Razib Khan One-stop-shopping for all of my content

October 29, 2011

Ancient DNA in the near future

Filed under: Ancient DNA,Cheddar Man,Genomics,Human Genetics,Human Genomics — Razib Khan @ 12:27 pm

I recently inquired if anyone was sequencing Cheddar Man. In case you don’t know, this individual died ~9,000 years ago in Britain, but the remains were well preserved enough that mtDNA was retrieved from him. He was of haplogroup U5, which is still present in the local region. Cheddar Man is also particularly interesting because he is definitely a Paleolithic hunter-gatherer, predating the Neolithic in Britain by thousands of years.

It turns out that no one is looking at Cheddar Man now. But that’s probably because money and time are finite. I was told that there are plenty of other specimens which would also probably be good candidates for sequencing in the Museum’s collection (this doesn’t seem to be a case where curators are being stingy and overprotecting of their specimens). That’s not too surprising. We’ll probably answer a lot of questions about the roles of demographic diffusion vs. cultural diffusion when it comes to agriculture soon enough (as in, over the next 10 years as techniques for getting signal out of old degraded and contaminated samples get better).

September 14, 2011

Ötzi, first, but not last, farmer?

Filed under: Ancient DNA,Anthroplogy,Human Genetics,Iceman,Ötzi — Razib Khan @ 8:59 pm

Dienekes relays that Ötzi the Iceman carried the G2a4 male haplogroup. He goes on to observe:

We now have G2a3 from Neolithic Linearbandkeramik in Derenburg and G2a in Treilles in addition to Ötzi from the Alps. G2a folk got around. He joins Stalin and Louis XVI as a famous G2a.

It was already clear with the discovery of G2a in France and Central Europe, that this otherwise uncommon present-day haplogroup in Europe was more prominent during the Neolithic, and Ötzi’s data point seals the case.

In a sense, the triple G2a finds in Neolithic Europe confirm the origins of the European Neolithic population in West Asia, but renew the mystery as to how all the rest of the “players” of the European Y-DNA scene appeared on the scene, with everything except G and I first appearing in the ancient DNA record after the end of the Neolithic.

Yes, I believe that the Paleolithic-Neolithic dichotomy is more hindrance than help in understanding the European past (the Paleolithic itself may have exhibited more population turnover than we can appreciate). I suspect that the two most common European Y haplogroups, R1a and R1b, underwent rapid increase in frequency over the past ~5,000 years. I do not believe that this is necessarily representative of the rest of the genome. The spread of male lineages can be rather unrepresentative.

In other news, Ötzi’s genome is going to drop any day now. My prediction that it’s more West Asian than we might have expected seems more plausible, though less surprising and risky, at this point.

Image credit: 23andMe

August 9, 2011

The hunt for ancient DNA

Ewen Callaway has a good survey of what’s been going down in ancient human genomics over the past year in Nature, Ancient DNA reveals secrets of human history. It’s not paywalled, so read the whole thing. Most of it won’t be too surprising for close readers of this weblog, but this part is new:

By comparing individual DNA letters in multiple modern human genomes with those in the Neanderthal genome, the date of that interbreeding has now been pinned down to 65,000–90,000 years ago. Montgomery Slatkin and Anna-Sapfo Malaspinas, theoretical geneticists from the University of California, Berkeley, presented the finding at the Society for Molecular Biology and Evolution meeting in Kyoto, Japan, held on 26–30 July.

Slatkin says that their result agrees with another study presented at the meeting that came from the group of David Reich, a geneticist at Harvard Medical School in Boston, Massachusetts, who was involved in sequencing both the Neanderthal and Denisova genomes. The dates also mesh with archaeological finds bookending early human migrations out of Africa to between about 50,000 and 100,000 years ago. Reich’s team is now developing tools to find signs of more recent interbreeding that might have occurred after humans arrived in Asia ...

