What Ethic Group is This?

 

map

23 and Me map of genetic relatives, rounded. 

An ethnic group is a set of people with a common ancestry, culture, and language. The Han Chinese, at a 1.3 billion strong, are an ethnic group; the Samaritans, of whom there are fewer than a thousand, are also an ethnic group. Ishi was, before his death, an ethnic group of one: the last surviving member of the Yahi people of California. 

We sit within nested sets of genetic relatives:

Family<clan<tribe<ethnic group<race<species<genus

(You are most likely part Homo neanderthalensis, because different species within the Homo genus have interbred multiple times.)

Interestingly, Wikipedia lists African American as an ethnicity on its list of ethnic groups page (as they should, because it is). 

Four or five hundred relatives, from parents and children to fifth cousins, are enough to begin to describe an ethnic group. It certainly looks, based on the map, like I hail from an ethnic group–yet neither Wikipedia nor 23 and Me recognize this group.

According to Wikipedia

Larger ethnic groups may be subdivided into smaller sub-groups known variously as tribes or clans, which over time may become separate ethnic groups themselves due to endogamy or physical isolation from the parent group. Conversely, formerly separate ethnicities can merge to form a pan-ethnicity, and may eventually merge into one single ethnicity. Whether through division or amalgamation, the formation of a separate ethnic identity is referred to as ethnogenesis.

Of course, no one wants to submit their DNA to 23 and Me and get the result “You’re a white person from America.” (Nor “You’re a black person from America.”) We know that. People take these tests to look at their deeper history. 

But focusing only on the past makes it easy to lose sight of the present. You aren’t your ancestors. The world didn’t halt in 1492. I’m no more “British” or “European” than I am “Yamnaya” or “Anatolian farmer.” 

History moves on. New ethnic groups form. The past tells us something about where we’ve been–but not where we’re headed. 

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Two Denisovan Admixture Events?

Recent genetic analysis suggests that humans mated with the mysterious Denisovans not once, but twice

Asian genomes carry introgressed DNA from Denisovans and Neanderthals

East Asians show evidence of introgression from two distinct Denisovan populations

South Asians and Oceanians carry introgression from one Denisovan population

I can’t read the whole paper, because it’s paywalled, but if correct, this is quite the change. Previously, only small amounts of Denisovan were detected in East Asians, while large amounts (2-6%) were detected in Oceanians (ie, Melanesians, Papuans, and Australian Aborigines.) 

According to Wikipedia:

Statistical analysis of genomic DNA sequences from different Asian populations indicates that at least two distinct populations of Denisovans existed,[50][51] and that a second introgression event from Denisovans into humans occurred. A study of Han ChineseJapanese and Dai genomes revealed that modern East Asian populations include two Denisovan DNA components: one similar to the Denisovan DNA found in Papuan genomes, and a second that is closer to the Denisovan genome from the Altai cave. These components were interpreted as representing separate introgression events involving two divergent Denisovan populations. South Asians were found to have levels of Denisovan admixture similar to that seen in East Asians, but this DNA only came from the same single Denisovan introgression seen in Papuans.[52]  …

The Denisovans, in case you’re new here, are a human species similar to the Neanderthals who lived… well, we’re not sure exactly where they lived, other than the Altai Cave, Siberia. We also don’t know what they looked like, because we have only found a few of their bones–a finger bone and some teeth–but they might have looked a bit like the Red Deer Cave People. Remarkably, though, these were in good enough condition (Siberia preserves things very well,) to allow scientists to extract sufficient DNA to determine that they are indeed a human species, but one that split from the ancestors of Homo sapiens about 600,000-750,000 years ago, and from the Neanderthals about 200,000 years later. 

Just as Homo sapiens mated with Neanderthals, so Denisovans mated with Neanderthals and Homo sapiens–the human family tree is growing increasingly complex. 

We don’t know exactly where these interbreeding events happened, since we know so little about the Denisovans (at least one of the Neanderthal interbreeding events probably happened in the Middle East, given that all non-Africans [and some Africans] have Neanderthal DNA,) but a clue lies in the DNA of the Negrito peoples. 

The Negritoes are a variety of peoples who live in south east Asia and, like the Pygmies of Africa, are rather short. Some of them, like the Aeta of the Philippines, have almost Papuan levels of Denisovan admixture, while others, like the Onge of India, have almost none. Assuming the Negritos are related to each other and not just isolated examples of island dwarfism, this suggests that the interbreeding event really did take places somewhere east of the major Indonesian islands of Sumatra and Borneo (which probably weren’t islands at the time, but connected to the mainland). The Denisovans may have been clever enough to build boats and cross the Wallace Line, surviving in the more isolated islands of Indonesia and the Philippines. 

On a related note, the article I just linked to from John Hawks, “This is where Scientists Might Find the Next Hobbits,” is truly excellent: 

In May, an international team of scientists led by Thomas Ingicco revealed new archaeological findings from Kalinga, in the northernmost part of Luzon, Philippines. Until now, scientists have mostly assumed that the Philippines were first inhabited by modern humans, only after 100,000 years ago. But the artifacts unearthed by Ingicco and coworkers were much older, more than 700,000 years old. …

Luzon was never connected to the Asian mainland, even when sea level was at its lowest during the Ice Ages. To get there, ancient hominins had to float. Who were they, and how did they get there?

Timeline of ancient Indonesian and Filipino hominin findings, from John Hawks’s article

I recommend you read the whole thing.

What’s all of this Denisovan DNA good for, anyway? Quoting Wikipedia again:

The immune system’s HLA alleles have drawn particular attention in the attempt to identify genes that may derive from archaic human populations. Although not present in the sequenced Denisova genome, the distribution pattern and divergence of HLA-B*73 from other HLA alleles has led to the suggestion that it introgressed from Denisovans into humans in west Asia. As of 2011, half of the HLA alleles of modern Eurasians represent archaic HLA haplotypes, and have been inferred to be of Denisovan or Neanderthal origin.[54] The apparent over-representation of these alleles suggests a positive selective pressure for their retention in the human population. A higher-quality Denisovan genome published in 2012 reveals variants of genes in humans that are associated with dark skin, brown hair, and brown eyes – consistent with features found with Melanesians today.[16] A study involving 40 Han Chinese and 40 people of ethnic Tibetan background identified a region of DNA around the EPAS1 gene that assists with adaptation to low oxygen levels at high altitude found in Tibetans is also found in the Denisovan genome.[55][56] In Papuans, introgressed Neanderthal alleles have highest frequency in genes expressed in the brain, whereas Denisovan alleles have highest frequency in genes expressed in bones and other tissues.[57]

It is a great era in genetics. 

Finnis, Saami, and Fennoscandian DNA

 

800px-Lenguas_finougrias
Distribution of the Finno-Ugric languages

I’ve long wondered which group arrived first in Europe: the Indo-Europeans or the Finno-Ugrics. Most Europeans speak one of the hundreds of languages in the Indo-European family tree, but a few groups speak languages from the mostly Siberian Finno-Ugric branch of the Uralic family.

(Sorry, guys, I’m out of practice writing and these sentences don’t sound good to me, but the only way to improve is to forge ahead, so let’s go.)

Major countries/ethnic groups that speak Finno-Ugric languages include the Finns (obviously,) Saami/Lapps, Hungarians, and Estonians. The most southerly of this family, Hungarian, arrived in the Carpathian Basin within the span of recorded History (in 894 or 895, followed by a few years of warfare to secure their territory,) but the origins of the other European Finno-Ugric languages remains mysterious.

Who arrived first, the Indo Europeans or the Finns? Did the Saami always live in their current homelands, or did they once range much further south or east? Did they migrate here recently or long ago (since the entire area was under ice sheets during the ice age, no one lived there tens of thousands of years ago.)

With the exception of Hungarian, these languages all hail from the far north (especially if you include the Samoyidic languages, which hail from north of Komi on the map,) a cold and forbidding land where herding, hunting, gathering, and fishing have remained the primary way of life until quite recently–the long winters making agriculture very difficult.

