Mitochondrial control-region sequence variation in aboriginal Australians

Aboriginal Australian mitochondrial genome variation - an increased understanding of population antiquity and diversity

Aboriginal Australians represent one of the oldest continuous cultures outside Africa, with evidence indicating that their ancestors arrived in the ancient landmass of Sahul (present-day New Guinea and Australia) ~55 thousand years ago. Genetic studies, though limited, have demonstrated both the uniqueness and antiquity of Aboriginal Australian genomes. We have further resolved known Aboriginal Australian mitochondrial haplogroups and discovered novel indigenous lineages by sequencing the mitogenomes of 127 contemporary Aboriginal Australians. In particular, the more common haplogroups observed in our dataset included M42a, M42c, S, P5 and P12, followed by rarer haplogroups M15, M16, N13, O, P3, P6 and P8. We propose some major phylogenetic rearrangements, such as in haplogroup P where we delinked P4a and P4b and redefined them as P4 (New Guinean) and P11 (Australian), respectively. Haplogroup P2b was identified as a novel clade potentially restricted to Torres Strait Islanders. Nearly all Aboriginal Australian mitochondrial haplogroups detected appear to be ancient, with no evidence of later introgression during the Holocene. Our findings greatly increase knowledge about the geographic distribution and phylogenetic structure of mitochondrial lineages that have survived in contemporary descendants of Australia’s first settlers.

Mitochondrial DNA diversity of present-day Aboriginal Australians and implications for human evolution in Oceania

Aboriginal Australians are one of the more poorly studied populations from the standpoint of human evolution and genetic diversity. Thus, to investigate their genetic diversity, the possible date of their ancestors' arrival and their relationships with neighboring populations, we analyzed mitochondrial DNA (mtDNA) diversity in a large sample of Aboriginal Australians. Selected mtDNA single-nucleotide polymorphisms and the hypervariable segment haplotypes were analyzed in 594 Aboriginal Australians drawn from locations across the continent, chiefly from regions not previously sampled. Most (~78%) samples could be assigned to mtDNA haplogroups indigenous to Australia. The indigenous haplogroups were all ancient (with estimated ages >40 000 years) and geographically widespread across the continent. The most common haplogroup was P (44%) followed by S (23%) and M42a (9%). There was some geographic structure at the haplotype level. The estimated ages of the indigenous haplogroups range from 39 000 to 55 000 years, dates that fit well with the estimated date of colonization of Australia based on archeological evidence (~47 000 years ago). The distribution of mtDNA haplogroups in Australia and New Guinea supports the hypothesis that the ancestors of Aboriginal Australians entered Sahul through at least two entry points. The mtDNA data give no support to the hypothesis of secondary gene flow into Australia during the Holocene, but instead suggest long-term isolation of the continent.

Human settlement history between Sunda and Sahul: a focus on East Timor (Timor-Leste) and the Pleistocenic mtDNA diversity

BACKGROUND

Distinct, partly competing, "waves" have been proposed to explain human migration in(to) today's Island Southeast Asia and Australia based on genetic (and other) evidence. The paucity of high quality and high resolution data has impeded insights so far. In this study, one of the first in a forensic environment, we used the Ion Torrent Personal Genome Machine (PGM) for generating complete mitogenome sequences via stand-alone massively parallel sequencing and describe a standard data validation practice.

RESULTS

In this first representative investigation on the mitochondrial DNA (mtDNA) variation of East Timor (Timor-Leste) population including >300 individuals, we put special emphasis on the reconstruction of the initial settlement, in particular on the previously poorly resolved haplogroup P1, an indigenous lineage of the Southwest Pacific region. Our results suggest a colonization of southern Sahul (Australia) >37 kya, limited subsequent exchange, and a parallel incubation of initial settlers in northern Sahul (New Guinea) followed by westward migrations <28 kya.

CONCLUSIONS

The temporal proximity and possible coincidence of these latter dispersals, which encompassed autochthonous haplogroups, with the postulated "later" events of (South) East Asian origin pinpoints a highly dynamic migratory phase.

Brief communication: the Australian Barrineans and their relationship to Southeast Asian negritos: an investigation using mitochondrial genomics

The existence of a short-statured Aboriginal population in the Far North Queensland (FNQ) rainforest zone of Australia's northeast coast and Tasmania has long been an enigma in Australian anthropology. Based on their reduced stature and associated morphological traits such as tightly curled hair, Birdsell and Tindale proposed that these "Barrinean" peoples were closely related to "negrito" peoples of Southeast Asia and that their ancestors had been the original Pleistocene settlers of Sahul, eventually displaced by taller invaders. Subsequent craniometric and blood protein studies, however, have suggested an overall homogeneity of indigenous Australians, including Barrineans. To confirm this finding and determine the degree of relatedness between Barrinean people and Southeast Asian negritos, we compared indigenous Australian mitochondrial DNA (mtDNA) sequences in populations from the FNQ rainforest ecozone and Tasmania with sequences from other Australian Aboriginal populations and from Southeast Asian negrito populations (Philippines Batek and Mamanwa, and mainland Southeast Asian Jahai, Mendriq, and Batak). The results confirm that FNQ and Tasmanian mtDNA haplogroups cluster with those of other Australian Aboriginal populations and are only very distantly related to Southeast Asian negrito haplogroups.

