3 0 Volume 35 Issue 3 | Skeptical Inquirer

[ SCIENCE WATCH K E N N E T H W . K R A U S EKenneth W. Krause is a contributing editor, books editor, and “The Good Book” columnist for the Humanist and a contributing editor and columnist for the SKEPTICAL INQUIRER. E-mail: krausekc@msn.com.

If God created man in his own image,as the opening chapter of Genesisdemands, he must have first created

the carnival fun-house mirror as a refer-ence tool. Since the ancestors of chim-panzees and modern humans split be-tween six and eight million years ago,different species of hominin have evolvedor retained bizarre muddles of seeminglystrange and unlikely features—branch-grasping feet, sprawling pelvises, flaredrib cages, chinless mandibles, protrudingbrow ridges, and, of course, ex pandedbrains, just to name a few.

But recent discoveries have compli-cated the more contemporary humannarrative too. When our direct ances-tors—a small but well-fated populationof Homo sapiens—emigrated fromAfrica into the Near East over 50,000years ago, the Eurasian landmass hadalready been inhabited by a variety ofhumans. The Neandertals, for example,flourished in the west until about28,000 years ago, while Homo floresiensispersisted in present-day Indonesia untilaround 17,000 years ago.

Were there others? If so, did our an-cestors simply wipe them out, alongwith all genetic remnants of their exis-tence? Or did they interbreed with theother humans as their numbers swiftlyexpanded into both Europe and Asia?

Two schools of thought have longdominated the debate. Led by ChrisStringer at the National History Mu-seum in London, disciples of the majori-tarian “complete replacement” modelargue that our ancestors simply sup-

planted other humans, by whatevermeans, rather than mixing with them.Contrarily, “classic multiregionalists” tendto follow University of Michigan’s Mil-ford Wolpoff, who, with the minority,contends that modern H. sapiens wereconceived outside of Africa through thegenetic intermingling of perhaps manyhuman groups.

But, to nearly everyone’s surprise,both paradigms were challenged onMay 7, 2010, when an internationalteam of scientists led by Svante Pääbopublished a draft sequence of the Nean-dertal genome in Science magazine

(Green 2010; the subject of my “ScienceWatch” column of September/October2010). A paleogeneticist at the MaxPlanck Institute in Leipzig, Germany,Pääbo revealed that 1–4 percent of themodern, non-African human genomewas derived from our burly cousins. Inother words, Neander tals and modernhumans, whose lineages split between440,000 and 270,000 years ago, likelyinterbred in the Middle East between80,000 and 50,000 years ago.

Unfortunately, the Neandertal Ge -nome Project largely obscured anotherimportant hominin discovery, from

Denisovans and Human Hybrids in theGame-Changing Age of Paleogenetics

New Hominid Joins the FamilyDNA sequencing shows new primate species that may

have shared a common ancestor with humans

RUSSIAAltai mountainsAltai mountainsAltai mountainsHomo

Sapiens

Neanderthals

DNA taken from bone fragment of smallchild 30,000 – 48,000 years old found in theDenisova Cave

The Siberianhominid

NEW!

NEW!

UNDER

DISPUTEUNDER

DISPUTE

Four hominid speciesMay have roamed theearth at the same time,around 40,000 years ago

Flores “hobbit” manWas it a separatespecies?Source: Nature 250310

SI May June 11 CUT_SI new design masters 3/25/11 10:02 AM Page 30

Skeptical Inquirer | May / June 2011 31

which two major papers eventually re-sulted. First, on April 8, 2010, a spare,seven-member team led by Pääbo andhis Leipzig colleague Johannes Krausepublished its findings vis-à-vis the mi-tochondrial genome of an unfamiliarhuman recovered from a deep forest insouthern Siberia (Krause 2010).

In 2008, Russian archaeologist Ana-toli Derevianko—who would ulti-mately join the Pääbo-Krause team—found a female child’s distal manualphalanx, or pinkie bone, in DenisovaCave in the Altai Mountains of pres-ent-day Russia. Although the fingercouldn’t be tested directly, its surroundingstratum was radiocarbon dated to be-tween 48,000 and 30,000 years old. Re-luctant to grant the child a taxonomicdesignation as a Linnaean species or sub-species, the team would later identify thenew humans simply as the “Denisovans.”

