Published May 8, 2014
Written by Razib Khan and Rui H, Family Tree DNA
 
Abstract

The aim of this survey is to review the methods and results that serve as the basis for myOrigins. After generating a reference data set pruned of related individuals, we used the the Admixture package’s model-based clustering framework to capture the genetic variation of the world’s populations, and infer ancestral proportions for particular individuals. Eighteen clusters were defined spanning extant modern human genetic variation, but reflective of ancient migrations and admixtures.

1  Introduction

Over the past 50,000 years since modern humans have left Africa numerous populations have diverged [Mendez2013] and recombined [Hellenthal2014] to generate the diversity we see around us today. Though most human genetic variation is apportioned within, rather than across, populations, there have been barriers to gene flow on an inter-continental scale [Jorde2004]. This has resulted in genetic distances between groups being great enough so as to identify them accurately with molecular markers [Rosenberg2002]. The markers are diverse, from microsatellites to alloyzomes. But for our purposes it is critical to note that the the human genome has approximately 10 million single nucleotide polymorphisms (SNPs) [Reich2003]. These are single base pairs of A, C, G, and T, which vary across populations, and can be used for purposes of inferring deep history on a paleontological scale [Patterson2006a], as well as individual forensic identification [Tian2008].

With a sufficient density of markers very fine-grained inferences can be made as to the ancestral makeup of any given individual, assuming a finite number of discrete ancestries. Though the reality of human variation and its history is more nuanced than any given population genetic summary, importance aspects of deep ancestry and genetic relatedness can be established through methods which reduce the complexity of the data into a finite set of dimensions. These are represented visually in a manner so as to impart the general qualitative result to a non-specialist audience.

2  Model-based inferences of genetic variation

There are many ways to represent genetic distance and clustering between individuals and populations. A classic method is Principal Component Analysis (PCA), which reduces the total variation into a set of independent dimensions ordered by proportion of variation explained for each dimension [Patterson2006]. Therefore, PC 1 is the dimension which explains the largest proportion of variation, and PC 2 explains the second largest proportion of the variation, and so on. Populations or individuals can then be represented along a two-dimensional plane which exhibits patterns of clustering which correspond to genetic relatedness. More recently dense multi-locus marker sets have allowed for the development of robust model-based methodologies which give more explicit results [Pritchard2000].

These methods posit a model which includes a “K” number of ancestral populations as a parameter, assuming that true populations will be in Hardy-Weinberg Equilibrium. The genotypic variation of individuals is configured as a composite of these ancestral populations according to their weights. Assuming K = 2 an individual may have assignments of 50 percent to each of the posited clusters, or any pairwise values which sum to 100 percent (e.g., 10 percent and 90 percent for each component). Note that the “K” does not necessarily dennote “real” populations in a concrete sense which underwent discrete admixture events, though it may. But often a given number of populations will still be highly informative of population and individual relatedness, setting aside any necessary correspondence to historical genetic fact.

3  Admixture

The modern era of model-based admixture analysis using multi-locus data began with the release of the Structure program [Pritchard2000]. It utilizes a Bayesian approach and an Markov chain Monte Carlo (MCMC) algorithm to sample the distribution of probabilities. Given the range of models and parameters which can fit the genotypic data the ultimate outcomes are a series of assignments to explicit K values which are fixed as inputs. The ultimate outputs of weighted assignment of individuals to each K is generally visualized in the form of colored barplots.

 structure_image

Figure 1: Hubisz, Melissa J., et al. “Inferring weak population structure with the assistance of sample group information.” Molecular ecology resources 9.5 (2009): 1322-1332.

Because Structure implements a computationally intensive Bayesian method, it has a relatively long run-time. Several packages have emerged that operate within the same model-based framework of Structure, but utilize more computationally efficient algorithms and a less exhaustive maximum likelihood approach. Foremost among these is the Admixture program, which has widely become the standard model-based admixture analysis package [Alexander2009]. Though there are differences in the technical details between Structure and Admixture, both generate results that are visually represented as barplots. With dense SNP data, Admixture has been shown to be as accurate and much faster than Structure.

4  Reference Populations

Model-based methods of admixture inference are sensitive to the input data which is evaluated to establish population substructure. To maintain consistency, it is important to fix a reference set that can be used across runs of individual ancestry predictions. In other words, though individuals whose ancestries are being computed may vary, the reference genotypes against which they are compared to infer those ancestries will remain constant. To construct a reference set, we collected populations from multiple sources:

•     GeneByGene DNA customer database

•     Human Genome Diversity Project

•     International HapMap Project

•     Estonian Biocentre

The GeneByGene data derives from a custom Illumina OmniExpress 710K microarray chip. The HGDP data was from Illumina HumanHap650K Beadchips [Li2008]. The Estonian Biocentre data derives from Illumina 610K or 660K bead arrays [Behar2010] or Illumina HumanOmniExpress BeadChip.

PCA

Figure 2: PCA used to remove outliers

We assembled a large number of candidate reference populations which were relatively unadmixed and sampled widely in terms of geography. From these, we removed related or outlier individuals with the Plink software, utilizing identity-by-descent (IBD) analysis and visually inspecting multi-dimensional scaling plots (MDS). Further visualization established that the reference population sets were indeed genetically distinct from each other. We also ran Admixture and MDS with specific populations to asses if any individuals were outliers or exhibited notable gene flow from other reference groups, removing these. Admixture was run on an inter and intra-continental scale to establish a plausible number of K values utilizing the cross-validation method [Alexander2011]. After removing markers that were missing in more than 5 percent of loci and those with minor allele frequencies below 1 percent, the total intersection of SNPs across the pooled data set was 290,874. The final number of individuals in was 1,353.

To validate our Reference Population set, we tested them against a list of well studied benchmark groups whose ancestral background in the literature has been well attested. Additionally, we also cross-checked against individuals with attested provenance within the GeneByGene DNA database.

5  Generation of cluster maps

To generate the contour maps of the distribution of a particular cluster as a function of geography, we used the fraction of representation in a myOrigins cluster at latitude-longitude points derived from distinct populations within our benchmark list and produced smoothed density maps. The R packages spatstat and maps were employed to generate polygons overlain upon a world map.

6  Table of reference populations

Population N Population N
Armenian 46 Lithuanian 6
Ashkenazi 60 Masai 140
British 39 Mbuti 15
Burmese 8 Moroccan 7
Cambodian 26 Mozabite 24
Danish 13 Norwegian 17
Filipino 20 Pashtun 33
Finnish 49 Polish 35
French 17 Portuguese 25
German 17 Russian 41
Gujarati 31 Saudi 19
Iraqi 12 Scottish 43
Irish 45 Slovakian 12
Italian 30 Spanish 124
Japanese 147 Surui 21
Karitiana 23 Swedish 33
Korean 15 Ukrainian 10
Kuwaiti 14 Yoruba 136

 

 

7  myOrigins Cluster Descriptions

7.1  Trans-Ural Peneplain

Overview

From the girdle of Eastern Europe, exploding eastward across the vast plains of Eurasia, Trans-Ural Peneplain was carried along with the explosion of the Slavs over the past 2,000 years. Despite the vast distances involved, these peoples are closely related because of their recent origins in the same zone of east-central Europe. Cleavage of religion and national rivalries cannot mask the fact that the languages are nearly intelligible, giving a clue as to their deep affinities.

Neolithic Revolution

While the other Indo-European groups waxed in more fertile climes, the Slavic and Baltic core of Trans-Ural Peneplain languished in the relatively marginal forest zones of the northeast, living a lifestyle not altogether dissimilar from the Finnic hunter-gatherers to their north. Like the European Northlands, this cluster is a hybrid of farmer and northern hunter with the preponderance of the latter, though sprinkled with exotic elements from the east.

Bronze Age

It seems likely that the Indo-Europeans came early to this zone and Trans-Ural Peneplain probably has a genesis in the Corded Ware culture. Additionally, there are suggestions that earlier outliers of this cluster ventured far to the east. The connections along the great steppe were already being forged though the core ethnicities, which later contributed to the demographic expansion, were limited to the western forest zone.

Early Recorded History

The ancients knew them as Sclaveni, and they were small tribes which rose to prominence in the vacuum created by the collapse of institutional order on the eastern frontier of Rome. Led by nomadic confederations such as the Avar, the Slavs filled the interior of the Balkan peninsula, absorbing all the peoples that had previously lived in that region excepting the Romanians and Albanians. In the west, they pushed into the territories of the Germans, who were themselves decamping to the collapsing provinces of the fallen Western Roman Empire.

Middle Ages

Christianity turned the tribes into kingdoms, Poland, Bohemia, Bulgaria, and Russia, just to name a few. The Russians were led by a motley array of Scandinavian and Finnic warriors, the Rus, who established the uniqueness of their polity by aligning themselves to the Byzantine rite. While the West Slavs experienced the onslaught of the German “drive to the east” during the Middle Ages, most viciously in the form of the Teutonic Knights, the Russians expanded south and east as the nomad empires collapsed. By the end of the medieval period, Russia was poised to become the largest empire in the world, breaking out of Europe and venturing past the Urals explosively, sending a sliver of influence all the way across Siberia to the Pacific.

