Fossil DNA: on the trail of human evolution

At the end of 2016, the news hit the head­lines. Euras­i­ans carry around 2% of the genes of Neander­thals, who dis­ap­peared around 40,000 years ago. This dis­cov­ery, which was awar­ded the Nobel Prize in 2022, sheds light on the links between this spe­cies and our own and even sug­gests that they may have inter­bred on sev­er­al occa­sions. Since then, new aven­ues have been opened up to under­stand the causes of Neander­th­al extinc­tion, as well as the factors that favoured the sur­viv­al and sub­sequent expan­sion of Homo sapi­ens in the his­tory of human evolution.

Ancient (or fossil) DNA is the key to access­ing the genet­ic inform­a­tion of our ancest­ors. This tool is used by palaeo­ge­n­om­ics, a dis­cip­line that com­bines DNA sequen­cing tech­niques with the ana­lys­is of ancient bio­lo­gic­al remains. By extract­ing and deci­pher­ing the DNA pre­served in bones, teeth, hair, seeds and wood, sci­ent­ists can access the genet­ic inform­a­tion of spe­cies, includ­ing that of our dis­tant ancestors.

One of the first to suc­ceed in ‘read­ing’ a fossil DNA sequence was bio­lo­gist Allan Wilson, who in the mid-1980s sequenced DNA from a quagga, a zebra-like equine that had been extinct since the 19^th Cen­tury. Bio­lo­gist Svante Pääbo then went fur­ther back in time by sequen­cing pre­served DNA from an Egyp­tian mummy. “Even though the DNA molecule is chem­ic­ally more stable than RNA, its con­ser­va­tion over sev­er­al mil­len­nia remained hypo­thet­ic­al. It was only after sev­er­al dec­ades of effort that we real­ised we could work on such ancient DNA”, explains Jean-Louis Mergny, Inserm research dir­ect­or and head of the bio­logy depart­ment at Insti­tut Poly­tech­nique de Par­is. Since then, the Swede’s work was rewar­ded with a Nobel Prize in Medi­cine (2022) and palaeo­ge­n­om­ics is mak­ing giant strides. Jean-Louis Mergny emphas­ises that the emer­gence of this dis­cip­line “is a sci­entif­ic revolu­tion that enables us to go back in time to remote periods”.

This bio­chem­ist who is “fas­cin­ated by the unusu­al con­form­a­tions and oddit­ies of DNA” developed a pas­sion for ancient DNA “after read­ing books on Neander­thals dur­ing lock­down and suc­cess­ive vis­its to the Musée de l’Homme”. As such, he ini­ti­ated a research pro­ject to look for unusu­al struc­tures in ancient gen­omes, first on a vir­us¹², then on extinct human species.

The work that inspired the Jur­as­sic Park saga was wrong; insect DNA is not pre­served in amber.

The research­er has focused in par­tic­u­lar on Den­iso­vi­an and Neander­th­al pop­u­la­tions, two spe­cies for which the data (DNA lib­rar­ies) are “avail­able in open access and open to the sci­entif­ic com­munity”. The aim: to com­pare their meta­bol­isms with those of ana­tom­ic­ally mod­ern humans (Homo sapi­ens) and detect gen­om­ic vari­ations that could explain any select­ive disadvantage.

The prob­lem is that fossil DNA is a fra­gile mater­i­al. Time, chem­ic­al agents, micro-organ­isms and human manip­u­la­tion degrade and con­tam­in­ate it. Even Svante Pääbo, one of the lead­ing fig­ures in the dis­cip­line, encountered this dif­fi­culty when work­ing on Egyp­tian mum­mies dur­ing his first attempts in the 1980s.  “He real­ised after­wards that what he had sequenced con­tained parts of gen­omes that undoubtedly belonged to people who had manip­u­lated the mum­mies”, recounts Jean-Louis Mergny.

Worse still, oth­er less scru­pu­lous teams sub­sequently pub­lished erro­neous res­ults based on DNA sup­posedly extrac­ted from insects pre­served in amber – the work that inspired the Jur­as­sic Park saga. “We now know that DNA is poorly pre­served in amber, and cer­tainly not over tens of mil­lions of years… sci­ence pro­gresses through its mis­takes!” smiles Jean-Louis Mergny.

