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

Delineating the dispersal of Y-chromosome sub-haplogroup O2a2b-P164 among Austronesian-speaking populations

This article reports on an exploration of the Y-chromosome sub-haplogroup O2a2b-P164 in Austronesian-speaking populations. Moderate to high abundance of the P 164 mutation is seen in the West Pacific including the Amis of Formosa (36%) and the Filipinos of Mindanao (50%) as well as in the Kiritimati of Micronesia (70%), and Tonga and Samoa of West Polynesia (54% and 33%, respectively), and it drops to low frequencies in populations of East Polynesia. The communities of Polynesia and Micronesia exhibit considerable inter- and intra-population haplotype sharing suggesting extensive population affinity. The observed affinities, as well as the ages and diversity values within the P 164 sub-haplogroup among Austronesian-speaking populations signal an ancestral migration route and relationships that link the Amis of Taiwan with distant communities in West and East Polynesia, Micronesia, and the Maori of New Zealand. High resolution sequencing of the Austronesian Y chromosome indicate that the P 164 lineage originated about 19,000 ya and then split into three branches separating the Ami aborigines, Southeast Asian and Polynesian/Micronesian populations about 4700 ya, roughly coinciding with the initiation of the Austronesian diaspora. The Y-chromosomes of all the Polynesian and Micronesian population examined belong to the new FT 257096 haplogroup.

A novel system for classifying tooth root phenotypes

Human root and canal number and morphology are highly variable, and internal root canal form and count does not necessarily co-vary directly with external morphology. While several typologies and classifications have been developed to address individual components of teeth, there is a need for a comprehensive system, that captures internal and external root features across all teeth. Using CT scans, the external and internal root morphologies of a global sample of humans are analysed (n = 945). From this analysis a method of classification that captures external and internal root morphology in a way that is intuitive, reproducible, and defines the human phenotypic set is developed. Results provide a robust definition of modern human tooth root phenotypic diversity. The method is modular in nature, allowing for incorporation of past and future classification systems. Additionally, it provides a basis for analysing hominin root morphology in evolutionary, ecological, genetic, and developmental contexts.

The Ami and Yami aborigines of Taiwan and their genetic relationship to East Asian and Pacific populations

This article reports on the genetic characteristics of the Ami and Yami, two aboriginal populations of Taiwan. Y-SNP and mtDNA markers as well as autosomal SNPs were utilized to investigate the phylogenetic relationships to groups from MSEA (mainland Southeast Asia), ISEA (island Southeast Asia), and Oceania. Both the Ami and Yami have limited genetic diversity, with the Yami having even less diversity than the Ami. The partitioning of populations within the PCA plots based on autosomal SNPs, the profile constitution observed in the structure analyses demonstrating similar composition among specific populations, the average IBD (identical by descent) tract length gradients, the average total length of genome share among the populations, and the outgroup f3 results all indicate genetic affinities among populations that trace a geographical arc from Taiwan south into the Philippine Archipelago, Borneo, Indonesia, and Melanesia. Conversely, a more distant kinship between the Ami/Yami and MSEA based on all the markers examined, the total mtDNA sequences as well as the admixture f3 and f4 analyses argue against strong genetic contribution from MSEA to the Austronesian dispersal. The sharing of long IBD tracts, total genome length, and the large number of segments in common between the Ami/Yami and the Society Archipelago populations East Polynesia standout considering they are located about 10,700 km apart.

Seagrass ecosystem contributions to people's quality of life in the Pacific Island Countries and Territories

Seagrass ecosystems provide critical contributions (goods and perceived benefits or detriments) for the livelihoods and wellbeing of Pacific Islander peoples. Through in-depth examination of the contributions provided by seagrass ecosystems across the Pacific Island Countries and Territories (PICTs), we find a greater quantity in the Near Oceania (New Guinea, the Bismarck Archipelago and the Solomon Islands) and western Micronesian (Palau and Northern Marianas) regions; indicating a stronger coupling between human society and seagrass ecosystems. We also find many non-material contributions historically have been overlooked and under-appreciated by decision-makers. Closer cultural connections likely motivate guardianship of seagrass ecosystems by Pacific communities to mitigate local anthropogenic pressures. Regional comparisons also shed light on general and specific aspects of the importance of seagrass ecosystems to Pacific Islanders, which are critical for forming evidence-based policy and management to ensure the long-term resilience of seagrass ecosystems and the contributions they provide.