Modern History

Empires and kingdoms became unions and republics in the 20th century. As these great nations at the heart of Eurasia expanded, they absorbed a host of peoples, Jews and Germans in the west and Turks in the east. But the consequence of the nationalisms of the age is that many of these people no longer reside in the territory of the central Eurasian states, leaving the field to Trans-Ural Peneplain.

Review Summary

Rather than venturing across oceans, the expansion of Trans-Ural Peneplain has been through the interiors of Eurasia, the vast zones between Western Europe and the rest of the Eurasian world. Originally cohesive and geographically constrained, this distinctively European cluster is now one of the most expansive and widespread. And its heritage of Western European hunter leavened with Middle Eastern farmer and Siberian nomad reflect this.

Sources

Li, Chunxiang, et al. “Evidence that a West-East admixed population lived in the Tarim Basin as early as the early Bronze Age.” BMC biology 8.1 (2010): 15.

Treadgold, Warren T. A history of the Byzantine state and society. Stanford University Press, 1997.

Barford, Paul M. The early Slavs: culture and society in early medieval Eastern Europe. Cornell University Press, 2001.

7.2  North Mediterranean

Overview

From Spain to Greece, the North Mediterranean cluster defines an arc from Gibraltar to Bosphorus. Ancient and robust, this group is dominant in Southern Europe. Its strongest source is from the first farmers to migrate out of Western Eurasia. They absorbed those who were there before, holdovers from the Ice Age.

A long history of traveling merchants and seafarers shaped this cluster. The great empires of Rome and Greece carried it away to distant lands. They also brought a second wave of Western Eurasian influence into the cluster. Its modern geography speaks to the history of those who moved, either willingly or in chains, under the Roman Empire. Because of this, the cluster’s signature is strongest in the western part of the Mediterranean. It is particularly strong on the isolated island of Sardinia. It reaches also upwards to the British Islands as well as east into modern Turkey.

The politics of empire and of a later Rome may explain why the cluster is part of many Southern European and non-European Jewish Diaspora populations.

Stone Age

Southern Europe was a place of refuge for Europeans during the Ice Age. Both Neanderthals and modern humans took shelter on the peninsulas. There, they lived in areas shielded by mountains and fringed by oceans. Until recently, historians thought that most of the ancestry of modern Europeans was from these sheltered groups. New findings are challenging that thinking. The modern population has a more complex origin. Humans did exist in these clement zones though. Some of their ancestry is present in modern Europeans from the region.

Neolithic Revolution

Nearly 10,000 years ago the first farmers arrived in the North Mediterranean region. They came from Western Eurasia. Reaching Southern Europe’s sea shores, this group took over ownership from previous residents. On the Iberian Peninsula, this became the main signature.

They have the same genetic origin as those who reached north to what is now Sweden. However, while the culture survived there, the genetic signature was largely replaced by later migrations.

Bronze Age

There is Tartessos in the west, and there is Mycenae in the east. Civilization and long distance trade have long marked the North Mediterranean cluster’s homeland. The Bell Beakers came to this region. Northern peoples moved south into the Italian Peninsula. In the Bronze Age, the North Mediterranean cluster blended with the European Coastal Plain cluster across the Alps. Thus, where the piedmont turns to steep slopes, the genetic lines blur.

Early Recorded History

The rise of Rome is the source of legions of historic texts on the peoples of the North Mediterranean cluster. Before Latin and Greek dominated, there was the Pelasgian, Ligurian, Celtiberian, and Tartessian. Yet, the rise of Greece and then Rome brought consistency to the region. Many languages passed away and left a single language with many dialects. Many peoples passed away and left local variants on a common core. Even while Rome brought new people to its eastern edge and islands, so too,Rome made a whole mosaic from many stones.

Middle Ages

Genoa in the west and Venice in the east. The fall of Byzantium, and the rise of the Papacy. Politics was the bread and butter of the history of the medieval period. It was a culture that gave rise to the ideas of Machiavelli. By now though, history had set the core North Mediterranean signature.

Modern History

The North Mediterranean peoples have circled back to their own history. Ideas of ethnic nation states again dominate. However, economic change has done more to shift the modern geography of this cluster. Colonialism spread its peoples to the New World. Opportunity now takes them into Northern Europe.

Review Summary

The North Mediterranean cluster is a distinct European cluster. It brackets the southern flank of the continent. Its origin is a mix of the first hunter-gatherers to reach Europe and later migrations from the Western Eurasia. The later migrations came in two waves. First came the founders of farming culture after the Ice Age. Second came those under the Roman Empire. The first wave European farmers is the cluster’s primary heritage.

The power of Rome spread this cluster far and wide. While long term gene flow has also helped move its presence north of the Alps and Pyrenees.

Sources

Lazaridis, Iosif, et al. “Ancient human genomes suggest three ancestral populations for present-day Europeans.” arXiv preprint arXiv:1312.6639 (2013).

Pala, Maria, et al. “Mitochondrial DNA signals of late glacial recolonization of Europe from near eastern refugia.” The American Journal of Human Genetics 90.5 (2012): 915-924.

Brandt, Guido, et al. “Ancient DNA reveals key stages in the formation of central European mitochondrial genetic diversity.” Science 342.6155 (2013): 257-261.

Skoglund, Pontus, et al. “Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe.” Science 336.6080 (2012): 466-469.

7.3  North Circumpolar

Overview

Localized around Finland, North Circumpolar nevertheless has affinities deep into Eurasia due to the ancient connections of Uralic peoples

Stone Age

Hunter-gatherers, no doubt, have long lived on the edge of the ice sheets or at least, since the expansion of the Gravettian people into the heart of Eurasia  25,000 years ago. The North Circumpolar cluster reflects the legacy of these ancient people, who shifted north with the weather.

Neolithic Revolution

The Neolithic came late to the north, with the Saami living as hunters and fishers down to the modern era. The influence of Middle Eastern farmers is minimal among the North Circumpolar for this reason. By the time farming arrived, the age of wanderings was over, and that lifestyle spread through cultural diffusion.

Bronze Age

As amber was traded south and gold poured into Scandinavia, the Finns were on the margins of history; their rivers and coastlines byways rather than at the center of the action. While the Scandinavians and Slavs pushed up against the margins of the civilized world, the Finns remained rumors deep in the north to the Classical writers.

Early Recorded History

The Uralic peoples came to history late despite their antiquity, because the institutions of modern statecraft did not penetrate the deep north. This changed with the rule of the Russian Czars and Swedish Kings, which nevertheless rested lightly upon a people with few material possessions and barely beyond slash and burn agriculture.

Middle Ages

A Crusade brought the Swedes to the land of the Finns. And yet, the ostensibly Scandinavian Rurikids have a Y-chromosomal lineage that is normally Finnish, suggesting fluid boundaries between the North Circumpolar and European Northlands, clear in the relatedness between the two clusters. To the east, the Russian state expanded north and began assimilating its own Finnic peoples into the Russian identity, leaving isolates such as the Mari and Mordvian.

Review Summary

With a strong peak in Finland, the North Circumpolar bleeds over at varying fractions across much of Northern Eurasia and even into the New World. It is an ancient cluster bringing together threads of deep Eurasian history on the coldest fringe of habitation. While agricultural civilizations developed on the western and eastern antipodes of Eurasia, the resilient people of the far north persisted. Even with the washing over of farmers across the rest of the continent on the Arctic fringe, the North Circumpolar cluster persisted and flourished, maintaining east-west connections that might otherwise have been erased.

Sources

Huyghe, Jeroen R., et al. “A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies.” European Journal of Human Genetics 19.3 (2011): 347-352.

Kriiska, Aivar. “From hunter-fisher-gatherer to farmer–Changes in the Neolithic economy and settlement on Estonian territory.” Archaeologia Lituana 4 (2003): 11-26.

Balanovsky, Oleg, et al. “Two sources of the Russian patrilineal heritage in their Eurasian context.” The American Journal of Human Genetics 82.1 (2008): 236-250.

7.4  North African Coastlands

Overview

The Arabs call it the Maghreb, the westernmost edge of the world. The nations of Morocco, Algeria, and Tunisia anchor the North Africa Coastlands. But its influence goes further out south into Sub-Saharan Africa and east toward the Middle East because of the Afro-Asiatic connections. North, the Moorish influence and Roman connections have brought segments on the other shore of the Mediterranean. Though geographically constrained, this cluster has been at the heart of events in the history of the Western world.

Stone Age

Though the origin of anatomically modern humans is presumed to be in southern or eastern Africa, the ancient Aterian culture of the northwest has also been a candidate. It is unclear how strong the influence of the hunter-gatherers of this region is in the genetics of the modern North African Coastlands cluster, but if it is significant, then it suggests that these people have lines going back to one of the most ancient distinct populations in the world. There seem to be deep connections between the peoples of North Africa and those of far Northern Europe on some uniparental lineages, suggesting perhaps that these groups harbor a very deep residual ancestral component indeed.

Neolithic Revolution

With the innovation of farming in the Middle East, streams of folk migrations went north, west, east, and south. One thread seems to have traversed the northern fringe of the Sahara, pastoralists herding goats, and pushed all the way to the Atlantic.