Lamnidis et al have a new paper out on Ancient Fennoscandian DNA that sheds a fascinating light on the subject:

Here we analyse ancient genomic data from 11 individuals from Finland and north-western Russia. We show that the genetic makeup of northern Europe was shaped by migrations from Siberia that began at least 3500 years ago. This Siberian ancestry was subsequently admixed into many modern populations in the region, particularly into populations speaking Uralic languages today. Additionally, we show that ancestors of modern Saami inhabited a larger territory during the Iron Age, which adds to the historical and linguistic information about the population history of Finland.

41467_2018_7483_fig1_htmlLet’s cut to the pictures, because they are worth a thousand words:

Just in case you are unclear on the geography, the Modern Saami come from northern part of the Finnoscandian peninsula. Six of the ancient remains came from Bolshoy Oleni Ostrov in the Murmansk Region on the Kola Peninsula–that’s the topmost dot on the map, now in Russia. These remains are very old–dated to about 1610-1436 BC.

Seven remains came from Levänluhta in Isokyrö, Finland, from a more recent burial dated to around 300-800 AD. (Actually, I think Levanluhta is a lake, so  This is the most southwestern burial on the map, in an area where the modern Finns live.

And the remains of two people came from a much more recent Saami cemetery in the Kola peninsula, Chalmny Varre, dating from the 17 or 1800s.

All of this DNA was compared against a variety of reference populations:

41467_2018_7483_fig2_html

(I would just like to pause for a moment to appreciate both the beauty and hard work that went into these graphs.)

PC2 graphs are a little complicated, but what we’re basically looking at (in color) are two different human population axes. They very roughly correlate to north-south (up and down) and east-west, (left to right), because people tend to be more closely related to their neighbors than people thousands of miles away, but there’s another, more fascinating story going on here.

On the right-hand side, we have a cline that maps very nicely to north and south, from the Yukagir–a people from a part of Russia that’s so far to the northeast it’s almost in Alaska–at the top and the Semende of Indonesia and the Atayal, an indigenous Taiwanese group, at the bottom. (Most Taiwanese you meet are either newly arrived Han Chinese or older Han Chinese; the aboriginal Taiwanese are different, but likely the ancestors of Polynesians.)

AsianDNA1
DNA from various Asian peoples

Most east Asian DNA shows up as a blend of these two groups (which we may call roughly polar and tropical). In the chart to the right, taken from Haak et al, the polar DNA is red and the tropical is yellow. So the up-down cline on the right side of the map represents which particular mix of Polar/Tropical DNA these folks have.

On the left side of the graph, we have a farming/hunter-gatherer cline. The first farmers hailed from Anatolia (now Turkey, but that was before the Turks moved to Turkey,) and subsequently spread/conquered most of Europe and probably a few other places, because agriculture was quite successful. So the orange is Middle Easterners; above them are southern Europeans like Albanians and Basques; then the English, French, Hungarians, Finns, etc; and finally some older burials of people with descriptive names like “Eastern Hunter-Gatherer” [EHG] or “Scandinavian Hunter-gatherers” [SHG].

(I have to constantly remind myself what these little abbreviations mean, but The Genetic Prehistory of the Baltic Region probably clears things up a bit:

Similarly, in the Eastern Baltic, where foraging continued to be the main form of subsistence until at least 4000 calBCE15, ceramics technology was adopted before agriculture, as seen in the Narva Culture and Combed Ceramic Culture (CCC). Recent genome-wide data of Baltic pottery-producing hunter-gatherers revealed genetic continuity with the preceding Mesolithic inhabitants of the same region as well as influence from the more northern EHG21,22, but did not reveal conclusively whether there was a temporal, geographical or cultural correlation with the affinity to either WHG or EHG.

The transition from the Late (Final) Neolithic to the Early Bronze Age (LNBA) is seen as a major transformative period in European prehistory, accompanied by changes in burial customs, technology and mode of subsistence as well as the creation of new cross-continental networks of contact seen in the emergence of the pan-European Corded Ware Complex (CWC, ca. 2900–2300 calBCE) in Central2 and north-eastern Europe21.

If you remember your Guns, Germs, and Steel, Turkish farmers had a really hard time getting their wheat to grow up in really cold places like Northern Russia,  Scandinavia and Narva (near the border between Estonia and Russia on the Baltic Sea,) which is why modern Finland is super poor and Turkey and Mexico, where corn was domesticated, are rich–what it doesn’t quite work like that?

Okay.

Anyway.

So most Europeans today are a mix of Anatolian farmers and various European hunter gatherer groups, with exactly how much you got depending a lot on whether the local environment was hospitable to farming. The pure hunter-gatherer genomes therefore show up as “further north” than the mixed, modern genomes of modern French and British folks.

There were additional events besides the Anatolian conquest that shaped modern European genetics–mostly the aforementioned Indo-European conquest–but the Indo-Europeans were at least part hunter-gatherer by DNA (nomadic pastoralists by profession,) so on this scale, their contributions look a lot like the older hunter-gatherer DNA.

So the interesting part of the graph is the middle, where all of the central Eurasian peoples are plotted. The purple band is various Finno-Ugric/Uralic speakers.

Hungarians are solidly in Europe because the ancient conquering Magyars left behind their language, but not much of their DNA (as we’ve discussed previously.) The Nganasan are one of the most thoroughly Siberian peoples you can imagine; they historically survived by hunting reindeer.

The green swaths (light and dark teal) are mostly Turkic-language speaking peoples; the Turkic peoples originated near Mongolia/Korea and spread out from there, mostly absorbing the DNA of whomever they encountered and passing on their language. The authors have also included Mongolian (which is not in the Turkic language family) in the light green group and some Caucuses groups in the dark teal.

Interestingly, the Yukaghir language (far upper right) is (according to Wikipedia,) potentially in the greater Finno-Ugric/Uralic family:

The relationship of the Yukaghir languages with other language families is uncertain, though it has been suggested that they are distantly related to the Uralic languages, thus forming the putative Uralic–Yukaghir language family.[5]

Based on the genetics, I’d say it looks very likely that the ancestors of Uralic-speaking Nganasan and the Yukagirs were conversing in some sort of mutually intelligible language. Unfortunately, Yukaghir has very few speakers and is likely to die, so there’s not much time to research it.

Finally in the Light Teal we have some groups from Pakistan/Afghanistan, like the Balochi.

(Note that all of the colors used in these studies are arbitrary; DNA doesn’t really have a color.)

So where do our ancient DNA remains fall on this graph?

Today, the Levanluhta site is in Finland, surrounded solidly by Finns (and maybe some random Scandinavians; who knows;) in 300-800 AD, the population was almost identical to modern Saami. So even though Saami and Finns both speak Finno-Ugric languages, the Finns replaces the Saami in this area sometime in the past 1,500 years or so.

One Levanlughta skeleton is an exception–the one marked Levanlughta_B; it is clearly closer to the Finns and English on this graph, but deeper mathematical analysis disputes this conclusion:

One of the individuals from Levänluhta (JK2065/Levänluhta_B) rejects a cladal position with modern Saami to the exclusion of most modern Eurasian populations. This individual also rejects a cladal position with Finns. We analysed low coverage genomes from four additional individuals of the Levänluhta site using PCA (Supplementary Figure 3), confirming the exclusive position of Levänluhta_B compared to all other six individuals (including the four low-coverage individuals) from that site, as is consistent with the ADMIXTURE and qpAdm results. The outlier position of this individual cannot be explained by modern contamination, since it passed several tests for authentication (see Methods) along with all other ancient individuals. However, no direct dating was available for the Levänluhta material, and we cannot exclude the possibility of a temporal gap between this individual and the other individuals from that site.

In other words, it is a mystery.

The remains from Chalmny Varre, which we know was a Saami cemetery, unsurprisingly cluster with the other Saami.

The Bolshoy remains, though, are quite interesting. They are shifted slightly in the direction of the ancient hunter-gatherers (perhaps their descendants, if still around, have mixed a bit with the agriculturalists.) Their physical location is about as far east as the Red Squares (ethnic Russians,) yet the more closely resemble the Mansi or the Selkups. (The modern Mansi live here; the modern Selkups live nearby.)

Getting down to the bar graphs, we see this data presented in a different way.

