IANUJAHY !H ARTCLFS Mitochondrial DNa and human evolution Rebecca L Cann", Mark Stoneking Allan C. wilson Department of Biochemistry, University of California, Berkeley, Califomia94720,USA Mitochondrial DNAs from 147 people, drawn from fve geographic populations hate been analysed by restriction mapping All these mitochondrial DNAs stem from one woman who is postulated to have lived about 200, 000 years ago, probably In A ica. All the populations examined except the African population have multiple origins, implying that each area was colonised repeatedly MoLECULAR bIology is now a major source of quantitative and allows recombination to occur. Recombination makes it hard objective information about the evolutionary history of the to trace the history of particular segments of DNA unless tightly human species. It has provided new insights into our genetic linked sites within them are considered divergence from apesl' and into the way in which humans are Our world-wide survey of mitochondrial DNA (mt DNA)adds ted to one another genetically"4. Our picture of genetic to knowledge of the history of the human gene pool in three evolution within the human species is clouded, however, because ways. First, mtDNA gives a magnified view of the diversity it is based mainly on comparisons of genes in the nucleus. present in the human gene pool, because mutations accumulate Mutations accumulate slowly in nuclear genes. In addition, this DNA several times faster than in the nucleus. Second nuclear genes are inherited from both parents and mix in every because mt DNA is inherited maternally and does not recom generation. This mixing obscures the history of individuals and bine, it is a to i for relating individuals to one anothe hex m address: Ipartment ot (e netty, University of Hawai, Honolulu, Hawai 96 there are about 10mt DNA molecules within a typical human and they are usually identical to one another. Typical mam-
ARTICLES NATUR! VOL 325 I JANUARY 198 Number ot dfference D loop IRNA 12SRNA 16S RNA Fig. I Histogram showing the number of site differences between ion maps of mtDNA for all possible pairs of 147 humai Fig. 2 Sequence divergence within 5 geographic areas for (8 )was estimated from co bols for the a,△ malian females consequently behave as haploids, owing to a zontal axis are the bottleneck in the genetically effective size of the population of umbeis of restriction sites in each functional region(D loop mt DNA molecules within each oocyte. This maternal and transfer RNA genes, 12S and 16s ribosomal RNA genes, NADH haploid inheritance means that mt DNA is more sensitive than dehydrogenase subunits 1-5, cytoch nuclear dna to severe reductions in the number of individuals other protein- coding regions) in a population of organisms. A pair of breeding individuals n transmit only one type of mt dNa but carry four haploid sets of nuclear genes, all of which are transmissible to offspring. these 18 people are a reliable source of African mt DNA, we Ihe fast evolution and peculiar mode of inheritance of mt DNa found that 12 of them bear restri provide new perspectives on he where and when the human occur exclusively or predominantly in native sub-Saharan gene pool arose and grew Africans (but not in Europeans, Asians or American Indian Restriction maps nor, indeed, in all such Africans). The mt DNA types in these 12 people are 2-7, 37-41 and 82(see below ) Methods used to MtDNA was highly purified from 145 placentas and two cell puny mt DNA and more detailed ethnographic information on lines, Hela and GM 3043, derived from a Black American and the first four groups are as described.; the New Guinea an aboriginal South African(' Kung), respectively. Most placen. are mainly from the Eastern Highlands of Papua New guinea tas (9%)were obtained from US hospitals, the remainder coming Each purified mI DNA was subjected to high resolution map- ere wtre presentatives of 5 geographic regions: 20 Africans (represent. Hhal, Hpall, Mbol, Taql, Rsal, Hinfl, Haelll, AluI an g the sub-Saharan region), 34 Asians(originating from China Ddel). Restriction sites were mapped by comparing observe ilippines, Indonesia Caucasians (originating from Europe, North Africa, and the mtDNA sequence".In this e identified 467 i Middle East), 21 aboriginal Australians, and 26 aboriginal New sites, of which 195 were polymorphic(that is, absent Guineans. Only two of the 20 Africans in our sample, those one individual). An average of 370 restriction site bearing mtDNA types I and 81(see