Early Recorded History

History begins with the Greeks and Phoenicians. In a word, Carthage. Some Y chromosomal studies have suggested deep Phoenician connections along the North Africa coast as the ancient Middle Eastern relatives of North African Coastlands moved west. But the backcountry remained dominated by the people which we think of today as Berbers, ruling client kingdoms, first to the Carthaginians and later to Romans. It was likely during this period that one began to see Sub-Saharan Africans in large numbers, contributing to the genetic mix. This was also the age of the Latin settler, such as St. Augustine’s father and the Vandal from distant Germany. Though these are minor contributions, it is likely they are not trivial.

Middle Ages

With the end of Rome and the fall of Byzantine rule in the west came Islam. Migrations into Iberia due to the expansion of the Arab Empire brought Berbers to the north shore of the Mediterranean, while the rise of self-consciously Berber Empires in the early medieval period brought their rule to to the southern edge of the Sahara. The Tuareg are the nomads of the Sahara and are a testimony to the dynamic, which might have spread this cluster to the shores of that great desert.

Modern History

European colonialism partitioned the Maghreb into distinct nation-states, but another phenomenon of note is the transformation of these Berber regions into Arab ones. But Arab here is a language, an identity, without much genetic consequence. The distinctiveness of these people is indelibly in their genes, spanning Cadiz to Timbuktu.

Review Summary

The North African Coastlands is one of the children of the West Asian Neolithic revolution. Its southwestern child, its influence has been found in Europe due to the vicissitudes of trans-Mediterranean commerce and perhaps even more significantly south of the Sahara due to the migration of camel driven nomads and warriors. Though the closest relatives of this cluster are those of the Middle East, it also bears hallmarks of being deeply influenced an indigneous substrate with roots which back to the Paleolithic.

Sources

ARCHAEOLOGISTS EXCAVATING. “Was North Africa the launch pad for modern human migrations? .” Science 16 (2004): 369.

Achilli, Alessandro, et al. “Saami and Berbers—an unexpected mitochondrial DNA link.” The American Journal of Human Genetics 76.5 (2005): 883-886.

Pereira, Filipe, et al. “Tracing the history of goat pastoralism: new clues from mitochondrial and Y chromosome DNA in North Africa.” Molecular biology and evolution 26.12 (2009): 2765-2773.

Zalloua, Pierre A., et al. “Identifying genetic traces of historical expansions: Phoenician footprints in the Mediterranean.” The American Journal of Human Genetics 83.5 (2008): 633-642.

Henn, Brenna M., et al. “Genomic ancestry of North Africans supports back-to-Africa migrations.” PLoS genetics 8.1 (2012): e1002397.

Botigué, Laura R., et al. “Gene flow from North Africa contributes to differential human genetic diversity in southern Europe.” Proceedings of the National Academy of Sciences 110.29 (2013): 11791-11796.

7.5  Niger-Congo Genesis

Overview

Dominated by West African and Bantu populations, Niger-Congo Genesis is deeply rooted in Africa. Niger-Congo Genesis takes up most of Sub-Saharan Africa. This is due to expansions that took place as part of a farming cultural shift in Africa.

It is also prominent in African Diaspora groups such as African Americans.

Stone Age

The earliest history of the Niger-Congo Genesis cluster is not well understood. Though of Africa, some have suggested that it contains part of an old migration into Africa from Eurasia. Others suggest that it shows traces of modern human interbreeding with an older African branch of the Homo lineage.

In the Stone Age, it was present only in the forests to the west of the Congo.

Neolithic Revolution

Farming culture came late to Africa. The shift was separate from the post Ice Age farming changes in Eurasia. For the Niger-Congo Genesis cluster, farming began in eastern Nigeria. It quickly swept east, south, and then southeast. Within  2,000 years, Bantus had spread to the southern tip of Africa. The migrations reshaped the genetic landscape of much of Africa in the process. There was admixture with resident populations. Yet, the average South African is genetically much like the average Nigerian, indicating only marginal admixture.

Middle Ages

The medieval period brought Arab slavery as millions were taken north. A substantial fraction of Arab ancestry is now Sub-Saharan, though rarely a preponderant component.

Modern History

Slavery in the New World by Europeans created a vast Diaspora of African ancestry people. Most of these come from West Africa and the Niger and Congo basins. Thus, Niger-Congo Genesis reached the New World.

Review Summary

There are three main clusters in Africa: Kalahari Basin, East African Pastoralist, and Niger-Congo Genesis. In the past few thousands of years, Niger-Congo Genesis has pushed aside the other two. This is the genetic signature of the farming related Bantu expansions. It now dominates the continent.

Sources

Hammer, Michael F., et al. “Genetic evidence for archaic admixture in Africa.” Proceedings of the National Academy of Sciences 108.37 (2011): 15123-15128.

de Filippo, Cesare, et al. “Bringing together linguistic and genetic evidence to test the Bantu expansion.” Proceedings of the Royal Society B: Biological Sciences 279.1741 (2012): 3256-3263.

Moorjani, Priya, et al. “The history of African gene flow into Southern Europeans, Levantines, and Jews.” PLoS genetics 7.4 (2011): e1001373.

Bryc, Katarzyna, et al. “Genome-wide patterns of population structure and admixture in West Africans and African Americans.” Proceedings of the National Academy of Sciences 107.2 (2010): 786-791.

7.6  Kalahari Basin

Overview

Kalahari Basin is a thin substrate across much of Sub-Saharan Africa, peaking in the southern regions where agricultural presence is minimal. Though very rarely dominant in any individual, its widespread distribution indicates how ubiquitous it was until recently.

Stone Age

It is cliche to say the Bushmen are the most “ancient” of human lineages. More accurate is the reality that they are the first branch off from all the others. Where in other locales one might posit the arrival of modern humans at a particular time, here we are confronted by a case where they were always there.

Early Recorded History

No one knows the original languages of the Pygmies as they speak Bantu or Nilotic dialects now. But the Hadza and Khoisan of the south maintain their own languages with distinctive clicks. The spread of the Bantu was so fast and thoroughgoing that the hunter-gatherer populations were marginalized rather quickly. If the archaeology of the Bantu expansion is correct, these hunters may have occupied a wide swath of Africa between the Congo to the Kenyan coast and south until  2,000 years ago.

Middle Ages

By about 1,000 years ago, the expansion of the Bantu into southern Africa ended due to ecological limitations. Though pushed to the edge of the sea, the Khoikhoi and Bushmen maintained a precarious existence with animal husbandry and hunting and gathering respectively. The former suggests that these are not a people lost in time, and recent work indicates Eurasian influences on the genetic character of many of these populations.

Modern History

The modern era has not been kind to indigenous and marginalized peoples. It seems likely that most of the ancestry of Kalahari Basin is now in Bantu speaking populations and therefore, in the African Diaspora. This may be the ultimate form of immortality, but it is cold comfort to these peoples as lived cultures as opposed to being segments of DNA.

Review Summary

The most distinct and diverged of clusters, Kalahari Basin is one you can suggest never left its homeland, for it occupies humankind’s ancient stomping grounds. Limited to Africa its recent history has been one of decline and assimilation.

Sources

Schuster, Stephan C., et al. “Complete Khoisan and Bantu genomes from southern Africa.” Nature 463.7283 (2010): 943-947.

Henn, Brenna M., et al. “Hunter-gatherer genomic diversity suggests a southern African origin for modern humans.” Proceedings of the National Academy of Sciences 108.13 (2011): 5154-5162.

Pickrell, Joseph K., et al. “Ancient west Eurasian ancestry in southern and eastern Africa.” arXiv preprint arXiv:1307.8014 (2013).

7.7  Jewish Diaspora

Overview

Judaism is a religion, but the Jewish people are also a nation. The latter implies genetic relatedness, with the mythos implying descent from the twelve tribes of Israel. More concretely, modern Jews have diversified into numerous branches, Ashkenazi, Sephardi, Mizrahi, as well as odds and ends such as the Bene and Beta Israel. But unifying many of these populations are genetic commonalities, likely derived from a Middle Eastern ancestry.

The Jewish Diaspora puts the particular focus on the Ashkenazi Jews, who are the majority of the world’s Jewish population. Derived from populations which were located within Central Europe, these Jews are now scattered across the world, with the largest concentrations in Israel and the United States. They represent a unique mix of Middle Eastern and European genetic elements which crystallized within the last  2,000 years.

Neolithic Revolution

The European ancestors of the Jewish Diaspora arrived predominantly with the Neolithic revolution to the shores of southern Europe, while the Middle Eastern ancestors remained in the Levantine homeland. In Europe, the farmers absorbed the remnants of the hunter-gatherers of Spain and Italy, altering the Middle Eastern genetic profile subtly.

Bronze Age

The Bronze Age in the Middle East saw the rise of three superpowers, Egypt, the Hittites of Anatolia, and the states of Mesopotamia. Between these were small states, such as that of the Syrians of Mitanni and the Hebrews of Palestine, the Israelites, and Judaeans. While the machinations of the great powers ground most peoples away, the Hebrews became something different, with their eventual conquest and scattering to Babylonia resulting not in their extinction but in their reinvention from a Levantine tribe to a nation united by ideals.

