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Early human interbreeding may go back much further than thought

Sept. 6, 2011
Courtesy of the University of Arizona
and World Science staff

In­ter­breed­ing be­tween an­ces­tors of mod­ern hu­mans and our ex­tinct ev­o­lu­tion­ary rel­a­tives hap­pened much ear­lier—and more ex­ten­sive­ly—than sci­en­tists have thought, a study sug­gests.

Sci­en­tists be­lieve our spe­cies, Ho­mo sapi­ens, orig­i­nat­ed in Af­ri­ca and even­tu­ally spread world­wide. Sev­er­al past stud­ies have al­so in­di­cat­ed that af­ter reach­ing Eu­rope, Ho­mo sapi­ens in­ter­bred with Ne­an­der­thal peo­ple. But the new work sug­gests in­ter­breed­ing with oth­er lin­eages had al­ready tak­en place in Af­ri­ca, per­haps with not­ed ex­tinct hu­man lin­eages such as Ho­mo erec­tus, the “upright walk­ing man,” or Ho­mo ha­bilis, “tool-using man.”

New research sug­gests an­cest­ors of mod­ern hu­mans in­ter­bred with oth­er lin­eages in Af­ri­ca, per­haps with not­ed ex­tinct lin­eages such as Ho­mo erec­tus, the “upright walk­ing man,” or Ho­mo ha­bilis, “tool-using man,” pictured above in an artist's con­cep­tion. (Cour­tesy NA­SA)


“We think there were probably thou­sands of in­ter­breed­ing events... It looks like our line­age has al­ways ex­changed genes” with oth­ers, said Mi­chael Ham­mer of the Uni­vers­ity of Ar­i­zo­na, who led a team re­port­ing the new find­ings. The re­search ap­pears in this week’s early online edition of the jour­nal Pro­ceed­ings of the Na­tional Acad­e­my of Sci­ences.

Sci­en­tists can now ex­tract DNA from fos­sils tens of thou­sands of years old, which has en­abled re­search in­to pro­posed in­ter­breed­ing with Ne­an­der­thals. But the Af­ri­ca spec­i­mens that Ham­mer’s team stud­ied were much old­er, Ham­mer not­ed, so “we don’t have fos­sil DNA from Af­ri­ca to com­pare with ours.” Al­so, “Ne­an­der­thals lived in cold­er cli­mates, but the cli­mate in more trop­i­cal ar­eas make it very tough for DNA to sur­vive that long.”

Thus “our work is dif­fer­ent from the re­search that led to the break­throughs in Ne­an­der­thal ge­net­ics,” he ex­plained. “We could­n’t look di­rectly for an­cient DNA that is 40,000 years old and make a di­rect com­par­i­son.” To get around this, Ham­mer’s team used com­put­ers and sta­tis­tics. “We looked at DNA from mod­ern hu­mans be­long­ing to Af­ri­can popula­t­ions and searched for un­usu­al re­gions in the ge­nome,” he ex­plained.

Be­cause no­body knows the DNA se­quences of those ex­tinct hu­mans, Ham­mer’s team first had to fig­ure out what fea­tures of mod­ern DNA might rep­re­sent frag­ments brought in from ar­cha­ic forms. “What we do know is that the se­quences of those forms, even the Ne­an­der­thals, are not that dif­fer­ent from mod­ern hu­mans,” he said. “They have cer­tain char­ac­ter­is­tics that make them dif­fer­ent from mod­ern DNA.”

The re­search­ers used sim­ula­t­ions to pre­dict what an­cient DNA se­quences would look like had they sur­vived. “You could say we sim­ulated in­ter­breed­ing and ex­change of ge­net­ic ma­te­ri­al,” Ham­mer said.

Ac­cord­ing to Ham­mer, the first signs of an­a­tom­ic­ally mod­ern fea­tures ap­peared about 200,000 years ago.

First, the team se­quenced vast re­gions of hu­man ge­nomes from sam­ples tak­en from six dif­fer­ent popula­t­ions liv­ing in Af­ri­ca to­day and tried to match up their se­quences with what they ex­pected those se­quences to look like in ar­cha­ic forms. The re­search­ers fo­cused on “non-coding” re­gions of the ge­nome, stretches of DNA that don’t con­tain actual genes.

“Then we asked our­selves what does the gen­er­al pat­tern of varia­t­ion look like in the DNA that we se­quenced in those Af­ri­can popula­t­ions, and we started to look at re­gions that looked un­usu­al,” Ham­mer said. “We dis­cov­ered three dif­fer­ent ge­net­ic re­gions fit the cri­te­ria for be­ing ar­cha­ic DNA still pre­s­ent in the ge­nomes of sub-Saharan Af­ri­cans. In­ter­est­ing­, this sig­na­ture was strongest in popula­t­ions from cen­tral Af­ri­ca.”

The sci­en­tists ap­plied sev­er­al cri­te­ria to tag a DNA se­quence as ar­cha­ic. For ex­am­ple, if a DNA se­quence dif­fered radic­ally from the ones found in a mod­ern popula­t­ion, it was con­sidered likely an­cient in or­i­gin. Anoth­er tell­tale sign is how far it ex­tends along a chro­mo­some, Ham­mer and col­leagues con­tend: if an un­usu­al piece is found to stretch a long por­tion of a chro­mo­some, it’s a sign of hav­ing en­tered the popula­t­ion rel­a­tively re­cent­ly.