below) were born in sub. were surveyed, representing about 9% of the 16,569 base-pair sharan Africa. The other 18 people in this sample human mt DNA genome mencans, who bear many non- African nuclear genes probably contributed mainly by Caucasian males. Those males would not Map comparisons be expected to have introduced any mt DNA to the Black The 147 mt DNAs mapped were divisible into 133 distinct types American population. Consistent with our view that most of Seven of these types were found in more than one individual; Table I MtDNA divergence within and between 5 human populations Table 2 Clusters of mI DNA Iypes that are specific to one geographic 0.350 3. Australian 0 Africa 90-180 4. Cauc:stan 021 New une: n 0.31 029 025 43-8 Fur The New guinea 28-55 mean pair wise divergence between hin populations (8,) appear on the diagonal values belov nal(8. y))are the mean For clusters represented by two or more individuals (and calculated genees bet for individuals not I DN es)in variation within those populations with mtDNA divergence occurs at the rate of 2-4% per million years,.ar X and Y. values above the diagonal(8)are interpopulation divergences, corrected Average age in thousands of years based on the assumption lon (I k
ARTICLES &d no individual contaned more than None of t following features with Fig 3 (1)two primary branches, one he five geographic composed entirely of Africans, the other including all 5 of the in two Australia populations studied; and(2)each population stems from multi Among C hree times and two ple lineages connected to the tree at widely dispersed positi more types occured twice. In New Guinea, two additional types Since submission of this manuscript, Horai et al built a tree for our samples of African and Caucasian populations and their found in six individuals sample of a Japanese population by another method their tree A histogram showing the number of restriction site diflerences shares these two feature between pairs of individuals is given in Fig. 1; the average Among the trees investigated was one consisting of five jumber of differences observed between any two humans is 95. primary branches with each branch leading exclusively to one The distnbution is approximately normal, with an excess of of the five populations. This tree, which we call the population pairwise comparisons involving large numbers of differences. specific tree, requires 5l more point mutations than does the d tree of minimum length in Fig 3. The minimum-length tree the extent of nucleotide sequence divergence for eac individuals. These estimates ranged from zero to 1.3 cquires fewer changes at 22 of the 93 phylogenetically-inform tive res on sites than does the population-specific tree, while tions per 100 base pairs, with erage sequence divergence the latter tree required fewer changes at four sites; both trees d of 0.32%, which agrees with that of Brown,who examined require the same number of changes at the remaining 67 sites only 21 humans The mi m-length tree is thus favoured by a score of 22 to Table 1 gives three measures of sequence divergence within 4. The hypothesis that the two trees are equally compatible with and between each of the five populations examined. These the data is statistically rejected, since 22: 4 is significantly measures are related to one another by equation (I different from the expected 13: 13. The minimum-length tree is 5=5y-0.5(6,+8,) (1) hus significantly more parsI an the population specifc tree. where 8, is the mean pairwise divergence (in percent)between a single po African origin ing value for another population(Y),8, We in fer from the tree of minimum length( Fig 3) divergence between individuals belonging to two different popu- is a likely source of the human mitochondrial gene pool. This lations(x and Y), and 8 is a measure of the interpopulation ference comes from the observation that one of the two primary divergence corrected for intrapopulation divergence. Af branches leads exclusively to African mt DNAs (types 1-7, as a group are more vanable(8,=0.47)than other groups. Fig 3)while the secor mary branch also leads to Afr Indeed, the variation within the African population is as great mt DNAs(types 37-41, 45, 46, 70, 72, 81, 82, 111 and 113).By as that between Africans and postulating that the common ancestral mt DNA (type a in Fig. 3) ne within-group variation of Asians(8-0.3 able to that which exists between groups. For Australians, tions needed to account for the geographic distributionof ucaslans, and