Early Recorded History

The reestablishment of the Jewish kingdom under the Persians and later their independence from the Greeks under the Maccabees allowed for the Jews to further develop their identity by becoming more than just another Near Eastern tribe. The Jews of Persia developed a distinct identity under the tolerant regime of the shahs, while the subjugation under the Greeks and Romans transformed the Western Jews from a parochial people into a cosmopolitan nation which traveled the shores of the Mediterranean. The confrontation with the Classical World resulted in the brilliance of synthesists such as Philo and arguably birthed Christianity as a sectarian form of Judaism. But it also gave rise to a unique tradition that challenged Hellenism on its own terms, typified by the first century rabbi Hillel the Elder. By the sixth century, the Jews of Persia and Palestine had formulated a new religious identity around the Talmud, and this message spread westward to those which lived around the shores of the Mediterranean.

Middle Ages

With luminaries as brilliant as Rashi, the Jews of Europe, of Ashkenaz, spread out into the cold darkness with the re-emergence of civilization in the wake of Rome’s collapse. Issuing north from the warm cities of Latin civilization to the isolated outposts of urbanity such as Trier, these Jews were the same yet different. United by a common religious tradition, the understanding of Judaism was that of the Pharisaical tradition led by rabbis. But in the long sojourn in the western provinces of Rome, the European Jews had taken on proselytes; those who were sympathetic to the Jewish message in the relative tolerance of the days of pagan Rome or those who had entered into unions with Jews and joined the tribe of their own free will. Two ancient streams of people, separated by the migrations of the Neolithic, had rejoined in Rome and began to spread north and east.

Modern History

As Poland-Lithuania waxed in the early modern era so did the Jews of Ashkenaz. In the centuries before their emancipation, due to the influence of the Enlightenment and liberalism, the Ashkenazi Jews became fixtures in the towns of Central Europe serving a role as an urban “Middleman Minority” for the nobility of Poland-Lithuania and the many peoples whom they ruled. With the division of Poland between Russia, Germany, and Austria-Hungary, the Jews were also divided and apportioned between the nations, but the stamp of their common heritage is clear, whether or not it be their Rabbinical Judaism or Yiddish language, a form of German with Hebrew and Slavic influences.

 These Jews of Ashkenaz prospered so much that by the early 20th century they were 90% of the world’s Jews, the Diaspora in near totality. Migration out of Russia and Central Europe resulted in a reversal of the great eastward expansion, as they moved west to the cities of Germany, France, the Netherlands, and London in England. With the opportunities offered in the United States contrasting with the escalating oppression in their homelands in the late 19th and early 20th century, a massive swell of migrants arrived on the shores of America. The subsequent Holocaust cut a hole in the ancient demographic homeland of the Ashkenazi Jews in Europe, resulting in a population resident in Israel, Western Europe, and the United States as well as Russia.

Review Summary

The heritage of the Jewish Diaspora stretches back to deep antiquity as two streams of Middle Eastern farmers separated during the Neolithic revolution. One ventured west and mixed its heritage with that of the hunter-gatherers of Western Europe. Another remained in the hillocks of the Levant and gave rise to a singular tribe of religious theorists that birthed the Jewish nation. The scattering of the Roman period brought them back together, in the great cosmopolitan centers of the western Mediterranean. The fall of Rome and the rise of Europe resulted in the Jewish Diaspora’s demographic expansion and cultural evolution in the milieu of Mitteleuropa.

Sources

Thomas, Mark G., et al. “Origins of old testament priests.” Nature 394.6689 (1998): 138-140.

Behar, Doron M., et al. “The genome-wide structure of the Jewish people.” Nature 466.7303 (2010): 238-242.

Keller, Andreas, et al. “New insights into the Tyrolean Iceman’s origin and phenotype as inferred by whole-genome sequencing.” Nature communications 3 (2012): 698.

Pala, Maria, et al. “Mitochondrial haplogroup U5b3: a distant echo of the epipaleolithic in Italy and the legacy of the early Sardinians.” The American Journal of Human Genetics 84.6 (2009): 814-821.

Thomas, Mark G., et al. “Founding mothers of Jewish communities: geographically separated Jewish groups were independently founded by very few female ancestors.” The American Journal of Human Genetics 70.6 (2002): 1411-1420.

Weinryb, Bernard Dov. The Jews of Poland: a social and economic history of the Jewish community in Poland from 1100 to 1800. Jewish Publication Society, 1973.

7.8  Indian Tectonic

Overview

South Asia consists of India, Pakistan, Bangladesh, Nepal, Sri Lanka, Bhutan, and Afghanistan. Bhutan is truly of the world of Tibet and Central Asia, but the other nations are clearly of a piece. Bounded on the west, north, and east by mountains and water all around, the genetics and geography have a clear correspondence in South Asia, which to the ancient Aryans, also had an obvious coherency as a domain apart.

Stone Age

Hominins have long been resident in the Indian subcontinent, but the origins of modern humanity in the subcontinent are fuzzy. Due to the reality of location, it seems plausible that this was one of the first regions outside of Africa which was inhabited by modern humans and has long played an important role in the posited “Southern Route” out of Africa, which might have made the mad dash to Australia. Others have argued that most Eurasian lineages derive from India, which as the first ecologically friendly zone for humans after exiting Africa.

Neolithic Revolution

Agriculture came to South Asia from the west, in Mehrgarh in modern Balochistan, nearly 10,000 years ago. With a Middle Eastern set of crops, it seems likely that people from the west arrived too. But the expansion of agriculture suited to the Middle East was slow into tropical South Asia with the Neolithic taking 5,000 years to reach South India. During this period, it seems likely that the the Indian Tectonic cluster took shape as a synthesis between the ancient populations of the region and the western farmers. After this melting pot, the only “pure” Stone Age populations with roots in the subcontinent were found in the isolated Andaman Islands.

Bronze Age

The half-light of history shines upon the subcontinent with the rise of the Indus Valley civilization, which was an expansive constellation of cities that spanned modern Pakistan and the fringes of north and west India. Due to the inability to translate the seals, which are ubiquitous in the cities of the Indus Valley civilization, its political history and cultural character is unknown. But there are mentions in Sumerian and Babylonian chronicles that refer to the land of Meluhha, almost certainly the Indus valley, that point to a flourishing trade between these two civilizations.

But the denouement of the civilization was its mysterious collapse in the early second millennium. The great cities disappeared, and the society reverted to a simpler and earlier mode of production. Mentions of Meluhha disappear from the annals of the Near Eastern civilizations as the people of the Indian subcontinent began to look inward.

The major controversy here is whether or not the Indus Valley civilization collapsed on its own or if it was pushed off a cliff by the Indo-Aryans. These pastoralists arrived in the second millennium and likely were the authors of the simpler society which spread across the north and west of the subcontinent in that era. There is also evidence of a secondary phase of genetic admixture in this zone during this period.

Early Recorded History

After the long dark period of the collapse of the Bronze Age cities, India comes back into the light of history in the first millennium with a flourishing society in the Gangetic plain. This is the era of the Buddha and the Mauryas. Alexander the Great reached the Punjab, and his armies were confronted by a dense land of plenty, where people wore cotton, and elephants served the rajas in military capacity. The early Indians termed the north Aryavarta, the land of Aryans, as the language of these people spread east and south with rapidity. Buddhism and Hinduism developed in a dialectical fashion as multiple strands in Indian spirituality contended for the hearts and souls.

Finally, the Mauryas of Magadha brought some political order to the subcontinent in the fourth and third centuries and expanded the boundaries of their hegemony to what we term South Asia, from Afghanistan to the southern tip. In the process, they brought Indo-Aryan culture to the southern regions, which retained a Dravidian linguistic basis but assimilated the values and ideas which we term Hindu, producing a fused subcontinent, unitary in self-identity but retaining a fundamental diversity.

Middle Ages

As had occurred in centuries past, the end of the first millennium A.D. saw the intrusion into the subcontinent of Muslims from Central Asia and Iran. Over the next few hundred years, these warriors conquered the whole subcontinent and reshaped it culturally. But their genetic impact was minimal, as they transformed themselves into a ruling caste, set apart from the native converts. But underneath the veneer of Islamic rule, Hindu India remained vibrant and evolved at its own pace and to its own tune, as a parallel society.

It was during this period, under Muslim rule, that the languages of modern India began to take form in an inchoate manner. Though the Muslims brought Persian as the lingua franca, they also patronized the local dialects, and so brought into being regional identities tied around ethno-linguistic markers. The contrast with the external Islamic migrants allowed for the crystallization of a native Indian identity and the formalization of a Hindu religious identity.

Far to the east, Indian civilization also expanded into Southeast Asia through Hindu and Buddhist religious ideas and motifs. The kingdoms of Java and Cambodia were being framed on explicitly Indian terms, and some migration of people did occur in the process, though this was a marginal aspect.

Modern History

Like so many outsiders the British brought external changes and broad institutional rearrangements but did not change the underlying structure. The key fissure of religion remains and has produced a fracturing of South Asia into Pakistan and India, while a subsequent ethnic division resulted in the shearing off of Bangladesh from Pakistan. The map may be simple in its neat lines, but the underlying diversity remains.

Review Summary

The Indian Tectonic cluster is a unique cluster that emerged as the synthesis of external and native elements, deep ancestry with South Asia, as well as farmers from the West, and perhaps Aryans on horses later. It is confined predominantly to the subcontinent, and to a great extent, it defines subcontinental ancestry.

Sources

Armitage, Simon J., et al. “The southern route “out of Africa”: evidence for an early expansion of modern humans into Arabia.” Science 331.6016 (2011): 453-456.