There are three groups that we can see contributing to most modern Europeans–Farmers, represented by the Orange LBK DNA; exclusively Indo-European, Green, notably not found in the Basque; and hunter-gatherers in Dark Blue. (Note that the ancestors of the Indo-Europeans hailed from the Central Eurasian steppes and so their DNA could have gotten around there, too.)

The modern Saami also have a Purple component to their DNA, which finds its highest expression in the Nganasan of far eastern polar Russia.

So the oldest burials–the Bolshoy–show no agricultural DNA. They are hunter-gatherers+Siberians, with a touch of Indo-European (probably from a steppe population that might have contributed to the Indos as well) and a bit they share with… the Karitiana of Brazil? Well, the Native Americans did descend from Paleo Siberians, so some genetic relatedness is expected.

The more recent burials, which cluster with the modern Saami, all show agricultural DNA–probably due to marrying a few of the local Finns/Russians who carry some agricultural DNA (who are almost genetically identical on this scale) rather than a pure LBK agriculturalist.

Here we see why the one outlier, Levanlughta_B, doens’t group with the Finns, either–modern Finns and Russians have some of that Nganasan-style Siberian DNA (probably from the same process that gifted Finnish/Russian DNA to the Saami), but Levanlughta_B doesn’t. Levanlughta_B looks more like the Baltic BA sample (Baltic Bronze Age.) Perhaps this individual was just a merchant, traveler, or lost–or represents a stage before the modern Finnish population had been produced.

The Finnish population itself is interesting, because it is genetically very similar to the Russian, but obviously speaks a language far more closely related to Saami (Lapp) than anything in the Indo-European tree. While it is therefore likely that the Finns replaced the Saami in the area around Lake Levanlughta, it seems also probable that in the process, they absorbed a large number of Uralic-speaking people. Who conquered (or married) whom? Did an ancient Balto-Slavic population move into what is now Finland, marry the local Saami girls, and adopt their language? Did an ancient Siberian population speaking a Uralic language conquer some ancient group of Russians, take their women, pass on their Uralic language, and later move into Finland and drive out the locals? Or perhaps something even more complicated occurred.

As for the Bolshoy, are they related (closely) to the modern Saami, or are they a group that simply died out?

The paper goes on:

 While the Siberian genetic component presented here [Purple] has been previously described in modern-day populations from the region1,3,9,10, we gain further insights into its temporal depth. Our data suggest that this fourth genetic component found in modern-day north-eastern Europeans arrived in the area before 3500 yBP. It was introduced in the population ancestral to Bolshoy Oleni Ostrov individuals 4000 years ago at latest, as illustrated by ALDER dating using the ancient genome-wide data from the Bolshoy samples. The upper bound for the introduction of this component is harder to estimate. The component is absent in the Karelian hunter-gatherers (EHG)3 dated to 8300–7200 yBP as well as Mesolithic and Neolithic populations from the Baltics from 8300 yBP and 7100–5000 yBP respectively8

Karelia is a region that crosses the border between Finland and Russia, so it is significant that this Siberian component isn’t found in ancient Karelian hunter-gatherers. Of course, the Siberians could have just been further north, however, the authors note that we have archaeological evidence of the spread of the Bolshoy people:

The large Nganasan-related component in the Bolshoy individuals from the Kola Peninsula provides the earliest direct genetic evidence for an eastern migration into this region. Such contact is well documented in archaeology, with the introduction of asbestos-mixed Lovozero ceramics during the second millennium BC50, and the spread of even-based arrowheads in Lapland from 1900 BCE51,52. Additionally, the nearest counterparts of Vardøy ceramics, appearing in the area around 1,600-1,300 BCE, can be found on the Taymyr peninsula, much further to the East51,52. Finally, the Imiyakhtakhskaya culture from Yakutia spread to the Kola Peninsula during the same period24,53. Contacts between Siberia and Europe are also recognised in linguistics. The fact that the Nganasan-related genetic component is consistently shared among Uralic-speaking populations, with the exceptions of absence in Hungarians and presence in the non-Uralic speaking Russians, makes it tempting to equate this genetic component with the spread of Uralic languages in the area.

The authors qualify this with a bit of “it’s complicated; people move around a lot,” but basically it’s People: not pots.

That was an enjoyable read; I look forward to the next paper from these folks.

Neanderthal DNA–hey!–what is it good for?

Quite a bit.

First, a bit of history:

neanderthalmap
map of Neanderthal DNA in humans

It appears that there were (at least) 3 main cross-breeding events with Neanderthals. The first event most likely happened when one small band of humans had left Africa and ventured into the Middle East, where Neanderthals were living. The DNA acquired from that partnership can be found in all modern non-Africans, since they are all descended from this same group. (Since there has also been back-migration from the Middle East into Africa sometime in the past 70,000 years, many African groups also have a small amount of this DNA.)

Soon after, the group that became the Melanesians, Papuans, and Aborigines split off from the rest and headed east, where they encountered–and interbred with–the mysterious Denisovans, a third human species that we know mostly from DNA. Various sources claim this happened before the second neanderthal inter-breeding event, but just looking at the amount of admixed neanderthal in Oceanans suggests this is wrong.

Meanwhile, the rest of the non-African humans, probably still living in the Middle East or Eurasian Steppe, encountered a second band of Neanderthals, resulting in a second admixture event, shared by all Asians and Europeans, but not Melanesians &c. Then the Asians and Europeans went their separate ways, and the Asians encountered yet a third group of Neanderthals, giving them the highest rates of Neanderthal ancestry.

nature-siberian-neanderthals-17.02.16-v2

During their wanderings, some of these Asians encountered Melanesians, resulting in a little Denisovan DNA in today’s south Asians (especially Tibetans, who appear to have acquired some useful adaptations to Tibet’s high altitude from ancient Denisovans.)

There were other interbreeding events, including a much older one that left homo sapiens DNA in Neanderthals, and one that produced Denny, a Neanderthal/Denisovan hybrid. There were also interbreeding events in Africa, involving as-yet unidentified hominins. (In the human family tree to the right/above, Melanesians are included within the greater Asian clade.)

Who married whom? So far, we’ve found no evidence of Neanderthal mitochondrial DNA–passed from mothers to their children–in modern humans, so the pairings most likely involved Neanderthal men and human women. But we have also found extremely little Neanderthal DNA on the Y chromosome–so it is likely that they only had female children, or any male children they had were infertile.

Anthropogenesis-DenisovaAlleleMapInterestingly, we find higher amounts of Neanderthal DNA in older skeletons, like the 40,000 year old Tianyuan Man, or this fellow from Romania with 10% Neanderthal DNA, than in modern humans. Two potential explanations for the decrease: later mixing with groups that didn’t have Neanderthal DNA resulted in dilution, or people with more Neanderthal DNA just got out-competed by people with less.

Given the dearth of DNA on the Y chromosome and the number of diseases linked to Neanderthal DNA, including Lupus, Crohn’s, cirrhosis, and Type-2 diabetes, the fact that morphological differences between Sapiens and Neanderthals are large enough that we classify them as different species, and the fact that Neanderthals had larger craniums than Sapiens but Sapiens women attempting to give birth to hybrid children still had regular old Sapiens pelvises, gradual selection against Neanderthal DNA in humans seems likely.

However, the Neanderthals probably contributed some useful DNA that has been sorted out of the general mix and come down the ages to us. For example, the trait that allows Tibetans to live at high altitudes likely came from a Denisovan ancestor:

Researchers discovered in 2010 that Tibetans have several genes that help them use smaller amounts of oxygen efficiently, allowing them to deliver enough of it to their limbs while exercising at high altitude. Most notable is a version of a gene called EPAS1, which regulates the body’s production of hemoglobin. They were surprised, however, by how rapidly the variant of EPAS1spread—initially, they thought it spread in 3000 years through 40% of high-altitude Tibetans, which is the fastest genetic sweep ever observed in humans—and they wondered where it came from.

Modern humans have Neanderthal DNA variants for keratin (a protein found in skin, nails, hair, etc.,) and UV-light adaptations that likely helped us deal with the lower light levels found outside Africa. There’s circumstantial evidence that microcephalin D could have Neanderthal origins (it appeared about 37,000 years ago and is located primarily outside of Africa,) but no one has found microcephalin D in a Neanderthal, so this has not been proven. (And, indeed, another study has found that Neanderthal DNA tends not to be expressed in the brain.)