June 20, 2011

Hints of Ötzi’s genome

Filed under: Ancient DNA,Ancient Genomes,Genetics,Genomics,Ötzi — Razib Khan @ 7:39 pm

John Hawks points to a report in Science on some morsels of information about Ötzi-the-Iceman’s genetics, The Iceman’s Last Meal:

Also at the meeting, researchers led by geneticist Angela Graefen of the Institute for Mummies and the Iceman reported that they have succeeded in sequencing the Iceman’s whole genome, despite the highly fragmented nuclear DNA. The genome has already revealed some surprises. One preliminary finding shows that the Iceman probably had brown eyes rather than the blue eyes found in many facial reconstructions done by artists. Graefen and her colleagues are also examining the DNA to see if Ötzi possessed genetic predispositions to diseases such as arthritis, which other researchers have diagnosed based on radiological and other evidence.

I’m assuming we’ll know a whole lot more before the end of summer. So I’m going to go out on a limb and make a prediction based on what I suspect about the southern European genetic landscape ~5,000 years ago: Ötzi will be more like contemporary West Asian people, Georgians, Armenians, etc., than modern north Italians and south Germans are. Right or wrong, I hope the results will be interesting!

May 31, 2011

Mediterranean men on the move

ResearchBlogging.orgSeriously, sometimes history matches fiction a lot more than we’d have expected, or wished. In the early 2000s the Oxford geneticist Bryan Sykes observed a pattern of discordance between the spatial distribution of male mediated ancestry on the nonrecombinant Y chromosome (NRY) and female mediated ancestry in the mitochondrial DNA (mtDNA). To explains this he offered a somewhat sensationalist narrative to the press about possible repeated instances of male genocide against lineage groups who lost in conflicts.

Here is a portion of the book of Numbers in the Bible:

15 – And Moses said unto them, Have ye saved all the women alive?

16 – Behold, these caused the children of Israel, through the counsel of Balaam, to commit trespass against the LORD in the matter of Peor, and there was a plague among the congregation of the LORD.

17 – Now therefore kill every male among the little ones, and kill every woman that hath known man by lying with him.

18 – But all the women children, that have not known a man by lying with him, keep alive for yourselves.

Then there is the rape of the Sabine women. The ethnogenesis of the mestizo and mulatto populations of ...

January 26, 2011

Neandertal admixture, revisiting results after shaken priors

After 2010′s world-shaking revolutions in our understanding of modern human origins, the admixture of Eurasian hominins with neo-Africans, I assumed there was going to be a revisionist look at results which seemed to point to mixing between different human lineages over the past decade. Dienekes links to a case in point, a new paper in Molecular Biology and Evolution,  An X-linked haplotype of Neandertal origin is present among all non-African populations. The authors revisit a genetic locus where there have been earlier suggestions of hominin admixture dating back 15 years. In particular, they focus on an intronic segment spanning exon 44 of the dystrophin gene, termed dys44. Of the haplotypes in this they suggested one, B006, introgressed from a different genetic background than that of neo-Africans. The map of B006 shows the distribution of the putative “archaic” haplotype from a previous paper cited in the current one from 2003. As you can see there’s a pattern of non-African preponderance of this haplotype. So what’s dystrophin‘s deal? From Wikipedia:

Dystrophin is a rod-shaped cytoplasmic protein, and a vital part of a protein complex that connects the cytoskeleton ...

January 5, 2011

Hobbit DNA in 2011

Filed under: Ancient DNA,Genetics,Genomics,Hobbit,Human Evolution,Human Genetics — Razib Khan @ 9:03 am

I predicted earlier that Hobbit DNA would be extracted in 2011. It was pretty much an educated guess based on various omissions I sensed in papers in 2010. But it seems that an attempt is going to be made:

Scientists are planning an attempt to extract DNA from the ‘hobbit’ Homo floresiensis, the 1-metre-tall extinct distant relative of modern humans that was unearthed in Indonesia, following a study that suggests problems in standard sampling methods in ancient-DNA research could have thwarted previous efforts.

This year, geneticists at the Australian Centre for Ancient DNA (ACAD) at the University of Adelaide hope to recover DNA from a roughly 18,000-year-old H. floresiensis tooth, which was excavated in 2009 from the Liang Bua site on the Indonesian island of Flores.

No guarantees, but still exciting.

