Maternal History of Oceania from Complete mtDNA Genomes: Contrasting Ancient Diversity with Recent Homogenization Due to the Austronesian Expansion

Archaeology, linguistics, and existing genetic studies indicate that Oceania was settled by two major waves of migration. The first migration took place approximately 40 thousand years ago and these migrants, Papuans, colonized much of Near Oceania. Approximately 3.5 thousand years ago, a second expansion of Austronesian-speakers arrived in Near Oceania and the descendants of these people spread to the far corners of the Pacific, colonizing Remote Oceania. To assess the female contribution of these two human expansions to modern populations and to investigate the potential impact of other migrations, we obtained 1,331 whole mitochondrial genome sequences from 34 populations spanning both Near and Remote Oceania. Our results quantify the magnitude of the Austronesian expansion and demonstrate the homogenizing effect of this expansion on almost all studied populations. With regards to Papuan influence, autochthonous haplogroups support the hypothesis of a long history in Near Oceania, with some lineages suggesting a time depth of 60 thousand years, and offer insight into historical interpopulation dynamics. Santa Cruz, a population located in Remote Oceania, is an anomaly with extreme frequencies of autochthonous haplogroups of Near Oceanian origin; simulations to investigate whether this might reflect a pre-Austronesian versus Austronesian settlement of the island failed to provide unequivocal support for either scenario.     

A cautionary tale on ancient migration detection: mitochondrial DNA variation in Santa Cruz Islands,Solomon Islands

Over the past decade, the origin of the first Malayo-Polynesian settlers of the island Pacific has become a contentious issue in molecular anthropology as well as in archaeology and historical linguistics. Whether the descendants of the ancestral Malayo-Polynesian speakers moved rapidly through Indonesia and Island Melanesia in a few hundred years, or whether they were the product of considerable intermingling within the more westerly part of the latter region, it is widely accepted that they were the first humans to colonize the distant Pacific islands beyond the central Solomon Islands approximately 3,000 years ago. The Santa Cruz Islands in the Eastern Solomons would have most likely been the first in Remote Oceania to be colonized by them. Archaeologically, the first Oceanic Austronesian settlement of this region appears to have been overlain by various later influences from groups farther west in a complex manner. Molecular anthropologists have tended to equate the spread of various Austronesian-speaking groups with a particular mitochondrial variant (a 9-base-pair [bp] deletion with specific D-loop variants). We have shown before that this is an oversimplified picture, and assumed that the Santa Cruz situation, with its series of intrusions, would be informative as to the power of mitochondrial DNA haplotype interpretations. In the Santa Cruz Islands, the 9-bp deletion is associated with a small number of very closely related hypervariable D-loop haplotypes resulting in a star-shaped Bandelt median network, suggesting a recent population expansion. This network is similar to Polynesian median networks. In a pairwise mismatch comparison, the Santa Cruz haplotypes have a bimodal distribution, with the first cluster being composed almost entirely of the 9-bp-deleted haplotypes-again attesting to their recent origins. Conversely, the nondeleted haplogroups bear signatures of more ancient origins within the general region. Therefore, while the profiles of the two sets of haplotypes indicate very distinctive origins in different populations with divergent expansion histories, the sequence of their introduction into the Santa Cruz Islands clearly does not follow simply.     

The impact of the Austronesian expansion: evidence from mtDNA and Y chromosome diversity in the Admiralty Islands of Melanesia

