African Ecology: Benchmarks and Historical Perspectives


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That considerable epidemiological burden could, of course, be the result of recent introduction of the pathogen. India, for example, suffered millions of deaths due to plague in the early 20th century as part of the Third Pandemic. Yet in Africa, we can look back even earlier than the beginning of epidemiological data collected by colonial governments.

For this, we have genetic evidence; the written testimony of colonial authorities, visitors, and missionaries; and the testimony of Africans themselves.

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Figure 3: Detail of the 1. Supplementary Fig. Morelli et al. Green and reproduced with permission. That was because at the time, and still to this day, these were the only samples of 1. ANT that had been fully sequenced. ANT branch is fuller and shows much more divergence. Connecting 1. From the polytomy to 1. In other words, about half of the divergence that has occurred within the 1. ANT branch—which has likely occurred over the past years or more—is still documented in the surviving strains.

Only multiple, well-dated aDNA samples could prove that definitively. It is possible that this diversity could have already accrued in another reservoir and been imported into East Africa wholesale.

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But because some of the collection dates go back as far as the s IP and IP, both samples of 1. ANT2a and, by at the latest, comprises isolates from the furthest node, 1. ANT1c IP , we know that all of the documented diversity already existed in at least Kenya and Congo by the middle of the 20th century see Table 1. All these isolates were obtained from human patients, meaning we cannot be sure what role recent relocation may have played in their infection.

Nevertheless, it is interesting that all three groups 1. ANT3, 1. ANT2, and 1. All Congolese cases have come from the eastern portion of the country, pointing to the plague foci in those elevated regions near the headwaters of the Uele River and near Lake Albert. Studies from the s and s suggest that it was just becoming a new problem in the region then, though that may be an artifact of increased colonial scrutiny by foreign doctors.

Table 1. East African Yersinia pestis isolates used for study of plague. Information drawn from G. ANT1a and 1. ANT1b provided from G. Chain et al. As we saw earlier, a real-time study of an outbreak in Madagascar documented the production of 13 new SNPs in a ten-year period.

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Nevertheless, the Y. Most mutations get eliminated from the lineage. Only those that have successfully reproduced in long-term reservoirs survive. Out of the whole Y. ANT strains. When we add the genetic diversity of 1. ANT to the evidence for deep infestation in an area that is very minimally urbanized, distant from any seaports that might have recently introduced the disease, the question is raised whether this is not indicative of deeper historical roots of plague in the region.

Having been reassigned there from India where what we now call the Third Plague Pandemic had just broken out , Koch had good reason to reflect on the question of whether plague infestations were new or not. Summing up, he cited one of the leading colonial plague researchers of the day, W. Simpson, who wrote in that. Still, there can be no doubt that plague has been endemic in the western province of Uganda for many years and, if tradition is correct, it has been there for ages.

They were unanimous in their opinion that its presence in the region was of long duration, even if its manifestation in particular areas was variable. Indirectly, they also capture the experiences of East Africans themselves. In , British physician Cuthbert Christy recounted an expedition he made seeking to confirm the presence of sleeping sickness, only to find instead widespread presence of, and knowledge about, kaumpuli. At Mbarara, to the west of Lake Victoria, for example, Christy received testimony about kawumpuli from a missionary:.

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Father Gorgu informed me also that kaumpuli was well known to the natives and dreaded by them long before the missionaries came to Bikira, eight years previously. Feldmann said, too, that it was generally believed at Fort Bukoba that the plague was introduced each year into German East Africa from Budu because of its always occurring in the former place about June, when the rains had ceased, and when the natives were able to cross the Kagera River and journey southwards.

And there can be no doubt, however extraordinary it may seem to those who have studied the disease in India and elsewhere, that there exists at Bikira, in Budu, a province of the Uganda Protectorate, to the west of the Victoria Nyanza, a focus of bubonic plague, which annually gives rise to small, but very virulent epidemics, and that from this focus the disease is carried at certain times of the year into German East Africa. It is also probable that the Egyptian epidemics have had their origin in this endemic centre in Uganda.

That may well have been possible, and there is no reason there could not have been a mixing of plague strains in East Africa with those radiating from the Third Pandemic out of Hong Kong, which by the time Christy was writing was well underway.


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Not simply was kawumpuli the name of a disease; Kawumpuli was the name of the son of the historical kabaka king Kayemba c. Archaeologist Scheherazade Amin looked in detail at the material evidence for the Baganda lubaale ; although the majority of lubaale shrines were located on the islands of Lake Nyanza Lake Victoria , she identifies the Kawumpuli shrine in the far north of Buganda lands, in Bulemeezi County. Zupitza, into Bukoba Tanzania to gather clinical samples of an outbreak on-going in Kisiba.

The genetics of Y. ANT might have taken to reach equatorial East Africa. Did it cross the Sahara from the west, passing into Congo? Did it instead arrive from the east, via the Indian Ocean littoral?

African Ecology : Benchmarks and Historical Perspectives

In , microbiologist Achtman suggested that the Chinese explorer Zheng He — or may have been involved in the transmission of plague from Asia to East Africa, since his voyages extended to the East African coast. ANT strain than India, not because China did not witness plague in this period it almost certainly did , 97 nor even because there was insufficient maritime trade coming out of China and connecting with the Indian Ocean in this period an exceptional amount of trade had been going on for centuries , 98 but simply because, as already noted section II.