New Guineans, who show nearly identical mtDNA types. It follows that b is a likely common ancestor of amounts of within- group variation(8,=0.23-0.25), the variation all non- African and many African mt DNAs (types 8-134 in tween groups slightly exceeds that Fi lg When the interpopulational distances(, )are corrected for riation(Table 1), they Multiple lineages per race (8=0.01-0.06) The mean value of the corrected distance among The second implication of the tree Fig 3)that each nor populations(8=0.04)is less than one-seventh of the mean African population has multiple origins- can be illustrated most distance between individuals within a population (0.30). Most simply with the New Guineans. Take, as an example, mt DNA of the mt DNA variation in the human species is therefore shared type 49, a lineage whose nearest relative is not in New Guinea, bet ween populations. A more detailed analysis supports this but in Asia(type 50). Asian lineage 50 is closer genealogically to this New Guinea lineage than to other Asian mt DNA lineages functional constraint Six other lineages lead exclusively to New Guinean mtDNA gure 2 shows the sequence divergence(8, )calculated for each 26-29, 65, 95 and 127-134 in Fig 3). This small region of New population across seven functionally distinct regions of the Guinea (mainly the Eastern Highlands Province)thus seems to Is he d 3),th ding portion of the mtDNA molecule, and the least vari- In the same way, we calculate the minimum numbers of female region is the 16S ribosomal RNA gene(8,=0.2).In genera cans are the most diverse and Asians the next most, across and 3). Each estimate is based on the number of region-specific clusters in the tree(Fig 3, Tables 2 and 3). These umbers Evolutionary tree ranging from 15 to 36(Tables 2 and 3), wil probably rise as A tree relating the 133 types of human mt DNA and the reference more types of human mtDNA are discovered quence(Fig 3)was built by the parsimony method To inter Tentative time scale pret this tree, we make two assumptions, both of which have A time scale can be affixed to the tree in Fig 3 by assuming that ensive empirical support:(1)a strictly maternal mode of mI DNA sequence divergence accumulates at a constant rate in IDNA transmission(so that any variant appearing in a group humans. One way of estimating this rate is to consider the extent of lineages must be due to a mutation occurring in the ancestral of diferentiation within clusters specific to New Guinea(Tabl lineage and not recombination between maternal and patern 2; see also refs 23 and 30), Australia and the New World omes)and(2)each individual is homogeneous for its multi People colonised these regions relatively recently nle mtDNA genomes. We can therefore view the tree as a of 30, 000 years ago for New Guinea 40,000 years ago for tions tr gy linking maternal lineages in modern human popula Australia", and 12, 000 years ago for the New World. These Many trees of minimal or near-minimal length can be ma times enable us to calculate that the mean rate of mtDNA divergence within humans lies between two and four percent from the data; all trees that we have have examined share the per million years; a detailed account of this calculation appears
ARlICLES bD1oOp258973出83郡所611B.6a 0a7937110.1403 m2323131170,3:3m0012 23253032354143 49k11 ND1:315e11.333k94118133.3391e41105122.3537a4 40 33134.599687:6022z 656162 48,6957e4445.7025a758 ATF8:8391e 0.851527ATP6:859212 9526B60; 5:243341HA 10536164656 667.11329 4.11350a NCISTOH- 两23:14322192,1438510.!4509a68123126:1456768 460Bc5cYTb;74749 15723943.15790(1637 15925158190 49k15 LLLL t1L⊥J 1::392112享 quene owpgente5 eque nee dev9申n《 59 8297 8119.J649ct0.165↑ 11 5155 Fig-3 a, Genealogical tree for 1.34 types of human mt DNA(133 restriction maps plus reference sequence); b, comprehensive list of polymorphic d评yDDx;)9甲 oring every site present in only one type of mI DNA was obtained (using theAs witl8 rved bety PAUP from the aboriginal South African( Kung)cell line (GM 3043). no 45 being from the He La cell line and no. 110 being the published human sequence. Black bars, clusters of mtDNA types specific to a given geographic region; asterisks, mt DNA types found in more than I individu type 134 was in six individuals, types 29, 65 and 80 each occured thrice, and other types flagged with asterisks occurred twice. To place the nodes in the tree relative to the percent divergence scale, we took account of the differences observed at all 195 polymorphic sites.b, The I human