The role of genetic drift in shaping modern human cranial evolution: a test using microevolutionary modeling

The means by which various microevolutionary processes have acted in the past to produce patterns of cranial variation that characterize modern humans is not thoroughly understood. Applying a microevolutionary framework, within- and among-population variance/covariance (V/CV) structure was compared for several functional and developmental modules of the skull across a worldwide sample of modern humans. V/CV patterns in the basicranium, temporal bone, and face are proportional within and among groups, which is consistent with a hypothesis of neutral evolution; however, mandibular morphology deviated from this pattern. Degree of intergroup similarity in facial, temporal bone, and mandibular morphology is significantly correlated with geographic distance; however, much of the variance remains unexplained. These findings provide insight into the evolutionary history of modern human cranial variation by identifying signatures of genetic drift, gene flow, and migration and set the stage for inferences regarding selective pressures that early humans encountered since their initial migrations around the world.

Whole-genome genetic diversity in a sample of Australians with deep Aboriginal ancestry

Australia was probably settled soon after modern humans left Africa, but details of this ancient migration are not well understood. Debate centers on whether the Pleistocene Sahul continent (composed of New Guinea, Australia, and Tasmania) was first settled by a single wave followed by regional divergence into Aboriginal Australian and New Guinean populations (common origin) or whether different parts of the continent were initially populated independently. Australia has been the subject of relatively few DNA studies even though understanding regional variation in genomic structure and diversity will be important if disease-association mapping methods are to be successfully evaluated and applied across populations. We report on a genome-wide investigation of Australian Aboriginal SNP diversity in a sample of participants from the Riverine region. The phylogenetic relationship of these Aboriginal Australians to a range of other global populations demonstrates a deep common origin with Papuan New Guineans and Melanesians, with little evidence of substantial later migration until the very recent arrival of European colonists. The study provides valuable and robust insights into an early and important phase of human colonization of the globe. A broader survey of Australia, including diverse geographic sample populations, will be required to fully appreciate the continent's unique population history and consequent genetic heritage, as well as the importance of both to the understanding of health issues.

The human genetic history of Oceania: near and remote views of dispersal

The human history of Oceania is unique in the way that it encompasses both the first out-of-Africa expansion of modern humans to New Guinea and Australia as well as the last regional human occupation of Polynesia. Other anthropological peculiarities of Oceania include features like the extraordinarily rich linguistic diversity especially of New Guinea with about 1,000 often very distinct languages, the independent and early development of agriculture in the highlands of New Guinea about 10,000 years ago, or the long-term isolation of the entire region from the outside world, which lasted as long as until the 1930s for most of the interior of New Guinea. This review will provide an overview on the genetic aspects of human population history of Oceania and how some of the anthropological peculiarities are reflected in human genetic data. Due to current data availability it will mostly focus on insights from sex-specifically inherited mitochondrial DNA and Y-chromosomal DNA, whereas more genome-wide autosomal DNA data are soon expected to add additional details or may correct views obtained from these two, albeit highly complex, genetic loci.

The revolution that didn't arrive: A review of Pleistocene Sahul

There is a "package" of cultural innovations that are claimed to reflect modern human behaviour. The introduction of the "package" has been associated with the Middle-to-Upper Palaeolithic transition and the appearance in Europe of modern humans. It has been proposed that modern humans spread from Africa with the "package" and colonised not only Europe but also southern Asia and Australia (McBrearty and Brooks, 2000; Mellars, 2006a). In order to evaluate this proposal, we explore the late Pleistocene archaeological record of Sahul, the combined landmass of Australia and Papua New Guinea, for indications of these cultural innovations at the earliest sites. It was found that following initial occupation of the continent by anatomically and behaviourally modern humans, the components were gradually assembled over a 30,000-year period. We discount the idea that the "package" was lost en route to Sahul and assess the possibility that the "package" was not integrated within the material culture of the initial colonising groups because they may not have been part of a rapid colonisation process from Africa. As the cultural innovations appear at different times and locations within Sahul, the proposed "package" of archaeologically visible traits cannot be used to establish modern human behaviour. Whilst the potential causal role of increasing population densities/pressure in the appearance of the "package" of modern human behaviour in the archaeological record is acknowledged, it is not seen as the sole explanation because the individual components of the "package" appear at sites that are widely separated in space and time.

Mitochondrial DNA variation in Karkar Islanders

We analyzed 375 base pairs (bp) of the first hypervariable region (HVS-I) of the mitochondrial DNA (mtDNA) control region and intergenic COII/tRNALys 9-bp deletion from 47 Karkar Islanders (north coast of Papua New Guinea) belonging to the Waskia Papuan language group. To address questions concerning the origin and evolution of this population we compared the Karkar mtDNA haplotypes and haplogroups to those of neighbouring East Asians and Oceanic populations. The results of the phylogeographic analysis show grouping in three different clusters of the Karkar Islander mtDNA lineages: one group of lineages derives from the first Pleistocene settlers of New Guinea-Island Melanesia, a second set derives from more recent arrivals of Austronesian speaking populations, and the third contains lineages specific to the Karkar Islanders, but still rooted to Austronesian and New Guinea-Island Melanesia populations. Our results suggest (i) the absence of a strong association between language and mtDNA variation and, (ii) reveal that the mtDNA haplogroups F1a1, M7b1 and E1a, which probably originated in Island Southeast Asia and may be considered signatures of Austronesian population movements, are preserved in the Karkar Islanders but absent in other New Guinea-Island Melanesian populations. These findings indicate that the Karkar Papuan speakers retained a certain degree of their own genetic uniqueness and a high genetic diversity. We present a hypothesis based on archaeological, linguistic and environmental datasets to argue for a succession of (partial) depopulation and repopulation and expansion events, under conditions of structured interaction, which may explain the variability expressed in the Karkar mtDNA.

