North Africa in Genetics and History

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

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

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

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

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

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

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

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

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

Note that not much DNA is shared across the Sahara:

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

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

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

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

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

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

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

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

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

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

In other words, someone went a-conquering.

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

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

 

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

New Frontiers of the Bronze Age Collapse (Pt. 1/3)

(source)
Bronze Age Greek palace of Knossos

(Go to Part 2, Part 3)

The Bronze Age is difficult to study because written language was a lot less widespread back then, and all of the artifacts have had a lot longer to be destroyed than more recent ones. We tend to think, therefore, about the “start” of European history as the rise of the Greek city states of Athens and Sparta with their flowering of philosophy, mathematics, and literature. (In short, the Iron Age.) If we think back before Homer’s day, our focus shifts, from the edge of Europe to the edges of Asia and Africa–Egypt, Anatolia, and Judea. (Indeed, our notion that “continents” are important units by which people are defined is probably faulty in this context, where bodies of water are probably equally important.)

Sewers of Knossos (source)
Sewers of Knossos

But there were fortified towns of +5,000 people in Greece a good 6,000 years before Homer composed his epics, way back in the neolithic. By the Bronze Age, Greece had cities and palaces with aqueducts, sewers, tons of art, writing, and international trade. (The Greek Bronze Age began around 3,200 BC.)

Chalcolithic town of Los Millares, Spain
Model of the Chalcolithic town of Los Millares

Egypt in the Bronze Age built its famous pyramids; across the Mediterranean, in Spain, we find the pre-bronze fortified town of Los Millares (population +1,000), the many towns of El Agar, and the impressive city of La Bastida.

A few locations excepted (for reasons that will become clear in a moment,) the Bronze Age required long-term navigation, trade, and techno-social complexity.

Bronze is an alloy of copper and tin. Copper is abundant and relatively easy to find, but too soft to make good tools. Mixing it with tin makes it harder and more functional, but tin is much rarer and harder to find–and tends not to be located anywhere near the copper ores. Bronze Age peoples, therefore, had to engage in long-distance trade to make their bronze.

1024px-Metallurgical_diffusionSpain was one of the Mediterranean’s major sources of tin; Cornwall (southern Britain) and the Ore Mountains (Erzgebirge,) in southern Germany were the others.

The Nebra Sky Disk, c. 1600 BC Germany, contains Cornish tin, Austrian copper, and Cornish or Carpathian gold. Trade in Cornish tin was long believed to be controlled by the the Phoenician Empire of North Africa. While it may be that the Phoenicians only controlled the Mediterranean end of the tin trade, a great many Phoenician coins have been found in southern Britain.

The Amber Road
The Amber Road

Another major trade item was amber, probably used primarily for jewelry but also sometimes burned as incense. Amber hails from northern Europe/Scandinavia, whose trade routes I wrote about back in Elsewhere in the Baltic: Gotland; the “Amber Road” stretches from the southern shores of the Baltic to northern Italy. From there it was traded to Carthage, Egypt, and Syria. (King Tut was interred with ornaments made of Baltic amber.) If amber made it to the Silk Road, it could have traveled even further afield.

So I wonder: How advanced were things circa 1,000 BC? Certainly most people were subsistence farmers, but then again, most people today are still farmers. Did the Europe of 1,000 or 6,000 BC look much like the Europe of 1,000 AD, but with fewer cathedrals? Did the Roman and Greek eras introduce major changes in the level of organization and the general shape of European daily life (even allowing for the massive collapse that followed in the western half of the Roman Empire,) or was this more or less the road Europe was already on? Would the culture of bronze age Europe be remotely familiar to us, or was it totally different? And how much of an effect (if any) did all of this trade have on the lives of ordinary people?

To be continued… (Go to Part 2, Part 3)