Yet on the other hand, Neanderthal admixture affected sapiens’ skull shapes:

Here, using MRI in a large cohort of healthy individuals of European-descent, we show that the amount of Neanderthal-originating polymorphism carried in living humans is related to cranial and brain morphology. First, as a validation of our approach, we demonstrate that a greater load of Neanderthal-derived genetic variants (higher “NeanderScore”) is associated with skull shapes resembling those of known Neanderthal cranial remains, particularly in occipital and parietal bones. Next, we demonstrate convergent NeanderScore-related findings in the brain (measured by gray- and white-matter volume, sulcal depth, and gyrification index) that localize to the visual cortex and intraparietal sulcus. This work provides insights into ancestral human neurobiology and suggests that Neanderthal-derived genetic variation is neurologically functional in the contemporary population.

(Not too surprising, given Neanderthals’ enormous craniums.)

Homo sapiens also received Neanderthal genes affecting the immune system, which were probably quite useful when encountering new pathogens outside of Africa, and genes for the “lipid catabolic process,”[19] which probably means they were eating new, fattier diets that Neanderthals were better adapted to digest.

Even Neanderthal-derived traits that today we cast as problems, like Type II Diabetes and depression, might have been beneficial to our ancestors:

“Depression risk in modern human populations is influenced by sunlight exposure, which differs between high and low latitudes, and we found enrichment of circadian clock genes near the Neanderthal alleles that contribute most to this association.”

Why would we find an association between Neanderthal DNA and circadian clock genes? Neanderthals had thousands of years more exposure to Europe’s long nights and cold winters than homo Sapiens’; it is unlikely that they developed these adaptations in order to become less well-adapted to their environment. It is more likely that Neanderthals downregulated their activity levels during the winter–to put it colloquially, they hibernated.

No problem for furry hunter-gatherers who lived in caves–much more problematic for information age workers who are expected to show up at the office at 9 am every day.

Type II diabetes affects digestion by decreasing the production of insulin, necessary for transporting converting carbs (glucose) into cells so it can be transformed into energy. However, your body can make up for a total lack of carbs via ketosis–essentially converting fats into energy.

Our hunter-gatherer ancestors–whether Neanderthal or Sapiens–didn’t eat a lot of plants during the European and Siberian winters because no a lot of plants grow during the winter. If they were lucky enough to eat at all, they ate meat and fat, like the modern Inuit and Eskimo.

And if your diet is meat and fat, then you don’t need insulin–you need ketosis and maybe some superior lipid digestion. (Incidentally, the data on ketogenic diets and type II diabetes looks pretty good.)

In sum, Neanderthal and Denisovan DNA, while not always useful, seems to have helped Homo sapiens adapt to colder winters, high altitudes, new pathogens, new foods, and maybe changed how we think and perceive the world.

 

 

Best of EvX: How Turkic is Turkey?

 

dpfz16huuaatcs6
map of the spread of farming in Turkey/Anatolia/Europe

Hello my Turkish and Turkic readers! In honor of having written a lot on this blog, we’re taking a look back at our most popular posts, and today’s is on the genetic history of Turkey and the Turkic peoples.

Since my original post, I have learned many things about Turkey–mostly that Turks and other Turkic peoples love their culture and heritage. Note: I will probably use “Turkey” and “Anatolia”, interchangeably in this post. Turkey is the name for the modern state located in the region; Anatolia is a more generic name for the geography. I know that “Turkey” as a state or even a people didn’t exist 8,000 years ago.

Turkey has a long and fascinating history. It is possibly the cradle of civilization, as sites like Gobekli Tepe attest, and one of the birthplaces of agriculture.

1280px-j228y-dna29Early farmers spread out from Anatolia into Europe and Asia, contributing much of the modern European gene pool. There are many Y-DNA haplogroups in modern Turkey, which most likely means the Turkish male population hasn’t been completely replaced in recent invasions. (It’s not uncommon for an invasion to wipe out 80+% of the male population in an area.) About 24% of Turkish men carry haplogroup J2, which might not have originated in Turkey all of those centuries ago, but by 12,000 years ago it was common throughout Turkey (and today remains the most common haplogroup). This lineage spread with the Anatolian farmers into Europe around 8,000 years ago. and presumably Asia, as well.

TurkishDNA2fromHaak
From Haak et al

The second most common Y-haplogroup, at 16%, is good old R1b, which was carried into Turkey around 5-6,000 years ago by the Indo-European invaders. (The Indo-European invasion in Spain apparently wiped out all of the local men, but was not nearly so bad in Turkey.) These invaders spoke the Anatolian branch of the Indo-European tree, including Hittite and Luwian.

The Anatolian languages went extinct following Anatolia’s conquest by Alexander the Great in the 4th century BC (though it took several centuries for the languages to fall completely out of use.)

Haplogroup G–11%–is most common in the Caucasus, spread thinly over much of Anatolia and Iran, and even more thinly through Europe, North Africa, and central Asia. It’s probably a pretty old group–Otzi the Iceman was a member of the G clade.

Haplogroup E-M215 is found in about 10% of Turks and is most common in North Africa and the Horn of Africa, but is also quite common in Bedouin populations. It seems likely to be a very old haplogroup.

J1–9%–is common throughout the Middle East and amusingly reaches 46% among Jewish men named “Cohen.”

The rest of Turkish Y-chromosomes hail either from related haplogroups, like R1a, or represent smaller fractions of the population, like Q, 2%, commonly found in Siberia and Native Americans.

(Information on all Turkish Y-haplogroups.)

TurkmenSo how much Turkish DNA hails from Turkic peoples?

Modern Turks don’t speak Anatolian or Greek. They speak a Turkic language, which hails originally from an area near Mongolia. The Turkic-speaking peoples migrated into Anatolia around a thousand years ago, after a long migration/expansion through central Eurasia that culminated with the conquering of Constantinople. Today, the most notable Turkic-speaking groups are the Turks of Turkey,  AzerbaijanisUzbeksKazakhsTurkmen and Kyrgyz people.

The difficulty with tracing Turkic DNA is that, unlike the Mongols, Turkic DNA isn’t terribly homogeneous. The Mongols left a definite genetic signature wherever they went, but imparted less of their language–that is, they killed, raped, and taxed, but didn’t mix much with the locals. By contrast, the Turkic peoples seem to have mixed with their neighbors as they spread, imparting their language and probably not massacring too many people.

asia
Asian, Australian, and Melanesian ethic groups (including Indian, Middle Eastern, and Chinese) from Haak et al’s dataset

According to Wikipedia:

The largest autosomal study on Turkish genetics (on 16 individuals) concluded the weight of East Asian (presumably Central Asian) migration legacy of the Turkish people is estimated at 21.7%.[1]

Note that Turkey shares haplogroup J2 with its Turkic neighbors. This raises an interesting possibility: early Anatolian farmers spread into central Eurasia, mixed with local nomadic Turkic speakers, and then migrated back into Turkey. But 16 people isn’t much of a study.

“South Asian contribution to Turkey’s population was significantly higher than East/Central Asian contributions, suggesting that the genetic variation of medieval Central Asian populations may be more closely related to South Asian populations, or that there was continued low level migration from South Asia into Anatolia.”

“South Asian” here I assume means that Turkey looks more like Iran than Uzbekistan, which is true. The Turkic wanderers likely passed through Iran on their way to Turkey, picking up Iranian culture (such as Islam) and DNA–plus the pre-existing Anatolian population was probably closer to Iran than Uzbekistan anyway.

… the exact kinship between current East Asians and the medieval Oghuz Turks is uncertain. For instance, genetic pools of Central Asian Turkic peoples is particularly diverse and modern Oghuz Turkmens living in Central Asia are with higher West Eurasian genetic component than East Eurasian.[2][3][4]

I think “West Eurasian” is a euphemism for “Caucasian.” East Eurasian (aka Asian) DNA, you can see in the map above, tends to be red+yellow, tending toward all red in Siberia and all yellow in Taiwan. Indo-European groups, including Iranians, tend to have a teal/blue/orange pattern. Turkmen, Uzbeks, and Uygurs, as you can see in the graph, have a combination of both sets of DNA. The Turks also have a small amount of east Asian DNA–but much less–while their neighbors in Iran and central Eurasia share a little Indian DNA.