The genetic ancestry of Polynesians can be traced to both Asia and Melanesia, which presumably reflects admixture occurring between incoming Austronesians and resident non-Austronesians in Melanesia before the subsequent occupation of the greater Pacific; however, the genetic impact of the Austronesian expansion to Melanesia remains largely unknown. We therefore studied the diversity of nonrecombining Y chromosomal (NRY) and mitochondrial (mt) DNA in the Admiralty Islands, located north of mainland Papua New Guinea, and updated our previous data from Asia, Melanesia, and Polynesia with new NRY markers. The Admiralties are occupied today solely by Austronesian-speaking groups, but their human settlement history goes back 20,000 years prior to the arrival of Austronesians about 3,400 years ago. On the Admiralties, we found substantial mtDNA and NRY variation of both Austronesian and non-Austronesian origins, with higher frequencies of Asian mtDNA and Melanesian NRY haplogroups, similar to previous findings in Polynesia and perhaps as a consequence of Austronesian matrilocality. Thus, the Austronesian language replacement on the Admiralties (and elsewhere in Island Melanesia and coastal New Guinea) was accompanied by an incomplete genetic replacement that is more associated with mtDNA than with NRY diversity. These results provide further support for the "Slow Boat" model of Polynesian origins, according to which Polynesian ancestors originated from East Asia but genetically mixed with Melanesians before colonizing the Pacific. We also observed that non-Austronesian groups of coastal New Guinea and Island Melanesia had significantly higher frequencies of Asian mtDNA haplogroups than of Asian NRY haplogroups, suggesting sex-biased admixture perhaps as a consequence of non-Austronesian patrilocality. We additionally found that the predominant NRY haplogroup of Asian origin in the Admiralties (O-M110) likely originated in Taiwan, thus providing the first direct Y chromosome evidence for a Taiwanese origin of the Austronesian expansion. Furthermore, we identified a NRY haplogroup (K-P79, also found on the Admiralties) in Polynesians that most likely arose in the Bismarck Archipelago, providing the first direct link between northern Island Melanesia and Polynesia. These results significantly advance our understanding of the impact of the Austronesian expansion and human history in the Pacific region.     

Affinities among Melanesians,Micronesians, and Polynesians: a neutral biparental genetic perspective

The human colonization of Remote Oceania, the vast Pacific region including Micronesia, Polynesia, and Melanesia beyond the northern Solomon Islands, ranks as one of the greatest achievements of prehistory. Many aspects of human diversity have been examined in an effort to reconstruct this late Holocene expansion. Archaeolinguistic analyses describe a rapid expansion of Austronesian-speaking "Lapita people" from Taiwan out into the Pacific. Analyses of biological markers, however, indicate genetic contributions from Pleistocene-settled Near Oceania into Micronesia and Polynesia, and genetic continuity across Melanesia. Thus, conflicts between archaeolinguistic and biological patterns suggest either linguistic diffusion or gene flow across linguistic barriers throughout Melanesia. To evaluate these hypotheses and the general utility of linguistic patterns for conceptualizing Pacific prehistory, we analyzed 14 neutral, biparental genetic (short tandem repeat) loci from 965 individuals representing 27 island Southeast Asian, Melanesian, Micronesian, and Polynesian populations. Population bottlenecks during the colonization of Remote Oceania are indicated by a statistically significant regression of loss of heterozygosity on migration distance from island Southeast Asia (r = 0.78, p < 0.001). Genetic and geographic distances were consistently correlated (r > 0.35, p < 0.006), indicating extensive gene flow primarily focused among neighboring populations. Significant correlations between linguistic and geographic patterns and between genetic and linguistic patterns depended upon the inclusion of Papuan speakers in the analyses. These results are consistent with an expansion of Austronesian-speaking populations out of island Southeast Asia and into Remote Oceania, followed by substantial gene flow from Near Oceanic populations. Although linguistic and genetic distinctions correspond at times, particularly between Western and Central-Eastern Micronesia, gene flow has reduced the utility of linguistic data within Melanesia. Overall, geographic proximity is a better predictor of biparental genetic relationships than linguistic affinities.     

Ancient voyaging and Polynesian origins

The "Polynesian motif" defines a lineage of human mtDNA that is restricted to Austronesian-speaking populations and is almost fixed in Polynesians. It is widely thought to support a rapid dispersal of maternal lineages from Taiwan ~4000 years ago (4 ka), but the chronological resolution of existing control-region data is poor, and an East Indonesian origin has also been proposed. By analyzing 157 complete mtDNA genomes, we show that the motif itself most likely originated >6 ka in the vicinity of the Bismarck Archipelago, and its immediate ancestor is >8 ka old and virtually restricted to Near Oceania. This indicates that Polynesian maternal lineages from Island Southeast Asia gained a foothold in Near Oceania much earlier than dispersal from either Taiwan or Indonesia 3-4 ka would predict. However, we find evidence in minor lineages for more recent two-way maternal gene flow between Island Southeast Asia and Near Oceania, likely reflecting movements along a "voyaging corridor" between them, as previously proposed on archaeological grounds. Small-scale mid-Holocene movements from Island Southeast Asia likely transmitted Austronesian languages to the long-established Southeast Asian colonies in the Bismarcks carrying the Polynesian motif, perhaps also providing the impetus for the expansion into Polynesia.     

Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomes

The settlement of the many island groups of Remote Oceania occurred relatively late in prehistory, beginning approximately 3,000 years ago when people sailed eastwards into the Pacific from Near Oceania, where evidence of human settlement dates from as early as 40,000 years ago. Archeological and linguistic analyses have suggested the settlers of Remote Oceania had ancestry in Taiwan, as descendants of a proposed Neolithic expansion that began approximately 5,500 years ago. Other researchers have suggested that the settlers were descendants of peoples from Island Southeast Asia or the existing inhabitants of Near Oceania alone. To explore patterns of maternal descent in Oceania, we have assembled and analyzed a data set of 137 mitochondrial DNA (mtDNA) genomes from Oceania, Australia, Island Southeast Asia, and Taiwan that includes 19 sequences generated for this project. Using the MinMax Squeeze Approach (MMS), we report the consensus network of 165 most parsimonious trees for the Oceanic data set, increasing by many orders of magnitude the numbers of trees for which a provable minimal solution has been found. The new mtDNA sequences highlight the limitations of partial sequencing for assigning sequences to haplogroups and dating recent divergence events. The provably optimal trees found for the entire mtDNA sequences using the MMS method provide a reliable and robust framework for the interpretation of evolutionary relationships and confirm that the female settlers of Remote Oceania descended from both the existing inhabitants of Near Oceania and more recent migrants into the region.     

Melanesian and Asian origins of Polynesians: mtDNA and Y chromosome gradients across the Pacific

The human settlement of the Pacific Islands represents one of the most recent major migration events of mankind. Polynesians originated in Asia according to linguistic evidence or in Melanesia according to archaeological evidence. To shed light on the genetic origins of Polynesians, we investigated over 400 Polynesians from 8 island groups, in comparison with over 900 individuals from potential parental populations of Melanesia, Southeast and East Asia, and Australia, by means of Y chromosome (NRY) and mitochondrial DNA (mtDNA) markers. Overall, we classified 94.1% of Polynesian Y chromosomes and 99.8% of Polynesian mtDNAs as of either Melanesian (NRY-DNA: 65.8%, mtDNA: 6%) or Asian (NRY-DNA: 28.3%, mtDNA: 93.8%) origin, suggesting a dual genetic origin of Polynesians in agreement with the "Slow Boat" hypothesis. Our data suggest a pronounced admixture bias in Polynesians toward more Melanesian men than women, perhaps as a result of matrilocal residence in the ancestral Polynesian society. Although dating methods are consistent with somewhat similar entries of NRY/mtDNA haplogroups into Polynesia, haplotype sharing suggests an earlier appearance of Melanesian haplogroups than those from Asia. Surprisingly, we identified gradients in the frequency distribution of some NRY/mtDNA haplogroups across Polynesia and a gradual west-to-east decrease of overall NRY/mtDNA diversity, not only providing evidence for a west-to-east direction of Polynesian settlements but also suggesting that Pacific voyaging was regular rather than haphazard. We also demonstrate that Fiji played a pivotal role in the history of Polynesia: humans probably first migrated to Fiji, and subsequent settlement of Polynesia probably came from Fiji.     

