ancestry and kinships of native siberian populations: the hla evidence

ARTICLES

Ancestry and Kinships of Native SiberianPopulations: The HLA EvidenceTATIANA S. UINUK-OOL, NAOKO TAKEZAKI, AND JAN KLEIN

Siberia, the northern one-third ofthe Asian continent, extends from theUral Mountains in the west to the Pa-cific Ocean in the east, and from theArctic Ocean in the north to themountain ranges of Central Asia inthe south (Fig. 1). Topographically, itis divided into three regions: the WestSiberian Lowland, the Central Sibe-rian Plateau, and the East SiberianUpland. The first of these regions,bounded on the west by the UralMountains, encompasses the great ba-sins of the rivers Ob and Yenisey,which originate in the southernmountains and flow into the ArcticOcean. The entire area is low-lying,extremely flat, and swampy. The Cen-

tral Siberian Plateau, between the riv-ers Yenisey and Lena, rises 600 to 700meters above the lowlands, but it toois flat, if slightly undulating. The EastSiberian Upland comprises a series ofmountain ranges between the LenaRiver and the Pacific coast. The south-ern part of the region is drained by theAmur River, which flows into the Pa-cific Ocean. The flatlands are rem-nants of an ancient craton aroundwhich the whole Asian continent wasassembled in the most recent phase ofits more than 2,500-million-year his-tory.1

Latitudinally, Siberia is divided intothe arctic (tundra), subarctic (taiga),and southern (steppe) zones, each dis-tinguished by differences in soil types,vegetation, and climate. The arcticzone is a 320 km-wide strip of landalong the Arctic coast. Here the sub-soil remains permanently frozen to adepth of 300 m or more; only the shal-low upper layer thaws briefly in sum-mer. Because the permafrost preventsunderground drainage, numerouslarge but shallow lakes form all overthe area. The scanty vegetation con-sists of lichens, mosses, grasses, andlow perennial flowering plants, as wellas low shrubs of birches and willows.Animal life is limited to wolves, wol-verines, foxes, hares, lemmings, andsome migratory birds.

The border between the arctic andsubarctic zones is delineated by thetree line, but the transition is gradualvia a forest tundra with sparse,stunted trees, extensive sphagnumpeat bogs, and thinning of the perma-frost. The subarctic taiga, which en-compasses more than half of Siberia,is a zone of dense, mostly coniferousforest. Here, too, as in much of therest of Siberia, there are essentially

only two seasons: long, numbing win-ter and short, chilly summer. Al-though large animals (bears, lynxes,deer, and elk) occur in the taiga, theyare not abundant.

In the flat parts of southern Siberia,the taiga gradually gives way to grassysteppes, then to arid steppes, and far-ther south to deserts. The steppe beltstraddling 52° to 53°N latitude is morethan 300 km wide in places. Here thesummers are longer and warmer, theprecipitation is light to moderate in allseasons, and the wildlife is more plen-tiful. The winters, however, are longand cold.

THE PEOPLES

There are now approximately 31million people living in Siberia, mostof them ethnic Russians; ethnic mi-norities account for fewer than 1.3million people.2 Four centuries ago, incontrast, there were probably onlyabout 5 million inhabitants of Siberia.Russians and other Europeans wererestricted to a few explorers or trad-ers, while the indigenous peoples werediversified into many ethnic groups.3,4

The decline of the indigenous peoplesbegan with the Russification of Sibe-ria in the seventeenth century. Whilesome ethnic groups have disappearedaltogether, several others are on theverge of extinction. The populationsize of the remaining groups has beendrastically reduced. Forced resettle-ment, voluntary or involuntarychanges in lifestyle, population inter-mixing, poverty, and disease, as wellas other factors have conspired tochange the ratio of native people toimmigrants. It is to be feared that afew generations from now, there willbe hardly any unmixed representa-

Tatiana S. Uinuk-ool is a research asso-ciate at the Max-Planck-Institut fur Biolo-gie, Abteilung Immungenetik, Tubingen,Germany. Her research interests are fo-cused on the genetic anthropology of Si-berians and the origin of the adaptive im-mune system. E-mail: [email protected] Takezaki is a staff member at theMax-Planck-Institut fur Biologie, Abtei-lung Immungenetik, Germany. She is in-terested in theoretical aspects of molec-ular evolution and vertebrate phylogeny.Jan Klein is Professor at the EberhardKarls Universitat Tubingen and Director ofthe Max-Planck-Institut fur Biologie,Abteilung Immungenetik, Germany. He isan immunogeneticist and molecular evo-lutionary biologist. His current researchinterests include evolution of the majorhistocompatibility complex and molecu-lar aspects of speciation. E-mail:[email protected].

Key words: genetic variability; haplogroup; mi-gration; dispersal; molecular anthropology

Evolutionary Anthropology 12:231–245 (2003)DOI 10.1002/evan.10124Published online in Wiley InterScience(www.interscience.wiley.com).

Evolutionary Anthropology 231

tives of the ethnic groups left in Sibe-ria. When this happens, the geneticrecord of the history of these peopleswill be scrambled, if not lost alto-gether.

And what an invaluable record it is!Because the land could not sustainhigh population density, Siberia, untilrecently, remained sparsely popu-lated. Ground travel had always beendifficult in Siberia: Food resourceswere scarce, the climate extreme, theforests impenetrable, and the moun-tains impassable. Consequently, indi-vidual settlements had remained iso-lated from one another and from theworld outside Siberia. In this regard,the demographic conditions in north-ern Asia may have mimicked thosethat existed when modern humans be-gan to expand out of Africa. Further-more, the geographic proximity of Si-beria to Alaska has made the Siberianpopulations obvious candidates forthe source of expansion of modernhumans into the New World. Finally,because southern Siberia borders on

some of the most populous regions onthe Asian continent, the Siberian pop-ulation may hold important clues tothe origin and history of the Asianpeople. For all these and other rea-sons, it is exigent to salvage as much

of the genetic record carried by theSiberian ethnic groups as possible.

During the past century, the indige-nous people of Siberia were studiedby ethnographers, physical anthropol-ogists, and linguists. These studies,summarized in a monograph editedby Levin and Potapov5 (originallypublished in Russian and later trans-lated into English6), led to the recog-nition of approximately thirty ethnicgroups distinguished by their physicalappearance, culture, traditions, cus-toms, and language (Table 1).2,5,7,8

Some of the groups were found to besedentary or semi-nomadic and oth-ers mostly nomadic. None were spe-cialized to a particular mode of sub-sistence, although in some groups onemode dominated. The modes in-cluded hunting, fishing, and breedingor herding reindeer, horses, or cattle.In each group, the people banded to-gether to establish small camps andsettlements, permanent or temporary,depending on their mobility. The shel-ters and dwellings they erected varied

Figure 1. Distribution of native ethnic groups in Siberia as it was more than fifty years ago. The map is based on Levin and Potapov.5 Shadedareas are colonized predominantly by Russians.

It is to be feared that afew generations fromnow, there will be hardlyany unmixedrepresentatives of theethnic groups left inSiberia. When thishappens, the geneticrecord of the history ofthese peoples will bescrambled, if not lostaltogether.

232 Evolutionary Anthropology ARTICLES

but were often based on the principleof a yurt, a circular domed tent of skinand felt stretched over a collapsibleframework. Most groups practiced

shamanism founded on the belief thatsome individuals are endowed withthe ability to communicate with gods,demons, and ancestral spirits.

