals persisted down to 29,000 years ago in southern Spain, but those seem to be rejected). What I can say is that it is entirely expected that the Neanderthal range as it contracted would exhibit an s-shaped trajectory, with a tail where they persisted as relic populations in areas which they were particularly well adapted to.
As paleoanthropology and genetics progress I’m rather sure that we’ll drill-down on very detailed dynamics of interaction, and local succession and replacement. Though humans leave cultural artifacts behind, as a rule the first and last fossils in paleontology usually underestimate the time span that a species flourished. I wouldn’t be surprised if the same applied to Neanderthals, and some day someone with a suspiciously high Neanderthal ancestral fraction was sequenced or genotyped who lived just before the Last Glacial Maximum.
Also, I should mention for those of you looking for a pre-Christmas gift, my company’s Neanderthal product (which does a functional analysis of a set of characteristics where modern humans segregate ancestral and derived variants from the two lineages) can be had for $29.99, as Helix is discounting the $80.00 kit cost (the same applies to the $39.99 Metabolism product, though if you bought Neanderthal earlier then Metabolism is always$39.99 since Helix has banked your data).
People keep asking us the details of the Helix-Insitome relationship and how it works. So we decided to write a blog post addressing that (it’s very short), How does Helix work?.
P.S. we’re probably the only start-up in the world where regular office conversation occurs about Neanderthals.
Since the beginning of this weblog, a particular tick that is common to humans emerges over and over. A tick that is seductive, inevitable, and which I periodically react negatively to (and surely do engage in). That tick is the one where peculiar or exotic terms, or common terms in specific senses, are deployed to demarcate ingroup vs. outgroup.
This is clearly illustrated by example. Libertarians will often call non-libertarians statists. In some ways, this is a defensible term descriptively. But statists never call themselves statists, and often are confused what that even means. Really the term “statist” is just a way you can tell other libertarians that this person is not of the tribe. It’s not about communicating with the statist in question. It’s about labeling them…a witch!
Another example is ally. This is a banal and general word, but on the cultural Left it’s become transformed into a very specific thing. If you are a white male, you are by constitution an oppressor with privilege, so you must by necessity aim toward being an ally. Ally here means those with privilege joining the struggle against oppression and the liberation of marginalized people.
Almost all of the above terms are pretty standard English words, but bundled together into that paragraph you know the perspective and Weltanschauung it’s expressing.
In the United States those who oppose the right to an abortion because they think the fetus is a person define themselves as pro-life. Those who support the right to an abortion define themselves as pro-choice. Pro-choice people sometimes call pro-life people anti-choice, while pro-life people call pro-choice people pro-abortion. The terms themselves are not important as descriptions. Rather, they’re about tribal mobilization.
On occasion, I’ve seen the term TERF, for trans-exclusionary feminist. The people who are called TERFs never call themselves TERFs. Often people who are denounced as TERFs don’t see to be TERFs at all.
When someone brings up the term “civic nationalism,” I’m usually pretty sure that that person is probably a white nationalist, because that’s a term that they seem to use a lot (to describe non-racial nationalists). People who are civic nationalists don’t describe themselves as such in normal conversations.
Because my views are generally more conservative than liberal people on the Right often believe that I am aware of all the tribal divisions and lexical nuances deployed by conservatives today. Or, more honestly people who spend a lot of time reading and discussing politics online with the tribe. I have finite time, I don’t really really track of all the new fashionable terms. Political philosophy and history interest me, but the contemporary ephemera, not so much. One of the most irritating aspects of “Neoreaction” was that they had all those terms which made no sense to outsiders without a glossary.
This sort of behavior makes sense ingroup. But when you start spouting off in public forums with new-fangled vocabulary accessible to the initiates you exclude them. Which is fine, but you also make it clear you just want to hear yourself talk.
Though sometimes scientists are guilty of this sort thing, by and large the utilization of words in a peculiar context has a precise meaning which is clear and distinct. For example, the term heritable. Transformed into heritability, it is the proportion of variance in the phenotype explained by variance in the genotype. Now could say “the proportion of variance in the phenotype explained by variance in the genotype” every time, but it’s usually easier just to say “heritability.”