mtDNA lineage analyses: origins and migrations of Micronesians and Polynesians

The islands of Micronesia and Polynesia collectively comprise the last major region of the globe to be settled by humans. Both of these groups of islands were colonized within the last 4,000 years by Austronesian-speaking agriculturists. Based on biogeographic and linguistic patterns, central-eastern Micronesia and Polynesia are included by many in a single category called Remote Oceania. Similarities of biologic, linguistic, and cultural traits within Remote Oceania highlight a question central to Oceanic studies: Are similarities among islands due to a common origin of isolated communities, to ongoing interactions among islands, or both? Analyses of mitochondrial DNA (mtDNA) sequences reveal that most remote Oceanic populations are polyphyletic. These polyphyletic populations violate the assumptions of many genetic distance and population demography models and so are problematic to interpret. The majority of mtDNA sequences from Micronesian and Polynesian populations are derived from Asia, whereas others are inferred to have originated in New Guinea. These data support an Island Southeast Asian origin and a colonization route along the north coast of New Guinea. The Marianas and Yap proper (main island) appear to have been independently settled directly from Island Southeast Asia, and both have received migrants from Central-Eastern Micronesia since then. Palau clearly demonstrates a complex prehistory including a significant influx of lineages from New Guinea. Thus genetic similarities among Micronesian and Polynesian populations result, in some cases, from a common origin, and in others, from extensive gene flow.     

Brief communication: mitochondrial DNA variation suggests extensive gene flow from Polynesian ancestors to indigenous Melanesians in the northwestern Bismarck Archipelago

Archaeological, linguistic, and genetic studies show that Austronesian (AN)-speaking Polynesian ancestors came from Asia/Taiwan to the Bismarck Archipelago in Near Oceania more than 3,600 years ago, and then expanded into Remote Oceania. However, it remains unclear whether they extensively mixed with indigenous Melanesians who had populated the Bismarck Archipelago before their arrival. To examine the extent of admixture between Polynesian ancestors and indigenous Melanesians, mitochondrial DNA (mtDNA) variations in the D-loop region and the cytochrome oxidase and lysine transfer RNA (COII/tRNA(Lys)) intergenic 9-bp deletion were analyzed in the following three Oceanian populations: 1) Balopa Islanders as AN-speaking Melanesians living in the northwestern end of the Bismarck Archipelago, 2) Tongans as AN-speaking Polynesians, and 3) Gidra as non-Austronesian-speaking Melanesians in the southwestern lowlands of Papua New Guinea. Phylogenetic analysis of mtDNA sequences revealed that more than 60% of mtDNA sequences in the Balopa Islanders were very similar to those in Tongans, suggesting an extensive gene flow from Polynesian ancestors to indigenous Melanesians. Furthermore, analysis of pairwise difference distributions for the D-loop sequences with the 9-bp deletion and the Polynesian motif (i.e., T16217C, A16247G, and C16261T) suggested that the expansion of Polynesian ancestors possessing these variations occurred approximately 7,000 years ago.     

The Q2 Mitochondrial Haplogroup in Oceania

Many details surrounding the origins of the peoples of Oceania remain to be resolved, and as a step towards this we report seven new complete mitochondrial genomes from the Q2a haplogroup, from Papua New Guinea, Fiji and Kiribati. This brings the total to eleven Q2 genomes now available. The Q haplogroup (that includes Q2) is an old and diverse lineage in Near Oceania, and is reasonably common; within our sample set of 430, 97 are of the Q haplogroup. However, only 8 are Q2, and we report 7 here. The tree with all complete Q genomes is proven to be minimal. The dating estimate for the origin of Q2 (around 35 Kya) reinforces the understanding that humans have been in Near Oceania for tens of thousands of years; nevertheless the Polynesian maternal haplogroups remain distinctive. A major focus now, with regard to Polynesian ancestry, is to address the differences and timing of the ‘Melanesian’ contribution to the maternal and paternal lineages as people moved further and further into Remote Oceania. Input from other fields such as anthropology, history and linguistics is required for a better understanding and interpretation of the genetic data.     