Autosomal microsatellite variability of the Arrernte people of Australia

The genomic diversity of the Arrernte people of Australia or caterpillar people was investigated utilizing 13 autosomal short tandem repeat (STR) markers. Significant departures from Hardy-Weinberg equilibrium were detected at the D18S51, TPOX and CSF1PO loci, which persisted after applying the Bonferroni correction. Gene diversity values oscillate between 0.6302 (CSF1PO) and 0.8731 (D21S11). Observed heterozygosity (Ho) ranges from 0.2632 (D18S51) to 0.8333 (vWA) and is lower than the expected heterozygosity (He) for 12 of the 13 loci analyzed. The genetic relationships of the Arrernte with Middle Eastern, East Asian, South Asian and Indian populations were analyzed by distance-based methods, including Neighbor-Joining trees and nonmetric multidimensional scaling. In addition, the genetic contribution of the populations included in the analysis to the Arrernte gene pool was estimated utilizing weighted least square coefficients. Although the Arrernte population exhibits a remarkable level of genetic differentiation, results of the phylogeographic analyses based on autosomal microsatellite data suggest a certain degree of genetic relatedness between the Arrernte tribe of Australia and populations from the Indian subcontinent. In contrast, the STR diversity analyses failed to detect substantial East Asian contribution to the genetic background of the Arrernte group.

A comprehensive analysis of microsatellite diversity in Aboriginal Australians

Indigenous Australians have a unique evolutionary history that has resulted in a complex system of inter and intra-tribal relationships. While a number of studies have examined the population genetics of indigenous Australians, most have used a single sample to illuminate details of the global dispersal of modern humans and few studies have focussed on the population genetic features of the widely dispersed communities of the indigenous population. In this study we examine the largest Aboriginal Australian sample yet analysed (N = 8,868) at fifteen hypervariable autosomal microsatellite loci. A comprehensive analysis of differentiation indicates different levels of heterogeneity among indigenous peoples from traditional regions of Aboriginal Australia. The most genetically differentiated populations inhabit the North of the country, in particular the Tiwi of Melville and Bathurst islands, Arnhem Land (itself divided into West and East Arnhem), and Fitzmaurice regions. These tribal groups are most differentiated from other Aboriginal Australian tribes, especially those of the Central Desert regions, and also show marked heterogeneity from one another. These genetic findings are supportive of observations of body measurements, skin colour, and dermatoglyphic features which also vary substantially between tribes of the North (e.g. Arnhem Land) and Central Australian regions and, more specifically, between the Tiwi and West and East Arnhem tribes. This study provides the most comprehensive survey of the population genetics of Aboriginal Australia.

Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis

Published and new samples of Aboriginal Australians and Melanesians were analyzed for mtDNA (n=172) and Y variation (n=522), and the resulting profiles were compared with the branches known so far within the global mtDNA and the Y chromosome tree. (i) All Australian lineages are confirmed to fall within the mitochondrial founder branches M and N and the Y chromosomal founders C and F, which are associated with the exodus of modern humans from Africa approximately 50-70,000 years ago. The analysis reveals no evidence for any archaic maternal or paternal lineages in Australians, despite some suggestively robust features in the Australian fossil record, thus weakening the argument for continuity with any earlier Homo erectus populations in Southeast Asia. (ii) The tree of complete mtDNA sequences shows that Aboriginal Australians are most closely related to the autochthonous populations of New Guinea/Melanesia, indicating that prehistoric Australia and New Guinea were occupied initially by one and the same Palaeolithic colonization event approximately 50,000 years ago, in agreement with current archaeological evidence. (iii) The deep mtDNA and Y chromosomal branching patterns between Australia and most other populations around the Indian Ocean point to a considerable isolation after the initial arrival. (iv) We detect only minor secondary gene flow into Australia, and this could have taken place before the land bridge between Australia and New Guinea was submerged approximately 8,000 years ago, thus calling into question that certain significant developments in later Australian prehistory (the emergence of a backed-blade lithic industry, and the linguistic dichotomy) were externally motivated.

