Background: The Truku indigenous people of Taiwan share strong cultural and genetic relationships with the Atayal tribe. Archaeological and linguistic studies show that their line of descent is associated to Proto-Austronesian speaking groups from Southeast Asia who settled in Taiwan in the early Neolithic, 6000 years ago.

Many studies have described the diversity of Austronesian-speaking Taiwanese people to shed more light on their origin and their connection with the “Out of Taiwan” migrations. However, the genetic relationship between the non-Austronesian-speaking groups of Taiwan and the populations of continental Asia is still unclear. Here, we studied the diversity of mtDNA in 767 non-Austronesian speakers from 16 locations in Taiwan using partial sequencing obtained from the hypervariable segment I (HVS-I) and coding regions 8,001-9,000 and 9.801–10,900 and 85 complete mtDNA genome sequences. Bayesian analysis of population structure was used to examine their relationship with over 3662 individuals representing indigenous groups of Taiwan, continental East Asia, Japan, and Island Southeast Asia. The whole analysis identified 278 haplotypes. Complete genomes revealed 62 novel subhaplogroups, of which 31 were exclusive to Taiwan. Estimates of coalescence times of all subhaplogroups showed peaks of diversification greater than 5.0 kya, likely characterizing gene flow from continental East Asian groups but not excluding in situ Taiwanese ancestry. Furthermore, a significant number of clades exclusive to non-Austronesian speakers of Taiwan (NAN_Tw) showed coalescence peaks between 1.0 and 2.6 kya, suggesting possible late Neolithic to early metal age settlements of NAN_Tw and local expansion in Taiwan.

Anthropological and linguistic studies place the first settlement of Austronesian speaking Taiwanese (AN_Tw) in the mid-Holocene era. However, geneticists have revealed exclusive diversity among the Bunun indigenous people, implying that their ancestral origin needs further study. The mitochondrial DNA (mtDNA) polymorphism of the Bunun shows a homogeneous relationship with other AN_Tw. However, the Y-chromosome polymorphism shows two major haplogroups, O1a2-M50 (60.7%), also seen to a lesser extent among the Northern AN_Tw, and O1b1a1a1a1a1-M88 (37.5%), scarce among all other AN and non-AN groups in Taiwan, but prevailing in Southeast Asia (SEA) and Mainland Southeast Asia (MSEA). While the present-day mtDNA profile of the Bunun typifies the long-term demographic standard for all AN_Tw since the Neolithic era, their Y-chromosome profile suggests an arrival of male settlers in the last two to three millennia from SEA or MSEA, who mixed exclusively with the Bunun indigenous people.

This study investigates the genetic relationship of the Mazu peoples on the east coast of China in the Taiwan Strait. Using partial and complete mitochondrial DNA (mtDNA) sequences, we compare Mazu with surrounding East Asia populations. Mazu shows no exclusive affinities with either Southeast or Northeast Asia. High genetic diversity and a very high number of exclusive haplogroups of various Asian origins suggest that Mazu resulted from a process of continuous resettlement that started when it first became an archipelago at the end of the last glacial maximum and that continued till the last century. As a result, genetic drift did not contribute to an exclusive Mazu profile. The structure of haplogroups that show signatures of the Neolithic era (N9a10a), or influx from Island Southeast Asia (F1a4a) suggest recent gene flows and Mazu relationship with it's pre-Neolithic era (presence of pre-E1a or R9/pre-F from Liangdao man) was not seen.