Melanesian mtDNA complexity

Melanesian populations are known for their diversity, but it has been hard to grasp the pattern of the variation or its underlying dynamic. Using 1,223 mitochondrial DNA (mtDNA) sequences from hypervariable regions 1 and 2 (HVR1 and HVR2) from 32 populations, we found the among-group variation is structured by island, island size, and also by language affiliation. The more isolated inland Papuan-speaking groups on the largest islands have the greatest distinctions, while shore dwelling populations are considerably less diverse (at the same time, within-group haplotype diversity is less in the most isolated groups). Persistent differences between shore and inland groups in effective population sizes and marital migration rates probably cause these differences. We also add 16 whole sequences to the Melanesian mtDNA phylogenies. We identify the likely origins of a number of the haplogroups and ancient branches in specific islands, point to some ancient mtDNA connections between Near Oceania and Australia, and show additional Holocene connections between Island Southeast Asia/Taiwan and Island Melanesia with branches of haplogroup E. Coalescence estimates based on synonymous transitions in the coding region suggest an initial settlement and expansion in the region at approximately 30-50,000 years before present (YBP), and a second important expansion from Island Southeast Asia/Taiwan during the interval approximately 3,500-8,000 YBP. However, there are some important variance components in molecular dating that have been overlooked, and the specific nature of ancestral (maternal) Austronesian influence in this region remains unresolved.     

Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations

Genetic affinities between aboriginal Taiwanese and populations from Oceania and Southeast Asia have previously been explored through analyses of mitochondrial DNA (mtDNA), Y chromosomal DNA, and human leukocyte antigen loci. Recent genetic studies have supported the “slow boat” and “entangled bank” models according to which the Polynesian migration can be seen as an expansion from Melanesia without any major direct genetic thread leading back to its initiation from Taiwan. We assessed mtDNA variation in 640 individuals from nine tribes of the central mountain ranges and east coast regions of Taiwan. In contrast to the Han populations, the tribes showed a low frequency of haplogroups D4 and G, and an absence of haplogroups A, C, Z, M9, and M10. Also, more than 85% of the maternal lineages were nested within haplogroups B4, B5a, F1a, F3b, E, and M7. Although indicating a common origin of the populations of insular Southeast Asia and Oceania, most mtDNA lineages in Taiwanese aboriginal populations are grouped separately from those found in China and the Taiwan general (Han) population, suggesting a prevalence in the Taiwanese aboriginal gene pool of its initial late Pleistocene settlers. Interestingly, from complete mtDNA sequencing information, most B4a lineages were associated with three coding region substitutions, defining a new subclade, B4a1a, that endorses the origin of Polynesian migration from Taiwan. Coalescence times of B4a1a were 13.2 ± 3.8 thousand years (or 9.3 ± 2.5 thousand years in Papuans and Polynesians). Considering the lack of a common specific Y chromosomal element shared by the Taiwanese aboriginals and Polynesians, the mtDNA evidence provided here is also consistent with the suggestion that the proto-Oceanic societies would have been mainly matrilocal.     

Early Austronesians: Into and Out Of Taiwan

A Taiwan origin for the expansion of the Austronesian languages and their speakers is well supported by linguistic and archaeological evidence. However, human genetic evidence is more controversial. Until now, there had been no ancient skeletal evidence of a potential Austronesian-speaking ancestor prior to the Taiwan Neolithic ∼6,000 years ago, and genetic studies have largely ignored the role of genetic diversity within Taiwan as well as the origins of Formosans. We address these issues via analysis of a complete mitochondrial DNA genome sequence of an ∼8,000-year-old skeleton from Liang Island (located between China and Taiwan) and 550 mtDNA genome sequences from 8 aboriginal (highland) Formosan and 4 other Taiwanese groups. We show that the Liangdao Man mtDNA sequence is closest to Formosans, provides a link to southern China, and has the most ancestral haplogroup E sequence found among extant Austronesian speakers. Bayesian phylogenetic analysis allows us to reconstruct a history of early Austronesians arriving in Taiwan in the north ∼6,000 years ago, spreading rapidly to the south, and leaving Taiwan ∼4,000 years ago to spread throughout Island Southeast Asia, Madagascar, and Oceania.     

Mitochondrial and nuclear genetic relationships among Pacific Island and Asian populations.