Several studies have concluded that the genetic haplogroups indigenous to Western Asia have the largest share in the gene pool of the present-day Turkish population.[5][6][7][8][5][9][10][11] An admixture analysis determined that the Anatolian Turks share most of their genetic ancestry with non-Turkic populations in the region and the 12th century is set as an admixture date.[12]

Western Asia=Middle East.

So Turkish DNA is about 22% Turkic, from nomads who entered the country via Iran, and about 78% ancient Anatolian, from the people who had already lived there on the Anatolian plateau for centuries.

But as the Turkic peoples (and many of the comments on my original post) show, culture doesn’t have to be genetic, and many Turkic people feel a strong cultural connection to each other. (And many people report that various Turkic languages are pretty easy to understand if you speak one Turkic language–EG:

hello everyone I’m an Uzbek,

… tatars played a great role in Genghis’s empire and they had an empire after dividing the empire called Golden Horde, it was mongol state but after it became to turki with a time. and their sons are kazakh and kirgiz. Thats why we uzbeks can understand turkish easly more than our neighboors kazakhs. and we uzbeks are not mongoloid like kazakhs.because uzbek language has oghuz and karluk dialect. uzbek-uygur are like turkish-azerbaijani or turkish-crimean tatar. thats why uzbek dialect is most understandable language for every turkic people. but we can understand %95 uygur, %85 turkish-turkmen, %70 azerbaijani %50 kazakh.

Our Uzbeki friend’s full comment is very interesting, and I recommend you read the whole thing.

For that matter, many thanks to everyone who has left interesting comments sharing your family’s histories or personal perspectives on Turkish/Turkic culture and history over the years–I hope you have enjoyed this update.

Which Groups Have the most Neanderthal and Denisovan DNA?  

 

beautifulneanderthalDenisovan
Neanderthal and Denisovan contributions to different populations by chromosome (source)

Here are the numbers I’ve found so far for Neanderthal and Denisovan DNA in different populations:

 et al, in The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans, 2016, report:

Native Americans: 1.37%
Central Asia: 1.4%
East Asia: 1.39%
Oceana (Melanesians): 1.54%
South Asia: 1.19%
Europeans: 1.06%

(I have seen it claimed that the high Neanderthal percents for Oceanan populations (that is, Melanesians and their relatives,) could be a result of Denisovan DNA being incompletely distinguished from Neanderthal.)

Prufer et al, [pdf] 2017, report somewhat higher values:

East Asians: 2.3–2.6%
Europeans: 1.8–2.4%

While Lohse and Frantz estimate an even higher rate of between 3.4–7.3% for Europeans and East Asians. (They found 5.9% in their Chinese sample and 5.3% in their European.)

The Mixe and Karitiana people of Brazil have 0.2% Denisovan (source); other estimates for the amount of Denisovan DNA in Native populations are much lower–ie, 0.05%.

I found an older paper by Prufer et al with estimates for three Hispanic populations, but doesn’t clarify if they have Native American ancestry:

Population Individuals Neandertal ancestry (%)
Autosomes X
Europeans CEU–Euros from Utah 85 1.17±0.08 0.21±0.17
FIN–Finnish 93 1.20±0.07 0.19±0.14
GBR–British 89 1.15±0.08 0.20±0.15
IBS–Spain 14 1.07±0.06 0.23±0.18
TSI–Tuscan 98 1.11±0.07 0.25±0.20

East Asians CHB–Han Chinese Beijing 97 1.40±0.08 0.30±0.21
CHS–Han Chinese South 100 1.37±0.08 0.27±0.21
JPT–Japan, Tokyo 89 1.38±0.10 0.26±0.21

Americans CLM: Colombians from Medellin 60 1.14±0.12 0.22±0.16
MXL: Mexicans from LA 66 1.22±0.09 0.21±0.15
PUR: Puerto Ricans 55 1.05±0.12 0.20±0.15

Africans LWK: Luhya in Webuye, Kenya 97 0.08±0.02 0.04±0.07
ASW: African Americans South West US 61 0.34±0.22 0.07±0.11

Since the paper is older, all of its estimates are lower than current estimates, because we now have more Neanderthal DNA to compare against. However, you can still see the general trend.

The difference between “autosomes” and “X” highlighted here is that (IIRC) autosomes includes all chromosomes except the XY pair, and X is the X from that pair. They’re breaking them up this way because the X chromosome tends to have very little Neanderthal on it (and the Y even less), probably because Neanderthal DNA on these particular chromosomes was selected against.

Neanderthal DNA appears to have been selected for in areas that control hair and skin–people who had just left Africa were adapted to the African environment, and Neanderthal hair and skin traits helped them survive in colder, darker winters. We also see a lot of Neanderthal DNA influencing inflammation/immune response–these may have helped people fend off new diseases. But we see almost no Neanderthal (or Denisovan) DNA in areas of the genome that code for sperm, eggs, testes, ovaries, etc. These parts of people were probably already finely tuned to work together, didn’t need to change with the environment, and changing anything probably just made them less efficient–so Neanderthal (and Denisovan) DNA on the X and Y chromosomes has been purged from the Homo Sapiens gene pool.

North African Populations Carry Signature of Admixture with Neanderthals reports its data relative to the European average (which I believe is the CEU pop, 1.17%, so I’ll do the math for you to figure how much Neanderthal they have.)

Algeria 44.57% = 0.52% Neanderthal
Tunisia 100.16% = 1.172 N
Tunisia 138.13% = 1.6% N (This is an interesting population that has been highly endogamous and thus better reflects historical populations in the area.)
Egypt 58.45% = 0.68% N
Libya 56.36% = 0.66% N
Morroco North 69.17% = 0.81% N
Morocco South 17.90% = 0.21% N
Saharawi 50.90% = 0.6% N
Canary Island* 101.44% = 1.187% N
China Beijing 193.43% = 2.26 % N
China 195.41% = 2.29% N
Texas Indu Gupti 84.37% =0.987% N
Andalusia*118.66% = 1.39% N
Tuscan 94.90% = 1.11% N
Basque BASC 129.48% = 1.51% N
Galicia* GAL 115.86% = 1.36% N
Yoruba YRI  0.00% = 0% N
Luyha LWK  −14.89% = N

The authors note that they are not sure how the Luyha received a negative score–perhaps the presence of admixed DNA from yet another species is interfering with the results.

According to Wikipedia:

Denisovan DNA is most commonly found in Melanesians, Papulans, Aboriginal Australians and Aboriginal Filipinos, who all have similar amounts around 4-6%, indicating that they probably were all one group when their ancestors met the Denisovans. However, the similar-looking but historically quite isolated Onge people have no Denisovan–so they split off before the event.

In Papuans, Neanderthal DNA tends to be expressed in brain tissue, Denisovan in bones and other tissues.

Asians have a small amount of Denisovan DNA; Tibetans have a particular gene that lets them absorb oxygen effectively at high altitudes that they got from the Denisovans.

The Mende People of Sierra Leon may derive 13% of their DNA from an as-yet unknown hominin species (ancient DNA and bones do not preserve well in parts of Africa, so finding remains and identifying the species may be difficult.)

The Yoruba derive 8 or 9% of their DNA from the same hominin.

Masai have a small fraction of Neanderthal–since they are 30% non-African, probably about 0.35% of their genome–but you can read the paper yourself. 

Biaka Pygmies and Bushmen (San): 2% from an unknown archaic.

With more testing, better and more comprehensive numbers are sure to turn up.

Greatest Hits: Native Americans and Neanderthal DNA.

Native-American-populations
Source: Ancient Beringians: A Discovery Changing Early Native American History

Over the years, a few of my posts have been surprisingly popular–Turkey: Not very Turkic, Why do Native Americans Have so much Neanderthal DNA?, Do Black Babies have Blue Eyes? and Can Ice packs help stop a seizure (in humans)?

It’s been a while since these posts aired, so I thought it was time to revisit the material and see if anything new has turned up.