The child’s mitochondrial DNA(mtDNA) proved exceptional, diverg-ing from that of modern humans andNeandertals at 385 and 202 nucleotidepositions, respectively. Indeed, this pre-liminary study disclosed no sign of in-terbreeding. But Pääbo couldn’t rule itout because both H. sapiens and Nean-dertals had evidently inhabited theneighboring environs at the same time.In fact, humans had probably occupiedthe site beginning around 280,000years ago.

In any case, Pääbo’s soon-to-be-ex-panded squad immediately beganworking on the Denisovans’ unusuallywell-preserved nuclear genome. Atabout three billion letters long, the nu-clear sequence promised a much morelucid account because it consisted ofcountless unlinked, neutrally evolvingloci. The mitochondrial genome, bycontrast, is inherited maternally as oneunit without recombination and is sub-ject to genetic drift.

And so the latest, though certainlynot the last, word on the Denisovans waspublished in Nature on December 23,2010. In their genetic history of the newhuman specimen, Pääbo and HarvardMedical School geneticist David Reichled a veteran group of twenty-eight au-thors from Germany, Spain, China, Rus-

sia, Canada, and the United States(Reich 2010). Wasting no time, they re-analyzed the finger bone and another in-dividual’s tooth—a second or thirdupper-left molar—discovered in thesame cave by Dere vianko back in 2000.

Pääbo’s combined results from 2010might prove so profound as to forevertransform our conceptions of recenthuman evolution—and thus, the relativeconstitution of every contemporary pop-ulation. At the very least, we’re left witha fascinating yet frustratingly complexweb of human migrations, interactions,and colonizations following the ances-tors’ final exodus from Africa.

Having sequenced the Denisovannuclear genome to 1.9-fold coverage—that is, on average, identifying sequencefrom nearly two DNA fragments thatcover any given nucleotide base in thegenome—Pääbo first explored the newhominin’s relationship to both Nean der -tals and modern humans.

To that end, Pääbo estimated the di-vergence between the Denisovan andthe human genome reference sequenceas a fraction of the divergence betweenpresent-day H. sapiens and our last com-mon ancestor with chimpanzees. TheDenisovan separated 11.7 percent of theway back. The point of digression for theVindija Cave, Croatia Neandertal ge -nome, by contrast, was 12.2 percent.

Hypothesizing a closer relationship

between Denisovans and Neandertals,Pääbo then performed a separate yet sim-ilar comparison between seven an cientand modern genomes—Deniso van, Ne-andertal, French, Han, Papuan, San(southern Africa), and Yoruba (WestAfrica). The Denisovan and Neandertalsequences separated 9.84 percent of theway back, and both of them separatedfrom the sequences of present-dayAfricans 12.38 percent of the way back.

To confirm, Pääbo’s team lined upthe Denisovan, Neandertal, and Yorubasequences to the chimp genome andcompared derived (evolved) and ances-tral alleles. They found that theDenisovan and Neandertal clustered tothe exclusion of the Yoruba and chim-panzee at 46,362 sites, compared withan average of 22,012 sites for the othertwo possible patterns, Yoruba andDenisovan or Yoruba and Neandertal.The team’s conclusion: “The Denisovaindividual and Neandertals share acommon history since separating fromthe ancestors of modern humans.”

So should the new humans be de-fined geographically and morphologi-cally as Neandertals or as their sister

A researcher extracts DNA from a fossil. Inset: The mtDNA within this tooth, found in Denisova Cave, suggeststhat Denisovans were distinct from both Neandertals and modern humans.

Natu

re m

agaz

ine

SI May June 11 CUT_SI new design masters 3/25/11 10:02 AM Page 31

32 Volume 35 Issue 3 | Skeptical Inquirer

group? Pääbo et al. evaluated more Ne-andertal sequences to find out. Aftercomparing the Vindija genomes tothose of Neandertals from Russia,Spain, and Germany, they ascertainedthat Neandertals descended from acommon population that experienced adrastic genetic bottleneck since diverg-ing from the ancestors of the Deni -sovans. Thus, the authors resolved, “Ne-

andertals across a broad geographicalrange have a population history distinctfrom that of the Denisova individual.”