Human cranial anatomy and the differential preservation of population history and climate signatures

Cranial morphology is widely used to reconstruct evolutionary relationships, but its reliability in reflecting phylogeny and population history has been questioned. Some cranial regions, particularly the face and neurocranium, are believed to be influenced by the environment and prone to convergence. Others, such as the temporal bone, are thought to reflect more accurately phylogenetic relationships. Direct testing of these hypotheses was not possible until the advent of large genetic data sets. The few relevant studies in human populations have had intriguing but possibly conflicting results, probably partly due to methodological differences and to the small numbers of populations used. Here we use three-dimensional (3D) geometric morphometrics methods to test explicitly the ability of cranial shape, size, and relative position/orientation of cranial regions to track population history and climate. Morphological distances among 13 recent human populations were calculated from four 3D landmark data sets, respectively reflecting facial, neurocranial, and temporal bone shape; shape and relative position; overall cranial shape; and centroid sizes. These distances were compared to neutral genetic and climatic distances among the same, or closely matched, populations. Results indicate that neurocranial and temporal bone shape track neutral genetic distances, while facial shape reflects climate; centroid size shows a weak association with climatic variables; and relative position/orientation of cranial regions does not appear correlated with any of these factors. Because different cranial regions preserve population history and climate signatures differentially, caution is suggested when using cranial anatomy for phylogenetic reconstruction.

Mitochondrial genomics identifies major haplogroups in Aboriginal Australians

We classified diversity in eight new complete mitochondrial genome sequences and 41 partial sequences from living Aboriginal Australians into five haplogroups. Haplogroup AuB belongs to global lineage M, and AuA, AuC, AuD, and AuE to N. Within N, we recognize subdivisions, assigning AuA to haplogroup S, AuD to haplogroup O, AuC to P4, and AuE to P8. On available evidence, (S)AuA and (M)AuB are widespread in Australia. (P4)AuC is found in the Riverine region of western New South Wales, and was identified by others in northern Australia. (O)AuD and (P8)AuE were clearly identified only from central Australia. Our eight Australian full mt genome sequences, combined with 20 others (Ingman and Gyllensten 2003 Genome Res. 13:1600-1606) and compared with full mt genome sequences from regions to the north that include Papua New Guinea, Malaya, and Andaman and Nicobar Islands, show that ancestral connections between regions are deep and limited to clustering at the level of the N and M macrohaplogroups. The Australian-specific distribution of the five haplogroups identified indicates genetic isolation over a long period. Ancestral connections within Australia are deeper than those reflected by known linguistic or culturally based affinities. Applying a coalescence analysis to a gene tree for the coding regions of the eight genomic sequences, we made estimates of time depth that support a continuity of presence for the descendants of a founding population already established by 40,000 years ago.

Ancient mitochondrial DNA from Malaysian hair samples: Some indications of Southeast Asian population movements

The late Pleistocene and early Holocene population history of Southeast Asia is not well-known. Our study provides new data on mitochondrial DNA (mtDNA) lineages of the aboriginal inhabitants of the Malay Peninsula, and through an extensive comparison to the known mtDNA diversity in Southeast and East Asia, provides some new insights into the origins and historical geography of certain mtDNA lineages in the region. We extracted DNA from hair samples (dating back 100 years) preserved in the Duckworth Collection and belonging to two Peninsular Malaysian individuals identified as "Negrito." Ancient DNA was analyzed by sequencing hypervariable region I (HVS-I) of the mtDNA control region and the mtDNA region V length polymorphism. The results show that the maternal lineages of these individuals belong to a recently defined haplogroup B sub-branch called B4c2. A comparison of mitochondrial haplotypes and haplogroups with those of 10,349 East Asian individuals indicates their very restricted geographical distribution (southwestern China, Southeast Asia Peninsula, and Indonesia). Recalculation of the B4c2 age across all of East Asia ( approximately 13,000 years) and in different subregions/populations suggests its rapid diffusion in Southeast Asia between the end of the Last Glacial Maximum and the Neolithic expansion of the Holocene.

Mandibular fossa of fossil Australians

Many questions about the skeletal adaptations and morphology of hunter-gatherers on the Australian continent remain unanswered. One anatomical region receiving little research in Australian fossils to date is the mandibular fossa. Here we report a study of three size dimensions, three shape indices and three morphological (non-metric) features of the mandibular fossa in 11 fossil Australians comparing them with modern Australo-Melanesian samples. We find broad similarities in past and modern populations in this region. Early and modern Australians and modern Papua New Guineans have elongate, broad and shallow fossae. All three populations show similarity in articular tubercle size, but postglenoid tubercle and entoglenoid process sizes show unexpected affinities. We also test for the possible presence of temporal trends in mandibular fossa size among fossil Australians. Our analyses indicate that none are present.

MITOCHONDRIAL DNA AND HUMAN EVOLUTION

Several unique properties of human mitochondrial DNA (mtDNA), including its high copy number, maternal inheritance, lack of recombination, and high mutation rate, have made it the molecule of choice for studies of human population history and evolution. Here we review the current state of knowledge concerning these properties, how mtDNA variation is studied, what we have learned, and what the future likely holds. We conclude that increasingly, mtDNA studies are (and should be) supplemented with analyses of the Y-chromosome and other nuclear DNA variation. Some serious issues need to be addressed concerning nuclear inserts, database quality, and the possible influence of selection on mtDNA variation. Nonetheless, mtDNA studies will continue to play an important role in such areas as examining socio-cultural influences on human genetic variation, ancient DNA, certain forensic DNA applications, and in tracing personal genetic history.