sequence, with 12 restriction enzymes indicated by the following single letter code a, Alul; b, Apall; c, Ddel; d, Fnu Dll; e, Haelll: f, Hhal, g, Hin/, h, Hpal; i, Hpall; j, Mbol; k, Rsal; 1, Taql. Italicized sites are present in the indicated mt DNA types and nonitalicized sites are absent in the indicated types, parentheses refer to alternative placements of inferred etters in encoding regions and genes for transfer RNA, ribosomal RNA and proteins (ND, NADH dehydrogenase; CO, cytochrome oxidase, AT P, adenosin position 8 in the D Joop that was not found in mIDNA lype I but was present in type 2, etc. Note that since this site is not present in the position 8 is actually a semisite, differing from the Mbol recognition sequence at method of mapping such inferred sites). Not all sites were scored 69. 63. 68. and all of the New Guinea int DNAs: mtDNAs 114 and 121 could D e typed with Rsal. The locations of some om those reported before?3., as do the individuals in which some sites oc n re-examination of previously-studied mtDNAS. elsewhere. This rate is similar to previous estimates from apparent age of this cluster (calculated in Table 3)is 90,0001 ever, it is equally possible that the exodus occurred, estimate of 2%-4% to be reasonable for humans, although as recently as 23-105 thousand years ago(Table 2). The mt DNA additional comparative work is needed to obtain a more exact results cannot tell us exactly when these migrations took placci As Fig. 3 shows, the common ancestral mt DNA(type a)links Other mt dNA studies mtDNA types that have diverged by an average of nearly 0.57 Assuming a rate of 2%.-4% per million years, this implies that individuals". 2 both support an African origin for the human 140,000-290,000 years ago. Similarly, ancestral types b-j may sites in each of 200 mt DNAs from Africa, Asia, Europe and the have existed 62, 000-225, 000 years ago(Table 3) New World, and found 35 mt DNA types. This much smalle When did the migrations from Africa take place? The oldest number of mI DNA types probably reflects the inability of their of the clusters of mI DNA types to contain no African members methods to distinguish between mt DNAs that differ by less thad stems from ancestor r and included types 11-29(Fig 3). The 03% and may account for the greater clustering of mIDNA
---ARTICLES diff ng an African origin for the human nuclear gene poo/ i 1.35 More recent studies of restriction site polymorphisms in nucle Relation to fossil record Our tentative interpretation of the tree( Fig 3)and the time scale (Table 3)fits with one view of the fossil re Homo sapiens occurred first in Africa 3-4). about 140,000 years ago, and that all present-day humans are descet dants of that African population. Archaeologists have observed that blades we go,long before they replaced flake tools in Asia or Europe"6. 47 But the ment between our molecular view and the evidence from palaeoanthropology and archaeology should be treated cautiously for two reasons. First, there is much uncertainty about the ages of these remains. Second, our placement of the common n any other ancestor of all human mtdNa diversity in Africa 140,000 280,000 years ago need not imply that the transformation to anatomically modern Homo sapiens occurred in Africa at this Symbols●, African on time. The mtDNA data tell us nothing of the contributions to this transformation by the genetic and cultural traits of males and females whose mt DNA became extinct types by geographic origin that they observed. (By by hey too Homo has been present in Asia as well as in Africa for at least An alternative view of human evolution rests on evidence that ethods distinguish between mtDNAs that diffe Although Johnson ef al. favoured an Asian origin, they too one million year found that Africans possess the greatest amount of mtDNA to anatomically modern humans occurred in parallel in different variability and that a midpoint rooting of their tree leads to an parts of the Old World33, 49. This hypothesis leads us to expect genetic difierences of great antiquity within widely separated S al. sequenced the large noncoding region, parts of the modern pool of mtDNAs. It is hard to reconcile which includes the displacement loop(D loop), from four the mt DNA results with this hypothesis. The greatest divergences Caucasians and three Black Americans. A parsimony tree for within clusters specific to non-African parts of the World corre- Fig. 4 d to times of only 90,, 000 years. This might imply that th (such as J d Pck