A shared past for East Africa's hunter-gatherers18 February 2019

A local official helps translate into Amharic informationabout the research project to people from the Amharapopulation in Ethiopia. Credit: Tishkoff Lab

Languages that involve "clicks" are relatively rareworldwide but are spoken by several groups inAfrica. The Khoisan language family includes ahandful of these click languages, spoken by hunter-gatherer groups in southern and eastern Africa.But the grouping of these populations into a singlelanguage family has been controversial, with somelinguists convinced that a few of the languages aretoo different to be classified together.

A genomic study of 50 African populations led byresearchers at the University of Pennsylvania addssome clarity to the relationships between theseclick-speaking groups and many others. Theresults point to a relatively recent shared ancestryfor a few of the click-speaking hunter-gathererpopulations, indicating they are more closelyrelated to one another than to their neighbors thatpractice other subsistence lifestyles, such asfarming or animal herding.

The analysis, one of the most extensive of its kindof ethnically diverse populations in Africa, alsodemonstrates the importance of infectious disease,immunity, and diet in shaping the diversity ofpopluations across Africa. The work is published inthe journal Proceedings of the National Academy ofSciences.

"It's very rare to have a study of this many groupsthat are genetically different in terms of ancestry, intheir susbsistence patterns, and are geographicalydispersed as well," says Sarah Tishkoff, ageneticist and Penn Integrates KnowledgeProfessor who was the senior author on the paper."This allows us to characterize population structureand demographic history as well as to look atsignatures of natural selection acting on thesepopulations."

The analysis builds upon decades of work by theTishkoff lab and African collaborators to exploreAfrican genetic diversity. The research, saysTishkoff, facilitates genomics research overall byexamining populations that have been otherwiseunderstudied, and it can play a role in identifyinggenetic variants that influence health and diseasein Africa and around the world.

This study probes deeply into the genomiclandscape of 840 Africans, identifying 621,000separate nucleotides in the DNA of eachparticipant.

The 50 groups surveyed are spread across sub-Saharan Africa and include almost all groups thatpractice a hunting-and-gathering lifestyle, or haveuntil recently.

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The Penn-led study examined genetic data from 50distinct African populations, including many who practicehunter-gatherer lifestyles, such as the (clockwise fromupper left) Sabue, San, Hadza, and Sandawe. The teamfound that some of these hunting and gathering groupsshare a common ancestry, and also underscored theimportant role of diet and disease as drivers of localadaptation around the continent. Credit: Tishkoff lab

Tishkoff, Scheinfeldt, and colleagues wereparticularly interested in what these studyparticipants' genomes would reveal about ancientrelationships among hunter-gatherer populations,particularly those speaking languages that hadbeen classified as Khoisan. East Africa's Hadzaand Sandawe hunter-gatherers had been labeledKhoisan by some linguistic analyses, grouped withsouthern Africa's San hunter-gatherers.

"Some linguists say it's not correct to place all ofthese into the Khoisan family, arguing that theHadza and Sandawe languages are so differentfrom each other and from the San that they reallyshould be in separate language classifications,"says Tishkoff.

The researchers also included study participantsfrom the Dahalo of Ethiopia, who have never beenstudied genetically but speak a language withremnant clicks. "It's an ongoing question inlinguistics and genetics," Tishkoff says, "and wewanted to ask the question, 'Do these groups withclick phonemes have a common genetic

ancestry?'"

They were also curious to know whether a sharedsubsistence lifestyle practice—that of hunting andgathering—indicated a shared ancestry. Among the16 hunter-gatherer populations they studied was agroup called the Sabue who live in southwesternEthiopia, surrounded by pastoralist groups. TheSabue had never before participated in genomicresearch and speak a language that is thus farunclassified.

Using the genetic information they obtained to mapout the populations' likely relationships to oneanother, the researchers unexpectedly found thatfour hunter-gatherer populations—the Hadza,Sandawe, Dahalo, and Sabue, each of whom dwellin distinct areas of eastern Africa—clusteredtogether.

"Typically what we see is that populations clusterby geography, but here we're seeing an exceptionto that," Tishkoff says. "Here you have three groupsthat either speak a click language, have remnantclicks, or have an unclassified language, andthey're showing a common ancestry even thoughthey're spread across different countries."

Although the researchers could not identify auniquely shared ancestry between these fourgroups of eastern African Khoisan hunter-gatherersand the southern African San people, who alsospeak a language with clicks, they did observeshared ancestry between the San and rainforest hunter-gatherers from Central Africa, despite beinggeographically far apart.

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With the help of a local translator, Simon Thompson fromSarah Tishkoff's lab (University of Pennsylvania) andDawit Wolde-Meskel (collaborator from Addis AbabaUniversity) explain the research project on Africanpopulation genetics to the Argobba population, Ethiopia.After the project is presented, the researchers answerany questions. Credit: Tishkoff lab

In contrast, other hunter-gatherer groups, such asthe Wata, El Molo, and Yaaku, appeared moregenetically similar to neighboring agriculturalist andpastorlist groups.

The common ancestry for the four East Africa hunter-gatherer groups dates back more than20,000 years ago, according to the team's analysis,around the beginning of the last glacial maximum,when ice covered extensive portions of Earth andthe climate was much different than it is today.

"The idea is that this may have changedenvironmental conditions and introduced a barrierbetween populations," says Laura Scheinfeldt, thelead author who was a research associate inTishkoff's lab, and is now with the Coriell Institutefor Medical Research.

The researchers' techniques also allowed for abetter understanding of the forces that have actedto differentiate the groups they studied.

"What we found was the strongest signatures ofadaptation tended to be population-specific," says

Scheinfeldt. In other words, targets of naturalselection were different in the different groups andmay well have contributed to the uniqueness ofeach.

Despite these individual differences, the categoriesof the genes that were selected were sharedamong populations, the researchers discovered.

"Genes involved in immune responses, diet, andmetabolism were the broad categories that we sawcoming up over and over again," Scheinfeldt notes."We know infectious disease in general is a verystrong pressure, and, when you look solely at howprevalent malaria is, that also explains some of thepatterns we see in adaptive signatures. Just thatone disease is a very strong selective pressure."

In future studies, Tishkoff and colleagues will bezooming in to see how particular genetic variantsmay affect physical traits in the people whopossess them, studies that could shed light ongenetic causes of disease susceptibility. They'llalso be using powerful whole-genome sequencingtechniques to further illuminate the relationshipsamong Africa's diverse populations.

More information: Laura B. Scheinfeldt el al.,"Genomic evidence for shared common ancestry ofEast African hunting-gathering populations andinsights into local adaptation," PNAS (2019). www.pnas.org/cgi/doi/10.1073/pnas.1817678116

Provided by University of Pennsylvania

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APA citation: A shared past for East Africa's hunter-gatherers (2019, February 18) retrieved 16December 2021 from https://medicalxpress.com/news/2019-02-east-africa-hunter-gatherers.html

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