Island Southeast Asia has recently produced several surprises regarding human history, but the region's complex demography remains poorly understood. Here, we report ∼2.3 million genotypes from 1,028 individuals representing 115 indigenous Philippine populations and genome-sequence data from two ∼8,000-y-old individuals from Liangdao in the Taiwan Strait. We show that the Philippine islands were populated by at least five waves of human migration: initially by Northern and Southern Negritos (distantly related to Australian and Papuan groups), followed by Manobo, Sama, Papuan, and Cordilleran-related populations. The ancestors of Cordillerans diverged from indigenous peoples of Taiwan at least ∼8,000 y ago, prior to the arrival of paddy field rice agriculture in the Philippines ∼2,500 y ago, where some of their descendants remain to be the least admixed East Asian groups carrying an ancestry shared by all Austronesian-speaking populations. These observations contradict an exclusive "out-of-Taiwan" model of farming-language-people dispersal within the last four millennia for the Philippines and Island Southeast Asia. Sama-related ethnic groups of southwestern Philippines additionally experienced some minimal South Asian gene flow starting ∼1,000 y ago. Lastly, only a few lowlanders, accounting for <1% of all individuals, presented a low level of West Eurasian admixture, indicating a limited genetic legacy of Spanish colonization in the Philippines. Altogether, our findings reveal a multilayered history of the Philippines, which served as a crucial gateway for the movement of people that ultimately changed the genetic landscape of the Asia-Pacific region.

Multiple lines of evidence show that modern humans interbred with archaic Denisovans. Here, we report an account of shared demographic history between Australasians and Denisovans distinctively in Island Southeast Asia. Our analyses are based on-2.3 million genotypes from 118 ethnic groups of the Philippines, including 25 diverse self-identified Negrito populations, along with high-coverage genomes of Australopapuans and Ayta Magbukon Negritos. We show that Ayta Magbukon possess the highest level of Denisovan ancestry in the world--30%-40% greater than that of Australians and Papuans-consistent with an independent admixture event into Negritos from Denisovans. Together with the recently described Homo luzonensis, we suggest that there were multiple archaic species that inhabited the Philippines prior to the arrival of modern humans and that these archaic groups may have been genetically related. Altogether, our findings unveil a complex intertwined history of modern and archaic humans in the Asia-Pacific region, where distinct Islander Denisovan populations differentially admixed with incoming Australasians across multiple locations and at various points in time.

Following publication of the original article [1], we have been notified that Additional file 3 was published with track changes.

The genetic profile of Negritos of the Philippines differs from the non-Negrito groups with mitochondrial DNA haplogroups B4b1a2, B5, D6a, M, M52a, and N11b. Although Negritos are not seen in Taiwan, the strong genetic affinity between the Philippines and Taiwan Mountain Tribe Aborigines (TwMtA), and Folks tales of TwMtA, Saisiyat and Atayal recounting past contacts with Negritos, warrant the search for a Negrito signature in Taiwan. Material and Method: Discriminant Analysis of Principal Component (DAPC) was used to determine the genetic relationship between TwMtA, Filipino and non-TwMtA groups. Results: The deep coalescence of B4b1a2 in the Philippine Negritos, Saisiyat, Atayal, Island Southeast Asia, and SEA (Southeast Asia) suggested a deeply rooted common ancestry, but could not support a past Negrito presence in Taiwan. Conversely, the sharing of cultural components and mtDNA (mitochondrial DNA) haplogroup D6a2 in Saisiyat, Atayal and Philippine Negritos may characterize a Negrito signature in Taiwan. Although the molecular variation of D6a2 determines its presence in Taiwan back to middle Neolithic, other markers, Y-SNP haplogroups C-M146 and K-M9, warrant further analysis. Conclusion: Most likely, the physical characteristics, languages, and the genetic makeup of the Negritos in Taiwan have been diluted as the result of heavy migration from the mainland in the last 400 years.