for the D loop(at least five times faster than other other mtDNA contributed no surviving mtDNA lineages to the gene pool of regions),(2)a greater diversity among Black American D loop our sequences and (3) that the common ancestor was African Consistent with this implication are features, found recently in the skeletons of the ancient Asian forms, that make Nuclear DNA studies it unlikely that Asian erectus was ancestral to Homo sapiens$e 52 Estimates of genetic distance based on comparative studies of Perhaps the non-African erectus population was sapiens migrants from Africa; incomplete fossils indicating the ar genes their products differ in kind fr mt DNA estimates, The latter are based on the actual number of muta estern Asia at uttiych(75,000-150,000 years ago)and Qafzeh (50,000-70.000 tional differences between mt DNA genomes, while the former years ago)might reflect these frst migrati rely on differences in the frequencies of ecs a and we should expect to find extremely divergent types of mIDNA If there was hybridization between the resident archaic form easured bet ween and within populations. Gene frequencies in Asia and anatomically modern forms emerging from Africa in be infuenced by recombination, genetic drift, selec igration, so the direct relationship found between time ar mutational distance for mtDNA would not be expected in present-day Asians, more divergent than any mtDNA found genetic distances based on nuclear DNA. But studies based of mtDNA polymorphic blood groups, red cell enzymes, and serum protein the Asians studied. 4-6. Although such archaic types of show that( 1) ditferences bet ween racial groups are mtDNA could have been lost from the hybridizing population, those within such groups and (2)the largest gene frequen expanding population is low. Thus we propose that Homo Table 3 Ancestors, lineages and extents of divergence in the geneaological tree for 134 types of human mtDNA Ances endant hneages or clusters specific to a region 85-170 0-140 65-130 025 34 15 Assuming that the mtDNA divergence rate is 2.4 n per million years3,so
--… ETTERS TONATURE NATURE VOL I JANUARY 1987 erectus in Asia was replaced without much mixing with the the overall extent of nuclear dna diversity in both human and ading Homo sapiens from Africa African ape populations. By comparing the nuclear and Conclusions and prospects drial DNA may be possible to find out Studies of mI DNA suggest a view of how, where and when accompanied the t or prolonged bottleneck in population whether a trans modern humans arose that fits with one interpretation of action bet ween palaeoanthropology, archaeology and molecu evidence from ancient human bones and tools. More extensive lar biology will allow a deeper analysis of how our specie molecular comparisons are needed to improve our rooting of arose the mt dNA tree and the calibration of the rate of mtDNA We thank the Foundation for Research into the Origin ergence within the human species. This may provide a more M Man, the National Science Foundation and the NIH for suppe reliable time scale for the spread of human populations and We also thank P. Andrews, K. Bhatia, F.C.Howell,w better estmates of the number of maternal lineages involved Howells,R..Kirk, E. Mayr, E. M. Prager, V M. Sarich, ck founding the non- African populations Stringer and T. White for discussion and help in obtaining It is also important to obtain more quantitative estimates of placentas 29. Horai, s, Gojobori, T& Matsunaga, R, M. Bhatia, k& wiison, A Goodman, M. Humm. Biod 35, 37]-424(1963 &winn,A.C.sne11200.12034967) 3 D. C, Garrson, K. & Kno hrop445-466199 A. E cf oL Th D Cavall,-Sr 4,362-37941961 36. Munay, J.C. er aL Poc nain. Acad. Sci. U.S.A 81, 3486-3490(1984) 91982} 38. Coope d.n e of Hum g mnet 62. orm205 4i9856 hin.5.L&Higs,D.R.Cf42809-819(985 pp68,107-12241985 34 16. oho. P D. Van dr Walle. M ). Ea of the Fossil Etidence Hauswinh, ww. Nature 306. 40004c 4车B Acad Sn L.s.A7,3605-3601980 sUsA82,2895-2899(1985) mans: A world Suruey of the Fossil Evidence icds L.& Eocb. L A. Cancer Res 45 1809-1814(1985 1 y 49 Cope, c. s. The nri d rd SINISa n w x 92 293) 71 ey, Ca ilson,A.C in Genetic vernal ropical Porulanons (eds Roberts, (. T. Destefan Cann, R. L Brown. w, M,& wilson.AC wy of the Fossil Eanence(tds Smith, F. H.& Spencer, F)51-136(Liss. New a06、4794991984) 54 et632433201984) M. Cann. RL& wi 煤 Farris,J.S.Am. Nat. 106, 645-66(/0298 4visa:, . &. Naiscpae.. 105(1984) 28. Greenberg. B. D, Newbold, I. E. Sugino, A Gene 21 33-49(1983)