Update of the global distribution of human gammaherpesvirus 8 genotypes

Human gammaherpesvirus 8 (HHV-8) consists of six major clades (A–F) based on the genetic sequence of the open reading frame (ORF)-K1. There are a few conflicting reports regarding the global distribution of the different HHV-8 genotypes. This study aimed to determine the global distribution of the different HHV-8 genotypes based on phylogenetic analysis of the ORF-K1 coding region using sequences published in the GenBank during 1997–2020 and construct a phylogenetic tree using the maximum likelihood algorithm with the GTR + I + G nucleotide substitution model. A total of 550 sequences from 38 countries/origins were analysed in this study. Genotypes A and C had similar global distributions and were prevalent in Africa and Europe. Genotype B was prevalent in Africa. Of the rare genotypes, genotype D was reported in East Asia and Oceania and genotype E in South America, while genotype F was prevalent in Africa. The highest genotypic diversity was reported in the American continent, with Brazil housing five HHV-8 genotypes (A, B, C, E, and F). In this study, we present update of the global distribution of HHV-8 genotypes, providing a basis for future epidemiological and evolutionary studies of HHV-8.

Ancient DNA from Guam and the peopling of the Pacific

Humans reached the Mariana Islands in the western Pacific by ∼3,500 y ago, contemporaneous with or even earlier than the initial peopling of Polynesia. They crossed more than 2,000 km of open ocean to get there, whereas voyages of similar length did not occur anywhere else until more than 2,000 y later. Yet, the settlement of Polynesia has received far more attention than the settlement of the Marianas. There is uncertainty over both the origin of the first colonizers of the Marianas (with different lines of evidence suggesting variously the Philippines, Indonesia, New Guinea, or the Bismarck Archipelago) as well as what, if any, relationship they might have had with the first colonizers of Polynesia. To address these questions, we obtained ancient DNA data from two skeletons from the Ritidian Beach Cave Site in northern Guam, dating to ∼2,200 y ago. Analyses of complete mitochondrial DNA genome sequences and genome-wide SNP data strongly support ancestry from the Philippines, in agreement with some interpretations of the linguistic and archaeological evidence, but in contradiction to results based on computer simulations of sea voyaging. We also find a close link between the ancient Guam skeletons and early Lapita individuals from Vanuatu and Tonga, suggesting that the Marianas and Polynesia were colonized from the same source population, and raising the possibility that the Marianas played a role in the eventual settlement of Polynesia.

Rocker jaw: Global context for a Polynesian characteristic

Our goal is to describe the global distribution of the "rocker jaw" variant in human populations. Rocker jaw refers to mandibles that lack the antegonial notch, making them unstable on a flat surface. Data were collected by C.G. Turner II on 9,207 individuals from Asia, Europe, the Pacific, and the Americas, and by J.D. Irish on 3,526 individuals from North and South Africa. With a focus on Polynesia, where the trait is most common, frequencies are presented for subdivisions of Oceania, Australasia, Eurasia, the Americas, and Africa. While the rocker jaw is a Polynesian characteristic, the trait is found throughout the world. Within major geographic regions, there are interesting contrasts, for example, (a) the similarity of Jomon and Ainu and their difference from modern Japanese; (b) Aleuts and Northwest Coast Indians are similar and both are distinct from the Inuit and other Native Americans; and (c) North and Sub-Saharan Africans show a regional difference that parallels genetic and dental distinctions. Skeletons in South America that exhibit the rocker jaw have been interpreted as Polynesian voyagers who ventured to the west coast of South America. The rarity of rocker jaw in South American natives supports this view. The rocker jaw can be attributed to the unique basicranium morphology and large upper facial height of Polynesians, which highlights the integrated growth of a functional module (i.e., mastication) of the craniofacial complex. The unusually high frequency of the trait in Polynesians is a product of both function and founder effect/genetic drift.

Partial-AZFc deletions in Chilean men with primary spermatogenic impairment: gene dosage and Y-chromosome haplogroups

PURPOSE

To investigate the association of partial-AZFc deletions in Chilean men with primary spermatogenic failure and their testicular histopathological phenotypes, analyzing the contribution of DAZ dosage, CDY1 copies, and Y-chromosome haplogroups.

SUBJECTS AND METHODS

We studied 479 Chilean men: 334 infertile patients with histological examination (233 cases with spermatogenic defects and 101 normal spermatogenesis, obstructive controls, OC), and 145 normozoospermic controls (NC). AZFc subdeletions were detected by single-tagged sequences and single nucleotide variants analysis. DAZ-copy number was quantified by real-time qPCR. Y-chromosome haplogroups (Y-hg) were hierarchically genotyped through 16 biallelic-markers.