There is a consensus that gene flow characterizing modern Mainland Chinese arrived in Taiwan during the last 400 years, mostly from East China. However, primary genetic studies of ancient human remains of the middle Neolithic era, revealing inconsistencies between the archaic genes profile and that of modern Mainland Chinese, raised debates about the time of arrival of modern Chinese in Taiwan. To resolve this problem, this study focuses on the analysis of 3000 years BP human remains excavated from the Neolithic east coast archeological Ling-Ding site II near Hualien in Taiwan. The mitochondrial DNA (mtDNA) recovered from five archeological human remains was analyzed to elucidate their genealogy, and to characterize their genetic relationship with the present-day aboriginal and non-aboriginal people of Taiwan. Five mtDNA haplogroups were characterized from the Ling-Ding site II skeletons, C4a2, N9a1, B4c1b2a, Z, and B4b. Except for mtDNA haplogroups B4c1b2a, commonly seen among the present-day central Taiwan Aborigines and scarce in the heavily sinicised Taiwan western plain tribes, all other haplogroups were common to urban Taiwanese and modern Mainland Chinese. It is proposed that a middle Neolithic gene flow, characterizing Modern Mainland East Asians, was introduced to Taiwan by settlers who reached the East coast of Taiwan in Hualien (Ling- Ding site II) and co-habited with Taiwan Mountain tribe Aborigines. The findings of this study may be relevant for the understanding of the middle Neolithic peopling of Taiwan by non-Austronesian speakers.

There are two very different interpretations of the prehistory of Island Southeast Asia (ISEA), with genetic evidence invoked in support of both. The "out-of-Taiwan" model proposes a major Late Holocene expansion of Neolithic Austronesian speakers from Taiwan. An alternative, proposing that Late Glacial/postglacial sea-level rises triggered largely autochthonous dispersals, accounts for some otherwise enigmatic genetic patterns, but fails to explain the Austronesian language dispersal. Combining mitochondrial DNA (mtDNA), Y-chromosome and genome-wide data, we performed the most comprehensive analysis of the region to date, obtaining highly consistent results across all three systems and allowing us to reconcile the models. We infer a primarily common ancestry for Taiwan/ISEA populations established before the Neolithic, but also detected clear signals of two minor Late Holocene migrations, probably representing Neolithic input from both Mainland Southeast Asia and South China, via Taiwan. This latter may therefore have mediated the Austronesian language dispersal, implying small-scale migration and language shift rather than large-scale expansion.

BACKGROUND:Cytokine gene single nucleotide polymorphisms (SNPs) are widely used to study susceptibility to complex diseases and as a tool for anthropological studies.MATERIALS AND METHODS:To investigate cytokine SNPs in an Iranian multi-ethnic population, we have investigated 10 interleukin (IL) SNPs (IL-1β (C-511T, T-31C), IL-2 (G-384T), IL-4 (C-590T), IL-6 (G-174C), IL-8 (T-251A), IL-10 (G-1082A, C-819T, C-592A) and tumor necrosis factor-alpha (TNF-α) (G-308A) in 415 Iranian subjects comprising of 6 different ethnicities. Allelic and genotypic frequencies as well as Hardy-Weinberg equilibrium (HWE) were calculated by PyPop software. Population genetic indices including observed heterozygosity (Ho), expected heterozygosity (He), fixation index (FIS), the effective number of alleles (N e) and polymorphism information content (PIC) were derived using Popgene 32 software. Multidimensional scaling (MDS) was constructed using Reynold's genetic distance obtained from the frequencies of cytokine gene polymorphism.RESULTS:Genotypic distributions were consistent with the HWE assumptions, except for 3 loci (IL-4-590, IL-8-251 and IL-10-819) in Fars and 4 loci (IL-4-590, IL-6-174, IL-10-1082 and TNF-α-308) in Turks. Pairwise assessment of allelic frequencies, detected differences at the IL-4-590 locus in Gilakis versus Kurds (P = 0.028) and Lurs (P = 0.022). Mazanis and Gilakis displayed the highest (Ho= 0.50 ± 0.24) and lowest (Ho= 0.34 ± 0.16) mean observed heterozygosity, respectively.CONCLUSIONS:MDS analysis of our study population, in comparison with others, revealed that Iranian ethnicities except Kurds and Mazanis were tightly located within a single cluster with closest genetic affinity to Europeans.

