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Mitochondrial lineage M1 traces an early human backflow to Africa

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  BioMed   Central Page 1 of 12 (page number not for citation purposes) BMC Genomics Open Access Research article Mitochondrial lineage M1 traces an early human backflow to Africa  AnaMGonzález* †1 , JoséMLarruga †1 , KhaledKAbu-Amero 2 , YufeiShi 2 , JoséPestano 3  and VicenteMCabrera 1  Address: 1 Department of Genetics, Faculty of Biology, University of La Laguna, Tenerife 38271, Spain, 2 Department of Genetics, King Faisal Specialist Hospital & Research Center, Riyadh 11211, Saudi Arabia and 3 Department of Genetics, Faculty of Medicine, University of Las Palmas de Gran Canaria, Las Palmas 35080, SpainEmail: AnaMGonzález*-amglez@ull.es; JoséMLarruga-jlarruga@ull.es; KhaledKAbu-Amero-kamero@kfshrc.edu.sa;  YufeiShi-yufei@kfshrc.edu.sa; JoséPestano-jpestano@dbbf.ulpgc.es; VicenteMCabrera-vcabrera@ull.es* Corresponding author †Equal contributors Abstract Background: The out of Africa hypothesis has gained generalized consensus. However, manyspecific questions remain unsettled. To know whether the two M and N macrohaplogroups thatcolonized Eurasia were already present in Africa before the exit is puzzling. It has been proposedthat the east African clade M1 supports a single srcin of haplogroup M in Africa. To test the validityof that hypothesis, the phylogeographic analysis of 13 complete mitochondrial DNA (mtDNA)sequences and 261 partial sequences belonging to haplogroup M1 was carried out. Results: The coalescence age of the African haplogroup M1 is younger than those for other MAsiatic clades. In contradiction to the hypothesis of an eastern Africa srcin for modern humanexpansions out of Africa, the most ancestral M1 lineages have been found in Northwest Africa andin the Near East, instead of in East Africa. The M1 geographic distribution and the relative ages of its different subclades clearly correlate with those of haplogroup U6, for which an Eurasianancestor has been demonstrated. Conclusion: This study provides evidence that M1, or its ancestor, had an Asiatic srcin. Theearliest M1 expansion into Africa occurred in northwestern instead of eastern areas; this earlyspread reached the Iberian Peninsula even affecting the Basques. The majority of the M1a lineagesfound outside and inside Africa had a more recent eastern Africa srcin. Both western and easternM1 lineages participated in the Neolithic colonization of the Sahara. The striking parallelismbetween subclade ages and geographic distribution of M1 and its North African U6 counterpartstrongly reinforces this scenario. Finally, a relevant fraction of M1a lineages present today in theEuropean Continent and nearby islands possibly had a Jewish instead of the commonly proposedArab/Berber maternal ascendance. Background  The reconstruction of human history is a multidiscipli-nary objective. Alternative models proposed to explainthe srcin and dispersion of modern humans on the basisof paleoanthropological data [1] have received unevensupport from other disciplines. From a genetic perspec-tive, uniparental non-recombining markers have depictedthe most complete and coherent picture of the srcin of  Published: 9 July 2007 BMC Genomics  2007, 8 :223doi:10.1186/1471-2164-8-223Received: 4 September 2006Accepted: 9 July 2007This article is available from: http://www.biomedcentral.com/1471-2164/8/223© 2007 González et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the srcinal work is properly cited.  BMC Genomics  2007, 8 :223http://www.biomedcentral.com/1471-2164/8/223Page 2 of 12 (page number not for citation purposes) modern humans, clearly favoring the recent out-of-Africahypothesis. The greatest diversity and the deepest phylo-genetic branches for both Y-chromosome [2,3] and mtDNA [4,5] have been found in Africa. These African lin- eages have coalescence ages [6-9] compatible with a recent   African srcin of modern humans as proposed by fossil[10,11] and archaeological studies [12]. Furthermore, only more derived lineages have been found out of Africasupporting the hypothesis that, in their worldwide disper-sion, modern humans replaced archaic humans insideand outside Africa. It seems that radiation in Africa of Y-chromosome M168 derived lineages [13] and L3 mtDNA lineages [14] preceded the out-of-Africa expansion. Focus-ing on mtDNA, all non-African lineages belong to twofounder clusters, named M and N, which share a commonroot with their L3 African counterpart. Two possible out-of-Africa routes have been proposed: A southern coastalroute bordering the Read Sea