The haematology of indigenous Australians

Prior to European settlement indigenous Australians were hunter-gatherers who lived in geographically isolated small clan groups, also separated by elaborate totemic rules. Today they still reside in isolated communities throughout Australia but many have moved to the cities. They share a high incidence of a range of health problems including cardiovascular disease, renal disease and infectious diseases largely attributed to a change to a more sedentary lifestyle. This paper reviews the haematology of indigenous Australians, including blood count, frequency and causes of anaemia, inherited risk factors for thrombophilia, blood groups and the incidence and types of haematological malignancies. There are some significant genetic differences between indigenous and non-indigenous Australians particularly in the frequency of blood groups, factor V Leiden and prothrombin mutations and presence of -alpha3.7 kb thalassaemia. These findings may have practical therapeutic implications (e.g. HPA phenotype for transfusion therapy and pregnancy risk) and in predicting disease risk. Other differences are acquired, related to lifestyle and living conditions (e.g. eosinophilia secondary to parasitic infections; iron and folate deficiencies), and are largely preventable.

Mitochondrial genome variation and evolutionary history of Australian and New Guinean aborigines

To study the evolutionary history of the Australian and New Guinean indigenous peoples, we analyzed 101 complete mitochondrial genomes including populations from Australia and New Guinea as well as from Africa, India, Europe, Asia, Melanesia, and Polynesia. The genetic diversity of the Australian mitochondrial sequences is remarkably high and is similar to that found across Asia. This is in contrast to the pattern seen in previously described Y-chromosome data where an Australia-specific haplotype was found at high frequency. The mitochondrial genome data indicate that Australia was colonized between 40 and 70 thousand years ago, either by a single migration from a heterogeneous source population or by multiple movements of smaller groups occurring over a period of time. Some Australian and New Guinea sequences form clades, suggesting the possibility of a joint colonization and/or admixture between the two regions.

Mitochondrial DNA analysis reveals diverse histories of tribal populations from India

We analyzed 370 bp of the first hypervariable region of the mitochondrial DNA (mtDNA) control region in 752 individuals from 17 tribal and four nontribal groups from the Indian subcontinent, to address questions concerning the origins, genetic structure and relationships of these groups. Southern Indian tribes showed reduced diversity and large genetic distances, both among themselves and when compared with other groups, and no signal of prehistoric demographic expansions. These results probably reflect enhanced genetic drift because of small population sizes and/or bottlenecks in these groups. By contrast, northern groups exhibited more diversity and signals of prehistoric demographic expansions. Phylogenetic analyses revealed that southern and northern groups (except northeastern ones) have related mtDNA sequences albeit at different frequencies, further supporting the larger impact of drift on the genetic structure of southern groups. The Indian mtDNA gene pool appears to be more closely related to the east Eurasian gene pool (including central, east and southeast Asian populations) than the west Eurasian one (including European and Caucasian populations). Within India, northeastern tribes are quite distinct from other groups; they are more closely related to east Asians than to other Indians. This is consistent with linguistic evidence in that these populations speak Tibeto-Burman languages of east Asian origin. Otherwise, analyses of molecular variance suggested that caste and tribal groups are genetically similar with respect to mtDNA variation.

Mitochondrial DNA variability of West New Guinea populations

This paper reports human mitochondrial DNA variability in West New Guinea (the least known, western side of the island of New Guinea), not yet described from a molecular perspective. The study was carried out on 202 subjects from 12 ethnic groups, belonging to six different Papuan language families, representative of both mountain and coastal plain areas. Mitochondrial DNA hypervariable region 1 (HVS 1) and the presence of the 9-bp deletion (intergenic region COII-tRNA(Lys)) were investigated. HVS 1 sequencing identified 73 polymorphic sites defining 89 haplotypes; the 9-bp deletion, which is considered a marker of Austronesian migration in the Pacific, was found to be absent in the whole West New Guinea study sample. Statistical analysis applied to the resulting haplotypes reveal high heterogeneity and an intersecting distribution of genetic variability in these populations, despite their cultural and geographic diversity. The results of subsequent phylogenetic approaches subdivide mtDNA diversity in West New Guinea into three main clusters (groups I-III), defined by sets of polymorphisms which are also shared by some individuals from Papua New Guinea. Comparisons with worldwide HVS 1 sequences stored in the MitBASE database show the absence of these patterns outside Oceania and a few Indonesian subjects, who also lack the 9-bp deletion. This finding, which is consistent with the effects of genetic drift and prolonged isolation of West New Guinea populations, lead us to regard these patterns as New Guinea population markers, which may harbor the genetic memory of the earliest human migrations to the island.