(via Dienekes)

November 9, 2010

European man of many faces: Cain vs. Abel

UE-1

When it comes to the synthesis of genetics and history we live an age of no definitive answers. L. L. Cavalli-Sforza’s Great Human Diasporas would come in for a major rewrite at this point. One of the areas which has been roiled the most within the past ten years has been the origin and propagation of the agricultural lifestyle across the European continent between 10,000-6,000 years before the present (starting in Europe’s southeast fringe a few thousand years after the origination of the Neolithic lifestyle in the Levant, and finally pushing into the southern Scandinavian peninsula only ~6,000 years ago). The reasons for this particular debate about the origin of the European are manifold. First, most scholars are of European ancestry, and some of the debates have roots going back a century. So a natural interest exists based on normal human biases. Second, when it comes to genetics the climate of Europe is ideal for the preservation and extraction of ancient DNA. Third, there are relatively clear and distinct theoretical models which can be tested by the data, whether to verify or refute.

ResearchBlogging.orgI have already reviewed earlier work in three previous posts, European man perhaps a Middle Eastern farmer, European man perhaps not a Middle Eastern farmer, and Völkerwanderung back with a vengeance. Instead of rehashing everything I’ll take it as a given that you’ve read or skimmed those posts. Rather, let’s move on to a new paper in PLoS Biology, Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities:

In Europe, the Neolithic transition (8,000–4,000 B.C.) from hunting and gathering to agricultural communities was one of the most important demographic events since the initial peopling of Europe by anatomically modern humans in the Upper Paleolithic (40,000 B.C.). However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. To date, inferences about the genetic make up of past populations have mostly been drawn from studies of modern-day Eurasian populations, but increasingly ancient DNA studies offer a direct view of the genetic past. We genetically characterized a population of the earliest farming culture in Central Europe, the Linear Pottery Culture (LBK; 5,500–4,900 calibrated B.C.) and used comprehensive phylogeographic and population genetic analyses to locate its origins within the broader Eurasian region, and to trace potential dispersal routes into Europe. We cloned and sequenced the mitochondrial hypervariable segment I and designed two powerful SNP multiplex PCR systems to generate new mitochondrial and Y-chromosomal data from 21 individuals from a complete LBK graveyard at Derenburg Meerenstieg II in Germany. These results considerably extend the available genetic dataset for the LBK (n = 42) and permit the first detailed genetic analysis of the earliest Neolithic culture in Central Europe (5,500–4,900 calibrated B.C.). We characterized the Neolithic mitochondrial DNA sequence diversity and geographical affinities of the early farmers using a large database of extant Western Eurasian populations (n = 23,394) and a wide range of population genetic analyses including shared haplotype analyses, principal component analyses, multidimensional scaling, geographic mapping of genetic distances, and Bayesian Serial Simcoal analyses. The results reveal that the LBK population shared an affinity with the modern-day Near East and Anatolia, supporting a major genetic input from this area during the advent of farming in Europe. However, the LBK population also showed unique genetic features including a clearly distinct distribution of mitochondrial haplogroup frequencies, confirming that major demographic events continued to take place in Europe after the early Neolithic.

sommer-nadachowski-2006-figAs I’ve indicated before the archaeological jargon is rather mystifying to me. Some of this is due to translation, the Linear Pottery Culture is abbreviated “LBK” because in the German it is Linearbandkeramik. Rather, I try and focus on some basic concrete parameters: time and space. So we have the first agricultural society with a focus on Central Europe flourishing ~7,000 years before the present. Some now we have the time and space in mind around which we can bracket all the background variables. The big question being asked, and answered, is whether the practitioners of LBK were descendants of Ice Age Europeans who expanded from the “refugia” in the south of Europe during the Last Glacial Maximum (LGM) ~20,000 years ago. To speak intelligently about these issues you need some basic intuition, so you see the map which I found on John Hawks’ weblog showing the line of settlement during the LGM. As the ice retreated presumably the European hunter-gatherers would have rapidly pushed northward, following the species which they consumed.