Mitochondrial and autosomal short tandem-repeat (STR) genetic distances among 28 Pacific Island and Asian populations are significantly correlated (r=.25, P<.01) but describe distinct patterns of relationships. Maternally inherited-mtDNA data suggest that Remote Oceanic Islanders originated in island Southeast Asia. In contrast, biparental STR data reveal substantial genetic affinities between Remote Oceanic Islanders and Near Oceanic populations from highland Papua New Guinea and Australia. The low correlation between maternal and biparental genetic markers from the same individuals may reflect differences in genome-effective population sizes or in sex-biased gene flow. To explore these possibilities, we have examined genetic diversity, gene flow, and correlations among genetic, linguistic, and geographic distances within four sets of populations representing potential geographic and cultural spheres of interaction. GST estimates (a measure of genetic differentiation inversely proportional to gene flow) from mtDNA sequences vary between 0.13 and 0.39 and are typically five times greater than GST estimates from STR loci (0.05-0.08). Significant correlations (r>.5, P<.05) between maternal genetic and linguistic distances are coincident with high mtDNA GST estimates (>0.38). Thus, genetic and linguistic distances may coevolve, and their correspondence may be preserved under conditions of genetic isolation. A significant correlation (r=.65, P<.01) between biparental genetic and geographic distances is coincident with a low STR GST estimate (0.05), indicating that isolation by distance is observed under conditions of high nuclear-gene flow. These results are consistent with an initial settlement of Remote Oceania from island Southeast Asia and with extensive postcolonization male-biased gene flow with Near Oceania.     

Unexpected island effects at an extreme: reduced Y chromosome and mitochondrial DNA diversity in Nias

The amount of genetic diversity in a population is determined by demographic and selection events in its history. Human populations which exhibit greatly reduced overall genetic diversity, presumably resulting from severe bottlenecks or founder events, are particularly interesting, not least because of their potential to serve as valuable resources for health studies. Here, we present an unexpected case, the human population of Nias Island in Indonesia, that exhibits severely reduced Y chromosome (non-recombining portion of the Y chromosome [NRY]) and to a lesser extent also reduced mitochondrial DNA (mtDNA) diversity as compared with most other populations from the Asia/Oceania region. Our genetic data, collected from more than 400 individuals from across the island, suggest a strong previously undetected bottleneck or founder event in the human population history of Nias, more pronounced for males than for females, followed by subsequent genetic isolation. Our findings are unexpected given the island's geographic proximity to the genetically highly diverse Southeast Asian world, as well as our previous knowledge about the human history of Nias. Furthermore, all NRY and virtually all mtDNA haplogroups observed in Nias can be attributed to the Austronesian expansion, in line with linguistic data, and in contrast with archaeological evidence for a pre-Austronesian occupation of Nias that, as we show here, left no significant genetic footprints in the contemporary population. Our work underlines the importance of human genetic diversity studies not only for a better understanding of human population history but also because of the potential relevance for genetic disease-mapping studies.     

Human Genetics, Paleoenvironments, and Malaria: Relationships and Implications for the Settlement of Oceania

Lapita is a distinctive ceramic style that first appeared in the Bismarck Archipelago about 3600 B.P. and over the next few centuries spread throughout island Melanesia. For many prehistorians the distribution of Lapita sherds identifies the expansion of Austronesian-speaking populations through Oceania. This article addresses the Lapita language question by exploring the implications of the relationship among gamma globulin (Gm) genetics, paleoenvironments, malaria, natural selection, and prehistoric settlement patterns. Archeological sites with Lapita ceramics are consistently located in coastal lowlands, which in some parts of Oceania would have been malarious areas. Drawing on recent evidence that Austronesian-speaking populations in Near Oceania possess a genetic advantage over Non-Austronesian speakers with regard to malaria, we contend that Austronesian speakers have been able to occupy—on a permanent basis—malarious coastal lowlands that were detrimental to Non-Austronesian speakers. It follows, therefore, that the inhabitants of those Lapita sites spoke one or more of the Austronesian languages.     