Today, lets revisit Native Americans and Neanderthal DNA:

I’m sorry, but I no longer think Native Americans (aka American Indians) have higher than usual levels of Neanderthal DNA. Sorry. Their Neanderthal DNA levels are similar to (but slightly lower than) those of other members of the Greater Asian Clade. They also have a small amount of Denisovan DNA–at least some of them.

Why the confusion? Some Neanderthal-derived alleles are indeed more common in Native Americans than in other peoples. For example, the Neanderthal derived allele SLC16A11 occurs in 10% of sampled Chinese, 0% of Europeans, and 50% of sampled Native Americans. (Today, this gene makes people susceptible to Type 2 diabetes, but it must have been very useful to past people to be found in such a large percent of the population.)

neanderthalmap

And there was one anomalously high Neanderthal DNA measure in Natives living near the Great Slave Lake, Canada. (Look, I didn’t name the lake.)

But this doesn’t mean all Native Americans possess all Neanderthal alleles in greater quantities.

So how much Neanderthal do Native Americans have? Of course, we can’t quite be sure, especially since only a few Neanderthals have even had their DNA analyzed, and with each new Neanderthal sequenced, we have more DNA available to compare against human genomes. But here are some estimates:

beautifulneanderthalDenisovan
Neanderthal and Denisovan contributions to different populations by chromosome (source)

 et al, in The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans, report:

Native Americans: 1.37%
Central Asia: 1.4%
East Asia: 1.39%
Oceana (Melanesians): 1.54%
South Asia: 1.19%
Europeans: 1.06%

I have seen it claimed that the high Neanderthal percents for Oceanan populations (that is, Melanesians and their relatives,) could be a result of Denisovan DNA being incompletely distinguished from Neanderthal.

Prufer et al, [pdf] 2017, report somewhat higher values:

East Asians: 2.3–2.6%
Europeans: 1.8–2.4%

While Lohse and Frantz estimate an even higher rate of between 3.4–7.3% for Europeans and East Asians. (They found 5.9% in their Chinese sample and 5.3% in their European.)

The Mixe and Karitiana people of Brazil have 0.2% Denisovan (source); other estimates for the amount of Denisovan DNA in Native populations are much lower–ie, 0.05%.

I found an older paper by Prufer et al with estimates for three Hispanic populations, but doesn’t clarify if they have Native American ancestry:

CLM–Colombians from Medellin: 1.14%
MXL–Mexicans in LA: 1.22%
PUR–Puerto Rico: 1.05%

Since this is an older paper, all of its estimates may be on the low side.

The absolute values of these numbers is probably less important than the overall ratios, since the numbers themselves are still changing as more Neanderthal DNA is uncovered. The ratios in different papers point to Native Americans having, overall, about the same amount of Neanderthal DNA as their relatives in East Asia.

Melanesians, though. There’s an interesting story lying in their DNA.

The Unbearable Whiteness of Elizabeth Warren

I almost feel sad for Senator Warren. One day, a little girl looked in the mirror, saw pale skin, brown hair, and blue eyes looking back at her, and thought, “No. This can’t be right. This isn’t me.”

So she found a new identity, based on a family legend–a legend shared by a suspicious number of white people–that one of her ancestors was an American Indian.

warren-penn-state
Elizabeth Warren changed her race at Penn: Source

This new identity conveyed certain advantages: Harvard Law claimed her as a Native American to boost claims of racial diversity among the faculty:

A majority [83%] of Harvard Law School students are unhappy with the level of representation of women and minorities on the Law School faculty, according to a recent survey. …

Law students said they want to learn from a variety of perspectives and approaches to the law. “A black male from a lower socioeconomic background will approach the study of constitutional law in a different way from a white upper-class male,” Reyes said. …

Of 71 current Law School professors and assistant professors, 11 are women, five are black, one is Native American and one is Hispanic, said Mike Chmura, spokesperson for the Law School.

Although the conventional wisdom among students and faculty is that the Law School faculty includes no minority women, Chmura said Professor of Law Elizabeth Warren is Native American.

In response to criticism of the current administration, Chmura pointed to “good progress in recent years.”

As did Penn:

The University of Pennsylvania chose not to tout in the press their newly minted Native American professor. But her minority status was duly noted: The university’s Minority Equity Report, published in April 2005, shows that Warren won a teaching award in 1994. Her name is in bold and italicized to indicate she was a minority. …

The law school was happy to have her count as a diversity statistic, however, and for at least three of the years she taught there — 1991, 1992, and 1994 — an internal publication drawing on statistics from the university’s federal affirmative action report listed one Native American female professor in the university’s law school.

Warren’s Native American identity may have played no role in her hiring (the committees involved appear not to have known or cared about her identity,) but it seems to have been important to Warren herself. As her relatives aged and died, and she moved away from her childhood home in Oklahoma and then Texas, she was faced with that persistent question: Who am I?

The truth, a white woman from a working class family in Oklahoma, apparently wasn’t enough for Elizabeth. (Oklahoma doesn’t carry many status points over in East Coast academic institutions.)

Each of us is the sum of many things, including the stories our families tell us and genetic contributions from all of our ancestors–not just the interesting ones (within a limit–after enough generations, each individual contribution has become so small that it may not be passed on in reproduction.)

I have also done the 23 and Me thing, and found that I hail from something like 20 different ethnic groups–including, like Warren, a little smidge of Native American. But none of those groups make up the majority of my DNA. All of them are me; none of them are me. I just am.

Warren’s announcement of her DNA findings vindicated her claim to a Native American ancestor and simultaneously unveiled the absurdity of her claim to be a Native American. What should have been a set of family tales told to friends and passed on to children and grandchildren about a distant ancestor became a matter of national debate that the Cherokee Nation itself felt compelled to weigh in on:

Using a DNA test to lay claim to any connection to the Cherokee Nation or any tribal nation, even vaguely, is inappropriate and wrong. It makes a mockery out of DNA tests and its legitimate uses while also dishonoring legitimate tribal governments and their citizens, whose ancestors are well documented and whose heritage is proven. Senator Warren is undermining tribal interests with her continued claims of tribal heritage.

Like them or not, the Cherokee have rules about who is and isn’t a Cherokee, because being Cherokee conveys certain benefits–for example, the tribe builds houses for members and helps them look for jobs. This is why conflicts arise over matters like whether the Cherokee Freedmen are official members. When membership in a group conveys benefits, the borders of that group will be policed–and claims like Warren’s, no matter how innocently intended, will be perceived as an attempt at stealing something not meant for her.

Note: I am not saying this kind of group border policing is legitimate. Many “official” Cherokee have about as much actual Cherokee blood in them as Elizabeth Warren, but they have a documented ancestor on the Dawes Rolls, so they qualify and she doesn’t. Border policing is just what happens when there are benefits associated with being part of a group.

I don’t have an issue with Warren’s own self-identity. After all, if race is a social construct,* then she’s doing it exactly right. She’s allowed to have an emotional connection to her own ancestors, whether that connection is documented via the Dawes Rolls or not. All of us here in America should have equal access to Harvard’s benefits, not just the ones who play up a story about their ancestors.

The sad thing, though, is that despite being one of the most powerful and respected women people in America, she still felt the need to be more than she is, to latch onto an identity she doesn’t truly possess.

You know, Elizabeth… it’s fine to just be a white person from Oklahoma. It’s fine to be you.

 

*Note: This blog regards “species” and nouns generally as social constructs, because language is inherently social. That does not erase biology.

Book Club: The Code Economy: The DNA of Business

“DNA builds products with a purpose. So do people.” –Auerswald, The Code Economy

McDonald’s is the world’s largest restaurant chain by revenue[7], serving over 69 million customers daily in over 100 countries[8] across approximately 36,900 outlets as of 2016.[9] … According to a BBC report published in 2012, McDonald’s is the world’s second-largest private employer (behind Walmart with 1.9 million employees), 1.5 million of whom work for franchises. …

There are currently a total of 5,669 company-owned locations and 31,230 franchised locations… Notably, McDonald’s has increased shareholder dividends for 25 consecutive years,[18] making it one of the S&P 500 Dividend Aristocrats.[19][20]

According to Fast Food Nation by Eric Schlosser (2001), nearly one in eight workers in the U.S. have at some time been employed by McDonald’s. … Fast Food Nation also states that McDonald’s is the largest private operator of playgrounds in the U.S., as well as the single largest purchaser of beef, pork, potatoes, and apples.  (Wikipedia)

How did a restaurant whose only decent products are french fries and milkshakes come to dominate the global corporate landscape?