I’ll pass over the methodological nuts & bolts; you can find them in the paper. Obviously this isn’t technically trivial; extracting, amplifying, and avoiding contamination, from DNA samples on the order of 7,000 years old is awesome. As usual they focused on mtDNA because this is found in much larger quantities than nuclear DNA. They did get a few Y chromosomal results though, though mtDNA is the star of the show here. The mtDNA is the maternal lineage, so it can tell you only so much. Additionally, there may be selection dynamics going on to change the frequencies of some of these variants. But with those caveats in hand I think mtDNA patterns can be very informative because if women are on the move that is a pointer to a classic folk-wandering, where a whole people transplant their culture via migration. Many more British women arrived in the New World than Spanish women, and therein lay one of the crucial factors in the difference between Anglo and Latin America.

The slide show below has all the major figures of interest. I’ve also replicated the full description, and made some minor edits. Please take in the table; much of the paper really presupposes an intuitive familiarity with mtDNA haplogroup frequencies.



mtDNA pairwise Fst by population
Hunter-Gatherers Near East LBK
Near East 4.46 * *
LBK 9.9 3.22 *
Central Europe 3.67 1 4.22

The authors also had an Fst table illustrating genetic distances using mtDNA of ancient and contemporary populations. I’ve cleaned up the table a bit, and standardized the values so that the smallest distance = 1. This is mostly so you can make immediate sense of it. What you clearly see is the enormous genetic distance between Central European hunter-gatherers and LBK, who were present in Germany right before the arrival of farmers. This comes very close to a falsification of the maximalist pots-not-people model, whereby farming spread from its point of origin in Anatolia and the Levant through a process of cultural diffusion, just like the alphabet or the potato. The relatively large distance between ancient and modern populations shouldn’t be too surprising, genetic distances operate across both time and space. There are interesting inferences one can make about the nature of gene flow over the past 10,000 years in Eurasia when viewing the relatively small distance between the two modern populations, but really the important point for the purposes of this paper is the high wall between the two cultures who practice differing modes of production.

In the paper the authors support, tentatively, a classic demic diffusion process. This is basically a very simple model whereby farmers with larger population growth rates expand into the “space” of hunter-gatherers. But as Dienekes Pontikos notes such a process would also be characterized by dilution of the original Middle Eastern “genetic signal” over time. Rather, what we see here seems to be a total transfer for a population across large distances. The authors themselves note that the LBK farmers seem to have followed the interior lines of rivers and flat-bottom plains. Farmers had discovered a new way to exploit nature, but in the end they were still ecologically constrained. The northern two-thirds of Scandinavia still had hunter-gatherer populations down to the period of the classical Greeks. This was not because of the powerful magic wielded by Väinämöinen. The Middle Eastern derived agricultural toolkit no doubt began to run into its natural ecological limits on Europe’s northern fringe. Without knowing anything further I suspect that the death of the southern Sami culture in the face of Norwegian and Swedish expansion in the early modern period was probably driven by the emergence of more systematic agricultural science, which could push the ecological limits beyond the long-standing equilibrium established in the Iron Age.

But I don’t think this is just a story of ecology. It is clearly a story of culture. We assume that culture is easily transferable from society to society. In some ways it is. The original phonetic script of Upper Mesopotamia and Syria seems to have quickly triggered imitation and appropriation from India to Italy within a few centuries of its widespread use by the Aramaeans. But farming is not like the idea of writing. The original farmers seem to have expanded rather slowly initially out of the Middle East. Not only did they perfect the biological character of their crops, they probably perfected the customs and traditions which would go along with farming. A complex suite of explicit rules and implicit norms. Perhaps it was not so easy to simply copy the farming lifestyle? Or, perhaps more interestingly, the hunter-gatherers by and large did not want to copy the farming lifestyle? (this is a tendency among some modern non-farming groups, who would rather work temporarily on farms themselves rather than become full-time obligate peasants) The large genetic distances between the LBK and the hunter-gatherers around them may indicate not only the relatively endogenous growth of the LBK in “virgin” land (e.g., compare to the Yankees of New England in the 17th and 18th century), but, also the emergence of an ideological aversion to mixing with the “savages.” We have plenty of textually attested de-humanization of the “savage” and “barbarian” by the “civilized.” It is likely that the gap between the LBK and the hunter-gatherers of Europe was only somewhat smaller than that between the Aborigines of Australia and Tasmania and the European settlers!