Oppenheimer, Stephen. “A single southern exit of modern humans from Africa: Before or after Toba? .” Quaternary International 258 (2012): 88-99.

Petrie, C. A., and K. D. Thomas. “The topographic and environmental context of the earliest village sites in western South Asia.” Antiquity 86.334 (2012).

Shipton, Ceri, et al. “Lithic technology and social transformations in the South Indian Neolithic: The evidence from Sanganakallu–Kupgal.” Journal of Anthropological Archaeology 31.2 (2012): 156-173.

Reich, David, et al. “Reconstructing Indian population history.” Nature 461.7263 (2009): 489-494.

Moorjani, Priya, et al. “Genetic evidence for recent population mixture in India.” The American Journal of Human Genetics 93.3 (2013): 422-438.

Schlingloff, Dieter. “Cotton-manufacture in ancient India.” Journal of the Economic and Social History of the Orient/Journal de l’histoire economique et sociale de l’Orient (1974): 81-90.

Eaaswarkhanth, Muthukrishnan, et al. “Traces of sub-Saharan and Middle Eastern lineages in Indian Muslim populations.” European Journal of Human Genetics 18.3 (2010): 354-363.

Eaton, Richard Maxwell. The rise of Islam and the Bengal frontier, 1204-1760. No. 17. Univ of California Press, 1993.

Karafet, Tatiana M., et al. “Balinese Y-chromosome perspective on the peopling of Indonesia: genetic contributions from pre-neolithic hunter-gatherers, Austronesian farmers, and Indian traders.” Human biology 77.1 (2005): 93-114.

7.9  European Northlands

Overview

The ancients thought Scandinavia was an island, and it might as well have been. The nations of Norden were once united under the Kalmar Union, and genetically, they bear strong resemblances to each other. A sister cluster to European Coastal Plain and European Coastal Islands, the European Northland has developed in modest isolation, inflected by the arctic heritage that it shares with North Circumpolar.

Stone Age

Humankind only came to the north during the Holocene after the cold retreated. Today the peninsula is still rising after being weighed down by the ice sheets. It was settled rapidly by hunters and fishers who managed to hold off the farmers until  5,000 years before the present. The cold northern clime made the wheat and other crops developed in the Middle East difficult exports, while the extensive marine resources supported a dense coastal population of hunter-gatherers, the cousins to those in the south which were being absorbed by the farmers.

Neolithic Revolution

Eventually farming crossed the Kattegat with agro-pastoralism and northern adapted cereals such as oats. But the hunters were thick on the ground and did not entirely cede ground. Ancient DNA suggests that modern Scandinavians are a hybrid but lean more toward their hunter-gatherer ancestors, indicating that the cultural transformation was one that did not leave the original inhabitants behind.

Bronze Age

The continental cultures such as the Corded Ware affected Scandinavia, as evidenced by the linguistic commonalities between Germany and the peninsula. Though these changes did not transform the genetic landscape, it is likely to have altered it, perhaps introducing the R1 paternal lineages from the southwest and southeast.

Early Recorded History

What the ancients knew as Thule became the mother of nations. Barbaric tribes such as the Goths, Vandals, and Cimbri had their origins in Scandinavia, which seems to have been uniformly Germanic south of the zone of Finnic habitation. Driven by a deficit of land or wealth they ventured south repeatedly and made trouble on the margins of civilized lands and sometimes struck at the heart of the rich southern lands.

Middle Ages

What had been a nuisance became an apocalypse as the word Viking became part of the European lexicon. The Vikings in their many iterations smashed England, conquered Ireland, discovered Iceland, and threatened Paris and Constantinople. Others ventured into the Mediterranean to pillage the towns of Muslim Spain. In the islands north of Britain, and in the Danelaw, they established roots and settled down. In parts of France, they were tamed and went from being poachers to game wardens. Civilized as Normans, they became Christian adventurers who conquered southern Italy and threatened Byzantium itself.

Modern History

From Gustavus Adolphus’ adventures in Germany during the Thirty Years’ War to Charles XII’s Great Northern War, Scandinavia remained geopolitically active in the modern era, if less fearsome. But more important has been the great migration out of the peninsula, especially to the United States, of whole villages. Arguably this has had a greater effect than all the Viking invasions combined.

Review Summary

The legacy of the ancient hunter-gatherers of Europe strongly leavened with the heritage of incoming farmers the people of Scandinavia are the purest distillation of Europe’s age of ice in the modern world. Though kin to other Europeans of the north, their isolation and later association with the Finnic peoples have changed them in ways that are genetically clear. An expansion over the past two thousand years has brought this heritage from the nearer shores of continental and Atlantic Europe, all the way to the plains of the Dakotas.

Sources

Ekman, Martin, and Jaakko Mäkinen. “Recent postglacial rebound, gravity change and mantle flow in Fennoscandia.” Geophysical Journal International 126.1 (1996): 229-234.

Malmström, Helena, et al. “Ancient DNA reveals lack of continuity between neolithic hunter-gatherers and contemporary Scandinavians.” Current Biology 19.20 (2009): 1758-1762.

Skoglund, Pontus, et al. “Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe.” Science 336.6080 (2012): 466-469.

Fellows-Jensen, Gillian. “Scandinavian influence on the place-names of England.” Language Contact in the British Isles (1991): 337-54.

Blegen, Theodore Christian. Norwegian Migration to America, 1825-1860. Arno Press, 1969.

7.10  European Coastal Plan

Overview

From the Bay of Biscay toward the Pripet Marshes, the coastal plain of Northern Europe is particularly clement for its latitude, warmed by the Gulf Stream and maritime Westerlies. Along these shores have long been fertile lowlands amenable to farming, and the rise and fall of many nations of renown. A variegated mass of peoples nevertheless united by distinct strands, the European Coastal Plain is the genetic outcome of the synthesis between farmer, hunter, and nomad in the years after the retreat of the ice.

Stone Age

After the extinction of the Neanderthal and the rise of the Cro-Magnon, cultures came and went in succession along this fertile stretch of the Pleistocene landscape, south of the ice and north of the forest. Aurignacian, Gravettian, Solutrean, and Magdalenian are just a few of the names familiar to many. These were the first great visual artists of humanity whose works persist down to the present, such as the cave art of Lascaux. Moving west and east, these cultures occupied a vast expanse of Western Eurasia and reshaped what it meant to be human on the ecological frontier of our species.

Neolithic Revolution

While the arrival of farmers in Europe’s south was a revolution in fact as well as metaphor, absorbing the hunter-gatherer substrate in toto, the northern face of Europe was rich in marine resources; and the spread of farming was often halting and punctuated. They moved up through valleys leaving the lands between for hunters and the shore to the fishers and beach-combers. Archaeology tells a story of both coexistence and conflict over thousands of years as some regions persisted in the old ways for hundreds of years, beyond the frontier of farming settlements. Eventually, farming spread to all corners, and the old and the new amalgamated to create the basis of a new culture.

Bronze Age

The age of metal brought different cultures, Bell Beaker and Corded Ware, from the southwest and east. Positioned at the center of Europe the core of European Coastal Plain has received many influences over the ages, including from populations as far afield as Siberia. In the years before recorded history, the region was reordered by the crystallization of the Indo-European languages, which were diversified by the time of the Classical Era. Migration to the peninsulas of northern and southern Europe from the coastal zone, and vice versa, have shaped the character of both regions.

Early Recorded History

With the light of history, we see both Celts and Germans dominating the plain between the Atlantic and Eastern Europe. Caesar’s conquest of Gaul resulted in the eventual shift of that zone to one of Latinate civilization, while the Germans remained predominantly outside of the purview of Romanitas, thanks to the victory of Arminius in Teutoburg Forest. On the southern fringes, remained unrelated peoples such as the Vascones, while the east saw the jostling between German and Slav, as the Germanic Goths moved toward the Black Sea while the Slavic Wends crossed the Elbe.

Middle Ages

After Rome came Charlemagne and the agricultural revolution of the mouldboard plough. The population increased, and the wealthy states which grew up in the shadow of Rome attracted raiders: Vikings from the north and Magyars from the east. But the genetic foundation of the European Coastal Plain had been established in previous ages, and the nation-states of Germany and France and the Low Countries reflected different aspects of that diversity and variation, elements of a landscape shaped by forces from all directions.

Modern History

The people on the European Coastal Plain were at the heart of recent history, the engines behind the Great Powers of the age. Great migrations of surplus population resulted in a Diaspora from the Volga in Russia to the vast expanses of the American heartland. Germans settled across Eastern Europe while Walloon miners brought their skills to Sweden. From being the resting place of wandering people, the people of the European Coastal Plain became dominant actors in the game of colonialism and settlement.

Review Summary

Many-layered and deep in history, the European Coastal Plain combines nearly all the threads of European genetic history in one. The hunter-gatherer, farmer, and intruder from the steppe were forged together as one people before the light of history, while the French and the German were created by the intersection between the civilized and barbarian during antiquity. With this diverse ancestry across the gentle plain, a relatively unified cluster was created, and modernity has brought its expansion along the wavefront of Western hegemony.

Sources

Skoglund, Pontus, et al. “Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe.” Science 336.6080 (2012): 466-469.

Keeley, Lawrence H. War before civilization. Oxford University Press, 1996.