Mitogenomes from Two Uncommon Haplogroups Mark Late Glacial/Postglacial Expansions from the Near East and Neolithic Dispersals within Europe

The current human mitochondrial (mtDNA) phylogeny does not equally represent all human populations but is biased in favour of representatives originally from north and central Europe. This especially affects the phylogeny of some uncommon West Eurasian haplogroups, including I and W, whose southern European and Near Eastern components are very poorly represented, suggesting that extensive hidden phylogenetic substructure remains to be uncovered. This study expanded and re-analysed the available datasets of I and W complete mtDNA genomes, reaching a comprehensive 419 mitogenomes, and searched for precise correlations between the ages and geographical distributions of their numerous newly identified subclades with events of human dispersal which contributed to the genetic formation of modern Europeans. Our results showed that haplogroups I (within N1a1b) and W originated in the Near East during the Last Glacial Maximum or pre-warming period (the period of gradual warming between the end of the LGM, ∼19 ky ago, and the beginning of the first main warming phase, ∼15 ky ago) and, like the much more common haplogroups J and T, may have been involved in Late Glacial expansions starting from the Near East. Thus our data contribute to a better definition of the Late and postglacial re-peopling of Europe, providing further evidence for the scenario that major population expansions started after the Last Glacial Maximum but before Neolithic times, but also evidencing traces of diffusion events in several I and W subclades dating to the European Neolithic and restricted to Europe.     

Mitochondrial DNA signals of late glacial recolonization of Europe from near eastern refugia

Human populations, along with those of many other species, are thought to have contracted into a number of refuge areas at the height of the last Ice Age. European populations are believed to be, to a large extent, the descendants of the inhabitants of these refugia, and some extant mtDNA lineages can be traced to refugia in Franco-Cantabria (haplogroups H1, H3, V, and U5b1), the Italian Peninsula (U5b3), and the East European Plain (U4 and U5a). Parts of the Near East, such as the Levant, were also continuously inhabited throughout the Last Glacial Maximum, but unlike western and eastern Europe, no archaeological or genetic evidence for Late Glacial expansions into Europe from the Near East has hitherto been discovered. Here we report, on the basis of an enlarged whole-genome mitochondrial database, that a substantial, perhaps predominant, signal from mitochondrial haplogroups J and T, previously thought to have spread primarily from the Near East into Europe with the Neolithic population, may in fact reflect dispersals during the Late Glacial period, ～19-12 thousand years (ka) ago.     

The Arabian cradle: mitochondrial relicts of the first steps along the southern route out of Africa

A major unanswered question regarding the dispersal of modern humans around the world concerns the geographical site of the first human steps outside of Africa. The "southern coastal route" model predicts that the early stages of the dispersal took place when people crossed the Red Sea to southern Arabia, but genetic evidence has hitherto been tenuous. We have addressed this question by analyzing the three minor west-Eurasian haplogroups, N1, N2, and X. These lineages branch directly from the first non-African founder node, the root of haplogroup N, and coalesce to the time of the first successful movement of modern humans out of Africa, ～60 thousand years (ka) ago. We sequenced complete mtDNA genomes from 85 Southwest Asian samples carrying these haplogroups and compared them with a database of 300 European examples. The results show that these minor haplogroups have a relict distribution that suggests an ancient ancestry within the Arabian Peninsula, and they most likely spread from the Gulf Oasis region toward the Near East and Europe during the pluvial period 55-24 ka ago. This pattern suggests that Arabia was indeed the first staging post in the spread of modern humans around the world.     

Rapid deployment of the five founding Amerind mtDNA haplogroups via coastal and riverine colonization

Numerous studies of variation in mtDNA in Amerindian populations established that four haplogroups are present throughout both North and South America. These four haplogroups (A, B, C, and D) and perhaps a fifth (X) in North America are postulated to be present in the initial founding migration to the Americas. Furthermore, studies of ancient mtDNA in North America suggested long-term regional continuity of the frequencies of these founding haplogroups. Present-day tribal groups possess high frequencies of private mtDNA haplotypes (variants within the major haplogroups), consistent with early establishment of local isolation of regional populations. Clearly these patterns have implications for the mode of colonization of the hemisphere. Recently, the earlier consensus among archaeologists for an initial colonization by Clovis hunters arriving through an ice-free corridor and expanding in a "blitzkrieg " wave was shown to be inconsistent with extensive genetic variability in Native Americans; a coastal migration route avoids this problem. The present paper demonstrates through a computer simulation model how colonization along coasts and rivers could have rapidly spread the founding lineages widely through North America.