How DNA can mis­lead re­searchers

Study­ing our an­ces­tral foot­print on the con­ti­nent hits stum­bling blocks when labs dis­agree, writes Alan G Mor­ris

The Star Late Edition - - INSIDE - Com­par­a­tive data.

AN­CIENT DNA is start­ing to re­veal the se­crets of how peo­ple emerged from, moved into or moved around Africa. Hu­man skele­tons from Sal­danha Bay in the Western Cape, Bal­lito in KwaZulu-Natal, and Mota Cave in Ethiopia, Tan­za­nia, and now Malawi have been an­a­lysed and the re­sults re­cently pub­lished.

I am part of a team work­ing on a whole se­ries of skele­tons from the Later Stone site of Faraoskop in the Western Cape. We are try­ing to find both mi­to­chon­drial and nu­clear DNA sam­ples to work out re­la­tion­ships be­tween in­di­vid­u­als in what may have been a case of mass killings some 2 000 years ago.

This rush of projects has pre­sented the cu­ra­tors of ar­chae­o­log­i­cal skele­tons with eth­i­cal is­sues, be­cause the re­search re­quires the destruc­tion of hu­man bone.

There are four cen­tral prob­lems that con­cern me and that have been echoed in my pri­vate cor­re­spon­dence with var­i­ous col­leagues: com­pe­ti­tion be­tween labs for sam­ples, the dan­ger of para­chute re­search (for­eign re­searchers who drop in, gather data and go home again), the dis­con­nec­tion be­tween the study of bones and ge­net­ics, and lab­o­ra­tory method­olo­gies and

THE CHAL­LENGES

Com­pe­ti­tion for sam­ples: This has be­come a very real prob­lem. At least five labs have been pro­cess­ing ar­chae­o­log­i­cal skele­tons from South Africa. Back in May 2014, I made a list of all an­cient DNA projects on South African spec­i­mens that had, up to that point, been pro­posed or were in ac­tion. I counted 13, though not all of these have taken place.

In some cases per­mis­sion to sam­ple has been re­fused. One rea­son for re­fusal is that the project is sim­ply an at­tempt to an­a­lyse skele­tons be­cause they are old and avail­able. This sort of anal­y­sis may be good for the lab­o­ra­tory con­cerned, but it is just plain bad sci­ence and is per­ilously close to “min­ing” of bone spec­i­mens from mu­se­ums.

Much of the com­pe­ti­tion for sam­ples is pub­li­ca­tion-driven, with labs chas­ing the next pa­per in Na­ture or other high-im­pact jour­nals. This is ob­vi­ously im­por­tant as it can drive fund­ing for labs or pro­mo­tions for their denizens.

Para­chute re­search: It’s very easy to do sam­pling in this kind of re­search. All that’s re­quired is a nub­bin of bone, and in most cases that is sent out of the coun­try for anal­y­sis to hap­pen else­where. So how should South African re­searchers fit in?

For a num­ber of years there was an ac­tive re­sis­tance to set­ting up a South African lab in the be­lief that it was too ex­pen­sive and fund­ing would be bet­ter spent on projects that have a more di­rect ben­e­fit to the coun­try’s pre­vi­ously dis­ad­van­taged peo­ple. That at­ti­tude is now chang­ing in some quar­ters and I have heard talk of set­ting up labs in Cape Town, Jo­han­nes­burg and Pretoria. How would such labs link to over­seas in­sti­tu­tions?

Genes ver­sus bones: There has been a def­i­nite ten­dency for ge­netic re­search to ig­nore in­for­ma­tion gath­ered in pre­vi­ous stud­ies of the bones of the skele­tons them­selves.

An­cient DNA re­search, like ge­netic re­search on liv­ing peo­ples, has been fo­cused on trac­ing back lin­eage lines through mi­to­chon­drial, Y-chro­mo­some or re­cently, nu­clear DNA. All that has been re­quired is a tiny frag­ment of bone that can yield DNA. But can such stud­ies give us a true pic­ture of the past?

The an­swer is “yes” in terms of lin­eage but “no” in terms of life ex­pe­ri­ence and adap­ta­tion. This is­sue is im­por­tant be­cause the first choice in sam­pling should be from as com­plete a skele­ton as pos­si­ble so that ge­netic and os­te­o­log­i­cal data – that is in­for­ma­tion about bones – can be com­pared.

Per­haps the most ex­treme ex­am­ple of this prob­lem is the con­struc­tion of the hu­man an­ces­tor known as the “Deniso­vans”. Much has been writ­ten about these dis­tant an­ces­tors’ ge­net­ics. But all of it has been based on one fin­ger bone and three teeth from one site.

We ac­tu­ally know noth­ing about these peo­ple ex­cept for their ge­netic shadow. The foren­sic an­thro­pol­o­gist in me screams that I must have a body be­fore draw­ing any con­clu­sions. The same goes for the dis­cus­sion of peo­ple from the com­par­a­tively re­cent African past.

Com­par­a­tive data: As a non-ge­neti­cist, it did not cross my mind that dif­fer­ent labs might pro­duce dif­fer­ent DNA re­sults. Some years ago I had my own Y-chro­mo­some and mi­to­chon­drial DNA an­a­lysed. The re­sults were fas­ci­nat­ing, but I was ex­tremely sur­prised to dis­cover that if I sent the same sam­ples to dif­fer­ent DNA her­itage lab­o­ra­to­ries I could get dif­fer­ent re­sults.

It is not the anal­y­sis it­self that is dif­fer­ent, but the ref­er­ence sam­ples that are cho­sen for com­par­i­son. This can be re­solved as the an­a­lysed sam­ples be­come more nu­mer­ous – as long as the dif­fer­ent labs share their re­sults – but I have re­cently dis­cov­ered that not all labs are the same when it comes to piec­ing to­gether long strands of nu­clear DNA from the frag­ments dis­cov­ered in the process of ex­tract­ing an­cient DNA from bones.

The pro­cess­ing meth­ods are not in­ter­change­able and there are at least two dif­fer­ent method­olo­gies that pro­duce dif­fer- ent suc­cess rates. This means it is pos­si­ble that re­sults from dif­fer­ent labs may not be com­pa­ra­ble.

This would make the com­pe­ti­tion be­tween labs even more in­tense and might even re­sult in mul­ti­ple re­quests for sam­ples from the same skele­ton.

KNOWL­EDGE ABOUT AFRICAN HER­ITAGE

Ul­ti­mately, the most im­por­tant is­sue is that African sci­en­tists need to be part of the re­search and African de­scen­dant com­mu­ni­ties need to be able to ac­cess the in­for­ma­tion dis­cov­ered about their an­ces­tors.

We need to en­sure that both train­ing and jobs in an­cient DNA re­search are avail­able in African coun­tries and that pub­li­ca­tions are sub­mit­ted to lo­cal sci­en­tific and mu­seum jour­nals. This re­search is not about the next pro­mo­tion for the lab sci­en­tists. It is about build­ing the knowl­edge base of our African her­itage. – The Con­ver­sa­tion

This ar­ti­cle has been adapted from a piece in the SA Jour­nal of Sci­ence.

Mor­ris is pro­fes­sor of bi­o­log­i­cal an­thro­pol­ogy at the Univer­sity of Cape Town

PIC­TURE: DUMISANI DUBE

SHED­DING NEW LIGHT: A skele­ton in grave 127 is one of as many as 650 that lie in a ceme­tery near Crown Mines, south of Jo­han­nes­burg. The re­mains are be­ing ex­humed for sci­en­tific stud­ies and will be re­buried at a later stage.

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