IKEA is not only the world’s largest furniture store, but also among the globe’s top 10 retailers of anything and the 25th most beloved corporation. (Disney ranks number one.) Even I feel a strange, heartwarming emotion at the thought of IKEA, which somehow comes across as a sweet and kind multi-national behemoth.

In The Code Economy, Auerswald suggests that the secret to McDonald’s success isn’t (just) the french fries and milkshake machines:

Kroc opened his first McDonald’s restaurant in 1955 in Des Plaines, California. Within five years he had opened two hundred new franchises across the country. [!!!] He pushed his operators obsessively to adhere to a system that reinforced the company motto: “Quality, service, cleanliness, and value.”

h/t @simongerman600

Quoting Kroc’s1987 autobiography,

“It’s all interrelated–our development of the restaurant, the training, the marketing advice, the product development, the research that has gone into each element of the equipment package. Together with our national advertising and continuing supervisory assistance, it forms an invaluable support system. Individual operators pay 11.5 percent of their gross to the corporation for all of this…”

The process of operating a McDonald’s franchise was engineered to be as cognitively undemanding as possible. …

Kroc created a program that could be broken into subroutines…. Acting like the DNA of the organization, the manual allowed the Speedee Service System to function in a variety of environments without losing essential structure or function.

McDonald’s is big because it figured out how to reproduce.

source: Statista

I’m not sure why IKEA is so big (I don’t think it’s a franchise like McDonald’s,) but based on the information posted on their walls, it’s because of their approach to furniture design. First, think of a problem, eg, People Need Tables. Second, determine a price–IKEA makes some very cheap items and some pricier items, to suit different customers’ needs. Third, use Standard IKEA Wooden Pieces to design a nice-looking table. Fourth, draw the assembly instructions, so that anyone, anywhere, can assemble the furniture themselves–no translation needed.

IKEA furniture is kind of like Legos, in that much of it is made of very similar pieces of wood assembled in different ways. The wooden boards in my table aren’t that different in size and shape from the ones in my dresser nor the ones in my bookshelf, though the items themselves have pretty different dimensions. So on the production side, IKEA lowers costs by producing not actual furniture, but collections of boards. Boards are easy to make–sawmills produce tons of them.

Furniture is heavy, but mostly empty space. By contrast, piles of boards stack very neatly and compactly, saving space both in shipping and when buyers are loading the boxes into their cars. (I am certain that IKEA accounts for common car dimensions in designing and packing their furniture.)

And the assembly instruction allow the buyer to ultimately construct the furniture.

In other words, IKEA has hit upon a successful code that allows them to produce many different designs from a few basic boards and ship them efficiently–keeping costs low and allowing them to thrive.

From Anatomy of an IKEA product:

The company is also looking for ways to maximize warehouse efficiency.

“We have (only) two pallet sizes,” Marston said, referring to the wooden platforms on which goods are placed. “Our warehouses are dimensioned and designed to hold these two pallet sizes. It’s all about efficiencies because that helps keep the price of innovation down.”

In Europe, some IKEA warehouses utilize robots to “pick the goods,” a term of art for grabbing products off very high shelves.

These factories, Marston said, are dark, since no lighting is needed for the robots, and run 24 hours a day, picking and moving goods around.

“You (can) stand on a catwalk,” she said, “and you look out at this huge warehouse with 12 pallets (stacked on top of each other) and this robot’s running back and forth running on electronic eyebeams.”

IKEA’s code and McDonald’s code are very different, but both let the companies produce the core items they sell quickly, cheaply, and efficiently.

In The Code Economy, Chapter 8: Evolution, discusses the rise of Tollhouse Cookies, McDonald’s, the difference between natural and artificial objects, and the development of evolutionary theory from Darwin through Watson and Crick and through to Kauffman and Levine’s 1987 paper, “Toward a General Theory of Adaptive Walks on Rugged Landscapes.” (With a brief stop at Erwin Shrodinger along the way.)

The difficulty with evolution is that systems are complicated; successful mutations or even just combinations of existing genes must work synergistically with all of the other genes and systems already operating in the body. A mutation that increases IQ by tweaking neurons in a particular way might have the side effect of causing neurons outside the brain to malfunction horribly; a mutation that protects against sickle-cell anemia when you have one copy of it might just kill you itself if you have two copies.

Auerswald quotes Kauffman and Levin:

“Natural selection does not work as an engineer works… It works like a tinkereer–a tinkerer who does not know exactly what he is going to produce but uses… everything at his disposal to produce some kind of workable object.” This process is progressive, moving form simpler to more complex forms: “Evolution doe not produce novelties from scratch. It works on what already exists, either transforming a system to give it new functions or combining several systems to produce a more elaborate one [as] during the passage from unicellular to multicellular forms.”

Further:

The Kauffman and Levin model was as simple as it was powerful. Imagine a genetic code of length N, where each gene might occupy one of two possible “states”–for example, “o” and “i” in a binary computer. The difficulty of the evolutionary problem was tunable with the parameter K, which represented the average number of interactions among genes. The NK model, as it came to be called, was able to reproduce a number of measurable features of evolution in biological systems. Evolution could be represented as a genetic walk on a fitness landscape, in which increasing complexity was now a central parameter.

You may remember my previous post on Local Optima, Diversity, and Patchwork:

Local optima–or optimums, if you prefer–are an illusion created by distance. A man standing on the hilltop at (approximately) X=2 may see land sloping downward all around himself and think that he is at the highest point on the graph. But hand him a telescope, and he discovers that the fellow standing on the hilltop at X=4 is even higher than he is. And hand the fellow at X=4 a telescope, and he’ll discover that X=6 is even higher.

A global optimum is the best possible way of doing something; a local optimum can look like a global optimum because all of the other, similar ways of doing the same thing are worse.

Some notable examples of cultures that were stuck at local optima but were able, with exposure, to jump suddenly to a higher optima: The “opening of Japan” in the late 1800s resulted in breakneck industrialization and rising standards of living; the Cherokee invented their own alphabet (technically a syllabary) after glimpsing the Roman one, and achieved mass literacy within decades; European mathematics and engineering really took off after the introduction of Hindu-Arabic numerals and the base-ten system.

If we consider each culture its own “landscape” in which people (and corporations) are finding locally optimal solutions to problems, then it becomes immediately obvious that we need both a large number of distinct cultures working out their own solutions to problems and occasional communication and feedback between those cultures so results can transfer. If there is only one, global, culture, then we only get one set of solutions–and they will probably be sub-optimal. If we have many cultures but they don’t interact, we’ll get tons of solutions, and many of them will be sub-optimal. But many cultures developing their own solutions and periodically interacting can develop many solutions and discard sub-optimal ones for better ones.

On a related note, Gore Burnelli writes: How Nassim Taleb changed my mind about religion:

Life constantly makes us take decisions under conditions of uncertainty. We can’t simply compute every possible outcome, and decide with perfect accuracy what the path forward is. We have to use heuristics. Religion is seen as a record of heuristics that have worked in the past. …

But while every generation faces new circumstances, there are also some common problems that every living being is faced with: survival and reproduction, and these are the most important problems because everything else depends on them. Mess with these, and everything else becomes irrelevant.

This makes religion an evolutionary record of solutions which persisted long enough, by helping those who held them to persist.

This is not saying “All religions are perfect and good and we should follow them,” but it is suggesting, “Traditional religions (and cultures) have figured out ways to solve common problems and we should listen to their ideas.”

From Ray Kurzweil

Back in The Code Economy, Auerswald asks:

Might the same model, derived from evolutionary biology, explain the evolution of technology?

… technology may also be nothing else but the capacity for invariant reproduction. However, in order for more complex forms of technology to be viable over time, technology also must possess a capacity for learning and adaptation.