I’ve made it pretty clear I take a dim view of the prospects for this liberal democracy of ours over the next generation or so. A day shall come when you stand with the Frost Giants or you stand with the Aesir. There’s really no avoiding a choice. I would recommend on that day pick you pick the strongest side, not who you think is the right side. Power is truth, truth is not power.
But this day is not that day. Until then there is still time to listen and cultivate one’s mind. Let’s dispense with bleeding private language into public. It’s just unseemly.
Cystic fibrosis is one of those ‘classical’ recessive diseases you learn about in medical genetics. It’s frequent enough that doctors will always be interested in it, and its inheritance pattern is relatively simple, following a rough Mendelian pattern of recessive expression. The reality is a little more complicated than that though, as there are different mutations in the CFTR gene, and some variants can complement so that two carriers don’t necessarily have a risk of producing a child which expresses the disease.
But CF is also interesting from an evolutionary perspective. Why is such a lethal disease present at such high frequencies in Northern Europeans? On the order of 1 out of 25 Northern Europeans carry a mutant allele on CFTR. Apparently, 1 in 19 Irish carries a mutation for CF, while Finland it’s prevalent at a frequency of around 1 in 90, which is actually in the range of non-European populations.
Though it is well known that inbred populations can manifest high frequencies of deleterious alleles, as a whole Northern Europe is not an inbred population. So what’s going on? One hypothesis is that heterozygotes for CF (carriers) have a higher fitness than wild-type individuals, so the low but persistent frequency of CF expressing individuals is an outcome of this overdominant effect. The analogy then presents to sickle-cell anemia. Heterozygotes are more resistant to malaria, an endemic and pervasive disease in much of the tropics and subtropics.
Applying spatial epidemiology, we studied the link between CF carriership rate and tuberculosis (TB) incidence in Brazil. We corrected for 5 potential environmental and 2 immunological confounders in this relation: monthly income, sanitary provisions, literacy rates, racial composition and population density along with AIDS incidence rates and diabetes mellitus type 2. Smoking data were incomplete and not available for analysis.
A significant, negative correlation between CF carriership rate and TB incidence, independent of any of the seven confounders was found.
The immediate objection is that one may not have controlled for all the confounds. Though do note there are molecular biological rationales for why CFTR heterozygotes may be more fit when infected with tuberculosis.
All that being said Brazil is a diverse place, and it is hard to imagine there might not be a confound out there geographically. Fortunately, we won’t be doing a randomized controlled field trial by infecting individuals with tuberculosis, so we’re just going to have to keep looking at these correlational studies.
Something has to be driving selection for this nasty disease as part of the genetic correlation.
I’ve spent a little time reading Oathbringer this week, mostly before I go to sleep. It’s a little hard to keep track of everything because it’s been seven years since the first book and over three since the last one. Since Brandon Sanderson projects ten books in the series I doubt I will finish this out. At the current rate of production I will be thinking about retirement when the Stormlight Archive is near completion!
But reading Oathbringer it did come to my mind that Sanderson has done a really good job in building a world which is fundamentally not just a European Middle Ages retread, as is the norm in much of fantasy. There are so many new words and characters to keep track of I think I didn’t internalize this in the earlier books. So I did a little Googling and found that Sanderson was trying to do the same thing that Frank Herbert did in Dune, by creating a whole new and novel ecology.
Secondly, he has mentioned that most of his characters are not white and that he has struggled to make sure that they are not depicted in stereotypical European fashion in cover art. The primary protagonists are in fact a people who he imagines to be a hybrid between East Asians and Middle Easterners (his time in Korea as a Mormon missionary inflected his world-building), though that is simply the closest analog. He specifically states that the one human race without epicanthic folds, and look the most European in feature and complexion, are often assumed to be East Asian in by readers because of their exoticism and name (Shin).
The day the Pintupi Nine entered the modern world. The story of nine people who were totally isolated from the modern world until 1984. They were scared when they met relatives who had lived in a town. To convince them to stay the relatives had them taste sugar.