Although most groups developedtheir own distinctive language, thedifferent languages can be classifiedinto four main families and at least

TABLE 1. Native Siberian Peoples: Basic Demographic Dataa

Peoples (Ethnonyms)

CensusPopulationSize (1989)

Language Family:Group Subsistence (Traditional)

TraditionalReligion

Aleut 650 Eskimo-Aleut: Aleut Sedentary; hunting of sea mammals,fishing

Shamanism

Altai (Tabular, ChelkanKumanda, Telengit, Tele,Teleut)

69,400 Altaic: Turkic Nomadic rearing; semi-sedentaryrearing; hunting

Shamanism

Buriat 417,400 Altaic: Mongolian Nomadic rearing; semi-sedentaryrearing

Buddhism,Shamanism

Chukchee 15,100 Chukchi-Kamchatkan:Northern

In coastal area: hunting of seamammals. In tundra: nomadicreindeer herding

Polytheisticanimism

Dolgan 6,600 Altaic: Turkic Semi-sedentary; reindeer herding,hunting, fishing

Shamanism

Eskimo 17,000 Eskimo-Aleut: Eskimo Hunting of sea mammals, fishing,hunting

Polytheisticanimism

Even 17,100 Altaic: Tungus Nomadic in tundra; semi-sedentaryin coastal areas; reindeer herding,fishing, hunting sea mammals

Shamanism

Evenki 29,900 Altaic: Tungus Nomadic; reindeer herding, hunting ShamanismItelmen (Kamchadal) 2,400 Chukchi-Kamchatkan:

SouthernHunting of sea mammals, fishing,

huntingPolytheistic

animismKet 1,100 Unknown Sedentary; hunting, fishing ShamanismKhakas 78,500 Altaic: Turkic Semi-sedentary rearing; fishing ShamanismKhanty (Ostyak) 22,300 Finno-Ugric: Ugric Nomadic reindeer herding, hunting,

fishingShamanism

Koryak 8,900 Chukchi-Kamchatkan:Northern

In coastal area: hunting of seamammals, fishing. In tundra:nomadic reindeer herding

Shamanism,animism

Mansi 8,300 Finno-Ugric: Ugric Hunting, fishing, reindeer herding ShamanismNegidal 600 Altaic: Tungus Sedentary; hunting, fishing ShamanismNenet 34,200 Altaic: Samoyedic Nomadic reindeer herding, hunting,

fishingShamanism

Nganasan 1,300 Uralic-Yukagir:Samoyedic

Nomadic reindeer herding, hunting,fishing

Shamanism

Nivkh (Gilyak) 4,600 Unrelated: uniqueTungus language

Sedentary; fishing, hunting of seamammals, crop farming, rearing ofdogs

Shamanism,bear cult

Orochi 900 Altaic: Tungus Sedentary; hunting, fishing ShamanismSelkup (Ostyako-Samoyed) 3,600 Uralic-Yukagir:

SamoyedicHunting, fishing Shamanism

Shor 15,700 Altaic: Turkic Hunting Shamanism,animisticelements

Tofalar (Karagasy) 700 Altaic: Turkic Nomadic reindeer herding, hunting ShamanismTuvan (Tuvinian) 206,200 Altaic: Turkic Nomadic; horse, cattle, and camel

breedingBuddhism

(Lamaism);Shamanism

Udegey (Udekhe, Udikhe) 1,900 Altaic: Tungus Sedentary; hunting, fishing Shamanism,tiger cult

Ulchi (Olchi) 3,200 Altaic: Tungus Sedentary; hunting, fishing ShamanismYakut 380,200 Altaic: Turkic Sedentary; rearing of horses and

domestic livestockShamanism

Yukagir 1,100 Altaic: Ural-Yukagirian Nomadic and sedentary; hunting,reindeer herding, breedinghunting dogs

Shamanism

a Some western Siberian populations shown in Figure 1 are not included.

ARTICLES Evolutionary Anthropology 233

two isolates. In the classification ofRuhlen,9 the four families are Uralic-Yukagir, Altaic, Chukchee-Kamchat-kan, and Eskimo-Aleut. The two lan-guage isolates are Ket and Nivkh(Gilyak).

The Yukagir, who speak a languageof the Uralic-Yukagir family, livealong the rivers Kolyma and Indigirkaand their tributaries in the arctic andsubarctic zones of northeastern Sibe-ria. Related languages belonging tothe Uralic branch of this family arespoken by Nenets, who live in both theEuropean (Kanin and Kola Peninsu-las) and the Asian (Taimyr Peninsula)parts of the Arctic; the Nganasan ofthe Taimyr Peninsula; and Khantyand Mansi distributed along the lowerOb and its tributaries in northeasternSiberia.

The Altaic family of languages is di-vided into three subfamilies, Turkic,Mongolian, Tungus. Languages be-longing to the Turkic subfamily arespoken by Yakut, Dolgan, Tuvan, andTofalar. Yakut once lived in southernSiberia but moved farther north along time ago and are now distributedover a vast region on both sides of theLena River called Yakutia. Dolgan ofthe Taimyr Peninsula speak a lan-guage closely related to Yakut, butwith elements of the Evenk language.Tuvan and Tofalar speak closely re-lated languages and live near eachother on the south side of the SayanMountains in southern Siberia. Thelanguage belonging to the Mongoliansubfamily is spoken by Buriatsaround Lake Baikal. Tungus lan-guages are spoken by Evenki. Evenkiscattered over a territory the size ofEurope in northeastern Siberia.Evenki, who occupy an even largerterritory stretching from the YeniseyRiver to the Pacific coast: Negidal,Orochi, Udegey, and Ulchi, all smallgroups distributed around the AmurRiver and its tributaries; and Orok ofthe Sakhalin Island.

Languages of the Chukchee-Kam-chatkan family are spoken by theChukchee and Koryaks, while those ofthe Eskimo-Aleut family are spokenby Inuit (“Siberian Eskimos”) andAleuts. These four small groups live inthe extreme northeastern part of Sibe-ria. The language of the Ket on theYenisey River and its tributaries, and

that of the Nivkh on Sakhalin Island,appear to be unrelated to each otherand to all other languages.

The physical appearance of indige-nous Siberians has been described asMongoloid; that is, the Siberians re-semble other native Asians.5 Differ-ences have been reported between theethnic groups with respect to stature,skin and eye color, hair texture, headand nose shape, face size and flatness,beard development, morphology ofeye folds and cheekbones, as well asother features.5 Very little can be in-ferred from these studies about theorigin of the entire Siberian popula-tion complex or the origin of the indi-vidual groups. Because none of thegroups acquired writing and theknown archeological record of the in-dividual groups is limited, virtually

the only sources of information re-garding their history before the seven-teenth century were oral tradition andlanguage affinities.

The archeological record of earlyhuman colonization of Siberia has re-cently been reviewed in this journal10

and elsewhere.11 The authors of thesereviews conclude that reliably datedarcheological sites indicate a sporadicoccupation of southwestern Siberiaby modern Homo sapiens during theLate Paleolithic. Less reliably datedsites suggest an even earlier set-tling.10–13

THE GENES

Recent advances in molecular biol-ogy make it possible to compare indi-viduals and populations at thegenomic (DNA) rather than the phe-

notypic (character) level. Nuclear ormitochondrial (mt) DNA is extractedand small fragments of it are exam-ined by one of the many methods nowavailable. Among the favorite frag-ments are part of or the entiremtDNA, a segment of the Y-chromo-some, and genes of the HLA complex.Variations of all three of these frag-ments have been studied in the indig-enous Siberian populations.14–31

Studies of mtDNA and Y-chromo-some variation have recently been re-viewed.32,33 The present review there-fore focuses on the HLA system.However, we will also compare theresults obtained with all three systemsas far as they pertain to the nativeSiberian and American populations.Although the studies based on thesethree systems are all aimed at recon-structing the history of human popu-lations (their genealogy), they use dif-ferent means by which to pursueattainment of this purpose. Themeans are comparisons of allele fre-quencies in the case of the HLA sys-tem, and the genealogy and distribu-tion of individual mutations in thecase of mtDNA and Y-chromosomesystems (Box 1).

The 19 active loci that comprise theHLA complex proper (Box 2) are di-vided into class I and class II loci,which differ structurally and func-tionally.34 Studies on the Siberianpopulations have focused on the classII loci, mainly for the methodologicalreason that it is somewhat easier todistinguish the individual class II locifrom one another than it is to distin-guish the class I loci (Box 3). Amongthe class II loci, three are particularlysuitable for population studies be-cause of their high variability. The al-leles at these three loci (HLA-DRB1,-DQA1, and DQB1) and the combina-tions (haplotypes) in which they occuron individual chromosomes havebeen shown to differentiate humanpopulations in terms of allele frequen-cies.23,35 By converting the differencesin frequencies to genetic distancesand evaluating these by proper statis-tical methods (Box 4), it is possible toquantitate the genetic relationshipsamong populations and construct amodel (a population tree) of theirlikely evolution from ancestral popu-lations. It is the extraordinary vari-

Most, if not all, of theHLA-DRB1 alleles nowfound in the Siberianpopulations must havebeen present in theancestral population ofH. sapiens before itspread onto the differentcontinents.


ability of the three class II and threeclass I loci that makes the HLA systemsuited to this purpose.