Finally, there’s one last issue I want to highlight: the authors find that many presumably hunter-gatherer lineages are found among the LBK, while very common haplogroups (mtDNA and Y) in Europe today are not found among the LBK or the ancient hunter-gatherers. The clear inference then would be that Europe went through several periods of demographic change and migration within the last 10,000 years. A simple two-way admixture scenario will not suffice. Yesterday I posted this bar plot which contrasted the pattern of ancestry of French vs. French Basque using ADMIXTURE at K = 10:

French

The green element is nearly 100% in Sardinia, and drops off to nearly nothing somewhere around Iran. The light blue component is modal around the Caucasus, though is widely distributed, from Spain to Bengal (yeah, that’s me!) to Sweden. A simple model would be that the light blue arrived with Neolithic agriculturalists, as the Basques are the descendants of the original Ice Age Europeans. But this may not be correct, and our impression of the Basques may be totally false. It is not out of the question now that the Basque culture may have arrived via the ancient leap-frogging of agriculture from fertile regions around the Mediterranean before the seafarers passed into the Atlantic and swept around the western fringe of Iberia. What we may be seeing is a palimpsest of agriculturalists, where the Basques simply lack the last layer.

In any case, one can speculate a lot right. Ancient DNA has allowed us to refute maximalist versions of pots-not-people, but has also overturned our ability to hold to simple robust models. In science you prefer parsimony, unless parsimony simply can’t explain the patterns at hand. I think we’re there at this point.

Citation: Wolfgang Haak, Oleg Balanovsky, Juan J. Sanchez, Sergey Koshel, Valery Zaporozhchenko, Christina J. Adler, Clio S. I. Der Sarkissian, Guido Brandt, Carolin Schwarz, Nicole Nicklisch, Veit Dresely, Barbara Fritsch, Elena Balanovska, Richard Villems, Harald Meller, Kurt W. Alt, Alan Cooper, & Genographic Consortium (2010). Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities PLoS Biology : 10.1371/journal.pbio.1000536

August 2, 2010

Ancient DNA and Norden

Filed under: Ancient DNA,Genetics,Genomics,Scandinavia — Razib Khan @ 2:29 am

Genetics is now being brought to bear on whether there were non-trivial population movements in the prehistorical period. Or more precisely, a combination of genetics and archaeology, whereby the archaeologists retrieve and extract genetic material which the geneticists amplify and analyze. This has helped establish that European hunter-gatherers were not lactase persistent. This is totally unsurprising, but was a nice proof of principle. When it comes to ascertaining genetic relationships among populations, as opposed to specific traits whose genetic architecture is well established, it’s a bit trickier. Who knows how many population movements may have interposed themselves between the present and a particular period in the past from which you have samples?

A new paper in PLoS ONE reports findings which do little to clarify, though add weight to skepticism as to the definitiveness of earlier results, Genetic Diversity among Ancient Nordic Populations:

Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among the ancient Danes (average 13%) than among extant Danes and Scandinavians (~2.5%) as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type “diluted” by later immigration events. Interestingly, the two Neolithic samples (4,200 YBP, Bell Beaker culture) that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300–3,500 YBP) was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture.

Here’s a review of an earlier paper on this topic. Here’s an important section from the discussion of the current paper:

…Given our small sample sizes from these crucial time periods further studies are certainly required. However, the frequency of Hg U4 and U5 declines significantly among our more recent Iron Age and Viking Age Danish population samples to the level observed among the extant Danish population. Our study therefore would point to the Early Iron Age and not the Neolithic Funnel Beaker Culture as suggested by Malmström et al. (2009)…as the time period when the mtDNA haplogroup frequency pattern, which is characteristic to the presently living population of Southern Scandinavia, emerged and remained by and large unaltered by the subsequent effects of genetic drift. In contrast to Hg U4, which is only found in the Neolithic and Early Bronze Age samples, Hg U5 was observed in ~9% (5/53) of the remaining ancient samples and identified at all sites except Kongemarken and Skovgaarde.