BACKGROUND:Much of the data resolution of the haploid non-recombining Y chromosome (NRY) haplogroup O in East Asia are still rudimentary and could be an explanatory factor for current debates on the settlement history of Island Southeast Asia (ISEA). Here, 81 slowly evolving markers (mostly SNPs) and 17 Y-chromosomal short tandem repeats were used to achieve higher level molecular resolution. Our aim is to investigate if the distribution of NRY DNA variation in Taiwan and ISEA is consistent with a single pre-Neolithic expansion scenario from Southeast China to all ISEA, or if it better fits an expansion model from Taiwan (the OOT model), or whether a more complex history of settlement and dispersals throughout ISEA should be envisioned.RESULTS:We examined DNA samples from 1658 individuals from Vietnam, Thailand, Fujian, Taiwan (Han, plain tribes and 14 indigenous groups), the Philippines and Indonesia. While haplogroups O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 follow a decreasing cline from Taiwan towards Western Indonesia, O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 decline northward from Western Indonesia towards Taiwan. Compared to the Taiwan plain tribe minority groups the Taiwanese Austronesian speaking groups show little genetic paternal contribution from Han. They are also characterized by low Y-chromosome diversity, thus testifying for fast drift in these populations. However, in contrast to data provided from other regions of the genome, Y-chromosome gene diversity in Taiwan mountain tribes significantly increases from North to South.CONCLUSION:The geographic distribution and the diversity accumulated in the O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 haplogroups on one hand, and in the O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 haplogroups on the other, support a pincer model of dispersals and gene flow from the mainland to the islands which likely started during the late upper Paleolithic, 18,000 to 15,000 years ago. The branches of the pincer contributed separately to the paternal gene pool of the Philippines and conjointly to the gene pools of Madagascar and the Solomon Islands. The North to South increase in diversity found for Taiwanese Austronesian speaking groups contrasts with observations based on mitochondrial DNA, thus hinting to a differentiated demographic history of men and women in these populations.

The importance of mitochondrial DNA (mtDNA) polymorphism in the prediction of type 2 diabetes (T2D) in men and women is not well understood. We questioned whether mtDNA polymorphism, mitochondrial functions, age and gender influenced the occurrence of T2D with or without ischemic stroke (IS).

We present, to our knowledge, the first quantitative evidence that music and genes may have coevolved by demonstrating significant correlations between traditional group-level folk songs and mitochondrial DNA variation among nine indigenous populations of Taiwan. These correlations were of comparable magnitude to those between language and genes for the same populations, although music and language were not significantly correlated with one another. An examination of population structure for genetics showed stronger parallels to music than to language. Overall, the results suggest that music might have a sufficient time-depth to retrace ancient population movements and, additionally, that it might be capturing different aspects of population history than language. Music may therefore have the potential to serve as a novel marker of human migrations to complement genes, language and other markers.

Mitochondrial DNA (mtDNA) and non-recombining Y chromosome (NRY) are inherited uni-parentally from mother to daughter or from father to son respectively. Their polymorphism has initially been studied throughout populations of the world to demonstrate the "Out of Africa" hypothesis. Here, to correlate the distribution of nasopharyngeal carcinoma (NPC) in different populations of insular Asia, we analyze the mtDNA information (lineages) obtained from genotyping of the hyper variable region (HVS I & II) among 1400 individuals from island Southeast Asia (ISEA), Taiwan and Fujian and supplemented with the analysis of relevant coding region polymorphisms. Lineages that best represented a clade (a branch of the genetic tree) in the phylogeny were further analyzed using complete genomic mtDNA sequencing. Finally, these complete mtDNA sequences were used to construct a most parsimonious tree which now constitutes the most up-to-date mtDNA dataset available on ISEA and Taiwan. This analysis has exposed new insights of the evolutionary history of insular Asia and has strong implications in assessing possible correlations with linguistic, archaeology, demography and the NPC distribution in populations within these regions. To obtain a more objective and balanced genetic point of view, slowly evolving biallelic Y single nucleotide polymorphism (Y-SNP) was also analyzed. As in the first step above, the technique was first applied to determine affinities (macro analysis) between populations of insular Asia. Secondly, sixteen Y short tandem repeats (Y-STR) were used as they allow deeper insight (micro analysis) into the relationship between individuals of a same region. Together, mtDNA and NRY allowed a better definition of the relational, demographic, cultural and genetic components that constitute the make up of the present day peoples of ISEA. Outstanding findings were obtained on the routes of migration that occurred along with the spread of NPC during the settlement of insular Asia. The results of this analysis will be discussed using a conceptual approach.