HLA ALLELES AND HAPLOTYPESOF NATIVE SIBERIANS

The number of different HLA allelesfound in each of the Siberian ethnicgroups is only a fraction of the totalnumber of alleles described in the hu-man species. Thus, for example, at theHLA-DRB1 locus, 329 alleles havethus far been identified (see the web-site http://www.ebi.ac.uk/imgt/hla/stats.html), but of these only 16 to 25 allelesare present in any given Siberian pop-ulation.22–27 Altogether, 34 out of 329,eight out of 24, and 14 out of 53known HLA-DRB1, -DQA1, and -DQB1alleles, respectively, have been found inthe assemblage of the Siberian ethnicgroups.

Most, if not all, of the HLA-DRB1alleles now found in the Siberian pop-ulations must have been present in theancestral population of H. sapiens be-

fore it spread onto the different conti-nents. In fact, most of these allelesmust have existed in the ancestral spe-cies from which H. sapiens originated.36

This conclusion is indicated by threeobservations: the worldwide distribu-tion of the alleles; the age estimatesbased on the number of nucleotidedifferences between the alleles; andthe presence of closely related allelesin nonhuman primates.37 No allelehas been found that is restricted in itsdistribution to a single Siberian ethnicgroup or exclusively to all the nativeSiberian populations. This observationis consistent with similar findings innon-Siberian populations.35,38,39 Incomparison to the mtDNA, the HLAand other nuclear genes evolve moreslowly. Although new mutations arisecontinuously at the HLA loci, the greatmajority of them remains limited tothe people in whom they occurred orto a few of their immediate descen-dants. In a given population, onlyrarely does a mutation establish itself

as a polymorphism (that is, the fre-quency of its occurrence rises above0.01). As a result, there are two kindsof variability at the HLA loci: poly-morphism comprised of alleles thatare shared by many individuals in dif-ferent populations and rare variantsor alleles that are restricted to a fewindividuals. It appears that the major-ity of the described HLA-DRB1 allelesis of the latter type. The fact that norare HLA-DRB1 variants have thus farbeen found in the Siberian studies canbe explained by the relatively smallnumber of individuals tested and theshortness of the DNA segment (oneexon) analyzed.

The extent of polymorphism at theHLA-DQA1 and -DQB1 loci in Siberiaand worldwide is lower than that atthe DRB1 locus. Also, these alleles aregenerally more widely distributedamong the populations. In the case ofthe DRB1 locus, populations are dis-tinguished by the presence or absenceof alleles, as well as by the frequencies

Box 1. Gene Trees Versus Population Trees

Genetic relationships among popu-lations are commonly depicted in theform of trees, which, in turn, are usedto imply, directly or indirectly, a gene-alogy of the populations. The dataentered into the computation onwhich the trees are based are the ge-netic differences between the popu-lations. Genetic differences are usedin two distinct ways that lead to dif-ferent trees.

In one case, an attempt is made toreconstruct the pathway by whichmutations accumulated in a definedstretch of DNA (gene or haplotype)extracted from individuals represent-ing different populations. A graphicdepiction of the reconstruction is agene (haplotype) tree (network), inwhich furcations indicate individualmutations. Genealogy of populationsis then indirectly inferred from suchtrees from the distribution of the al-leles (haplotypes) among the popula-tions, taking into account the path-way by which the alleles presumablyarose.

In the second case, the genealogy

of the mutations is not of primary in-terest; rather, an attempt is made toreconstruct the pathway by which dif-ferences in allele (haplotype) frequen-cies between populations may havearisen. This pathway is then assumedto reflect directly the genealogy of thepopulations. A graphic depiction ofthe pathway is a population tree inwhich furcations are interpreted assplittings of populations. To give asimple example, an ancestral popula-tion may have split into two, whichbecame geographically separated.Random genetic drift, or the chancevariation in the transmission of allelesduring the formation of a new gener-ation, gradually differentiated the twopopulations with regard to allele fre-quencies at their loci. Subsequently,each of the two populations mighthave split again and the new popula-tions again drifted apart in their allelefrequencies. Because time plays arole in the divergence of the popula-tions, the difference between popula-tions on the same line of descent issmaller than that between popula-

tions on distinct lines. It is this diver-gence in allele frequencies that keepsa genealogical record of the popula-tions.

Obviously, it is most unlikely that thehistory of human population unfoldedin this simplistic manner. Populationsmay expand into new territories withoutsplitting; splitting populations may con-tinue to exchange genes; the split intotwo populations may be uneven andthe size difference between the found-ing populations may affect allele fre-quencies; a gene may come under se-lection pressure that skews theprocess determining allele frequencies.All these factors may obscure the ge-nealogy of the populations. A popula-tion tree must therefore be regarded asa simplified abstraction of complex re-ality. That the tree is not pure fantasy isindicated by the fact that major branch-ing patterns of human population treesbased on allele frequencies at manyloci68,69 are in agreement with evidenceprovided by geography, linguistics, andother independent sources of genea-logical information.


of alleles shared by the different pop-ulations.22–25 At the DQA1 and DQB1loci, the various populations are dis-tinguished largely by frequencies ofshared alleles. Apparently, the com-mon DQA1 and DQB1 alleles werepresent in the founding population ofmodern humans, after which their fre-quencies in the expanding popula-tions differentiated by random ge-netic drift.

Additional genetic information re-

garding the genealogy of native Sibe-rian populations is provided by theHLA haplotypes, the cis-combinationsof alleles at two or more HLA loci (Box2). Each of the Siberian ethnic groupstypically contains 20 to 30 differentHLA-DQB1-DQA1-DRB1 haplotypes,while the total number of these hap-lotypes in all the groups combined is�60.22–24 About half a dozen of thehaplotypes are widely shared not onlyby Siberian, but also non-Siberian

populations. These haplotypes, likethe widely shared alleles, may havearisen before the dispersion of the hu-man species onto the different conti-nents, perhaps in Africa.

In contrast to the HLA alleles, how-ever, population-specific haplotypesare found in the Siberian ethnicgroups. About a dozen such haplo-types have been reported thus far andanother dozen or so seem to be re-stricted to one Siberian population

Box 2. The HLA System

The acronym “HLA” stands for hu-man leukocyte antigen. It calls tomind the fact that originally the mol-ecules (antigens) were detected byantibodies on the surface of the leu-kocytes (see Box 3). The cluster of theHLA loci in a single chromosomal re-gion is the human’s version of themajor histocompatibility complex(Mhc), so designated because theHLA antigens are primarily responsi-ble for the incompatibility (immune)response against transplanted for-eign tissues or organs. The Mhc mol-ecules initiate the immune responsenot only against foreign HLA anti-gens, but also against antigens ofpathogens. Specifically, the mole-cules bind peptides derived from bro-ken-down proteins of the pathogen

and present them to receptors onlymphocytes, the main players in theresponse. The HLA complex is lo-cated on the short arm of chromo-some 6 (region 6p21.31) and con-tains, in addition to the 19 active HLAgenes, more than 150 other genes,some of which encode proteins in-volved in the degradation of patho-gen-derived proteins, transportationof the resulting peptides, and loadingof the peptides onto the HLA mole-cules.34,74

Six of the 19 HLA loci (HLA-A, -B,C, -DRB1, -DQB1, and DQA1) aredistinguished by their polymorphism:They occur in human populations innumerous variants (alleles), each al-lele at an appreciable frequency. Theidentities and frequencies of the al-

leles characterize a given population.Some of the alleles differ from theothers at only one nucleotide site ofthe coding part of the gene, whileothers differ at more than 30 sites. Acombination of HLA alleles at two ormore loci of a single chromosome isthe HLA haplotype. The frequenciesof HLA haplotypes are, like the fre-quencies of HLA alleles, distinguish-ing characteristics of individual hu-man populations. The different HLAloci are denoted by capital letters andnumbers. The alleles at a given locusare distinguished by two- or four-digitnumbers (depending on the degree ofresolution) separated from the locusdesignation by an asterisk. The loci ofinterest in the present context are HLA-DRB1, HLA-DQA1, and HLA-DQB1.


and very few non-Siberian popula-tions. These haplotypes presumablyarose by intergenic recombination inthe individual Siberian ethnic groups.Also, some of them probably arose in-dependently in non-Siberian popula-

tions. Indeed, theoretical consider-ations, taking into account thefrequency of recombination betweenthe three HLA loci as determined byfamily studies,40 the sizes of the pop-ulations, and other factors, suggest

that each Siberian ethnic group canbe expected to contain 4 HLA-DQA1-DQB1 and 10 DRB1-DQA1 new re-combinants at any given time.22 Theseconsiderations suggest further that,on average, 5 to 10 haplotypes could

Box 3. HLA Typing

Originally HLA alleles were distin-guished indirectly through the anti-genic properties of the proteins theyencode. During pregnancy and deliv-ery, some of the fetal cells or theirbreakdown products enter the moth-er’s circulation and the paternally de-rived fetal HLA antigens stimulate thesecretion of specific antibodies intothe mother’s blood. Similarly, duringblood transfusion the HLA antigenson the donor’s leukocytes are recog-nized as foreign by the recipient’s im-mune system and so trigger an anti-body response. The antisera thusproduced can then be used in sero-logical typing of large panels of leu-kocytes from blood donors. Suchtypings are routine in many transfu-sion stations and thus are a source ofvaluable information about the HLApolymorphism in various populations.However, serological HLA typingdoes not resolve all the alleles be-cause some of the changes in thegenes do not lead to the generation of

new antigenic determinants. To ob-tain a higher discrimination amongthe HLA alleles, it is necessary to re-sort to DNA typing.