In addi­tion to the risk of con­tam­in­a­tion, which has now been partly brought under con­trol thanks to strin­gent labor­at­ory hygiene stand­ards, multi-mil­len­nia-old DNA sequences are dam­aged and present them­selves to sci­ent­ists in highly frag­men­ted form.What is an obstacle is also an oppor­tun­ity, because, as the bio­chem­ist reveals, « we can more eas­ily recog­nise what is old and unstable, and sep­ar­ate it from more recent con­tam­in­at­ing sequences that remain intact”.

Tak­ing a jour­ney through our genet­ic her­it­age, shows that it bears traces of the “selec­tion pres­sures” that have shaped our spe­cies over the course of its his­tory. These pres­sures are linked to changes in cli­mate, the unavail­ab­il­ity of cer­tain resources, pred­a­tion, sexu­al selec­tion, para­sites, and the emer­gence of patho­gens. These con­straints have ‘pushed’ our spe­cies to adapt and mutate its allele fre­quen­cies over the gen­er­a­tions. In the cata­logue of these selec­tion pres­sures, palaeo­gen­et­i­cists are par­tic­u­larly inter­ested in the impact of major pan­dem­ics on the evol­u­tion of our immune system.

In this con­text, sci­ent­ists sug­ges­ted in 2022³ that European pop­u­la­tions pos­it­ively selec­ted cer­tain immune sys­tem genes that respon­ded bet­ter to Yersin­ia pestis, the bac­teri­um that caused the Black Death and decim­ated at least 50 mil­lion people in the 16^th Cen­tury. Genet­ic mark­ers of this epis­ode are still present in Europeans, unlike pop­u­la­tions in Asia or Africa, where the Black Death did not occur.

More broadly, in 2023, bio­lo­gists Gas­pard Kern­er and Lluís Quintana-Murci (Insti­tut Pas­teur, Collège de France) pub­lished the res­ults of a colossal palaeo­ge­n­om­ic study, which com­pared 503 mod­ern European gen­omes with more than 2,300 ancient gen­omes found on the con­tin­ent and span­ning the last 10 mil­len­nia. The sci­ent­ists iden­ti­fied selec­tion muta­tions in almost 90 dif­fer­ent genes, includ­ing those cod­ing for lactase (which enables milk to be diges­ted), skin pig­ment­a­tion (explain­ing the light­er skin col­our of Europeans), and the immune response to cer­tain infec­tious dis­eases (such as the Black Death).

Their work shows that these genet­ic muta­tions have a double-edged effect. They are pos­it­ive in terms of res­ist­ance to infec­tious dis­eases, but neg­at­ive in terms of the risk of devel­op­ing autoim­mune or chron­ic inflam­mat­ory dis­eases, such as dia­betes or Crohn’s dis­ease. This phe­nomen­on, known as ant­ag­on­ist­ic pleio­tropy, illus­trates the evol­u­tion­ary com­prom­ise that each liv­ing spe­cies makes to optim­ise its select­ive value.

Let’s go back to Neander­th­al. Jean-Louis Mergny has used this abil­ity to determ­ine the impact of selec­tion pres­sures on the genet­ic her­it­age of a spe­cies as the basis for his cur­rent research. The bio­chem­ist has ana­lysed Neander­th­al mito­chon­dri­al DNA for genet­ic mark­ers of evol­u­tion and links with Sapiens.

Remem­ber that our research­er prefers non-con­form­ing and ‘rebel­li­ous’ DNA to ‘the canon­ic­al double-helix struc­ture’. This is why he focused on ori­gin­al genet­ic sequences loc­ated in the G‑quadruplexes (G4). “These are four-stran­ded sec­ond­ary struc­tures that form nodes in the gen­ome”, he explains. How­ever, the Neander­th­al mito­chon­dri­al node “is much more ‘com­plic­ated’ than ours”, which would make rep­lic­a­tion of its mito­chon­dria more dif­fi­cult, “at least in the Homo sapi­ens con­text that we know”. Since these organ­elles are con­sidered to be the energy power­houses of cells, their poor repro­duc­tion is a pri­ori a select­ive dis­ad­vant­age for this spe­cies… “Unless Neander­th­al had more effi­cient enzymes for unwind­ing these knots”, he adds.