Mitochondrial DNA variation in an aboriginal Australian population: evidence for genetic isolation and regional differentiation

The mitochondrial DNA (mt-DNA) variation of in the Walbiri tribe of the Northern Territories, Australia, was characterized by high resolution restriction fragment length polymorphism (HR-RFLP) analysis and control region sequencing. Surveying each mt-DNA for RFLPs with 14 different restriction enzymes detected 24 distinct haplotypes, whereas direct sequencing of the control region hypervariable segment I (HVS-I) of these mt-DNAs revealed 34 distinct sequences. Phylogenetic analysis of the RFLP haplotype and HVS-I sequence data depicted that the Walbiri have ten distinct haplotype groups (haplogroups), or mt-DNA lineages. The majority of the Walbiri RFLP haplotypes lacked polymorphisms common to Asian populations. In fact, most of the Walbiri haplogroups were unique to this population, although a few appeared to be subbranches of larger clusters of mt-DNAs that included other Aboriginal Australian and/or Papua New Guinea haplotypes. The similarity of these haplotypes suggested that Aboriginal Australian and Papua New Guinea populations may have once shared an ancient ancestral population(s), and then rapidly diverged from each other once geographically separated. Overall, the mt-DNA data corroborate the genetic uniqueness of Aboriginal Australian populations.

Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins

DNA from ancient human remains provides perspectives on the origin of our species and the relationship between molecular and morphological variation. We report analysis of mtDNA from the remains of 10 ancient Australians. These include the morphologically gracile Lake Mungo 3 [ approximately 60 thousand years (ka) before present] and three other gracile individuals from Holocene deposits at Willandra Lakes (<10 ka), all within the skeletal range of living Australians, and six Pleistocene/early Holocene individuals (15 to <8 ka) from Kow Swamp with robust morphologies outside the skeletal range of contemporary indigenous Australians. Lake Mungo 3 is the oldest (Pleistocene) "anatomically modern" human from whom DNA has been recovered. His mtDNA belonged to a lineage that only survives as a segment inserted into chromosome 11 of the nuclear genome, which is now widespread among human populations. This lineage probably diverged before the most recent common ancestor of contemporary human mitochondrial genomes. This timing of divergence implies that the deepest known mtDNA lineage from an anatomically modern human occurred in Australia; analysis restricted to living humans places the deepest branches in East Africa. The other ancient Australian individuals we examined have mtDNA sequences descended from the most recent common ancestor of living humans. Our results indicate that anatomically modern humans were present in Australia before the complete fixation of the mtDNA lineage now found in all living people. Sequences from additional ancient humans may further challenge current concepts of modern human origins.

Independent histories of human Y chromosomes from Melanesia and Australia

To investigate the origins and relationships of Australian and Melanesian populations, 611 males from 18 populations from Australia, Melanesia, and eastern/southeastern Asia were typed for eight single-nucleotide polymorphism (SNP) loci and seven short tandem-repeat loci on the Y chromosome. A unique haplotype, DYS390.1del/RPS4Y711T, was found at a frequency of 53%-69% in Australian populations, whereas the major haplotypes found in Melanesian populations (M4G/M5T/M9G and DYS390.3del/RPS4Y711T) are absent from the Australian populations. The Y-chromosome data thus indicate independent histories for Australians and Melanesians, a finding that is in agreement with evidence from mtDNA but that contradicts some analyses of autosomal loci, which show a close relationship between Australian and Melanesian (specifically, highland Papua New Guinean) populations. Since the Australian and New Guinean landmasses were connected when first colonized by humans > or =50,000 years ago but separated some 8,000 years ago, a possible way to reconcile all the genetic data is to infer that the Y-chromosome and mtDNA results reflect the past 8,000 years of independent history for Australia and New Guinea, whereas the autosomal loci reflect the long preceding period of common origin and shared history. Two Y-chromosome haplotypes (M119C/M9G and M122C/M9G) that originated in eastern/southeastern Asia are present in coastal and island Melanesia but are rare or absent in both Australia and highland Papua New Guinea. This distribution, along with demographic analyses indicating that population expansions for both haplotypes began approximately 4,000-6,000 years ago, suggests that these haplotypes were brought to Melanesia by the Austronesian expansion. Most of the populations in this study were previously typed for mtDNA SNPs; population differentiation is greater for the Y chromosome than for mtDNA and is significantly correlated with geographic distance, a finding in agreement with results of similar analyses of European populations.

Close genetic similarity between two sympatric species of tephritid fruit fly reproductively isolated by mating time

Two sibling species of tephritid fruit fly, Bactrocera tryoni and B. neohumeralis, occur sympatrically throughout the range of B. neohumeralis in Australia. Isolation between the two species appears to be maintained by a difference in mating time: B. tryoni mates at dusk, whereas B. neohumeralis mates during the middle of the day. A morphological difference in humeral callus color also distinguishes the two species. Despite clear phenotypic evidence that B. tryoni and B. neohumeralis are distinct species, genetic differentiation as measured by four markers--nuclear DNA sequences from the white gene and the ribosomal internal transcribed spacer (ITS2), and mitochondrial DNA sequences from the cytochrome b (cytb) and cytochrome oxidase subunit II (COII) genes--is very small. Minor fixed differences occur in the ITS2 sequence, however, in all other cases the two species exhibit a high level of shared polymorphic variation. The close genetic similarity suggests either that speciation has occurred very rapidly and recently in the absence of any mitochondrial DNA sorting or that the sharing of polymorphisms is due to hybridization or introgression. A third species within the tryoni complex, B. aquilonis, is geographically isolated. Bactrocera aquilonis is also genetically very similar, but in this case there is clear differentiation for the mitochondrial loci. The three species form a group of considerable interest for investigation of speciation mechanisms.