A above we have no reason to believe that Branch 1 strains reached that far east at this early period. Moreover, transmission of plague across open desert landscapes is well attested, especially when camels which are very susceptible to plague are involved. Especially after the Ottoman conquest of Mamluk Egypt in , there would have been ample opportunity for the continued circulation of plague from the Caucasus area to North Africa.

ANT strain was imported from India, there are other scenarios that might involve introduction of plague from the east coast. As is becoming more and more apparent from archaeological researches, the Swahili Coast was a region of intense biological and commercial exchange with the Indian Ocean basin from at least the 7th century on. It has been noted that for some communities on the Indian Ocean littoral, there is a pattern of abandonment or decline in East African coastal trading zones in the 14th or 15th century just as in West Africa.

In the 16th century, for example, there was considerable wrangling between the Ottomans, the Portuguese, and the Mughal empire for control of the Red Sea, the crucial link between the Mediterranean and Indian Ocean spheres of trade. Although less well documented, those maritime interventions extended at times down the length of the East African coast, creating a potential disease trajectory that linked to the Black Sea, which the Ottomans controlled exclusively by this point.

In —97, soldiers from Oman attacked the Portuguese stronghold of Fort Jesus in Mombasa modern-day Kenya , part of the Portuguese buildup of defensive forts along the Swahili Coast at the end of the 16th century to halt Ottoman ambitions in the region. By August, the fort was completely depopulated of Portuguese. Although it has been implied that the Omani introduced the plague, no new arrivals from Oman are reported in this period. One commentator implies that it was the Portuguese themselves who brought the disease. Were the siege really the point of first entry of 1.

If the disease came from Oman, that would fit a Middle Eastern scenario of transmission currently demanded by the genetics narrative, though if it was brought by the Portuguese themselves, then that would likely have been from Goa, India, where, as noted above, we do not yet have evidence of Branch 1 strains. It is reported that one of the Portuguese commanders, who departed precipitously in January , had been ordered to make contact with a local group, the Musungulos.

An ecologically complex disease like plague, which thrives at high elevations yet flourishes as well in lower-elevation commensal rodent communities where it causes epizootics and consequently, epidemics , might readily have moved through an area such as this. Indeed, this is precisely the scenario of resurgence of plague that is now being envisaged for early modern Europe, with plague persisting at higher elevations and periodically erupting into outbreaks in cities below.

After its first arrival in , plague came in repeated waves, producing a total of forty outbreaks by the time the Ottomans claimed authority over Egypt in If the disruption of river traffic was as severe as the Arabic documents suggest, the cessation of economic activity may have effectively created a buffer, beyond which plague did not pass. The Christian kingdom of Nubia or Makuria Arab.

Muqurra ; Nub. Dotawo , stretching from the First to the Fifth Cataract, collapsed sometime around , the capital of Dongola being abandoned and a makeshift new capital being established further downriver at Daw Gebel Adda ; although recent archaeological finds show some continuing occupation of the area, that Nubia suffered political and economic disruption in the second half of the 14th century is clear. Such extreme devastation, which drastically reduced the economic activity that so effectively moved plague over long distances, may itself be an argument against further expansion of plague infestation up the Nile and into the White Nile and thence to the Great Lakes.

This is a topic on which bioarchaeological and palaeogenetic work could contribute importantly.

None of the 20th-century historical or epidemiological accounts of plague in Africa include Ethiopia, save for a nod to its possible role in the Justinianic Plague, which was already noted above. In their timing, at least, all of these accord approximately with outbreaks recorded not simply for Egypt, but for southern Russia as well.


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  8. ANT into the Great Lakes region because we still know so little about the experiences of plague in surrounding areas. The overall narrative of 1. Should any aDNA be retrieved from any of the regions where 1. But so will further interrogation of the cultural record of the Buganda and other peoples of the Great Lakes region, and investigation of cultural histories of plague in regions further to the north.

    ANT lineage of Y. I have also suggested that there are currently no grounds to connect the strain in East Africa with India, nor to view its importation as being due to the arrival of European colonialism—neither in the 19th century as postulated by Sussman nor even in the late 17th century, as supposed by earlier stories of the outbreak at Fort Jesus.

    The genetic histories of Y.

    African Ecology: Benchmarks and Historical Perspectives African Ecology: Benchmarks and Historical Perspectives
    African Ecology: Benchmarks and Historical Perspectives African Ecology: Benchmarks and Historical Perspectives
    African Ecology: Benchmarks and Historical Perspectives African Ecology: Benchmarks and Historical Perspectives
    African Ecology: Benchmarks and Historical Perspectives African Ecology: Benchmarks and Historical Perspectives
    African Ecology: Benchmarks and Historical Perspectives African Ecology: Benchmarks and Historical Perspectives
    African Ecology: Benchmarks and Historical Perspectives African Ecology: Benchmarks and Historical Perspectives
    African Ecology: Benchmarks and Historical Perspectives African Ecology: Benchmarks and Historical Perspectives
    African Ecology: Benchmarks and Historical Perspectives African Ecology: Benchmarks and Historical Perspectives
    African Ecology: Benchmarks and Historical Perspectives African Ecology: Benchmarks and Historical Perspectives

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