There are many methods of HLADNA typing, but they all have the firststep in common: amplification of theextracted DNA by the polymerasechain reaction. In this step, shortstretches of a DNA sequence corre-sponding to the opposite ends andcomplementary strands of a chosensegment of the HLA gene are used as“primers” to initiate repeated cyclesof strand separation and synthesis ofcomplementary strands. The meth-ods differ in the procedures used todistinguish the amplified DNAs of thedifferent genes. In the method used inour studies, the alleles are distin-guished by the single-stranded con-formation polymorphism and the dif-ferent patterns are identified by DNAsequencing. The single-strandedconformation polymorphism tech-nique is based on the observation

that the migration of short single-stranded DNA fragments in an elec-tric field generated in a nondenatur-ing gel depends not only on thelength of the fragments, but also ontheir sequence.75 Fragments differingby as little as a single nucleotide sub-stitution can usually be distinguishedin this manner. The resulting patternscan be visualized by the reduction ofAg(NO3)2 to elementary silver afterthe binding of the nitrate to the DNAin the presence of thiosulfate. Allelicfrequencies are calculated by count-ing and haplotypes are deduced fromthe genotypes of the typed individu-als. Where HLA genotypes of boththe parents and the offspring areknown, the haplotypes are obtaineddirectly from the segregation pat-tern of the allelic combinations.Where this information is not avail-able, haplotypes are deduced indi-rectly (and less reliably) from the as-sociations of the alleles found in thepopulations.


have been brought into Siberia withthe founding population and main-tained up to the present time, even ifthe founders reached Siberia as longas 40,000 years ago.22

A direct comparison of allelic fre-quencies provides only limited in-sight into the interrelationshipsamong populations. The relation-ships are revealed much better whenthe frequencies are converted to ge-netic distances between populationsand the distances are then used todraw population trees (Box 4). Fig-ure 2 shows a population tree basedon combined data for the DRB1,DQA1, and DQB1 loci; Figure 3shows a tree based on combinedDRB1 and DQB1 data; and Figure 4shows one based on DRB1 dataalone. This presentation is necessi-tated by the circumstance that notall of the non-Siberian populationshave been tested for all three HLAloci, but that some of these addi-tional populations are critical for theinterpretation of the relationship be-tween native Siberian and nativeAmerican populations. Some of thediscordances between the trees maybe accounted for by the observationthat data based on fewer loci gener-ally yield less reliable trees.

THE PLACE OF THE SIBERIANETHNIC GROUPS IN THE

FAMILY OF HUMANPOPULATIONS

Analysis of the HLA frequency datareveals the existence of a set of allelesand haplotypes that differentiates allthe indigenous Asian populationsfrom other Old World populations.On population trees this set is primar-ily responsible for the grouping of theAsian populations in a single cluster(Fig. 2), which can be interpreted asindicating a derivation from a singleancestral population. Borrowing aterm from taxonomists, such a clustercan be referred to as monophyletic. Itperhaps is not surprising that the Si-berian ethnic groups are included inthis cluster. Presumably they tracetheir origin to the same founding pop-ulation as do the other Asian popula-tions.

In some of the Siberian populations(Buriat and Mansi), however, HLA al-leles and mtDNA haplogroups20 (Fig.2) have been found that are otherwisecharacteristic of European Caucasianpopulations.23,24 These alleles havepresumably been introduced to Sibe-ria by Caucasians, but it is not clearwhen this took place. Archeologists

and anthropologists claim to havefound skulls with Caucasoid featuresat neolithic sites.41 These findings sug-gest that Asian-European exchangesmight have taken place much earlierthan the historical records document-ing the existence of the Silk Roadseem to indicate.

HLA alleles otherwise characteristicof European Caucasians are alsopresent in the Aleuts of the Com-mander Islands, which are part of theAleutian Island chain. This fact, com-bined with uncertainties about theirorigin, probably accounts for thesomewhat anomalous placing ofAleuts on the DRB1-based tree (Fig.2). Aleuts, who are closely related toEskimos in their language and cul-ture, have inhabited the western tip ofAlaska for more than 8,000 years, butit is not clear when they expanded tothe Aleutian Islands and whether theyreached the islands from Alaska orfrom northeastern Asia. It is thus de-batable whether the Commander Is-lands Aleuts should be considered na-tive Siberians or not.

Except for four populations (Buriat,Mansi, Tuvan, and Aleut), all the re-maining Siberian ethnic groups clus-ter together on the tree based on thecombined HLA frequencies (Fig. 2).Some of the Buriats are so heavily

Box 4. The Use of the HLA System in the Study of Populations

To use allele frequencies to drawtrees, they must first be convertedinto genetic distances. One way ofcomputing genetic distance (DA)76 isby using the formula

DA � 1 �1r �

j

r �i

mj

�xijyij

where r is the number of genetic lociand mj is the number of alleles at thej-th locus, while xij and yij are fre-quencies of the i-th allele at the j-thlocus in populations X and Y, re-spectively. The DA distance is basedon the idea of angular transforma-tion of allelic frequencies as pointson the surface of a hypersphere thatis specified in a coordinate system

with as many axes (dimensions) asthere are different alleles at a givenlocus. The distance between any twopopulations can then be computedfrom the angle between two linesprojecting from the system’s originto the points or the chord distancebetween the points. The DA distanceis known to have a small margin oferror, particularly when applied to asmall number of loci.

A phylogenetic tree can be drawnby using distance values calculatedfor all possible pairs of populationsstudied. Because the evolutionaryrate of the HLA loci is not the samein different populations, we usedthe neighbor-joining method,77 forwhich constancy of the evolutionaryrate is not a requirement. In this

method, initially the populationsare arranged into a star-like pattern,each population being at the tip of abranch radiating from the center.Next, two populations are chosen toform a cluster bifurcating from ashared branch (while the other pop-ulations remain in the star-like ar-rangement) and the sum of branchlengths of this tree is computed.This procedure is repeated for allthe possible pairwise combinationsof populations. The combinationthat gives the smallest sum (theshortest tree) is chosen. The chosenpair is then regarded as if it were asingle population and the wholeprocess is repeated, over and over,until all the branches of the treehave been specified.


admixed with Caucasian genes23 thaton the tree in Figure 2 they haveended up in the cluster of Caucasianpopulations. The outlier position ofthe Mansi population apparently isthe result of an admixture of Cauca-sian alleles, while that of the Tuvanpopulation appears to be the result ofan admixture of Central Asian alleles.Mansi live in northwest Siberia closeto the Ural Mountains, where theymay have had ample opportunity toexchange genes with European Cau-casians over an extended time. Tuvanpeople inhabit a region in Central Asia

that might be viewed as a melting potof Asian populations. Ethnographi-cally and culturally, Tuva peoples area heterogeneous population thatseems to have absorbed diverse influ-ences from ethnic groups passingthrough or temporarily settling intheir territory.42

The arrangement of the ethnicgroups within the Siberian cladeshows rough correlation with theirgeographical distribution (Fig. 2).Thus, the Todja and Tofalar (and,more distantly, Tuvan) cluster occu-pies a territory in south-central Sibe-

ria; the Ket, Yenisey Evenki, and Nga-nasan cluster is spread along theYenisey River in northwestern Sibe-ria; the Siberian Eskimo andChukchee groups are located in north-eastern Siberia; and the Negidal, Ok-hotsk Evenki, and Ulchi groups in-habit a region in southeastern Siberia.These correlations could reflect thehistory of splitting of the populationsfrom ancestors who moved into thesevarious regions. By contrast, there islittle correlation between the geneticaffinities among the Siberian popula-tions as indicated by the tree in Figure

Figure 2. Neighbor-joining tree of human populations based on genetic distances calculated from allele frequencies at the HLA-DRB1,-DQB1, and -DQA1 loci. Data from Uinuk-ool and coworkers23,24 and references therein, and for Moroccan Jewish, Ashkenazi Jewish, andSvanetian populations. From Roitberg-Tambur and coworkers38 and Sanchez-Velasco and Levya-Cobian.39 *Indicates data combinedfrom more than one study.