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.

BACKGROUND:Yami and Ivatan islanders are Austronesian speakers from Orchid Island and the Batanes archipelago that are located between Taiwan and the Philippines. The paternal genealogies of the Yami tribe from 1962 monograph of Wei and Liu were compared with our dataset of non-recombining Y (NRY) chromosomes from the corresponding families. Then mitochondrial DNA polymorphism was also analyzed to determine the matrilineal relationships between Yami, Ivatan, and other East Asian populations. RESULTS:The family relationships inferred from the NRY Phylogeny suggested a low number of paternal founders and agreed with the genealogy of Wei and Liu (P < 0.01). Except for one Y short tandem repeat lineage (Y-STR), seen in two unrelated Yami families, no other Y-STR lineages were shared between villages, whereas mtDNA haplotypes were indiscriminately distributed throughout Orchid Island. The genetic affinity seen between Yami and Taiwanese aborigines or between Ivatan and the Philippine people was closer than that between Yami and Ivatan, suggesting that the Orchid islanders were colonized separately by their nearest neighbors and bred in isolation. However a northward gene flow to Orchid Island from the Philippines was suspected as Yami and Ivatan peoples both speak Western Malayo-Polynesian languages which are not spoken in Taiwan. Actually, only very little gene flow was observed between Yami and Ivatan or between Yami and the Philippines as indicated by the sharing of mtDNA haplogroup B4a1a4 and one O1a1* Y-STR lineage. CONCLUSIONS:The NRY and mtDNA genetic information among Yami tribe peoples fitted well the patrilocal society model proposed by Wei and Liu. In this proposal, there were likely few genetic exchanges among Yami and the Philippine people. Trading activities may have contributed to the diffusion of Malayo-Polynesian languages among them. Finally, artifacts dating 4,000 YBP, found on Orchid Island and indicating association with the Out of Taiwan hypothesis might be related to a pioneering stage of settlement, as most dating estimates inferred from DNA variation in our data set ranged between 100-3,000 YBP.