and an Eurasian continentalroute through the Levant. Based on mitochondrial phylo-geography it was proposed that M lineages expanded withthe coastal route to southern Asia and Oceania and N lin-eages by the continental route to Eurasia [7]. However, theposterior detection of primitive N lineages in southernareas as India [15,16] and Australia [6,17] weakened that  hypothesis [18]. As, in addition, the founder ages of Mand N are very similar, the alternative hypothesis, that Mand N founders derived from a single African migration, was favored by several authors [16,19-21]. Another  related disjunctive yet not settled is whether M and N (andits main branch R) arose inside or outside Africa [20]. Thedetection of a basal branch of haplogroup M in Africa(M1) gave support to the idea that haplogroup M srci-nated in eastern Africa and was carried towards Asia withthe out-of-Africa expansion [22]. The alternative hypothe-sis, that haplogroup M1 could trace a posterior backflow to Africa from Asia, considered by several authors[7,21,23,24] has not yet gained experimental support  because, until now, no ancestral M1 lineages have beenfound outside Africa [21,24,25].  To shed light on this haplogroup we have constructed aphylogeny of the M1 clade based on the analysis of 13complete or nearly complete mitochondrial sequencesrepresenting the main branches of M1 and realized a phy-logeographic study using 261 partial M1 sequences todetermine the most probable age and srcin of this cladeand the temporal and spatial frame of its secondary expansions in Africa and Eurasia. Results  Although we have only completely sequenced a limitednumber of M1 lineages, the combination of HVSI haplo-types and RFLP status carried out for the rest of our M1samples allow us to be confident that we have not missedany new basic M1 lineage. As an outgroup of the M1 genomic phylogenetic tree (Fig.1) we used a published Indian M30 complete sequence[25]. When this M30 lineage is compared to the rare Msequence previously detected in two Palestinians [26], it isevident that it belongs to the Indian super-clade M4'30, asit shares the basal mutation 12007. More specifically it belongs to the M30 branch because it also has transition15431. M30 has a broad geographic, ethnic and linguistic range in India. It has been detected in northern and south-ern India, in Australoid and Caucasoids, and in Dravidand Indo-European speakers [24,25]. So, instead of an autochthonous Near East M lineage, its presence in Pales-tine is probably due to a recent gene flow from India. After careful re-reading and partial re-sequencing of two previ-ously published M1 sequences [7], we have detected inthem the following errors: both have the 12950C transver-sion, and, in addition M1,1 has the 6671 transition andM1,2 the 13111 transition. Taking these modificationsinto account, from the M basal type, haplogroup M1 ischaracterized by one transversion (12950C) and four transitions (6446, 6680, 12403, and 14110) in the coding region and by a five transitions motif (195, 16129, 16189,16249, and 16311) in the non-coding region (Fig. 1). Thishaplogroup can be RFLP diagnosed by a  Mnl I site loss at position 12402. Two main branches, M1c and M1abde,respectively defined by transitions 13111 and 6671,sprout from the root. Based on partial sequences M1c wasdefined by transition 16185 [21]. However, not all M1c lineages present this mutation that, in addition, recur-rently appears in a M1b1 lineage. It seems that for popu-lation studies M1c could be better diagnosed by a Dde Isite loss using a modified reverse primer (Table 1). It issurprising that none of the three M1c complete sequenceshave an eastern Africa ancestry: one (Jor771) has a Levan-tine srcin and the other two belong to West sub-Saharan Africa (SER558) and West Mediterranean (VAL1881)areas. The latter two sequences conform a new M1c1 sub-clade defined by transitions 10895 and 16399 that can beRFLP diagnosed at 10895 position (Table 1). In relation tothe M1abde cluster, it is also surprising that one lineagethat directly branched out from the root (BER957) has anorthwestern, not eastern, Berber ancestry. All the rest of lineages shared the 813 transition forming the M1abdcluster. Again, an isolate offshoot of Basque ancestry (BASV82) sprouts from its root. Subclade M1b was char-acterized by an RFLP site gain (+15882  Ava II) and loss of -15883 Hae III [22]. Later an M1b subclade defined by thenon-coding motif 16260–16320 and restricted to East  Africans was identified [21]. Consistently, none of our M1b sequences from western areas has that motif. The last cluster, M1a, was first distinguished by RFLP +12345 Rsa I[22] and, after that, further characterized by transition16359 [21]. In addition it also has transition 3705 at itsroot (Fig. 1). M1a is the most prominent clade in eastern Africa. However, its expansion occurred later than the  BMC Genomics  2007, 8 :223http://www.biomedcentral.com/1471-2164/8/223Page 3 of 12 (page number not for citation purposes) other M1 branches (Fig. 1). An M1a subclade, M1a2,defined by transition 9053, that can be RFLP diagnosed(Table 1), testifies a posterior spread of M1a to western Asia. Geographic distribution of M1 Figure 2 shows the reduced median network obtainedfrom the 261 M1 haplotypes found in a global searchcomprising more than 38,713 HVSI sequences. In Africa,haplogroup M1 has supra-equatorial distribution (seeadditional files 1 and 2). As previously reported its highest  frequencies and diversities (Table 2) are found in Ethiopiain particular and in East Africa in general. Two appreciablegradients exist. Frequencies significantly diminished fromEast to West and also going South to sub-Saharan areas.M1 is not uncommon in the Mediterranean basin show-ing a peak in the Iberian Peninsula. However, it is rare in Phylogenetic tree based on complete M1 sequences Figure 1Phylogenetic tree based on complete M1 sequences . Numbers along links refer to nucleotide positions. C, G indicate transversions; d deletions and i insertions. Recurrent mutations are underlined. Star differs from rCRS [62, 63] at positions: 73, 263, 311i, 750, 1438, 2706, 4769, 7028, 8701, 8860, 9540, 10398, 10873, 11719, 12705, 14766, 15301, 15326, 16223 and 16519. Subject srcins are: Asian (ASI HER; [54]) and 2 Ethiopians (AFR-KI43 and AFR-KI15; [55]) only analyzed for coding region; Georgian (GEO 2463); Indian (IND-B156; [25 2 Jordanians (JOR 771; [7] and JOR 841); 2 Moroccans (MOR 252; [7] and BER 957 = Berber); Saudi Arab (SAU ARA); Serere from Senegal (SER 558); 3 Spanish (Basque = BAS V82, Castilian = CAS 2490, and Valencian = VAL 1881). Doted branches include subjects only analyzed for RFLP and HVI region [22]. Roman num-bers refers to the Quintana-Murci et al. [22] nomenclature. 6446668012403195195A12007514dCA15431303i104004891478315043163111636216399 M4’30 14110161291618912950C M 162496671370512346147695301117647311176136371624916223 BER957 514iCA7091088512414160932438303ii131111631110895 813 BASV82 1622315884 M1 M1c M1abdeM1b 16249 SER558 5471514dCA55096251244213754161081636016399 M1c1M1abd 152311iii513151725938392919613149T AFRKI-43  1412716182C16183C303i MOR 252 108731618516190d CAS2490 M1b1 16359162606378 AFRKI-15 1593016399C JOR841 930785313152303ii83139053 GEO2463SAUARA 15249859869 M1a 4011852195451104414182 ASIHER 9053 M1a2 JOR771 303ii4661464515247G1567016129886816185 VAL1881 303ii27461495615212314416182C16183C1368116183C1614816183C9bp del827036044795G1363516278 M1a1 (III) M1a3 (IV)(II) M30 89111609316234 INDB156 Table 1: Diagnostic RFLPs for different M1 clusters ClusterDiagnostic RFLPM1-12402 Mnl I (1) +12950 Aci I, +14110 Ear IM1a+12345 RsaI (2) M1b-15883 HaeIII/+15882 Ava II (2) M1c-13110 Dde I (3) M1a2-9052 Hae II/-9053 Hha IM1b1-15172 Hae IIIM1c1+10893 Taq I 1 = [18] 2 = [21, 22] 3 = The primers used in the amplification were: L13069 = 5' AggCCCCACCCCAgTCTCAg 3' and the modify H13112* = 5' gCTAgggggTggAAgCggATgACTA 3'  BMC Genomics  2007, 8 :223http://www.biomedcentral.com/1471-2164/8/223Page 4 of 12 (page number not for citation purposes) continental Europe. Although in low frequencies, its pres-ence in the Middle East has been well established from theSouth of the Arabian Peninsula to Anatolia and from theLevant to Iran. The central HVSI haplotype (16129–16189–16223–16249–16311) has been found only oncein northwestern India [27]. Another possible Indian M1candidate is the derived sequence: 16086–16129–16223–16249–16259–16311 [28]. However, in two recent stud-ies in which 24 [24] and 56 [25] Indian M complete sequences were analyzed no ancestral M1 lineages havebeen found. M1 haplotypes have also been occasionally spotted in the Caucasus and the Trans Caucasus [23,29] and in Central Asia [30]. It seems that, going east, M1 evenreached the Tibet as the HVSI diagnostic motif was sam-pled there [31]. However, although haplotypes sharing four of the five HVSI transitions defining M1 (16129–16223–16249–16278–16311–16362; 16129–16223–16234–16249–16311–16362) have been sampled in Thailand and Han Chinese [32,33], complete sequencing  have unequivocally allocated them in the D4a branch of D, the most abundant haplogroup representing M in East  Asia. As commented previously, this is a clear example of the danger of establishing affinities between geographi-cally