2 and the languages these peoplesspeak. Thus, although Ulchi, Negidal,and Okhotsk Evenki, who all speakTungusic languages, cluster together,Tungus-speaking Yenisey Evenki andUdegeys are separated by populationsspeaking languages of different fami-lies. These discrepancies between ge-netic and linguistic classifications ofthe populations can be explained bygene flow between neighboring popu-lations or, in some cases, unrecordedconversions to a different languagewithout much gene flow.5

The HLA data lend themselves tothe interpretation that after the initialexpansion from Africa H. sapiens es-tablished two major expansion cen-ters, one in Southwest Asia and theother in Central Asia (Fig. 5). Thesouthwest center became the spring-head of the Near-Eastern and Euro-pean populations, whereas in CentralAsia the expansions continued withSiberians moving to the north, East

Asians heading east, and SoutheastAsians migrating toward present-dayIndonesia.

Trees based on gene frequenciescan be used not only to infer the prob-able sequence of population splittingbut also, under certain circumstances,to estimate the time at which the split-tings occurred. Taking as a startingpoint the European-Asian split 50,000to 55,000 years BP,43–45 we estimatethat the separation of the Paleosibe-rian population from most of theother Asian populations took place21,000 to 24,000 years BP.23 This esti-mate is consistent with archeologicalevidence on the spread of H. sapiensinto southern Siberia.10,11 Followingtheir emigration from the CentralAsian center, the Paleosiberiansspread over the vast expanses of Sibe-ria and fragmented into individualisolated populations that evolved intothe different ethnic groups.

NATIVE SIBERIANS AND NATIVEAMERICANS

In the three trees based on the fre-quencies of alleles at the HLA loci(Figs. 2–4), native American popula-tions assume positions within thecluster of Asian populations, as wouldbe expected if they originated in Asia.Hence, the HLA data support theAsian origin of native Americans sug-gested earlier by anthropological, eth-nographical, and archeological evi-dence (reviewed by Crawford46) andrecently by genetic studies ofmtDNA14,15 and Y-chromosome28–31

variants. As stated earlier, investiga-tors working with mtDNA and Y-chro-mosome loci commonly deduce gene-alogies of populations from thedistribution of mutations rather thanfrom the frequencies of alleles. In themtDNA system, investigators haveidentified haplotypes distinguished bymutations at specific sites and clus-

Figure 3. Neighbor-joining tree of human populations based on gene frequencies at two HLA class II loci, DRB1 and DQB1. The tree is takenfrom Uinuk-ool and colleagues,23 but non-Asian populations have been deleted for simplicity. For sources of frequency data, see Figure 2.


Figure 4. Neighbor-joining tree of human populations based on gene frequencies at the HLA-DRB1 locus. The tree is taken from Uinuk-ooland coworkers,23 but non-Asian populations have been deleted for simplicity. For sources of frequency data, see Figure 2.

Figure 5. An interpretation of the origin and dispersion of Siberian populations based on HLA allele frequency data.


tered them into haplogroups accord-ing to shared diagnostic mutations.Sets of these haplogroups appear todifferentiate populations on differentcontinents. Thus, European popula-tions are characterized by the posses-sion of haplogroups H, I, J, K, T, U, V,and W; Asian populations by haplo-groups F, G, M, Y, and Z; and nativeAmerican populations by haplogroupsA, B, C, and D.14,17,47–52 Because hap-logroups A, B, C, D are also found insome Asian populations, in particularin some of the Siberian ethnic groups,it can be argued that there is a gene-alogical link between populations onthese two continents. A similar deduc-tion can also be made from the distri-bution of the various haplotypes de-fined for DNA segments on theY-chromosome.28–31 However, the sit-uation is not as straightforward as itmay have seemed originally. For ex-ample, native Americans also possesshaplogroup X, which seems to be ab-sent in Asian populations but presentat relatively high frequencies in Euro-pean populations.53 To account forthese and other anomalies, ad hoc ex-planations have to be introduced.32

The HLA, mtDNA, and Y-chromo-some data can also be used to specifythe manner in which the colonizationof the American continent might havetaken place. While the origin of nativeAmericans from ancient Asian popu-lations is undisputed, the manner ofthis derivation remains contentious.In 1986, Greenberg, Turner, and Ze-gura54 published an influential butcontroversial paper in which theyclassified all of the numerous nativeAmerican languages into threegroups: American Indian (Amerind),Na-Dene, and Eskimo Aleut. On thebasis of this classification, they sug-gested that the New World was origi-nally colonized in three waves of mi-gration that founded the mainlanguage groups: Amerind, more than11,000 years BP; Na-Dene, about9,000 years BP; and Eskimo-Aleut,about 4,000 years BP. They arguedthat tooth morphology data (a batteryof 28 crown and root traits) and genefrequency data (blood group antigens,serum proteins, erythrocyte enzymes,immunoglobulins, and leukocyte anti-gens) match the linguistic classifica-tion and thus support the three-wave

hypothesis. In reviews published withthe paper, linguists and geneticistscriticized the three-wave hypothesis.The former pointed out that the clus-tering together of all American Indianlanguages into a single group is “dis-counted by nearly all specialists”; thelatter found the dental and geneticcorrelations unconvincing. In theyears that followed, the controversystirred by the three-wave hypothesisdid not die down. On the contrary, thehypothesis has remained a sort ofprobe by which all new data sets, in-cluding the HLA, mtDNA, and Y-chro-mosome data sets, must be con-fronted.

Clearly, if tentatively, the HLA datafavor three Siberian sources of HLAdiversity in native Americans. The Na-dler group of native Americans speakthe Carrier-Sekani language of theAthabascan family in the Na-Denelanguage group and live in British Co-lumbia. As shown by the trees in Fig-ures 3 and 4, the HLA-DRB1 andDQB1 frequencies of the Nadler groupare most similar not to those of any ofthe other groups of native Americanstested, but to those of the Nivkh onSakhalin Island and in the LowerAmur region in southeastern Siberia.This grouping suggests that Nivkh andnative Americans speaking Athabas-can languages are derived from acommon ancestral population, whileother native American groups tracetheir origin to other ancestral popula-tions. Similarly, Figure 4 reveals thatGreenland Eskimos are closest to agroup of Siberian populations that in-cludes Siberian Eskimos, Chukchee,and Udegey and excludes other Sibe-rian groups. Accordingly, GreenlandEskimos are presumably derived from adifferent ancestral population than areAthabascan-speaking native Ameri-cans. Finally, all three populationtrees suggest that all of the Amerindpopulations originated from a com-mon ancestral population that wasdifferent from the populations thatled to the Athabascan speakers andthe Greenland Eskimos. In all threepopulation trees, the branch leadingto the Amerinds splits off earlier thando the branches leading to the Atha-bascan speakers or to the Eskimos.This suggests, in agreement with theproposal of Greenberg, Turner, and

Zegura,54 that the founders of the Am-erind populations left Siberia muchearlier than did the founders of theAthabascan speakers and Eskimos.Thus, the HLA data support the viewthat there could have been at leastthree different founding populationsof the native American peoples andthat they came from different placesin Siberia at different times.