The tooth found in Denisova Cavealso tended to confirm that Denisovanswere distinct from both Neandertals andmodern humans. For one thing, analysisof the tooth’s mtDNA verified that itlikely belonged to an individual from thesame population as the finger. For an-other, its shape was odd, to say theleast—of ample proportions overall, withshort but robustly flaring roots.

If the tooth is a third molar, its sizeis consistent with Australopithecinesamples and falls outside the range ofnormal variation in all known fossilspecimens of the genus Homo, saveHomo habilis and Homo rudolfensis. If itis a second molar, it is larger than Ne-andertal and early modern human sam-ples and comparable to those fromHomo erectus and H. habilis specimens.Although confident, Pääbo could not,of course, completely rule out the pos-sibility that the tooth’s primitive mor-phology resulted from a reversion.

Finally, the team broached the al-ways-provocative question of geneflow—whether the new hominins mightbe more closely related to some present-day populations than to others. Pääbo

initially examined the relationship be-tween the Denisovan sequence and thegenomes of 938 contemporary humansfrom 53 different populations. He foundthat with respect to Neander tals andDeniso vans, “the Melanesian popula-tions stand out” compared to other non-African populations.

Following up, Pääbo compared theDenisovan genome with those of twelve

globally diverse persons, including ad-ditional sequences from Mela nesianPapua New Guinea and Bougain villeIsland. In sum, the authors revealed thetruly shocking news that “4.8 +/- 0.5%of the genomes of Melanesians derivefrom Deniso vans,” and, consideringPääbo’s previous study of the Neander -tal sequence as well, that “altogether, asmuch as 7.4 +/- 0.8% of the genomes ofMela nesians may thus derive from re-cent admixture with archaic hominins.”

The most plausible explanatorymodel for these landmark data, accord-ing to the Reich-Pääbo team, posits theDenisovans as an archaic population ge-netically distinct from all othersknown—including their sister group,the Neandertals, with whom they splitmore than 200,000 years ago while in-habiting the expansive Eurasian land-mass. The former migrated generallyeastward as the latter broke for the west.

As our direct ancestors departedfrom Africa, they interbred first withNeandertals and, shortly thereafter,with Denisovans. But Denisovansprobably mixed with modern humansonly as their numbers expanded alongAsia’s southern coastal areas and intoOceania. Evidently, the ancestors ofother non-African populations were

unaffected by the new humans. For now, the size and geographical

range of the Denisovan group must re -main unknown. Apparently, they madeno genetic contribution to either theHan Chinese or the Mongolians—twopopulations currently residing muchcloser to the Altai Mountains than theMelanesians, who lived a full 10,000kilometers away. So, whatever the Deni -sovans’ numbers at the time of admix-ture, they likely left their genetic marksomewhere far south of Denisova Cave.

One wonders as well why we haven’tdiscovered additional Denisovan re-mains. It may be that other fossils havebeen misclassified. Some specimensfrom China, for example, resemble nei-ther modern humans, Neander tals, norH. erectus. And even the Denisovan fin-ger bone was originally thought to be-long to a modern human. We shouldremember too that H. floresiensis wasn’tdiscovered until 2004. Only time willtell, of course, as the search for morefossils continues.

Perhaps most rousing of all is the re-alization that some of us carry more ar-chaic DNA than others. Some mightargue that DNA retained for almost50,000 years must confer a substantialadvantage or at least serve some practi-cal purpose. Accomplished paleogeneti-cists like Pääbo hope to provide answersto these questions and others in thevery near future.

Whatever the outcomes, as the sci-entific picture grows ever clearer, therest of us will no doubt be forced tocope with new realities, including un-expected forms of genetic diversity andincreasingly vague conceptions of whatit means to be human. nReferencesGreen, R.E., J. Krause, A.W. Briggs, et al. 2010.

A draft sequence of the Neandertal genome.Science 328: 710–22.

Krause, J., Q. Fu, J.M. Good, et al. 2010. Thecomplete mitochondrial DNA genome of anunknown hominin from southern Siberia.Nature 464: 894–97.

Reich, D., R.E. Green, M. Kircher, et al. 2010.Genetic history of an archaic hominin groupfrom Denisova Cave in Siberia. Nature 468,1053–60.

The tooth found in Denisova Cave also tended to confirm that Denisovanswere distinct from both Neandertalsand modern humans.

SI May June 11 CUT_SI new design masters 3/25/11 11:26 AM Page 32