I put up a poll without context yesterday to gauge people about what methods they preferred when it came to population genetic structure.* PCA came out on top by a plural majority. More explicitly model-based methods, such as Structure/Admixture, come in right behind them. Curiously, the oldest method, pairwise Fst comparisons (greater Fst means more variance partitioned between the groups), and Treemix, the newest method, have lower proportions of adherence.
Why is PCA so popular? Unlike Treemix or pairwise Fst you don’t have to label populations ahead of time. You just put the variation in there, and the individuals shake out by themselves. Pairwise Fst and Treemix both require you to stipulate which population individuals belong to a priori. This means you often end up using PCA or some other method to do a pre-analysis stage. Structure/Admixture model-based methods make you select the number of distinct populations you want to explore, and often assume an underlying model of pulse admixture between populations (Treemix does this too when you have an admixture edge).
PCA is also better at smoking out structure than Structure/Admixture for the same number of markers, and, it’s pretty fast as well. This is why the first thing I do when I get population genetic data where I want to explore structure is do a PCA and look for clusters and outliers. After this pre-analysis stage, I can move onto other methods.
* I stipulated “genotyped-based” methods to set aside some of the new-fangled techniques, which often assume phasing and analysis of haplotypes, such as Chromopainter or explicit local ancestry deconvolution (some local ancestry deconvolution does not require phased haplotypes, but the most popular do).
The arrival of Europeans to the American continent in AD 1492, with the consequent population decimation and impact on cultural practices, caused the domesticated traits to gradually disappear. The loss of domesticated varieties is a phenomena that has also occurred for other indigenously domesticated species in both South….
One of the novel arguments in Charles C. Mann’s 1491 is that our idea that the Amazon basin has always been a pristine wilderness could be incorrect. Mann relays the theories of revisionist scholars who argue that at one point in history much of the basin was subject human landscape manipulation, with concentrated burnings allowing for increased productivity in the normally poor soil of the region. Of course, this triggered a counterattack from classical scholars.
If these results about rice domestication are confirmed and become solid I think this would lean toward supporting the arguments of the revisionists, whose side Mann seems to favor in any case.
A major general theme in 1491 is that the Columbian Exchange was a disaster for New World peoples, though relatively positive for the Old World. European access to land surplus in the New World has been given as one reason for the economic takeoff of this region (“ghost acres”), while maize introduced into China was responsible for its great population expansion in the centuries leading up to 1800.
In contrast, the consensus seems to be that New World populations suffered massive population declines (some of this has been confirmed by genetic evidence) driven in large part, though not exclusively, by introduced Old World diseases. Mann argues that early fantastical reports of a dense network of villages along the Amazon (which may have fueled legends of El Dorado) actually reflect the reality that in the 16th century the riverine civilization had not collapsed due to disease. At least not yet.
Let’s stipulate that rice domestication in the Amazon was occurring before 1492. This adds another independent domestication event during the Holocene. Basically, agriculture seems to be something that pops up over and over again after the end of the last Ice Age. Why? As I have suggested before a lot had changed since the previous interglacial over 100,000 years before the present. Our cognitive orientation and our cultural toolkit seem to evoke agriculture relatively quickly and independently.
Second, the indigenous peoples of the Amazon today are predominantly hunters and gatherers or slash & burn agriculturalists. Relatively simple societies. In 1491 the author outlines that that mass death often resulted not directly from disease, but the fact that the debilitation of large proportions of the population then led to famine, which led to social disruption and institutional collapse, which then fed into more death and destruction. Today we perceive the Amazonians as “ancient” and “primal” nomads of the forest, just as their tropical homeland is seen to be eternal and everlasting. This, despite the fact that many of them even today are agriculturalists, albeit of a low-intensity sort. But as they are, perhaps so we could be. Complex societies seem to unravel awful quickly when subject to exogenous “shocks.” Perhaps we should be grateful for our “Pleistocene minds.” You never know when a swiss-army-knife mind is going to come in handy….