I wouldn’t put too much stock in these specific results. The sample sizes and representativeness issues are probably such that each new paper is going to change our assessment. But, I think the section which I emphasized points to a shift in the Zeitgeist. Until recently there’s been a very strong bias among historical geneticists to assume that the genetic variation is more strongly affected by deep time events, and that recent replacements and perturbations will have less impact. I think there were good reasons for this assumption, and still are, generalizing from broader patterns. But the over-extrapolation of the rule-of-thumb may have led to models which will soon be falsified in many specific instances.

On a slightly bittersweet note, ancient DNA will be able to answer questions about the origins of many circumpolar populations, but will have far less to tell us about societies and cultures further south, simply because of less favorable conditions for preservation. The main exception to this truism will presumably be desert societies. For example, Tutankhamun has been typed as of the R1b Y lineage.

April 20, 2010

Of pigs, people and porcine polygenism

800px-Wild_Pig_KSC02pd0873Jared Diamond famously argued in Guns, Germs and Steel that only a small set of organisms have the characteristics which make them viable domesticates. Diamond’s thesis is that the distribution of these organisms congenial to a mutualistic relationship with man shaped the arc of our species’ history and the variation in wealth that we see (though his a human-centric tale, we may enslave them, eat and use them as beasts of burden, but these are also species which have spread across the world with our expansion). This thesis has been challenged, but the bigger point of putting a focus on how humans relate to their domesticated animals, and the complex co-evolutionary path between the two, is something that we need to consider. In a plain biological and physical sense animals have utility; we eat them, and for thousands of years they were critical to our transportation networks. Some have argued that the rise of Islam, Arab monotheism, was contingent on the domestication of the camel (which opened up interior trade networks previously unaccessible). In The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World the argument is made that the distribution of the Indo-European languages has to do with the facility of Central Eurasian plainsmen with their steeds. And of course there is the domestic dog, arguably the one creature which is able to read our emotions as if they were a con-specific.

I suspect that the evolution and ethology of domesticated animals will offer a window into our own evolution and ethology. Konrad Lorenz famously believed that humans were going through their own process of domestication all the while that they were selecting organisms suited to their own needs. More pliable, less intelligent, faster growing and maturing, and so forth. Know thy companions, and know thyself, so to speak.

What about an animal as intelligent as a dog, but famously tasty? (the combination of the two characters causing some ethical tension in the minds of many) I speak here of the pig. A few years ago research came out which showed that pig-culture was introduced to Europe from the Middle East. That is, Middle Eastern pigs came with Middle Eastern people in all likelihood. But modern European pigs do not derive from these lineages, rather, by comparing modern genetic variation with ancient DNA the authors showed that the Neolithic pigs had been replaced by local breeds. Just as pigs can go feral and fend for themselves rather easily, it seems that their basic morph can be derived from wild boar populations easily as well (by contrast, it will perhaps take some effort to derive a pekingese from wolf populations, offering a reason for why small dogs seem to have emerged once). A new paper explores the evolutionary history and phylogeography of the pigs of the swine-loving societies par excellence, those of East Asia. Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA:

The establishment of agricultural economies based upon domestic animals began independently in many parts of the world and led to both increases in human population size and the migration of people carrying domestic plants and animals. The precise circumstances of the earliest phases of these events remain mysterious given their antiquity and the fact that subsequent waves of migrants have often replaced the first. Through the use of more than 1,500 modern (including 151 previously uncharacterized specimens) and 18 ancient (representing six East Asian archeological sites) pig (Sus scrofa) DNA sequences sampled across East Asia, we provide evidence for the long-term genetic continuity between modern and ancient Chinese domestic pigs. Although the Chinese case for independent pig domestication is supported by both genetic and archaeological evidence, we discuss five additional (and possibly) independent domestications of indigenous wild boar populations: one in India, three in peninsular Southeast Asia, and one off the coast of Taiwan. Collectively, we refer to these instances as “cryptic domestication,” given the current lack of corroborating archaeological evidence. In addition, we demonstrate the existence of numerous populations of genetically distinct and widespread wild boar populations that have not contributed maternal genetic material to modern domestic stocks. The overall findings provide the most complete picture yet of pig evolution and domestication in East Asia, and generate testable hypotheses regarding the development and spread of early farmers in the Far East.