Mitochondrial DNA (mtDNA) and non-recombining Y chromosome (NRY) are inherited uni-parentally from mothers to daughters or from fathers to sons respectively. Their high polymorphism (and rate of mutation) has been used to confirm the ‘Out of Africa’ hypothesis, and to time the spread of farming by Neolithic farmers (between 8000 and 5000 years ago) from the Levant to Europe and from Mainland Southeast Asia (MSEA) to Island Southeast Asia (ISEA). Here, we first combined results obtained from sequencing of the mtDNA hyper variable regions (HVS I and II) and other relevant coding regions among 1400 individuals from ISEA, Taiwan, Fujian and MSEA (Thailand, Vietnam). Analysis of the extensive polymorphism confirmed genetic continuity, revealing very specific genetic profiles gradually changing eastward across the regions. Lineages that best represented a clade in the initial phylogeny (a branch of the genetic tree) were further analysed using complete genomic mtDNA sequencing. Finally, a most parsimonious tree was constructed. While establishing the most up to date and informative mtDNA dataset available on populations of ISEA and Taiwan, we could infer more clearly, ancient population migration routes between MSEA and ISEA. When combined with worldwide studies, the African haplogroup L3 was, as expected, the precursor to super-haplogroups M and N. We note here that M and N are the ∼65 000 years’ ancestors of all haplogroups seen in populations of the northern hemisphere, Australia and the New World. In genetics, inferences about the genetic makeup of the past are drawn from studies of modern-day populations. According to archaeological and linguistics studies, it is now generally accepted that Western ISEA (Sumatra, Borneo, Java, Philippines and Sulawesi) have been a very active demographic platform of expansion and dispersal of the first eastern settlers in early Palaeolithic (∼55 000–45 000 years ago). The people who remained in the tropics are the Melanesian of today, and those who, very early, moved north, formed the east Asian populations. Some of them, much later (<10 000 years) after favourable climate changes, moved back to ISEA and even further to settle Polynesia in the Pacific and Madagascar in the Indian Ocean. The most favoured model, the ‘out of Taiwan’ was initially based on linguistic arguments, and suggests that the Austronesian-speaking populations of ISEA, Near Oceania, and Remote Oceania (the Polynesians) have a common origin among early Taiwanese agricultural groups who dispersed into ISEA ∼4000 years ago, reaching Near Oceania ∼3500 years ago [1,2]. In the process, these people completely replaced the culture (cultural diffusion) and the local populations of ISEA (demic diffusion). Interestingly, our study showed that 86% of mtDNA sequences in ISEA and Taiwan were characterized by sub-haplogroups of super haplogroup M (M7b3*, M7c3c*, M7b1*, D5b3*, D6*, E*; with ‘*’ indicating all subgroups thereafter) or N (B4a1a1*, B4a2*, B4c2*, B4d1*, B5a1b*, B5a2a*, F1a1a*, F1a3*, F1a4*, F3b*). These haplogroups are not seen among the Melanesian peoples (the descendants of the palaeolithic settlers such as the Australian Aborigines and the people of Near Oceania: Papua New Guinea, Bismark archipelago), but they are predominantly seen among Austronesian-speaking groups, in Taiwan and ISEA (Philippines and Indonesia). In the Pacific and Madagascar, their mtDNA diversity was mostly restricted to mtDNA haplogroup B4a1a1 and B4a1a1a (the precursor of the Polynesian motif and the Polynesian motif). Our analysis supported that these mtDNA haplogroups had Southeast Asian origin and were therefore the result of an ancient demic and cultural diffusion. To obtain a more objective and balanced genetic viewpoint, we re-analysed all poorly defined mtDNA haplogroups using complete sequencing and also extended the analysis to the study of the paternal polymorphism obtained from slowly evolving Y single nucleotide polymorphism (Y-SNP) and the much faster evolving Y chromosome short tandem repeats (Y-STR). Interestingly, in western ISEA, migration events inferred from Y chromosome analysis generally agreed with mtDNA and also suggested some possible bidirectional population movements from Taiwan to ISEA (the out of Taiwan) or from ISEA to Taiwan. On the contrary, further eastward, migration of Austronesian speakers into the pacific ended up with populations (the Polynesians, north coast New Guinea and many Bismark islands) displaying very different maternal and paternal genetic profiles: maternally Austronesian with a strongly reduced polymorphism, and paternally Melanesian). Together, the polymorphism of mtDNA and NRY chromosome unveiled outstanding findings on the evolutionary history of East Asia, insular Asia and near Oceania. For example, if