The grouping of the Nivkh with theAthabascan speakers deserves a briefcomment. Present-day Nivkh are be-lieved to be descendants of peoplewho, at least since Neolithic times,lived in the lower Amur region andperhaps along the coast of the Sea ofOkhotsk. They expanded to SakhalinIsland in two waves about 2,000 and1,000 BP.55 Although they have beenin contact with various south Tungustribes and Manchu (mainland Nivkh),as well as Ainu and Orok (SakhalinNivkh), they have until recently re-tained their identity, manifested par-ticularly in the uniqueness of theirlanguage. Although no direct link be-tween Nivkh and Athabascan (Na-Dene) speakers has, to our knowledge,been reported, certain parallels havebeen noted between Nivkh and nativeAmericans with respect to language,ethnography, and a system of kinship(http://www.raipon.org/Web_Database/nivkh.html). Like the Nivkh language,the Na-Dene family of languages is anisolate. Similarities of the Na-Denelanguages to Sino-Tibetan languageshave been described,56 but a recentreport claimed a relationship to theYenisey (Ket) family isolate.57

The mtDNA data have variouslybeen interpreted as supportingone,58,59 two,14 three,60 or four61

waves of migration. The evidenceclearly indicates that there were atleast three Siberian (Asian) sourcesfor mtDNA diversity among NativeAmericans. Whether the existence ofthese sources should be interpreted assuggesting one, two, or three migra-tion waves is debatable. One source isindicated by the distribution of haplo-group B. Although it is commonamong native Americans,61,62 in Sibe-ria haplogroup B is restricted to thesouthern parts, having been found inBuriat, Tuvan, and Northern Altaipopulations.15,18 Its presence in South-east Asia and Mongolia63,64 points to


southern Siberia and Central Asia asperhaps being the oldest source of ge-netic diversity among native Ameri-cans. A second source is indicated by amutation in the haplogroup A, specifi-cally by the substitution of C by T at thenucleotide site 16111 of the mtDNA se-quence. Haplogroup A is widely distrib-uted among both native Siberian andnative American populations.14 How-ever, while all native Americans whopossess haplogroup A have a versionwith T at site 16111, in Siberia onlySiberian Eskimos, Chukchee, and Ko-ryak do.16 Hence, northeastern Siberi-ans apparently contributed their shareto the mtDNA diversity of native Amer-icans. A third potential source is sug-gested by haplogroups C and D, which,like haplogroup A, are widespread inboth America and Siberia. The Ameri-can version of the haplogroups have Cor T at site 16325, whereas the Siberianversions have T at this site. Recently,however, the C-version of both haplo-groups has been found in Ulchi (R. Suk-ernik, personal communication) andthe C-version of the C haplogroup hasbeen found in Mongolians.65 This indi-cates that, taken together, central Asiaand southeastern Siberia may havebeen a third contributor to the geneticdiversity of indigenous Americans.

Three Siberian sources of Pre-Co-lumbian American genetic variabilityare also indicated by studies of the Ychromosome, specifically the M45haplogroup defined by a cluster of lociin the nonrecombining part of thechromosome. The haplogroup is di-vided into two subgroups: M45a,which lacks a restriction site calledM173, and M45b, which possessesthis site.31 The M45a subgroup is fur-ther divided into two types, C and T,by a mutation that changed the origi-nal C to T at site 181 of the Y-chromo-some locus called DYS199.66 The M45haplogroup is present in about 29% ofnative Americans.31 The M45a sub-group has been found in North, Cen-tral, and South America, as well as insouthern Siberia (Tuva).31 The M45bsubgroup is present in North and Cen-tral America as well as in eastern Si-beria (in the Udegey and Koryak).31

The T allele at the DYS199 locus (the“M3 marker”) occurs among nativeAmericans at a frequency of �60%and is present in northeastern Siberia

in Chukchee and Siberian Eskimopopulations.30,67 Thus, the M45a hap-logroup, the M45b haplogroup, andthe T-allelic lineage at the DYS199 lo-cus, like the mtDNA A, B, C, and Dhaplogroups and the HLA class IIgenes, identify three different regionsin Siberia in which haplotype lineagesnow characterizing native Americansmight have originated. Other Y-chro-mosome data are consistent with thisinterpretation.28

The main reason why the mtDNA

and Y-chromosome data are open toalternative interpretations is the modeof distribution of variability amongnative Americans. In general, the ge-netic differentiation of native Ameri-cans into the Amerind, Na-Dene, andEskimo-Aleut lineages is contestableas far as the mtDNA and Y-chromo-some systems are concerned. In thecase of mtDNA, the four main haplo-groups A, B, C, and D are found in allthree lineages. There are not enoughdata available on the various popula-

tions to determine whether or not thelineages can be differentiated in termsof gene frequencies. Similarly, in thecase of the Y-chromosome, the M45a,M45b, and M3 markers do not differ-entiate the three lineages unambigu-ously, although a partial demarcationis indicated.

This lack of a clear genetic demar-cation of Amerinds, Na-Denes, andEskimo-Aleuts has been seized uponby proponents of the single-migra-tion-wave hypothesis.58,59 Indeed, ifthe genetic variants are distributedpromiscuously among the three lin-guistic groups, then a single Asiansource containing the progenitors ofall the different present-day variantsmay seem to be a viable alternative.Most molecular anthropologists ap-pear to have little taste for other ex-planations, such as the possibilitythat the tripartite classification is in-correct or that languages are poorindicators of population genealo-gies.

To reconcile the linguistic and ge-netic data, some molecular anthropol-ogists have postulated a backflow ofvariants from the New to the OldWorld, or at least to the regions ofAsia close to the Bering Strait.67 Thispostulate underlies the two-wave hy-pothesis of Karafet and coworkers28:Although three sources of Y-chromo-some variability are indicated, theypropose that there were only two mi-gration waves, one from western Sibe-ria and the other from the eastern andnorthern regions of Lake Baikal,whereby the former is assumed tohave acquired variants in northeast-ern Siberia via gene backflow.Whether one denotes such a scenarioas a two- or three-wave hypothesisseems to us to be a semantic question.

Although gene backflow could alsohave conceivably influenced HLA al-lele frequencies, it seems unlikely thatit would have done so along the divi-sions indicated by the hypothesis ofGreenberg, Turner, and Zegura.54

Clearly, more HLA and other geneticdata will have to be generated before aconsensus can be reached on the peo-pling of America. In our view, allelefrequency data may prove to be moreinformative in this regard than willgene genealogy data.

There may be tworeasons for the specialstatus of the HLA system.First, HLA data oftenencompass not one, buttwo or more loci.Although these loci arelinked and hence arenot fully independentsources of information,when combined theynevertheless make theconclusions morerobust. Second, the highpolymorphism of the fewHLA loci seems tocompensate to somedegree for thelimitations imposed bythe use of a smallnumber of loci.


HOW RELIABLE IS THE HLAEVIDENCE?

HLA gene frequencies are widelyused in attempts to reconstruct gene-alogies of human populations (re-viewed by Roychoudhury and Nei68

and Cavalli-Sforza, Menozzi, and Pi-azza69). From time to time, however,concerns are voiced about the reliabil-ity of the inferences made from thesedata. These concerns are of two kinds,one general and the other specific. Thegeneral concern is that single-locusstudies are prone to a large statisticalerror. While this concern is justified,and inferences based on combineddata from multiple loci are certainly amore reliable source of informationthan are single-locus data, experiencehas shown that population trees basedon HLA data alone are generally ingood agreement with those based onmultilocus sets. There may be two rea-sons for the special status of the HLAsystem. First, HLA data often encom-pass not one, but two or more loci.Although these loci are linked andhence are not fully independentsources of information, when com-bined they nevertheless make the con-clusions more robust. Second, thehigh polymorphism of the few HLAloci seems to compensate to some de-gree for the limitations imposed bythe use of a small number of loci.

The specific concern about the useof HLA loci is that these loci are undernatural selection, which may skew al-lele frequencies independently of themode of population splitting. Indeed,associations of HLA alleles with sus-ceptibility or resistance to infectiousdiseases caused by Plasmodium falci-parum,70 the hepatitis B virus,71 andthe human immunodeficiency virus72

have been reported. However, skew-ing of HLA gene frequencies that isattributable to selection has proveddifficult to demonstrate. The reasonmight be that the selection operatingon HLA loci is of the balancing kind.73

In balancing selection, individualsgenerally have an advantage if theycarry two different alleles rather thanjust one allele. In this case, many al-leles are maintained in a population,but their distribution is determined bychance. Nonetheless, HLA character-ization of a group of populations mustbe regarded as only the first step in a

study of the genetic history of the hu-man species. A more complete pictureof the history will be obtained fromcombined studies of many differentloci.