Evolution of Pacific/Asian populations inferred from HLA class II allele frequency distributions

The allele frequency distributions for the HLA class II loci, DRB1, DQB1 and DPB1, in eight Pacific/Asian populations: Hawaiian, Samoan, Malay, Papua New Guinea (PNG) Highlands, and two Indonesian and PNG Lowland groups, were determined using high-resolution polymerase chain reaction/sequence-specific oligonucleotide probe (PCR/SSOP) typing methods. The allele frequency distributions for the HLA-DRB1 locus were determined for a third Indonesian population as well as for an additional Filipino population. DRB1 alleles in the DR2 serogroup (or allelic lineage) are very common in this region; in some populations, more than 50% of the alleles belong to this serogroup. The DRB1*1502 allele is frequent in nine of the ten populations studied, reaching a frequency of 0.48 in one Indonesian population and among Filipinos. Extensive DR-DQ haplotype diversity was detected in these populations. Seven different DR2-DQB1 haplotypes were observed in the Indonesian and PNG Lowland populations, eight in the PNG Highlands and ten in Malays and Filipinos. The DRB1*0410 allele, commonly observed in Australia, is observed in the PNG Highlands at a low frequency (f=0.03) and is absent in the other populations. Two additional DRB1 alleles commonly observed in Australia, DRB1*0405 and *1407, are also observed in the PNG Highlands at high frequencies (f=0.132 and 0.126), while they are rare in the PNG Lowlands (f=0.039 and 0.013). These alleles are generally rare or absent in the other populations. The DPB1*0501 allele, common in Chinese and Japanese populations, is most frequent in the Samoan, Hawaiian, Indonesian, and Malay populations, and the *0401 allele is the most frequent DPB1 allele in the PNG Lowlands. Both of these alleles have the same very high frequency (f=0.34) in the PNG Highlands. Analyses of homozygosity (the Ewens-Watterson F statistic) in these and other populations indicate that, while most allele frequency distributions are consistent with balancing selection, values of F for the Indonesian and Javan populations may reflect positive directional selection. Phylogenetic trees constructed using the allele frequencies at the DRB1 locus of the populations reported here, as well as those for additional Pacific, Asian, and Australian populations, indicate that the PNG Highland population is more closely related to Australian populations than to PNG Lowland populations, while the PNG Lowlands are more closely related to other Melanesian populations.

Extremely high levels of human mitochondrial DNA heteroplasmy in single hair roots

For many years it has been assumed that the vast majority of mitochondrial genomes of a single individual are identical, both in the same tissue and within different tissues. Incidences of heteroplasmy (i.e., the occurrence of two or more codominating types of molecules within the mitochondrial DNA population of the same individual) were thought to be extremely rare. This study strongly supports the thesis that heteroplasmy is a principle, rather than an exception, in mitochondrial DNA genetics. During direct sequencing of the first hypervariable segment of the human mitochondrial control region (HV1) in 100 single hair roots obtained from 35 individuals, 24 different heteroplasmic positions were identified. Unusually high levels of heteroplasmy (up to six positions in the HV1 region) were encountered in two individuals. Two individuals related in maternal lineage shared the same heteroplasmic positions. Moreover, highly variable levels of heteroplasmy were observed even among roots from the same individual. The most probable mechanisms involved in generating so many mismatches are mutations occurring presumably in the female germline, followed by differential segregation of mitotypes during the development of individual hairs. Generally, heteroplasmy complicates sequence comparisons in mitochondrial DNA testing performed for forensic purposes, but in some cases it can substantially increase the discriminating power of the analysis.

Human evolution: the southern route to Asia

Research on human origins has tended to focus on the origins of western Eurasians; only recently have genetic studies examined south and east Asian populations in depth. Recent work suggests that the supposed Aryan invasion of India 3,000-4,000 years ago was much less significant than is generally believed.

Mitochondrial DNA variation is an indicator of austronesian influence in Island Melanesia

Past studies have shown a consistent association of a specific set of mitochondrial DNA 9 base pair (bp) deletion haplotypes with Polynesians and their Austronesian-speaking relatives, and the total lack of the deletion in a short series of New Guinea Highlanders. Utilizing plasma and DNA samples from various old laboratory collections, we have extended population screening for the 9-bp deletion into "Island Melanesia," an area notorious for its extreme population variation. While the 9-bp deletion is present in all Austronesian, and many non-Austronesian-speaking groups, it is absent in the more remote non-Austronesian populations in Bougainville and New Britain. These results are consistent with the hypothesis that this deletion was first introduced to this region about 3,500 years ago with the arrival of Austronesian-speaking peoples from the west, but has not yet diffused through all populations there. The pattern cannot be reconciled with the competing hypothesis of a primarily indigenous Melanesian origin for the ancestors of the Polynesians. Although selection clearly has operated on some other genetic systems in this region, both migration and random genetic drift primarily account for the remarkable degree of biological diversity in these small Southwest Pacific populations.