RESULTS

The prevalence of AZFc-partial deletions was increased in cases (6%) compared with NC (1.4%) (P = 0.035). There was no difference between 143 Sertoli-cell only syndrome, 35 maturation arrest, or 35 mix atrophy patients and controls. However, gr/gr deletions were more frequent in 16 subjects with hypospermatogenesis compared with NC (P = 0.003) and OC (P = 0.013). Y-hg R was the most prevalent (~ 50%), but decreased among gr/gr deletions (21%, P = 0.03). The prevalence of Y-hg M increased in cases versus controls, both in total and non-deleted men (3.9 and 3.7% versus 0.4%, P = 0.009 and P = 0.016, respectively). Among gr/gr deletions, Y-hg H increased compared with non-deleted men (14.3% versus 0.4%, P = 0.0047).

CONCLUSION

Partial-AZFc deletions in a Chilean admixed population are associated with secretory azo/oligozoospermia and might have a role in the development of hypospermatogenesis. Low represented haplogroups, Y-hg M and Y-hg H, show an association with the occurrence of spermatogenic failure and gr/gr deletions respectively; however, additional studies are required.

A tale of textiles: Genetic characterization of historical paper mulberry barkcloth from Oceania

Humans introduced paper mulberry (Broussonetia papyrifera) from Taiwan into the Pacific over 5000 years ago as a fiber source to make barkcloth textiles that were, and still are, important cultural artifacts throughout the Pacific. We have used B. papyrifera, a species closely associated to humans, as a proxy to understand the human settlement of the Pacific Islands. We report the first genetic analysis of paper mulberry textiles from historical and archaeological contexts (200 to 50 years before present) and compare our results with genetic data obtained from contemporary and herbarium paper mulberry samples. Following stringent ancient DNA protocols, we extracted DNA from 13 barkcloth textiles. We confirmed that the fiber source is paper mulberry in nine of the 13 textiles studied using the nuclear ITS-1 marker and by statistical estimates. We detected high genetic diversity in historical Pacific paper mulberry barkcloth with a set of ten microsatellites, showing new alleles and specific genetic patterns. These genetic signatures allow tracing connections to plants from the Asian homeland, Near and Remote Oceania, establishing links not observed previously (using the same genetic tools) in extant plants or herbaria samples. These results show that historic barkcloth textiles are cultural materials amenable to genetic analysis to reveal human history and that these artifacts may harbor evidence of greater genetic diversity in Pacific B. papyrifera in the past.

Fluctuating and Geographically Specific Selection Characterize Rapid Evolution of the Human KIR Region

The killer-cell immunoglobulin-like receptor (KIR) region comprises a fast-evolving family of genes that encode receptors for natural killer (NK) cells and have crucial role in host defense. Evolution of KIR was examined in the context of the human genome. Gene-content diversity and single nucleotide polymorphisms (SNP) in the KIR genes and flanking regions were compared to >660,000 genome-wide SNPs in over 800 individuals from 52 populations of the human genome diversity panel (HGDP). KIR allelic diversity was further examined using next generation sequencing in a subset of 56 individuals. We identified the SNP rs587560 located in KIR3DL3 as a marker of KIR2DL2 and KIR2DL3 and, consequently, Cen A and Cen B haplotypes. We also show that combinations of two KIR2DL4 SNPs (rs35656676 and rs592645) distinguish KIR3DL1 from KIR3DS1 and also define the major KIR3DL1 high- and low-expressing alleles lineages. Comparing the diversity of the SNPs within the KIR region to remainder of the genome, we observed a high diversity for the centromeric KIR region consistent with balancing selection (p < 0.01); in contrast, centromeric KIR diversity is significantly reduced in East Asian populations (p < 0.01), indicating purifying selection. By analyzing SNP haplotypes in a region spanning ~500 kb that includes the KIR cluster, we observed evidence of strong positive selection in Africa for high-expressing KIR3DL1 alleles, favored over the low-expressing alleles (p < 0.01). In sharp contrast, the strong positive selection (p < 0.01) that we also observed in the telomeric KIR region in Oceanic populations tracked with a high frequency of KIR3DS1. In addition, we demonstrated that worldwide frequency of high-expression KIR3DL1 alleles was correlated with virus with virus (r = 0.64, p < 10⁻⁶) and protozoa (r = 0.69, p < 10⁻⁶) loads, which points to selection globally on KIR3DL1 high-expressing alleles attributable to pathogen exposure.