REFERENCES

1 Windley BF. 1995. The evolving continents, 3rded. Chichester: John Wiley & Sons.2 Friedrich P, Diamond N. 1994. Encyclopedia ofworld cultures, vol. VI. Russia and Euroasia/China. New York: G.K. Hall & Co.3 Bobrick B. 1992. East of the sun: the epic con-quest and tragic history of Siberia. New York:Poseidon.4 Forsyth J. 1992. A history of the peoples ofSiberia. Cambridge: Cambridge University Press.5 Levin MG, Potapov LP, editors. 1956. The peo-ples of Siberia. Moscow: Publishing House of theAcademy of USSR. In Russian.6 Levin MG, Potapov LP, editors. 1964. The peo-ples of Siberia. Dunn SP, Dunn E, translators.Chicago: University of Chicago Press.7 Gorbatcheva V, Federova M. 2000. The peoplesof the Great North: art and civilisation of Siberia.New York: Parkstone Press.8 Sokolov ZP. 1999. Arctis—my home: nations ofthe North; culture of nations of the North. Mos-cow: Severny Prostory. In Russian.9 Ruhlen M. 1987. A guide to the world’s lan-guages, vol. 1: classification. Stanford: StanfordUniversity Press.10 Goebel T. 1999. Pleistocene human coloniza-tion of Siberia and peopling of the Americas: anecological approach. Evol Anthropol 8:208–227.11 Derev’anko AP, Shimkin DB, Powers RW, ed-itors. 1998. The Paleolithic of Siberia. Urbana:University of Illinois Press.12 Goebel T, Aksenov M. 1995. Accelerator ra-diocarbon dating of the initial Upper Paleolithicin southeast Siberia. Antiquity 69:349–357.13 King ML, Slobodin SB. 1996. A fluted pointfrom the Uptar Site, northeastern Siberia. Sci-ence 273:634–636.14 Torroni A, Sukernik RI, Schurr TG, Starik-ovskaya YB, Cabell MF, Crawford MH, ComuzzieAG, Wallace DC. 1993. mtDNA variation of ab-original Siberians reveals distinct genetic affini-ties with native Americans. Am J Hum Genet53:591–608.15 Sukernik RI, Schurr TG, Starikovskaya YB,Wallace DC. 1996. Mitochondrial DNA variationin native Siberians, with special reference to theevolutionary history of American Indians: stud-ies on restriction endonuclease polymorphism.Genetika 32:432–439. In Russian.16 Starikovskaya YB, Sukernik RI, Schurr TG,Kogelnik A, Wallace DC. 1998. MitochondrialDNA diversity in Chukchi and Siberian Eskimos:implications for the genetic history of ancientBeringia and the peopling of the New World.Am J Hum Genet 63:1473–1491.17 Schurr TG, Sukernik RI, Starikovskaya YB,Wallace DC. 1999. Mitochondrial DNA variationin Koryaks and Itel’men: population replacementin the Okhotsk Sea-Bering Sea region during theneolithic. Am J Phys Anthropol 108:1–39.18 Derenko MV, Malyarchuk BA, Dambueva IK,Shaikhaev GO, Dorzhu CM, Nimaev DD, Zakha-rov IA. 2000. Mitochondrial DNA variation in twoSouth Siberian aboriginal populations: implica-tions for the genetic history of North Asia. HumBiol 72:945–973.19 Derbeneva OA, Sukernik RI, Volodko NV,Hosseini SH, Lott MT, Wallace DC. 2002. Analy-

sis of mitochondrial DNA diversity in the Aleutsof the Commander Islands and its implicationsfor the genetic history of Beringia. Am J HumGenet 71:415–421.20 Derbeneva OA, Starikovskaya EB, WallaceDC, Sukernik RI. 2002. Traces of earliest Euroa-sians in the Mansi of Northwest Siberia revealedby mitochondrial DNA analysis. Am J HumGenet 70:1009–1014.21 Mishmar D, Ruiz-Pesini E, Golik P, MacaulayV, Clark AG, Hosseini SH, Brandon M, Easley K,Chen E, Brown MD, Sukernik RI, Olckers A, Wal-lace DC. 2003. Natural selection shaped regionalmtDNA variation in humans. Proc Natl Acad SciUSA 100:171–176.22 Grahovac B, Sukernik RI, O’hUigin C,Zaleska-Rutczynska Z, Blagitko N, Raldugina O,Kosutic T, Satta Y, Figueroa F, Takahata N, KleinJ. 1998. Polymorphism of the HLA class II locusin Siberian populations. Hum Genet 102:27–43.23 Uinuk-ool TS, Takezaki N, Sukernik RI, NaglS, Klein J. 2002. Origin and affinities of indige-nous Siberian populations as revealed by HLAclass II gene frequencies. Hum Genet 110:209–226.24 Uinuk-ool TS, Takezaki N, Derbeneva O, Vo-lodko NV, Sukernik RI. n.d. Polymorphism of theHLA class II loci in three Siberian populations:Aleuts, Kets, and Nganasans. Submitted. Eur JImmunogenet.25 Krylov M, Erdesz S, Alexeeva L, Benevolen-skaya L, Arnett FC, Reveille JD. 1995. HLA classII and HLA-B27 oligotyping in two Siberian na-tive population groups. Tissue Antigens 46:382–386.26 Tokunaga K, Sideltseva EW, Tanaka H, Uch-ikawa C, Nieda M, Sideltsev VV, Zhuravleva E,Imanishi T, Itoh K, Akaza T, Takahashi K, Khal-turin V, Alexeev LP, Juji T. 1995. Distribution ofHLA antigens and haplotypes in the Buryat pop-ulation of Siberia. Tissue Antigens 45:98–102.27 Sartakova ML, Konenkov VI, Prokof’ev VF,Gel’fgat EL, Lamazhaa AM, Dongak LG, Kara-Mongush SI. 1998. Frequency of the HLA-DPgenes and the antigens of the HLA-A, -B, -Cw,and -DR loci in Tuvinians. Genetika 34:1127–1133. In Russian.28 Karafet TM, Zegura SL, Posukh O, Osipova L,Bergen A, Long J, Goldman D, Klitz W, HariharaS, de Knijff P, Wiebe V, Griffiths RC, TempletonAR, Hammer MF. 1999. Ancestral Asian sourc-e(s) of New World Y-chromosome founder hap-lotypes. Am J Hum Genet 64:817–831.29 Santos FR, Pandya A, Tyler-Smith C, PenaSD, Schanfield M, Leonard WR, Osipova L,Crawford MH, Mitchell RJ. 1999. The centralSiberian origin for native American Y chromo-somes. Am J Hum Genet 64:619–628.30 Lell JT, Brown MD, Schurr TG, Sukernik RI,Starikovskaya YB, Torroni A, Moore LG, TroupGM, Wallace DC. 1997. Y chromosome polymor-phisms in Native American and Siberian popula-tions: identification of Native American Y chro-mosome haplotypes. Hum Genet 100:536–543.31 Lell JT, Sukernik RI, Starikovskaya YB, Su B,Jin L, Schurr TG, Underhill PA, Wallace DC.2002. The dual origin and Siberian affinities ofNative American Y chromosomes. Am J HumGenet 70:192–206.32 Eshleman JA, Malhi RS, Smith DG. 2003. Mi-tochondrial DNA studies of Native Americans:conceptions and misconceptions of the popula-tion prehistory of the Americas. Evol Anthropol12:7–18.33 Hammer MF, Zegura SL. 1996. The role of theY chromosome in human evolutionary studies.Evol Anthropol 5:116–134.34 Klein J, Sato A. 2000. The HLA system, part I.N Engl J Med 343:702–709.


35 Imanishi T, Wakisaka A, Gojobori T. 1991.Genetic relationships among various humanpopulations indicated by MHC polymorphisms.In: Tsuji K, Aizawa M, Sasazuki T, Tsuji K,Aizawa M, Sasazuki TS, editors. 1991. Proceed-ings of the Eleventh International Histocompat-ibility Workshop and Conference. Oxford: Ox-ford University Press. p 627–632.

36 Mayer WE, Jonker M, Klein D, Ivanyi P, vanSeventer G, Klein J. 1988. Nucleotide sequencesof chimpanzee Mhc class I alleles: evidence fortrans-species mode of evolution. EMBO J 7:2765–2774.

37 Klein J, Sato A, Nagl S, O’hUigin C. 1998.Molecular trans-species polymorphism. Ann RevEcol Syst 29:1–21.

38 Roitberg-Tambur A, Witt CS, Friedmann A,Safirman C, Sherman L, Battat S, Nelken D,Brautbar C. 1995. Comparative analysis of HLApolymorphism at the serologic and molecularlevel in Moroccan and Ashkenazi Jews. TissueAntigens 46:104–110.