Why hunter-gatherer populations do not show signs of pleistocene demographic expansions

The mitochondrial DNA diversity of 62 human population samples was examined for potential signals of population expansions. Stepwise expansion times were estimated by taking into account heterogeneity of mutation rates among sites. Assuming an mtDNA divergence rate of 33% per million years, most populations show signals of Pleistocene expansions at around 70,000 years (70 KY) ago in Africa and Asia, 55 KY ago in America, and 40 KY ago in Europe and the Middle East, whereas the traces of the oldest expansions are found in East Africa (110 KY ago for the Turkana). The genetic diversity of two groups of populations (most Amerindian populations and present-day hunter-gatherers) cannot be explained by a simple stepwise expansion model. A multivariate analysis of the genetic distances among 61 populations reveals that populations that did not undergo demographic expansions show increased genetic distances from other populations, confirming that the demography of the populations strongly affects observed genetic affinities. The absence of traces of Pleistocene expansions in present-day hunter-gatherers seems best explained by the occurrence of recent bottlenecks in those populations, implying a difference between Pleistocene (approximately 1,800 KY to 10 KY ago) and Holocene (10 KY to present) hunter-gatherers demographies, a difference that occurred after, and probably in response to, the Neolithic expansions of the other populations.

Peopling of Sahul: mtDNA variation in aboriginal Australian and Papua New Guinean populations

We examined genetic affinities of Aboriginal Australian and New Guinean populations by using nucleotide variation in the two hypervariable segments of the mtDNA control region (CR). A total of 318 individuals from highland Papua New Guinea (PNG), coastal PNG, and Aboriginal Australian populations were typed with a panel of 29 sequence-specific oligonucleotide (SSO) probes. The SSO-probe panel included five new probes that were used to type an additional 1,037 individuals from several Asian populations. The SSO-type data guided the selection of 78 individuals from Australia and east Indonesia for CR sequencing. A gene tree of these CR sequences, combined with published sequences from worldwide populations, contains two previously identified highland PNG clusters that do not include any Aboriginal Australians; the highland PNG clusters have coalescent time estimates of approximately 80,000 and 122,000 years ago, suggesting ancient isolation and genetic drift. SSO-type data indicate that 84% of the sample of PNG highlander mtDNA belong to these two clusters. In contrast, the Aboriginal Australian sequences are intermingled throughout the tree and cluster with sequences from multiple populations. Phylogenetic and multidimensional-scaling analyses of CR sequences and SSO types split PNG highland and Aboriginal Australian populations and link Aboriginal Australian populations with populations from the subcontinent of India. These mtDNA results do not support a close relationship between Aboriginal Australian and PNG populations but instead suggest multiple migrations in the peopling of Sahul.

Mitochondrial DNA analysis: polymorphisms and pathogenicity

The investigation of mtDNA disease can be relatively straightforward if a person has a recognisable phenotype and if it is possible to identify a known pathogenic mtDNA mutation. The difficulties arise when no known mtDNA defect can be found, or when the clinical abnormalities are complex and not easily matched to those of the more common mitochondrial disorders. We will describe here the difficulties that can be encountered during the identification of pathogenic mtDNA mutations and the approaches that can be used to confirm, or eliminate, a likely pathogenic role, in either single gene diseases or in multifactorial disorders.

HLA class I allele distributions in six Pacific/Asian populations: evidence of selection at the HLA-A locus

The distributions of HLA-A alleles in six Pacific/Asian populations, Malay, Papua New Guinea (PNG) Highlands, two Indonesian groups, and two PNG Lowland groups, as well as the distribution of the HLA-B alleles in the PNG Highlands population, were determined using polymerase chain reaction (PCR) immobilized sequence-specific oligonucleotide (SSO) probe typing methods. The allele frequency distributions at the HLA class II loci, DRB1, DQB1 and DPB1 were also determined by PCR/SSO methods in an additional study of the same populations. In most of these populations, the HLA-A*2402 allele was the most frequent, attaining a frequency of 0.78 in the PNG Highlands. A*1101 was the next most frequent allele, followed in frequency by the *3401 allele. The HLA-B*1506, *4001, *5601 and *5602 alleles comprised 73% of the allele diversity at the B-locus in the PNG Highlands. Two previously unreported HLA-A alleles were identified in Indonesians and Malays, based on novel probe reactivity patterns. Cloning and sequencing identified these as A*1104 and *2410. Sequence comparisons show that these new alleles differ at codon 187 from their putative parental alleles (*1101 and *2403) by dinucleotide changes in the first two codon positions. These changes involve a Thr to Arg (CG to AC) and an Arg to Thr substitution (AC to CG) at position 187; residues at this position participate in pocket A of the peptide binding groove. Comparison of the HLA-A allele frequency distributions indicate that Malays are the most diverse (heterozygosity (h)=0.88) and the PNG Highlanders are, by far, the least diverse (h=0.37) of the groups studied. However, the diversity of B-locus alleles in the PNG Highlanders (h=0.91) was greater than that observed at the A-locus of any of the populations reported here. The remarkably high allele frequency of A*2402 in the PNG Highlands could reflect founder effects and population bottlenecks, genetic drift, or positive directional selection. The distribution of the HLA-B locus alleles and class II alleles, as well as mtDNA sequence data in the PNG Highlands indicates a reasonably high level of diversity at other loci, arguing that the high frequency of A*2402 cannot be attributed entirely to founder effects, bottlenecks, or drift and suggests the operation of positive selection for the A*2402 allele in this population.