Borić, Dušan, and Preston Miracle. “Mesolithic and Neolithic (dis) continuities in the Danube Gorges: new AMS dates from Padina and Hajdučka Vodenica (Serbia).” Oxford Journal of Archaeology 23.4 (2004): 341-371.

Raghavan, Maanasa, et al. “Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans.” Nature (2013).

7.11  European Coastal Islands

Overview

Facing the ocean on the northwest fringe of Eurasia are the Isles, Britain and Ireland. Due to their isolation from the continent, these islands have developed their own genetically distinct aspects, which nevertheless bind them to the continent through a history of gene flow. A sister cluster to European Coastal Plain and European Northlands, European Coastal Islands extend tendrils south and east, recapitulating connections with Celts and Germans on the mainland.

This group is typical to the British Isles, especially Ireland. Its reach includes all European Islands from the far north down to the Azores Islands off the coast of Spain. The continuous mixing of European populations means that this group is also present in lesser amounts on the mainland.

Stone Age

As the Ice Age ended, sea levels rose, and Doggerland sank into the North Sea. Their diet came from the sea, but it was also their enemy. The hunters from the refugia to the south had moved north with the warming, and Britain was rapidly resettled. To the east was Doggerland, now submerged in the North Sea. These were a strange folk, dark of skin, and blue of eye, whose roots in Europe went back deep into the Pleistocene. They exploited the marine resources extensively, likely resulting in a higher than typical population density for hunter-gatherers.

Neolithic Revolution

The farmers came to Britain late, but when they came, they wrought great change. The protein immediately switched from marine to mammal. The hunters were assimilated, and through the admixture emerged European Coastal Islands as we know it, a hybrid of two threads. It is now that the first monuments are built, and villages with stone houses appear.

Bronze Age

Though apart, the Isles were part of events on the European mainland. The Beaker People spread north and east and brought their distinctive culture to much of Western Europe. Some have suggested that it was this period which brought R1b to prominence in Europe.

Early Recorded History

Caesar brings Britain into history, while the Irish king Niall of the Nine Hostages straddles legend and truth. The Romans conquered under Claudius and found a relatively agrarian land of Celts of various degrees of ferocity. To the north, beyond the walls were the Picts, and Irish raiders were always a threat. It was in the last phases of Roman rule that the connections to the continent were reforged; Germans rushed in to fill the vacuum, giving the English their name and their language, and Celts fled south and established an outpost in Brittany. As the Dark Ages came upon Europe, the Vikings brought a new influx of blood resulting in a cosmopolitan melange that overlays the dominant genetic element of the Isles.

Middle Ages

The Normans conquered in 1066 and again established deep relationships to France, for they were as French as they were Norse. But the Hundred Years War produced a distinct English identity, apart, yet not alien to broader European sensibilities. The demographics did not shift, as the Normans were the faintest topping upon the class structure of Britain, dominated by Celts, Germans, and Vikings. And yet to this day Norman names are overrepresented among military elites, attesting to the power of family lineage.

Modern History

The Reformation and the Empire reordered Britain’s sympathies, while the famine resulted in a demographic collapse in Ireland. The influx of French and Dutch Protestants had a minimal effect on the genetics of Britain but changed its culture, tearing high from low church, Puritans and Royalists. Though the British Royal family has long been of German provenance, the character of the people remained unperturbed, maintaining the nature which coalesced over thousands of years upon to the Dark Ages.

Review Summary

Due to low gene flow because of water barriers Britain and Ireland have developed their own genetically distinctive cluster. But historical events have brought them back to the center, and people have migrated in both directions, from the continent and back to the continent. Genetically close to European Coastal Plain and European Northlands, European Coastal Islands has had an outsized impact on the demography of the world because of the explosion of population in the Anglosphere over the past few centuries.

Sources

Olalde, Iñigo, et al. “Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European.” Nature (2014).

Richards, Michael P., Rick J. Schulting, and Robert EM Hedges. “Archaeology: sharp shift in diet at onset of Neolithic.” Nature 425.6956 (2003): 366-366.

Skoglund, Pontus, et al. “Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe.” Science 336.6080 (2012): 466-469.

Myres, Natalie M., et al. “A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe.” European Journal of Human Genetics 19.1 (2011): 95-101.

Thomas, Mark G., Michael PH Stumpf, and Heinrich Härke. “Evidence for an apartheid-like social structure in early Anglo-Saxon England.” Proceedings of the Royal Society B: Biological Sciences 273.1601 (2006): 2651-2657.

Goodacre, S., et al. “Genetic evidence for a family-based Scandinavian settlement of Shetland and Orkney during the Viking periods.” Heredity 95.2 (2005): 129-135.

Clark, Gregory. “What is the true rate of social mobility?  evidence from the information content of surnames.” manuscript, UC Davis (2013).

7.12  Eurasian Heartland

Overview

Eurasian Heartland issues from the ancient eastern face of Western Eurasia, from Transoxiana south to the Indian ocean. With influence north, east, and west, it has galloped on the hoof of nomads and conquerors for four thousand years. It is found in most nations of Eurasia outside of East Asia because of this aspect of its history.

Stone Age

The desert zones of Central Eurasia were not thickly inhabited during the Stone Age, though clearly, humans traversed them to go to other regions.

Neolithic Revolution

Farmers arrived in this region from the eastern edge of the West Asian hearth, with crops perfectly transplantable. While some continued onward to India to create a new and distinct cluster through admixture, others remained and developed their own unique societies in the fertile upland valleys and riverine bottomlands. Pushing north into Transoxiana, the farmers confronted nomads, who were likely a distinct branch of the Indo-Europeans.

Bronze Age

In the lacunae between Babylon and the Indus Valley, this was an area famed for its lapis lazuli and a major source of raw material. In the north, the Bactria–Margiana culture flourished. In the steppes north of the Black Sea, it is likely that cousins were on the march into Europe, bringing horse and sword to the farmers of the western continent.

Early Recorded History

When the Persian Empire expanded to Khorosan and Transoxiana, Iranian languages were dominant, in particular Sogdian, which was long the lingua franca of the Silk Road. But these were distinct from the southern and western variants. Rather, they were more closely related to the far flung dialects of the Scythians and Sarmatians far to the north and west. Today, Iranian languages are relatively constrained, but in antiquity, they swept from the Danube to the Indus, and Eurasian Heartland mimics this distribution.

Middle Ages

Genghis Khan and Tamerlane reshaped Central Asia, making what was once Iranian Turk. Though the genetic character was radically altered, the Eurasian Heartland substrate remains and is still dominant further to the south beyond the pale of dominant Turkic settlement.

Modern History

With the movement of millions of the Indian subcontinent, Eurasian Heartland has appeared in the Pacific, the New World, and Southeast Asia. Millions of displaced Afghans have also brought it west into Iran and reinforced it in Pakistan.

Review Summary

Eurasian Heartland covers a vast swath in the center of the continent and reflects the edge of expansion of Middle Eastern farmers  10,000 years ago. Penetrating into South Asia and the steppes of Russia, its influence spans the Arctic Circle down toward the equator in a long arc bissecting Eurasia.

Sources

Hodoğlugil, Uğur, and Robert W. Mahley. “Turkish population structure and genetic ancestry reveal relatedness among Eurasian populations.” Annals of human genetics 76.2 (2012): 128-141.

Ostler, Nicholas. Empires of the word: A language history of the world. New York: HarperCollins, 2005.

Martínez-Cruz, Begoña, et al. “In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations.” European Journal of Human Genetics 19.2 (2011): 216-223.

7.13  Eastern Afroasiatic

Overview

The Persian Gulf up toward the Zagros mountains in Iraq and Iran serve as the hearth for the Eastern Afroasiatic genetic cluster. With a core zone sweeping up from Oman and turning east to Iran, this region encompasses one of the most critical pivots in modern geopolitics and was one of the roots of civilization. Facing south and east, this region has resulted in many enclaves along the shores of the Indian ocean, traveling the trade winds along the coasts of East Africa and India.

Stone Age

When anatomically modern humans left Africa over 50,000 years ago, they almost certainly arrived in the Middle East. But there is vigorous debate of whether or not the route was a “northern” one that swept up through the Levant or if there was an Arabian sojourn, implying an “Out of Arabia” model for the emergence of Eurasians. It may be that the answers about the origins of modern humans lay in excavations around and within the Persian Gulf.

Neolithic Revolution

The origins of agriculture are in the hills around the core zone of Eastern Afroasiatic populations. As such, it is likely that the populations to the east and south of the zone, which are the purview of this cluster, are the demographic consequences of this cultural revolution. Yet extensive habitation of the arid zones required subsequent developments, institutions that allowed for the development of hydraulic civilization in Mesopotamia and Iran and the domestication of the camel, which made the deep desert accessible to the peoples of Arabia.

Bronze Age

History began in Mesopotamia, and with it, we see the rise and fall of peoples in great textual narratives. The mysterious Sumerians arrive on the scene at the dawn of history, their language being unrelated to any other on record. They flourished for one thousand years, but slowly dissipated and became a memory by the second millennium before Christ. But in the same land between the Tigris and Euphrates were Semitic peoples, first the Akkadians and later the Amorites, Chaldaeans, and Aramaeans. These Semitic people were cousins, wanderers from the desert who spoke with a lilt alien and somehow altogether familiar to the people of the villages of the civilized world.