All that remains now is to ana­lyse the ‘nodes’ of its nuc­le­ar DNA: if the Neander­th­al gen­ome is now avail­able, it was at the cost of titan­ic efforts. There was a great deal of selec­tion pres­sure on this spe­cies and many hypo­theses have been put for­ward as to the causes of its dis­ap­pear­ance. For example, Homo neander­thalen­sis did not die out as a res­ult of a cas­cade of food pois­on­ing, poor tol­er­ance of smoke inhal­a­tion, an insuf­fi­ciently var­ied diet or excess­ive can­ni­bal­ism. It is even less true that his cog­nit­ive abil­it­ies were too weak; he was undoubtedly very cre­at­ive. But he had to con­tend with Homo sapi­ens, a “super-effi­cient” human­ity as described by archae­olo­gist Ludovic Sli­mak, who rushed to occupy the spaces left vacant by Neanderthal.

Neander­th­al is not the Homo stu­pidus we have long imagined

“Palaeo­ge­n­om­ics shows that Neander­thals were not the Homo stu­pidus we have long ima­gined, quite the con­trary,” main­tains Jean-Louis Mergny. We now know that they had the same genet­ic pre­dis­pos­i­tion to lan­guage as Homo sapi­ens (the FOXP2 gene has been iden­ti­fied, includ­ing in its pro­moter regions); that, by prac­tising pat­ri­loc­al­ity⁴, they avoided inbreed­ing as much as pos­sible; and that they not only cohab­ited with Sapi­ens, but also assim­il­ated (hybrid­ised) with him. Chil­dren were born of this hybrid­isa­tion, and humans of European ori­gin today retain a vis­ible trace of it in their genet­ic her­it­age, with an aver­age of 2% Neander­th­al DNA.

Many research teams around the world are now pay­ing close atten­tion to this her­it­age. Recent stud­ies have shown that Neander­th­al alleles have had an influ­ence on our spe­cies in terms of immune response⁵, sus­cept­ib­il­ity to Cov­id-19⁶, skin pig­ment­a­tion⁷ for UV res­ist­ance, the sleep cycle⁸ and lip­id cata­bol­ism⁹ (the break­down of lip­ids to pro­duce energy).

Palaeo­ge­n­om­ics sheds light on the evol­u­tion of human­kind and its immune sys­tem. But this dis­cip­line comes up against a major obstacle: the con­ser­va­tion of ancient DNA. This depends on the cli­mate of the regions where the human remains were dis­covered. Tem­per­ate or cold areas of Europe are more favour­able than trop­ic­al and humid zones, where oth­er spe­cies or human lin­eages that have now dis­ap­peared prob­ably lived. “This skews our per­cep­tion of human­ity », stresses Jean-Louis Mergny, espe­cially in Africa, the cradle of our spe­cies. Finally, he stresses that palaeo­ge­n­om­ics only makes sense “if it is com­bined with oth­er dis­cip­lines such as archae­ology and palae­on­to­logy”. It is dif­fi­cult, for example, to date a bone pre­cisely unless it has been dis­covered dur­ing rig­or­ous excav­a­tions, which are abso­lutely neces­sary but extremely time-con­sum­ing. Unfor­tu­nately, most of the samples we have come from rel­at­ively old excav­a­tions, with insuf­fi­cient or miss­ing doc­u­ment­a­tion. The prox­im­ity of two bones does not neces­sar­ily indic­ate that they are con­tem­por­ary – hun­dreds or even thou­sands of years may have elapsed between the two deaths. But extremely rig­or­ous ana­lyses can some­times answer this question.

New tech­nic­al advances will undoubtedly reveal new frag­ments of human­ity’s genet­ic her­it­age… or of these plur­al human­it­ies. “If I had dis­covered this uni­verse at the age of 20, you would prob­ably have inter­viewed me on an excav­a­tion site,” con­cludes Jean-Louis Mergny.

Samuel Belaud