distant areas only on the basis of HVSI homologiesas, often, they are the product of geographic isolation andmolecular convergence [18]. Within this sparse but geo-graphically wide range of M1 distribution its three identi-fied branches also had uneven radiations. Although M1a(HVSI identified by the 16359 transition) is present in allthe M1 range, its greatest frequencies and diversities arefound in Ethiopia and eastern Africa (Table 2), pointing tothis area as the most probable srcin of the M1a expan-sion in all directions, with particular incidence in western Asia and sub-Saharan Africa. Not all the M1b lineages canbe HVSI identified; however, several specific subcladeshave different locations. Those characterized by transi-tions 16260–16320 [21], and by presence of 16182 tran-sition and 16265C transversion [22] are restricted toEthiopia with occasional spreads to eastern Africa. Inaddition, there is an M1b branch, identified by 16185transition and 16190 deletion that has a northwestern dis-tribution excepting a Jordan haplotype (Fig. 2). Despitethat M1c cannot be unequivocally defined by transition16185, it can be stated that M1c is an overwhelmingly Northwest African clade which spreads to the Mediterra-nean and West sub-Saharan Africa areas. Finally, other unclassified M1 branches have also different geographic ranges. Those identified by the presence of 16357 transi-tion and by the reversion of the diagnostic position 16129are of Ethiopian eastern Africa adscription, while clusterscharacterized by loss of the diagnostic position 16223 andby the 16399 transition have a northwestern distribution(Fig. 2). However, M1 assignation of haplotypes, whichlack any of the basic positions, based only on HVSI infor-mation is risky when they share other diagnostic positions with different haplogroups. For instance, the Russian hap-lotype 16183C–16189–16249–16311, classified as M1on the basis of its HVSI sequence [34] also matches withhaplotypes assigned to the U1a clade [35]. The presence in the Mediterranean basin and in West sub-Saharan Africa of M1a and M1c lineages can be taken asproof that these areas received influences both from the West and East North African centers of M1 radiation.Quantitative confirmation of the above described patternsare provided by AMOVA and pairwise distances based onFST analyses using the groups and populations describedin Material and Methods and taking into account haplo-typic molecular differences. As usual the bulk of the vari-ation, 90%, is within populations, 6% is due todifferences among groups and 4% to differences among populations within groups. Pairwise differences betweenpopulations (Table 3) offer a more detailed view. There ishomogeneity between populations within eastern Africa,small differences (p < 0.05) within western Africa andstrong heterogeneity between these main areas (p <0.001). On the contrary, Iberian Peninsula has significant differences with the rest of Europe. In turn, West Asia con-forms an homogenous continuum with East Africa andEurope excepting Iberian Peninsula and the latter is not significantly different of western Africa. All these resultscan be explained as due to the differential radiation of M1a from East Africa and M1c from Northwest Africa, theIberian Peninsula being mostly influenced by Northwest  Africa and the rest of Europe and western Asia by East  Africa.  M1 haplotypes in Jews Several M1 haplotypes have been detected in Jewish com-munities albeit in low frequencies [36,37]. However,  when compared with non-Jew populations they show sig-nificantly higher frequencies for the whole M1 haplo-group (p = 33.54***) and for M1a in particular (p =24.90***). The only striking exception is that of theMoroccan Jews for which no M1 lineages have beendetected at all [36]. Interestingly, all M1 lineages found inJews, except two, belong to the eastern clade M1a (Fig. 2). Therefore, as for the bulk of the M1 Near East haplotypes,the most probable srcin of these Jewish M1 lineages isthe result of an eastern African expansion around 5000 years ago. Another peculiarity of M1 in Jewish communi-ties is its reduced haplotypic diversity (Table 2) which hasbeen already detected for other mtDNA lineages [36,38].In addition, there is a strong M1 geographic differentia-tion among Jewish communities. For example, all Euro-pean Ashkenazi Jews have only one M1a lineagecharacterized by a transition in the 16289 position that has not been detected in other Jew or non-Jew popula-tions. Similarly, all West Asian Jews shared an identicalM1a motif characterized by a transition in the 16209 posi-
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