To the east were the mysterious Elamites, rivals of the Sumerians who were later to fall in their own turn to the ancestors of the Iranians. The Persians became the heirs of Elam, in the hills above Khuzestan. As the Semites swept out of Iraq with the rise and fall of empires, Iran became the fortress of the Iranians who periodically expanded their influence north, west, and east.

Early Recorded History

This was the world of empire: the Babylonians, then the Assyrians, and finally the Persians. Early to the development of the city, so the eastern and southern fringes of the Middle East also came early to the concepts of imperial conglomerates of power and grandeur. Eventually, the insulated world was interrupted by outsiders, from Alexander the Great to the Romans, but the foreign touch was always light as the ancient peoples of this region became something new and yet remained true to their ancestors.

Middle Ages

History began here, and it continued to be driven along by greater world events. The rise of Islam placed Iraq at the center of the world, shimmering from Baghdad. The complacent world of early Islam, secure in its superiority, was soon shattered by the emergence of the power of the Turks who spilled over from the lands of Central Asia, and finally, the Mongol catastrophe that destroyed many ancient cities in these old lands.

But to the south, along the shores of the Persian Gulf, trade flourished; and the peoples of Oman were forging deep links with the cities of East Africa, and Arab sailors were establishing communities in western India. While the cities of Iraq and Iran were battered by the vicissitudes of history, ties of trade, which dated back to the mists of prehistory, tightened across the Indian ocean, held together by individuals whose roots lay around the Persian Gulf.

Modern History

With colonialism, the old boundaries were rearranged, and fuzzy frontiers became sharp lines upon the map. But the connections between the various nations around the Gulf remains due to the conflicts over oil and religion. Despite divisions over language and religion, the shared ties are deep and extend out toward a Diaspora which is the echo of historical events long forgotten.

Review Summary

The peoples of Eastern Afroasiatic ancestry crystallized early in our mind’s eye because history began in this region. They gave rise to the Arabs and were essential to the emergence of Iran. Their reach extends toward Africa and Asia due to the importance of trade around the Indian ocean. This is a cluster at the center of events and quite often the driver of events.

Sources

Fernandes, Verónica, et al. “The Arabian cradle: mitochondrial relicts of the first steps along the southern route out of Africa.” The American Journal of Human Genetics 90.2 (2012): 347-355.

Armitage, Simon J., et al. “The southern route “out of Africa”: evidence for an early expansion of modern humans into Arabia.” Science 331.6016 (2011): 453-456.

Rose, Jeffrey. “The Arabian Corridor Migration Model: archaeological evidence for hominin dispersals into Oman during the Middle and Upper Pleistocene.” Proceedings of the Seminar for Arabian Studies. Archaeopress, 2007.

Gopher, Avi, Shahal Abbo, and Simcha Lev-Yadun. “The “when”, the “where” and the “why” of the Neolithic revolution in the Levant.” Doc Praehist 28 (2001): 49-62.

Reilly, Benjamin J. “Revisiting Bedouin Desert Adaptations: Lactase Persistence as a Factor in Arabian Peninsula History.” Journal of Arabian Studies 2.2 (2012): 93-107.

Willis, Justin. “The Edge of Islam. Power, Personhood and Ethno-Religious Boundaries on the Kenya CoastBy Janet McIntosh.” Journal of Islamic Studie

7.14  East Asian Coastal Islands

Overview

From Shanghai south to the islands of Indonesia, the great rice cultures are the locus of East Asian Coastal Islands, in short, ASEAN plus China south of the Yangzi. But its farthest flung outposts can be found in Madagascar and Easter Island due to the Malayo-Polynesians.

Neolithic Revolution

Beginning as millet farmers in China  10,000 years ago, the agricultural revolution spread to the south and to  the cultivation of rice. Over time, these rice farmers moved through the valleys and coasts of southern China and arrived at the gates of Southeast Asia. 4,000 years ago the Austro-Asiatics moved into the mainland, while Austronesians began to drift south from Taiwan. Absorbing genetic ancestry from the indigenous populations, nonetheless East Asian Coastal Islands is a very close sister indeed to Asian Northeast.

Early Recorded History

The dawn of history in Southeast Asia has the Khmer and the Kinh, better known as Cambodians and Vietnamese. The former were outside of the purview of Chinese hegemony, while the latter fought hard for their independence. It is no surprise that later the Khmer entered the orbit of Indic civilization, while the Vietnamese were assimilated into Greater China. But genetically, their origins are the same, the Austro-Asiatic rice farmers of southern China. Cousins but not distantly so. To the west, the Mon were developing their own Austro-Asiatic civilization in Burma and Thailand.

Middle Ages

The medieval period brought the invasion of the Thai from southern China, a second wave of migration after the initial settlement. The hammer-blows of the Thai shattered the Austro-Asiatic hegemony of what became Thailand, while their cousins the Shan were not able to defeat the Burmese. Despite these mixed political results, the genetic effect was marginal in large part due to the relatively minor distinction between the newcomers and the Austro-Asiatic substrate.

Modern History

The Chinese Diaspora and the refugees who escaped the chaos of Southeast Asia have spread this cluster across the world.

Review Summary

Close to Asian Northeast, East Asian Coastal Islands heralds the arrival of farmers to Southeast Asia and mariners of grand ambition to the Indian and Pacific oceans. In China, it is a substantial presence with Asian Northeast and defines a north-south axis of ancestry and affinity.

Sources

Barker, Graeme, and Martin B. Richards. “Foraging–farming transitions in island southeast Asia.” Journal of Archaeological Method and Theory 20.2 (2013): 256-280.

Soares, Pedro, et al. “Climate change and postglacial human dispersals in Southeast Asia.” Molecular Biology and Evolution 25.6 (2008): 1209-1218.

7.15  East African Pastoralists

Overview

South of the Sahara and east of the forest, the East Africa pastoralists are an African cluster that is intercalated with the Bantu farmers who arrived from the west. Stretching from Sudan and south toward Tanzania, these people arrived as herders over the past few thousand years, coexistent and often politically dominant over the Bantus who are their near neighbors. On the northern Sudanic fringe, they seem to be indigenous and have connections to Eurasian populations expanding out of the Middle East.

Stone Age

Most of the ancestors of the East African Pastoralists never left Africa, but no doubt, their forebears fled south from the “Green Sahara.” The hunters and fishers along the upper Nile were optimally situated between the desert and the forest, exploring the open lands between.

Neolithic Revolution

With changes to the north, the proto-East African Pastoralist population also began to shift its way of life. Populations descending from Middle Eastern farmers were absorbed, and farming and pastoralism became part of the way of life for the people along the upper Nile. Over time, the herds moved south avoiding the zones of the tsetse flies. The original hunter-gatherers of East Africa gave way to the pastoralists on the one hand and the Bantu farmers on the other.

Others moved east into the Horn of Africa and co-mingled with Semitic peoples from the Arabian peninsula. Over time, this admixture gave rise to the populations of Ethiopia and Somalia.

Early Recorded History

In the highlands of Ethiopia, the civilization of Axum developed as a synthesis of indigenous African elements and Eurasian aspects, reflecting its genetic heritage. When Egypt fell to Islam, Ethiopia remained loyal to the Coptic Christianity that it had adopted in the centuries prior. In contrast, the lowlands gave way to Islam, which the Somalis took too enthusiastically.

Modern History

The kingdoms of Ethiopia and Somalia become enmeshed in conflicts between Omanis and Portuguese during the Age of Discovery, while the coastal cities of East Africa solidified their trans-Indian ocean networks. To the south, the Tutsi emerged as a hegemonic power among the Bantu farmers of the highlands of Rwanda-Burundi though in the process absorbing the Bantu culture. Nilotic peoples in Kenya and Tanzania such as the Luo and Masai have become part of the Bantu dominated landscape, defined by their distinctive physical features and pastoralist culture.

Review Summary

The East African Pastoralists are an ancient cluster which emerged on Sub-Saharan Africa’s north facing eastern expanse. The distinctive aspect of this cluster is its close association with pastoralism, allowing them to exist in symbiosis with the Bantu farmers. It is the dominant Sub-Saharan African contributor to the ancestry of Ethiopians.

Sources

Pickrell, Joseph K., et al. “Ancient west Eurasian ancestry in southern and eastern Africa.” arXiv preprint arXiv:1307.8014 (2013).

Pagani, Luca, et al. “Ethiopian genetic diversity reveals linguistic stratification and complex influences on the Ethiopian gene pool.” The American Journal of Human Genetics 91.1 (2012): 83-96.

7.16  Bering Expansion

Overview

From the Canadian Yukon south to Patagonia, the people of the New World are a unique expression of human genetic variation, the farthest edge of the migrations out of Africa. But their connections also stretch back to Siberia and even Europe, as their origins are a composite one.

Stone Age

15,000 years ago hunters, who were a motley mix of elements, moved from Siberia into Beringia. Subsequent to this, the tribes moved south, diversifying and settling an empty land. The original base of a few hundred were the root of the thousands of tribes and cultures that diversified over the continent.