Evolutionary theory as applied to the advance of code is the focus of the next chapter. Kauffman and Levin’s NK model ends up providing a framework for studying the creation and evolution of code. Learning curves act as the link between biology and economics.

Will the machines become sentient? Or McDonald’s? And which should we worry about?

North Africa in Genetics and History

detailed map of African and Middle Eastern ethnicities in Haaks et al’s dataset

North Africa is an often misunderstood region in human genetics. Since it is in Africa, people often assume that it contains the same variety of people referenced in terms like “African Americans,” “black Africans,” or even just “Africans.” In reality, the African content contains members of all three of the great human clades–Sub-Saharan Africans in the south, Polynesians (Asian clade) in Madagascar, and Caucasians in the north.

The North African Middle Stone Age and its place in recent human evolution provides an overview of the first 275,000 years of humanity’s history in the region(300,000-25,000 years ago, more or less), including the development of symbolic culture and early human dispersal. Unfortunately the paper is paywalled.

Throughout most of human history, the Sahara–not the Mediterranean or Red seas–has been the biggest local impediment to human migration–thus North Africans are much closer, genetically, to their neighbors in Europe and the Middle East than their neighbors across the desert (and before the domestication of the camel, about 3,000 years ago, the Sahara was even harder to cross.)

But from time to time, global weather patterns change and the Sahara becomes a garden: the Green Sahara. The last time we had a Green Sahara was about 9-7,000 years ago; during this time, people lived, hunted, fished, herded and perhaps farmed throughout areas that are today nearly uninhabited wastes.

The Peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages sheds light on how the Green (and subsequently brown) Sahara affected the spread (and separation) of African groups into northern and sub-Saharan:

In order to investigate the role of the last Green Sahara in the peopling of Africa, we deep-sequence the whole non-repetitive portion of the Y chromosome in 104 males selected as representative of haplogroups which are currently found to the north and to the south of the Sahara. … We find that the coalescence age of the trans-Saharan haplogroups dates back to the last Green Sahara, while most northern African or sub-Saharan clades expanded locally in the subsequent arid phase. …

Our findings suggest that the Green Sahara promoted human movements and demographic expansions, possibly linked to the adoption of pastoralism. Comparing our results with previously reported genome-wide data, we also find evidence for a sex-biased sub-Saharan contribution to northern Africans, suggesting that historical events such as the trans-Saharan slave trade mainly contributed to the mtDNA and autosomal gene pool, whereas the northern African paternal gene pool was mainly shaped by more ancient events.

In other words, modern North Africans have some maternal (female) Sub-Saharan DNA that arrived recently via the Islamic slave trade, but most of their Sub-Saharan Y-DNA (male) is much older, hailing from the last time the Sahara was easy to cross.

Note that not much DNA is shared across the Sahara:

After the African humid period, the climatic conditions became rapidly hyper-arid and the Green Sahara was replaced by the desert, which acted as a strong geographic barrier against human movements between northern and sub-Saharan Africa.

A consequence of this is that there is a strong differentiation in the Y chromosome haplogroup composition between the northern and sub-Saharan regions of the African continent. In the northern area, the predominant Y lineages are J-M267 and E-M81, with the former being linked to the Neolithic expansion in the Near East and the latter reaching frequencies as high as 80 % in some north-western populations as a consequence of a very recent local demographic expansion [810]. On the contrary, sub-Saharan Africa is characterised by a completely different genetic landscape, with lineages within E-M2 and haplogroup B comprising most of the Y chromosomes. In most regions of sub-Saharan Africa, the observed haplogroup distribution has been linked to the recent (~ 3 kya) demic diffusion of Bantu agriculturalists, which brought E-M2 sub-clades from central Africa to the East and to the South [1117]. On the contrary, the sub-Saharan distribution of B-M150 seems to have more ancient origins, since its internal lineages are present in both Bantu farmers and non-Bantu hunter-gatherers and coalesce long before the Bantu expansion [1820].

In spite of their genetic differentiation, however, northern and sub-Saharan Africa share at least four patrilineages at different frequencies, namely A3-M13, E-M2, E-M78 and R-V88.

A recent article in Nature, “Whole Y-chromosome sequences reveal an extremely recent origin of the most common North African paternal lineage E-M183 (M81),” tells some of North Africa’s fascinating story:

Here, by using whole Y chromosome sequences, we intend to shed some light on the historical and demographic processes that modelled the genetic landscape of North Africa. Previous studies suggested that the strategic location of North Africa, separated from Europe by the Mediterranean Sea, from the rest of the African continent by the Sahara Desert and limited to the East by the Arabian Peninsula, has shaped the genetic complexity of current North Africans15,16,17. Early modern humans arrived in North Africa 190–140 kya (thousand years ago)18, and several cultures settled in the area before the Holocene. In fact, a previous study by Henn et al.19 identified a gradient of likely autochthonous North African ancestry, probably derived from an ancient “back-to-Africa” gene flow prior to the Holocene (12 kya). In historic times, North Africa has been populated successively by different groups, including Phoenicians, Romans, Vandals and Byzantines. The most important human settlement in North Africa was conducted by the Arabs by the end of the 7th century. Recent studies have demonstrated the complexity of human migrations in the area, resulting from an amalgam of ancestral components in North African groups15,20.

According to the article, E-M81 is dominant in Northwest Africa and absent almost everywhere else in the world.

The authors tested various men across north Africa in order to draw up a phylogenic tree of the branching of E-M183:

The distribution of each subhaplogroup within E-M183 can be observed in Table 1 and Fig. 2. Indeed, different populations present different subhaplogroup compositions. For example, whereas in Morocco almost all subhaplogorups are present, Western Sahara shows a very homogeneous pattern with only E-SM001 and E-Z5009 being represented. A similar picture to that of Western Sahara is shown by the Reguibates from Algeria, which contrast sharply with the Algerians from Oran, which showed a high diversity of haplogroups. It is also worth to notice that a slightly different pattern could be appreciated in coastal populations when compared with more inland territories (Western Sahara, Algerian Reguibates).

Overall, the authors found that the haplotypes were “strikingly similar” to each other and showed little geographic structure besides the coastal/inland differences:

As proposed by Larmuseau et al.25, the scenario that better explains Y-STR haplotype similarity within a particular haplogroup is a recent and rapid radiation of subhaplogroups. Although the dating of this lineage has been controversial, with dates proposed ranging from Paleolithic to Neolithic and to more recent times17,22,28, our results suggested that the origin of E-M183 is much more recent than was previously thought. … In addition to the recent radiation suggested by the high haplotype resemblance, the pattern showed by E-M183 imply that subhaplogroups originated within a relatively short time period, in a burst similar to those happening in many Y-chromosome haplogroups23.

In other words, someone went a-conquering.

Alternatively, given the high frequency of E-M183 in the Maghreb, a local origin of E-M183 in NW Africa could be envisaged, which would fit the clear pattern of longitudinal isolation by distance reported in genome-wide studies15,20. Moreover, the presence of autochthonous North African E-M81 lineages in the indigenous population of the Canary Islands, strongly points to North Africa as the most probable origin of the Guanche ancestors29. This, together with the fact that the oldest indigenous inviduals have been dated 2210 ± 60 ya, supports a local origin of E-M183 in NW Africa. Within this scenario, it is also worth to mention that the paternal lineage of an early Neolithic Moroccan individual appeared to be distantly related to the typically North African E-M81 haplogroup30, suggesting again a NW African origin of E-M183. A local origin of E-M183 in NW Africa > 2200 ya is supported by our TMRCA estimates, which can be taken as 2,000–3,000, depending on the data, methods, and mutation rates used.

However, the authors also note that they can’t rule out a Middle Eastern origin for the haplogroup since their study simply doesn’t include genomes from Middle Eastern individuals. They rule out a spread during the Neolithic expansion (too early) but not the Islamic expansion (“an extensive, male-biased Near Eastern admixture event is registered ~1300 ya, coincidental with the Arab expansion20.”) Alternatively, they suggest E-M183 might have expanded near the end of the third Punic War. Sure, Carthage (in Tunisia) was defeated by the Romans, but the era was otherwise one of great North African wealth and prosperity.

 

Interesting papers! My hat’s off to the authors. I hope you enjoyed them and get a chance to RTWT.