Palaeolithic people did settle Taiwan, our study shows that demic diffusion by people from MSEA was complete (total replacement). On the other hand, we found that this was not the case for the Philippines and Indonesian where approximately 8–14% of Palaeolithic genetic markers (Melanesians) could still be found nowadays in the populations of western ISEA. In agreement with most recent studies, our analysis suggested that the relationship between linguistics, archaeology, demography and genetics was much more complex than first hypothesized. Some results of this analysis are discussed below using a conceptual approach. In 2005 and 2007, Friedlander and Hudjashov [1,2], produced trees of complete mtDNA sequences using founding super-haplogroups M and N. Initial analysis of the phylogeography of these haplogroups suggested that Aboriginal Australians were most closely related to the autochthonous populations of New Guinea/Melanesia. According to the molecular clock, it also indicated that prehistoric Australia and New Guinea were occupied initially during a unique Palaeolithic colonization event ∼50 000 years ago. The question still remained as to whether PNG and Australia were reached separately, sequentially, several times after an initial settlement event or if there were exchanges between them after an initial settlement. For this, Friedlaender and Hudjashov separately re-analysed the distribution of all subtypes of Melanesian mtDNA haplogroup M and N. Only one subtype of super haplogroup N (haplogroup P) will be described here [3,4] to show that it is during the early undifferentiated period of haplogroup P (∼51 000 years ago) that anatomically modern humans most likely moved separately to PNG and Australia. As the result of isolation, haplogroups P1 and P2 expanded in PNG while P5, P6, P7 and P9 expanded in Australia. More recently described subtypes of P, P3 and P4, were seen in PNG and Australia [5] and indicated possible gene flow between the two regions. The phylogenetic tree in Fig. 1 shows different subtypes of P3 or P4 in Australia (P3a and P4b1) and in PNG (P3b and P4a/b), suggesting gene flow. This also indicates a period of expansion of the undifferentiated P haplogroup in either Australia or PNG/Melanesia where P3 and P4 first appeared, (most possibly in PNG/Melanesia as the diversity there is highest). A later gene flow between 39 000 and 15 000 years of P3 and P4b from PNG/Melanesia to Australia must have been followed by an uninterrupted period of isolation till the present days. This allowed P3 and P4b to differentiate into P3a and P4b1 in Australia, while P3b and P4a speciated in PNG/Melanesia. Alternatively, P could have first differentiated in eastern ISEA into P3 and P4a/b and separately moved to Australia and PNG (39 000 years ago) where they differentiated locally. Phylogeography of mtDNA haplogroup P: most Parsimonious tree of haplogroup P (P is a subtype of super haplogroup N and macro haplogroup R). Before 2009, all known branches of P (P1–P6) were seen either in Australia or in Melanesia (PNG). Here, new branches, namely P8 and P10, were found in the Philippines [4]. Sequence accession number can be obtained from Phylotree [12]. P3a and P4b1 are only seen in Australia, and P3b and P4a are only seen in PNG. Their coalescent time estimate ranges between 15 000 and 30 000 years. This indicates either an early dispersal of the unspeciated P3 or P4 from PNG or from Australia, or separate dispersal of P3 and P4 from ISEA with no later gene flow between PNG and Australia. In summary, it appears that PNG and Australia were first reached separately (51 000 years ago). A later gene flow from PNG to Australia (<39 000 years ago) is most probable but will not be ascertained till further study is conducted among the populations of eastern ISEA. Our group later described the presence of two new subtypes of haplogroup P in the Philippines, haplogroups P10 and P8 [3,4]. Interestingly, there is no traces of haplogroup P in the region situated between PNG and the Philippines. P may have either disappeared by drift or has not yet been sampled. In any case, when ruling out the possibility of mutation recurrence, or back migration from PNG towards western ISEA, our findings suggest that haplogroup P made its first appearance in Western ISEA, very shortly before the settlement of PNG and Australia. This idea is further reinforced by the presence of another haplogroup P in Malaysia (R21). These findings strongly indicate that Western ISEA was an active platform for the Palaeolithic expansion and dispersal of the first modern human settlers. An unexpected high number of ‘basal lineages’ that, like haplogroup P, branch directly from super-haplogroups M or N, were also found throughout ISEA [3,4]. The presence of such unique and unshared basal