Neolithic Revolution

In the New World, independent instances of the Neolithic revolution occurred in Mesoamerica and the Andean region with the development of maize and potato. Just as in the Old World, it seems to result in demographic expansion of selected groups, evident in the dominance of Quechua and Nahuatl. But farming was never so thorough among many peoples who continued to hunt, fish, and gather. The demographic tsunamis characterized by the spread of farmers in the Old World did not occur in the New, and the underlying complexity of the hunter-gatherer world seems to have coexisted more consistently with an opportunistic attitude toward cultivation.

The Na-Dene languages of the northwest are evidence of a late migration, in part, due to their affinities with East Asians, at least going from from genetic data. The other languages are often classified as “Amerind,” but their underlying structure is not clear likely due to the deep  10,000 year time depth of diversification.

Modern History

The “Great Dying” due to the Columbian Exchange resulted in a massive demographic recession of the Bering Expansion cluster. Even in regions where it is resilient, as in Mesoamerica, there is evidence of admixture with Europeans and Africans. In the north and deep south, the native populations have been exterminated or absorbed into the settler populations. A world that was once all theirs is now owned by others.

Review Summary

The Bering Expansion is a distinct and compact cluster which emerged out of the late Pleistocene in Siberia. But like so many, it is a hybrid derived out of the mixture of an ancient Siberian population which also contributed to Europeans and East Asians. Today, it can be found across the New World at varying levels and even leaves its influence in Asia due to the Siberian connections of yore.

Sources

Raghavan, Maanasa, et al. “Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans.” Nature (2013).

Reich, David, et al. “Reconstructing native American population history.” Nature 488.7411 (2012): 370-374.

Bryc, Katarzyna, et al. “Genome-wide patterns of population structure and admixture among Hispanic/Latino populations.” Proceedings of the National Academy of Sciences 107.Supplement 2 (2010): 8954-8961.

7.17  Asian Northeast

Overview

China, Japan, and Korea form a single cultural and historical unit. This is Sinic civilization, and the locus of the Asian Northeast cluster is fittingly neatly encapsulated by this region, with a peak around Korea and Manchuria. Spreading north this cluster is dominant in Siberia and has connections to the New World with the Na-Dene. Declining as one goes south in China, it waxes as wheat and millet are replaced by rice.

Stone Age

Ancient DNA from  40,000 years before the present suggest that the ancestors of this cluster have long been resident in the region. Unlike other areas of Eurasia, intrusion into this sector has been minimal, and cultures and populations developed in situ. Early migrants crossed the water into Japan, creating the Jomon culture.

Neolithic Revolution

Around the Yellow river plain, a group of millet farmers who emerged nearly  10,000 years ago likely triggered off a set of migrations that reordered Eastern Eurasia’s demographic map. Facing the hunters and fishers north and south, these farmers expanded into demographic space and created synthetic populations which gave rise to the two East Asian clusters. Asian Northeast therefore spans the rice farmers of Korea as well as the Tungusic hunters and gatherers and the populations in between. Far to the north, the Neolithic never arrived because the ecology was not amenable. But whenever groups moved south, they seemed able to transition effectively to agro-pastoralism or farming.

Bronze Age

One of the early farming societies became what we know as the China, the Han, focused on the Shang state in the Yellow river valley. But this narrow delimited state was not the totality of East Asian agriculture, and admixture of indigenous mountaineers and lowlanders seem to have given rise to Tibetans on the edge of written history. Peoples were on the move long before the great Chinese writers put their thoughts down on paper.

Early Recorded History

As China came into its own during the Han dynasty, the genesis of Korea and Japan were both in the offing. The Yayoi rice farmers marginalized and absorbed their Jomon cousins in Japan  2,000 years ago after arriving from Korea. Subsequent to this migration, few newcomers arrived in the islands of Japan. In Korea, the melange of peoples shook themselves out into a few kingdoms at varying degrees of remove and vassalage to the great power that was China.

Middle Ages

With the Tang and Song  1,000 years ago, the geopolitical boundaries of East Asia came into being as we understand it with the proto-nation-states already outlined. Though the Mongols brought foreigners, their impact on the genetic landscape was minimal. The Hui, Chinese speaking Muslims, have only a minor element of non-East Asian ancestry, while Korea and Japan were closed off from the rest of the world by China. But the Mongols and Turks did transmit this heritage to the west at small fractions from Russia down to Egypt.

Modern History

With the rise of trade and globalization, a massive Diaspora of Chinese has spread to Southeast Asia and the New World, bringing Asian Northeast to new corners of the world. As Chinese power waxes no doubt this will continue, though within China itself the southerners are more often on the move, and they have somewhat less Asian Northeast. The major possibility in the near future is the north, as Russia declines militarily and demographically.

Review Summary

Distinct and isolated, Asian Northeast reflects the deep ancestry of the first settlers of Eastern Eurasia. Its influence can be felt in Amerindians through an ancient admixture event in Siberia as well as the more recent migration of Na-Dene across the Bering Strait.

Sources

Fu, Qiaomei, et al. “DNA analysis of an early modern human from Tianyuan Cave, China.” Proceedings of the National Academy of Sciences 110.6 (2013): 2223-2227.

Pickrell, Joseph, and David Reich. “Towards a new history and geography of human genes informed by ancient DNA.” bioRxiv (2014).

Liu, Xinyi, et al. “The earliest evidence of millet as a staple crop: new light on Neolithic foodways in North China.” American journal of physical anthropology 149.2 (2012): 283-290.

Jeong, Choongwon, et al. “Admixture facilitates genetic adaptations to high altitude in Tibet.” Nature communications 5 (2014).

Jinam, Timothy, et al. “The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations.” Journal of human genetics 57.12 (2012): 787-795.

Yao, Yong-Gang, et al. “Different matrilineal contributions to genetic structure of ethnic groups in the silk road region in china.” Molecular biology and evolution 21.12 (2004): 2265-2280.

Hodoğlugil, Uğur, and Robert W. Mahley. “Turkish population structure and genetic ancestry reveal relatedness among Eurasian populations.” Annals of human genetics 76.2 (2012): 128-141.

7.18  Anatolia and Caucasus Crossroads

Overview

Widespread and old, Anatolia and Caucasus Crossroads is linked to the rise and fall of many civilizations. It may even have been part of the rise of what we call civilization, and it lies at the crossroads of time and space for good and ill. From its core in the Caucasus mountains and the plateaus of Anatolia, it has expanded in all directions. Its reach shows its rich and sometimes checkered history. This group is the mark of those who moved east to west and back again along what would become the Silk Road.

Stone Age

The core Anatolia and Caucasus Crossroads geographic region was livable during the Stone Age. It may have been one of the first areas of modern human habitation during and after the extinction of Neanderthals. Early modern human settlers were hunter-gathers. The first farmers followed them, and the two groups likely intermixed. The farming lifestyle expanded from the hills to the south and outward in all directions. It is now central to the region.

Neolithic Revolution

Farming culture brought a settled life to members of the Anatolia and Caucasus Crossroads cluster. Large movements of people into the core region ended. Rather, the cluster began to spread across Eurasia in long curving sweeps. It was carried on the backs of horses and by the success of the plough.

Bronze Age

In the Bronze Age, the core lands of the Anatolia Crossroads cluster was home to the Hittites. They were one of the superpowers of the age and pioneered the use of iron. Their letters to the leaders of Egypt, Mycenae, and Babylon shed vital light on the ancient world.

Early Recorded History

The core Anatolia and Caucasus Crossroads region has a long recorded history. Its texts record the Phrygians, the Hurrians, the Hittites, the Hatti, and the Armenians. With the rise of Rome and Persia, these lands became a political center and a battleground. From here, came the emperors of Byzantium. They were Armenian in ancestry, Greek in speech, and Orthodox in religion. This history didn’t change genetic character of the people there. It was long set by their farming and herdsman ancestors.

Middle Ages

The Ottoman Empire brought a period of cultural stasis to the core Anatolia and Caucasus Crossroads region. This relative quiet lasted for over a thousand years.

The few exceptions were dramatic. The Turks swept down from Asia and brought those from the Asian Northeast cluster. The Arab expansion brought members of the Eastern Afroasiatic cluster to the southern borders.

These events had only a minor influence though on the Anatolia and Caucasus Crossroads signature. Closed social groups, such as the Druze and Assyrians, have clear signatures of Anatolia and Caucasus Crossroads. This suggests that their genes are native to the region.

Modern History

The modern history of the core Anatolia and Caucasus Crossroads region has been sad and unfortunate. It includes the ethnic cleansing of Armenians and forced removal from the Fertile Crescent of groups based on religion. These events did not alter the genetic signature of the region though.

Anatolia and Caucasus Crossroads is the strongest element in Turks. This is despite their cultural origins in Eastern Eurasia. It is also strongly present in Arabs of the northern Fertile Crescent. In Europe and Central Eurasia, it is present in groups with ancient links to the hearth of farming.

Review Summary

The Anatolia and Caucasus Crossroads cluster peaks at the crossroads of empires and cultures. Its center is in the highlands of Anatolia. The region’s open geography though has carried the signature north, south, east, and west. It spans national, religious, and cultural identity. Many of the farmers that arrived in Europe and Central Eurasia carry this heritage. Many of the ancient peoples of the Fertile Crescent do as well.

Sources

Hodoğlugil, Uğur, and Robert W. Mahley. “Turkish population structure and genetic ancestry reveal relatedness among Eurasian populations.” Annals of human genetics 76.2 (2012): 128-141.