The Marquesans at the fringes of the Austronesian expansion

In the present study, 87 unrelated individuals from the Marquesas Archipelago in French Polynesia were typed using mtDNA, Y-chromosome and autosomal (STRs) markers and compared to key target populations from Island South East Asia (ISEA), Taiwan, and West and East Polynesia to investigate their genetic relationships. The Marquesas, located at the eastern-most fringes of the Austronesian expansion, offer a unique opportunity to examine the effects of a protracted population expansion wave on population structure. We explore the contribution of Melanesian, Asian and European heritage to the Marquesan islands of Nuku-Hiva, Hiva-Oa and Tahuata. Overall, the Marquesas Islands are genetically homogeneous. In the Marquesan Archipelago all of the mtDNA haplogroups are of Austronesian origin belonging to the B4a1 subhaplogroup as the region marks the end of a west to east decreasing cline of Melanesian mtDNA starting with the West Polynesian population of Tonga. Genetic discrepancies are less pronounced between the Marquesan and Society islands, and among the Marquesan islands. Interestingly, a number of Melanesian, Polynesian and European Y-chromosome haplogroups exhibit very different distribution between the Marquesan islands of Nuku Hiva and Hiva Oa, likely resulting from drift, differential migration involving various source populations and/or unique trading routes.

Association study of CREBRF missense variant (rs373863828:G > A; p.Arg457Gln) with levels of serum lipid profile in the Pacific populations

BACKGROUND

A missense variant (rs373863828:G > A; p.Arg457Gln) of the CREBRF gene is strongly associated with a higher body mass index (BMI; kg/m²) in Polynesian populations. This variant has also been reported to be associated with lower total cholesterol in Samoans.

AIM

The aim of this study is to examine the association of rs373863828:G > A with levels of serum lipids in four Pacific populations.

METHODS

A total of 613 adult subjects were recruited from Tonga (Polynesians) and the Solomon Islands (Melanesians and Micronesians). Multiple regression analyses adjusted for age and sex were performed to examine the association of rs373863828 with levels of serum lipids in each population.

RESULTS

A significant association of rs373863828:G > A with lower level of HDL-cholesterol was detected in the Tonga population (β = -3.32 and p-value = 0.030). The expected change in HDL-cholesterol with respect to a single copy of the rs373863828-A allele was 3.32 mg/dL. However, the association between rs373863828-A and lower levels of HDL-cholesterol was not significant after further adjustment for BMI in the Tonga population (β = -2.32 and p-value = 0.13).

CONCLUSIONS

The rs373863828-A allele may not directly affect the level of serum HDL-cholesterol independent of BMI. To confirm the present findings, association studies with large sample sizes and functional analyses are required.

Walking backwards into the future: the need for a holistic evolutionary approach in Pacific health research

CONTEXT

The Pacific region has had a complex human history. It has been subject to multiple major human dispersal and colonisation events, including some of the earliest Out-of-Africa migrations, the so-called Austronesian expansion of people out of Island Southeast Asia, and the more recent arrival of Europeans. Despite models of island isolation, evidence suggests significant levels of interconnectedness that vary in direction and frequency over time. The Pacific Ocean covers a vast area and its islands provide an array of different physical environments with variable pathogen loads and subsistence opportunities. These diverse environments likely caused Pacific peoples to adapt (both genetically and culturally) in unique ways. Differences in genetic background, in combination with adaptation, likely affect their susceptibility to non-communicable diseases.

OBJECTIVES

Here we provide an overview of some of the key issues in the natural and human history of the Pacific region which are likely to impact human health. We argue that understanding the evolutionary and cultural history of Pacific peoples is essential for the generation of testable hypotheses surrounding potential causes of elevated disease susceptibility among Pacific peoples.

The evolutionary history and human settlement of Australia and the Pacific

Understanding the timing and processes involved in the human settlement of Australia and the Pacific has significance for addressing some key debates relating to human origins and population expansions worldwide. Despite this, for many years, Pacific populations were seriously under-represented in genetic studies of human origins. The last 15 years, however, have seen some major genetic studies involving Australian and Pacific populations which have shed light on their origins and interactions, and the last five years have seen some major developments that are challenging long-held concepts of Pacific settlement.