They used conventional phylogeographic techniques to catalog the variation in modern populations, as well as supplementing their data set with ancient samples. Here the genetic variance they’re looking at is the mtDNA, the maternal lineage. Easy to get at, and easy to analyze (lots of it, and non-recombinant). In general they seem to have found that there is a common genetic heritage of East Asian domestic pigs, who are embedded geographically among varieties of wild pig who exhibit localized genetic variants. Additionally, there are other varieties of domestic pig in Southeast and South Asia who seem to have arisen from their own boar populations (though there is a Pacific pig variant which seems to have been from mainland Southeast Asia, but that original source population has now been replaced by East Asian pigs). Finallythey find a strong continuity between ancient domestic East Asian pigs and the modern populations. This is a contrast with the findings in European which exhibited disjunction between past and present. Perhaps this has to do with the fact that East Asian pigs are more genuinely indigenous, derived from local wild lineages with regional adaptations, while the Middle Eastern pigs brought to Europe were short-term kludges easily superseded by domesticates derived from European boar populations.

pigfig2This figure shows the nature of haplotype sharing between wild and ancient & contemporary domestic pigs. The larger the pie, the more frequent the haplotype. The slices of the pie by color show wild (black), ancient (red) and modern domestic (white) shares of that haplotype. The line across the networks show the putative separation between the genetic variants relatively private to the wild populations, and those which lean toward a mix of wild & domesticates. The wild populations seem more diverse. 45 haplotypes out of 167 samples are found only in wild specimens, 92 haplotypes out of 339 samples are found only in domestic specimens, and 21 haplotypes are found in both 87 wild and 582 domestic pigs. One assumes that the domesticates are derived from a small subset of wild pigs, and that population underwent demographic expansion within the last 10,000 years. That’s not too different from our species, we’re descended from a small subset of H. sapiens, and we’ve undergone major demographic expansion. Our “wild” cousins among the great apes tend to have a lot more genetic variation even within their small populations because their demographic history has presumably been a bit more staid. As man was, so shall he turn his domesticates. And yet a major difference between the domestic pig and man seems to be that some variant of multiregionalism, the evolution of modern pigs from local lineages, and their subsequent hybridization to produce a genetically unified species, has been operative. One major caution with these studies is that they’re looking at mtDNA. The dog genomics work has been modified and overturned when they shifted from the mtDNA that most phylogeographers focus on to the total genome. One does not know the evolutionary history of an organism by one locus alone.

The pig is a peculiar beast, retaining its feral nature as evident by the periodic reemergence of morphs from released domestic populations which have no difficulty in going “wild.” There are 4 million feral hogs in the United States, and they can get quite large indeed. What would the pekingese do in a world without man? Probably be some other creature’s meal. But generalists like the pigs would no doubt flourish. The story of the pig is a story of piggybacking, so to speak, on the success of the upright ape and spreading across the world on the backs of the other white meat.

Let me finish from the author’s conclusion:

The evidence presented here suggests the following evolutionary history of pigs in East Asia. Having originally evolved in ISEA [Island Southeast Asia], wild Sus scrofa migrated (without human assistance) across the Kra Isthmus on the MalayPeninsula into Mainland Asia. From here, they spread across the landscape and, after traveling over land bridges, onto the islands of Japan, the Ryukyu chain, Taiwan, and Lanyu where they evolved unique mitochondrial signatures. After millennia of hunting and gathering, a major biocultural transition occurred early in the Holocene during which human populations in East Asia domesticated a variety of plants and animals, including pigs. This process took place at least once in the Yellow River drainage basin wheremilletmay have been first domesticated as early as 10,000 B.P…and may have also taken place independently in the downstream Yangtze River region where rice may have been domesticated…Two things are clear from the ancient DNA evidence presented here. First, unlike Europe, modern Chinese domestic pigs are the direct descendants of the first domestic pigs in this region. Second, despite the occurrence of a genetically distinct population of wild boar throughout modern China, this population has neither been incorporated into domestic stocks nor exterminated.

Citation: Larson, G., Liu, R., Zhao, X., Yuan, J., Fuller, D., Barton, L., Dobney, K., Fan, Q., Gu, Z., Liu, X., Luo, Y., Lv, P., Andersson, L., & Li, N. (2010). Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0912264107

Image credit: NASA

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