39 Sanchez-Velasco P, Leyva-Cobian F. 2001.The HLA class I and class II allele frequenciesstudied at the DNA level in the Svanetian popu-lation (Upper Caucasus) and their relationshipsto Western European populations. Tissue Anti-gens 58:223–233.

40 Begovich AB, McClure GR, Suraj VC, Hel-muth RC, Fildes N, Bugawan TL, Erlich HA.1992. Polymorphism, recombination, and link-age disequilibrium within the HLA class II re-gion. J Immunol 1481:249–258.

41 Alekseev V. 1998. The physical specificities ofPaleolithic hominids in Siberia. In: Derev’ankoAP, Shimkin DB, Powers RW, editors. The Paleo-lithic of Siberia. Urbana: University of IllinoisPress. p 329–335.42 Serdobov NA. 1971. History of formation ofTuvan Nation. Kyzyl: Tuvan. In Russian.43 Nei M, Roychoudhury AK. 1982. Genetic re-lationship and evolution of human races. EvolBiol 14:1–59.44 Ingman M, Kaessmann H, Paabo S, Gyllen-sten U. 2000. Mitochondrial genome variationand the origin of modern humans. Nature 408:708–713.45 Harding RM, Fullerton SM, Griffiths RC,Bond J, Cox MJ, Schneider JA, Moulin DS, CleggJB. 1997. Archaic African and Asian lineages inthe genetic ancestry of modern humans. Am JHum Genet 60:772–789.46 Crawford MH. 1998. The origins of NativeAmericans: evidence from anthropological genet-ics. Cambridge: Cambridge University Press.47 Wallace DC, Garrison K, Knowler WC. 1985.Dramatic founder effects in Amerindian mito-chondrial DNAs. Am J Phys Anthropol 68:149–155.48 Schurr TG, Ballinger SW, Gan YY, Hodge JA,Merriwether DA, Lawrence DN, Knowler WC,Weiss KM, Wallace DC. 1990. Amerindian mito-chondrial DNAs have rare Asian mutations athigh frequencies, suggesting they derived from

four primary maternal lineages. Am J HumGenet 46:613–623.49 Torroni A, Huoponen K, Francalacci P,Petrozzi M, Morelli L, Scozzari R, Obinu D,Savontaus ML, Wallace DC. 1996. Classificationof European mtDNAs from an analysis of threeEuropean populations. Genetics 144:1835–1850.50 Torroni A, Lott MT, Cabell MF, Chen YS, La-vergne L, Wallace DC. 1994. mtDNA and the or-igin of Caucasians: identification of ancient Cau-casian-specific haplogroups, one of which isprone to a recurrent somatic duplication in theD-loop region. Am J Hum Genet 55:760–776.51 Torroni A, Neel JV, Barrantes R, Schurr TG,Wallace DC. 1994. Mitochondrial DNA “clock”for the Amerinds and its implications for timingtheir entry into North America. Proc Natl AcadSci USA 91:1158–1162.52 Torroni A, Miller JA, Moore LG, Zamudio S,Zhuang J, Droma T, Wallace DC. 1994. Mito-chondrial DNA analysis in Tibet: implications forthe origin of the Tibetan population and its ad-aptation to high altitude. Am J Phys Anthropol93:189–199.53 Brown MD, Hosseini SH, Torroni A, BandeltH-J, Allen JC, Schurr TG, Scozzari R, Cruciani F,Wallace DC. 1998. mtDNA haplogroup X: an an-cient link between Europe/Western Asia andNorth America? Am J Hum Genet 63:1852–1861.54 Greenberg J, Turner IC, Zegura S. 1986. Thesettlement of the Americas: a comparison of lin-guistic, dental and genetic evidence. Curr An-thropol 27:477–497.55 Austerlitz R. 1994. Nivkh. In: Friedrich P, Di-amond N, Friedrich P, Diamond NS. Encyclope-dia of world cultures. New York: G.K. Hall. p283–286.56 Bengston JD. 1994. Edward Sapir and the“Sino-Dene” hypothesis. Anthropol Sci 102:207–230.57 Ruhlen M. 1998. The origin of the Na-Dene.Proc Natl Acad Sci USA 95:13994–13996.58 Stone AC, Stoneking M. 1998. mtDNA analy-sis of a prehistoric Oneota population: implica-tions for the peopling of the world. Am J HumGenet 62:1153–1170.59 Bonatto SL, Salzano FM. 1997. A single andearly migration for the peopling of the Americassupported by mitochondrial DNA sequence data.Proc Natl Acad Sci USA 9:1866–1877.60 Szathmary EJ. 1993. Genetics of aboriginalNorth Americans. Evol Anthropol 1:202–220.61 Horai S, Kondo R, Nakagawa-Hattori Y, Ha-yashi S, Sonoda S, Tajima K. 1993. Peopling ofthe Americas founded by four major lineages ofmitochondrial DNA. Mol Biol Evol 10:23–47.62 Torroni A, Schurr TG, Cabell MF, Brown MD,Neel JV, Larsen M, Smith DG, Vullo CM, WallaceDC. 1993. Asian affinities and continental radia-tion of the four founding Native AmericanmtDNAs. Am J Hum Genet 53:563–590.63 Merriwether DA, Hall WW, Vahlne A, FerrellRE. 1996. mtDNA variation indicates Mongoliamay have been the source for the founding pop-

ulation for the world. Am J Hum Genet 59:204–212.

64 Yao YG, Watkins WAS, Zhang YP. 2000. Evo-lutionary history of the mtDNA 9-bp deletion inChinese populations and its relevance to the peo-pling of east and southeast Asia. Hum Genet107:504–512.

65 Kolman CJ, Sambughin N, Bermingham E.1996. Mitochondrial DNA analysis of Mongolianpopulations and implications for the origin ofNew World founders. Genetics 142:1321–1334.

66 Underhill PA, Jin L, Zemans R, Oefner PJ,Cavalli-Sforza LL. 1996. A pre-Columbian Ychromosome-specific transition and its implica-tions for human evolutionary history. Proc NatlAcad Sci USA 93:196–200.

67 Karafet T, Zegura SL, Vuturo-Brady J, Po-sukh O, Osipova L, Wiebe V, Romero F, Long JC,Harihara S, Jin F, Dashnyam B, Gerelsaikhan T,Omoto K, Hammer MF. 1997. Y chromosomemarkers and trans-Bering Strait dispersals. Am JPhys Anthropol 102:301–314.

68 Roychoudhury AK, Nei M. 1988. Humanpolymorphic genes: world distribution. NewYork: Oxford University Press.

69 Cavalli-Sforza LL, Menozzi P, Piazza A. 1994.The history and geography of human genes.Princeton: Princeton University Press.

70 Hill AVS, Allsopp CEM, Kwiatkowski D, An-stey NM, Twumasi P, Rowe PA, Bennett S, Brew-ster D, McMichael AJ, Greenwood BM. 1991.Common West African HLA antigens are associ-ated with protection from severe malaria. Nature352:595–600.

71 Thursz MR, Thomas HC, Greenwood BM,Hill AV. 1997. Heterozygote advantage for HLAclass-II type in hepatitis B virus infection. NatGenet 17:11–12.

72 Carrington M, Nelson GW, Martin MP, Kiss-ner T, Vlahov D, Goedert JJ, Kaslow R, Buch-binder S, Hoots K, O’Brien SJ. 1999. HLA andHIV-1: heterozygote advantage and B*35-CW*04disadvantage. Science 283:1748–1752.

73 Hughes AL, Nei M. 1989. Nucleotide substi-tution at major histocompatibility complex classII loci: evidence for overdominant selection. ProcNatl Acad Sci USA 86:958–962.

74 Marsh SGE, Parham P, Barber LD. 2000. TheHLA facts book. San Diego: Academic Press.

75 Orita M, Iwahana H, Kanazawa H, HayashiK, Sekiya T. 1989. Detection of polymorphismsof human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc NatlAcad Sci USA 86:2766–2770.

76 Nei M, Tajima F, Tateno Y. 1983. Accuracy ofestimated phylogenetic trees from moleculardata. II. Gene frequency data. J Mol Evol 19:153–170.

77 Saitou N, Nei M. 1987. The neighbor-joiningmethod: a new method for reconstructing phylo-genetic trees. Mol Biol Evol 4:406–425.

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ancestry and kinships of native siberian populations: the hla evidence

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