“We are talk­ing about some­thing that hap­pened be­tween 20,000 and 60,000 years ago – not that long ago in the scheme of things,” Ham­mer said. “If in­ter­breed­ing oc­curs, it’s go­ing to br­ing in a whole chro­mo­some, and over time, re­com­bina­t­ion [ge­net­ic mix­ing] events will chop the chro­mo­some down to smaller pieces. And those pieces will now be found as short, un­usu­al frag­ments. By look­ing at how long they are we can get an es­ti­mate of how far back the in­ter­breed­ing event hap­pened.”

Ham­mer said that al­though the ar­cha­ic DNA se­quences ac­count for only two or three per­cent of what is found in mod­ern hu­mans, that does­n’t mean the in­ter­breed­ing was­n’t more ex­ten­sive. “It could be that this rep­re­sents what’s left of a more ex­ten­sive ar­cha­ic ge­net­ic con­tent to­day. Many of the se­quences we looked for would be ex­pected to be lost over time. Un­less they pro­vide a dis­tinct ev­o­lu­tion­ary ad­van­tage, there is noth­ing keep­ing them in the popula­t­ion and they drift out.”

In a next step, Ham­mer’s team wants to look for an­cient DNA re­gions that con­ferred some ad­van­tage to the an­a­tom­ic­ally mod­ern hu­mans once they ac­quired them.  In­ter­breed­ing, he added, “is quite com­mon in na­ture, and it turns out we’re not so un­usu­al af­ter all.”


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Interbreeding between ancestors of modern humans and our extinct evolutionary relatives happened much earlier—and more extensively—than scientists have thought, a study suggests. Scientists believe our species, Homo sapiens, originated in Africa and eventually spread throughout the world. Several past studies have also indicated that after reaching Europe, early humans interbred with Neanderthal people. But the new work suggests interbreeding with other lineages had already taken place in Africa, possibly with noted extinct human lineages such as Homo erectus, the “upright walking man,” or Homo habilis, “tool-using man.” “We think there were probably thousands of interbreeding events... It looks like our lineage has always exchanged genes” with others, said Michael Hammer of the University of Arizona, who led a team reporting the new findings. The research appears in the journal Proceedings of the National Academy of Sciences. Scientists can now extract DNA from fossils tens of thousands of years old, which has enabled research into proposed interbreeding with Neanderthals. But the Africa specimens that Hammer’s team studied were much older, Hammer noted, so “we don’t have fossil DNA from Africa to compare with ours.” Also, “Neanderthals lived in colder climates, but the climate in more tropical areas make it very tough for DNA to survive that long.” Thus “our work is different from the research that led to the breakthroughs in Neanderthal genetics,” he explained. “We couldn’t look directly for ancient DNA that is 40,000 years old and make a direct comparison.” To get around this, Hammer’s team used computers and statistics. “We looked at DNA from modern humans belonging to African populations and searched for unusual regions in the genome,” he explained. Because nobody knows the DNA sequences of those extinct humans, Hammer’s team first had to figure out what features of modern DNA might represent fragments brought in from archaic forms. “What we do know is that the sequences of those forms, even the Neanderthals, are not that different from modern humans,” he said. “They have certain characteristics that make them different from modern DNA.” The researchers used simulations to predict what ancient DNA sequences would look like had they survived. “You could say we simulated interbreeding and exchange of genetic material,” Hammer said. “We can simulate a model of hybridization between anatomically modern humans and some archaic form. In that sense, we simulate history so that we can see what we would expect the pattern to look like if it did occur.” According to Hammer, the first signs of anatomically modern features appeared about 200,000 years ago. First, the team sequenced vast regions of human genomes from samples taken from six different populations living in Africa today and tried to match up their sequences with what they expected those sequences to look like in archaic forms. The researchers focused on non-coding regions of the genome, stretches of DNA that do not contain genes, which serve as the blueprints for proteins. “Then we asked ourselves what does the general pattern of variation look like in the DNA that we sequenced in those African populations, and we started to look at regions that looked unusual,” Hammer said. “We discovered three different genetic regions fit the criteria for being archaic DNA still present in the genomes of sub-Saharan Africans. Interestingly, this signature was strongest in populations from central Africa.” The scientists applied several criteria to tag a DNA sequence as archaic. For example, if a DNA sequence differed radically from the ones found in a modern population, it was likely to be ancient in origin. Another telltale sign is how far it extends along a chromosome, Hammer and colleagues contend: if an unusual piece is found to stretch a long portion of a chromosome, it’s a sign of having entered the population relatively recently. “We are talking about something that happened between 20,000 and 60,000 years ago – not that long ago in the scheme of things,” Hammer said. “If interbreeding occurs, it’s going to bring in a whole chromosome, and over time, recombination [genetic mixing] events will chop the chromosome down to smaller pieces. And those pieces will now be found as short, unusual fragments. By looking at how long they are we can get an estimate of how far back the interbreeding event happened.” Hammer said that although the archaic DNA sequences account for only two or three percent of what is found in modern humans, that doesn’t mean the interbreeding wasn’t more extensive. “It could be that this represents what’s left of a more extensive archaic genetic content today. Many of the sequences we looked for would be expected to be lost over time. Unless they provide a distinct evolutionary advantage, there is nothing keeping them in the population and they drift out.” In a next step, Hammer’s team wants to look for ancient DNA regions that conferred some advantage to the anatomically modern humans once they acquired them. “Anatomically modern humans were not so unique that they remained separate,” he added. Interbreeding, he added, “is quite common in nature, and it turns out we’re not so unusual after all.”