lineages, all along the southern hemisphere coastlines, from the horn of Africa [6] through ISEA, and then New Guinea or Australia [1], suggested that the first colonists had a small effective population size, and progressed rapidly in their eastward migration, most likely at a rate of ∼700 m per year [7]. Moreover, the presence of this unexpectedly large number of novel basal haplogroups in West ISEA reinforced the idea that western ISEA was an active centre of expansion and of dispersal in early Palaeolithic. The high frequency of these basal haplotypes (14% in Java only), further suggest that maternal demic diffusion (total replacement), universally accepted as the result of an early Holocene wave of migration from MSEA, was not complete. The remaining 86% of sequences in ISEA were characterized by haplotypes that belong to an already well defined and much younger twig of haplogroup M, such as G1, D4, M9, M7, M13 and Z, and of haplogroup N such as B4, B5, F1 and N9a. Today, these haplogroups are all commonly seen in ISEA non-Melanesian populations, and most particularly among Austronesian speakers. Only one branch of super-haplogroup N (haplogroup B4 and its subgroup haplogroup B4a1a) is described here (Fig. 2). Using a large number of complete mtDNA B4 genomes, supplemented by data obtained from the analysis of control region genotyping, we show new and very convincing evidences that the most prevalent (80–90%) present days maternal lineages among Pacific islanders (haplogroup B4a1a1a) descended ∼20 000 years ago, during the last glacial maximal, from an east Asian mainland mtDNAs ancestor bearing haplogroup B4a1 [3,8,9]. The next descendant in line, haplogroup B4a1a, appeared at the beginning of the Holocene (8500 years ago), nowadays, it is only seen among Austronesian speakers in Western ISEA/Taiwan. B4a1a is the closest ancestor to the proto-Polynesian and Polynesian motifs. Since the origin of Austronesian languages is not older than 6000 years, this suggests that the ancestors of group of people speaking Austronesian languages today had already genetically differentiated from the mainland populations, and they had done this in insular Asia, before they actually spoke Austronesian. Some questions remain: were the bearers of B4a1a proto-Austronesians speakers? Is the absence of B4a1a on mainland Asia the result of drift? Till this is answered, the possibility for an origin in southeast Asia of proto-Austronesian speakers’ bearers of B4a1a remains open. Phylogeography of mtDNA haplogroup B4 and its of sub-haplogroups in mainland East and North Asia (green), in ISEA/Taiwan (the Taiwan motif: B4a1a, yellow), in Near Oceania (the proto-Polynesian motif: B4a1a1, black) and in the Pacific (the Polynesian motif: B4a1a1a, red). The four evolutionary stages of expansion of haplogroup B4 are region-specific. While there is strong correlation between archaeology and genetics on the path of migration taken by the bearers of all descendants of haplogroup B4a1a on their eastward movements towards the Pacific ocean, the timing of the staging of people movements determined by genetics and the timing associated to the ‘out of Taiwan’ model determined by linguistic and archaeological studies are not compatible. The ‘out of Taiwan’ proposes a dispersal beginning about 4000–5000 years ago. In contrast, the phylogeographic model (starting from B4a1a in western ISEA) reveals that its descendant haplogroup, the ‘Polynesian motif’ (B4a1a1a), has never been seen in Taiwan, and had its major expansion approximately 6650 years in the Bismarck Archipelago where it has now reached its higher frequency and diversity. Interestingly, these dating estimates are also compatible with recent Y-chromosome [10] and autosomal data [11], thus providing an excellent synthesis from all genetic systems [8]. These results describe an early B4a1a Holocene incubation period in ISEA/Taiwan and then expansion of the Polynesian motif (B4a1a1a) ∼6650 years ago in Near Oceania, which most importantly predated the development of the Lapita culture. The Lapita culture is a cultural complex including obsidian tools, finely decorated dentate-stamped pottery and shell ornaments that first appeared on the coasts of the Bismarck Archipelago ∼3500 years ago, spread into Remote Oceania ∼3000 years ago and is generally believed as the ‘land mark’ being the most strongly associated with the arrival of the first Austronesian speakers in Melanesia. In brief, during the first stage of the Austronesian Diaspora (West ISEA to Near Oceania), language and culture progressed when the genetic profile of people in ISEA was already well established, but in the second stage (Near Oceania to the Pacific), language, culture and genetic makeup moved in concert. No potential conflict of interests to declare.