Assessing the relative impact of historical divergence and inter-group transmission on cultural patterns: a method from evolutionary ecology

In the study of cultural evolution, observed among-group affinity patterns reflect the effects of processes such as mutation (e.g. innovation and copying error), between-group interaction (culture flow), drift and selection. As in biology, cultural affinity patterns are often spatially correlated, making it difficult to distinguish between the opposing geographically mediated forces of divergence and interaction, which cause groups to become more distinct or similar over time, respectively. Analogous difficulties are faced by evolutionary biologists examining the relationship between biological affinity and geography, particularly at lower taxonomic levels where the potential for gene flow between lineages is greatest. Tree models are generally used to assess the fit between affinity patterns and models of historical divergence. However, factors driving lineage divergence are often spatially mediated, resulting in tree models that are themselves geographically structured. Here, we showcase a simple method drawn from evolutionary ecology for assessing the relative impact of both geographically mediated processes simultaneously. We illustrate the method using global human craniometric diversity and material culture from the northern coast of New Guinea as example case studies. This method can be employed to quantify the relative importance of history (divergence) and geographically mediated between-group interaction (culture flow) in explaining observed cultural affinity patterns.This article is part of the theme issue 'Bridging cultural gaps: interdisciplinary studies in human cultural evolution'.

A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog

The accurate description of ancestry is essential to interpret, access, and integrate human genomics data, and to ensure that these benefit individuals from all ancestral backgrounds. However, there are no established guidelines for the representation of ancestry information. Here we describe a framework for the accurate and standardized description of sample ancestry, and validate it by application to the NHGRI-EBI GWAS Catalog. We confirm known biases and gaps in diversity, and find that African and Hispanic or Latin American ancestry populations contribute a disproportionately high number of associations. It is our hope that widespread adoption of this framework will lead to improved analysis, interpretation, and integration of human genomics data.

Human phylogeography and diversity

Homo sapiens phylogeography begins with the species' origin nearly 200 kya in Africa. First signs of the species outside Africa (in Arabia) are from 125 kya. Earliest dates elsewhere are now 100 kya in China, 45 kya in Australia and southern Europe (maybe even 60 kya in Australia), 32 kya in northeast Siberia, and maybe 20 kya in the Americas. Humans reached arctic regions and oceanic islands last-arctic North America about 5 kya, mid- and eastern Pacific islands about 2-1 kya, and New Zealand about 700 y ago. Initial routes along coasts seem the most likely given abundant and easily harvested shellfish there as indicated by huge ancient oyster shell middens on all continents. Nevertheless, the effect of geographic barriers-mountains and oceans-is clear. The phylogeographic pattern of diasporas from several single origins-northeast Africa to Eurasia, southeast Eurasia to Australia, and northeast Siberia to the Americas-allows the equivalent of a repeat experiment on the relation between geography and phylogenetic and cultural diversity. On all continents, cultural diversity is high in productive low latitudes, presumably because such regions can support populations of sustainable size in a small area, therefore allowing a high density of cultures. Of course, other factors operate. South America has an unusually low density of cultures in its tropical latitudes. A likely factor is the phylogeographic movement of peoples from the Old World bringing novel and hence, lethal diseases to the New World, a foretaste, perhaps, of present day global transport of tropical diseases.

How much impact do gains in height have on shoulder breadths within Taiwanese families?

OBJECTIVES

This study investigates allometric changes in shoulder breadths relative to changes in stature arising from rapidly changing developmental circumstances within 107 Taiwanese families. It speaks to broader issues related to the extent of phenotypic plasticity of body breadths humans are capable of in response to reductions in developmental stressors.

METHODS

An examination of relationships between shoulder breadth and height within individuals in each generation was followed by evaluation of patterns of difference between same-sex parent-offspring pairs in height and shoulder breadth.

RESULTS

Height was similarly positively correlated with shoulder breadth within fathers, mothers, sons, and daughters (P ≤ 0.002). Variance accounted for ranged from an adjusted R² of 0.201 among fathers to 0.151 for sons, with mothers' and daughters' values being 0.187 and 0.181, respectively. Comparisons of differences within families indicate that parents who were shorter than their same-sex offspring also tended to have modestly narrower biacromial breadths (father-son pairs: adjusted R²  = 0.112; t = 2.82, P = .007; mother-daughter pairs: adjusted R²  = 0.135; t = 2.97, P = 0.005).

CONCLUSIONS

Taken as a whole, results here support the view that secular changes in stature are not accompanied by similar changes in body breadths, perhaps so that responses to developmental environmental improvements do not alter thermoregulatory equilibria that reflect long-term evolutionary processes. These results indirectly constrain plausible hypotheses about how ancestors of Austronesian speakers altered their body size and shape as they voyaged to Fiji, Western Polynesia, and beyond.

The study of human Y chromosome variation through ancient DNA

High throughput sequencing methods have completely transformed the study of human Y chromosome variation by offering a genome-scale view on genetic variation retrieved from ancient human remains in context of a growing number of high coverage whole Y chromosome sequence data from living populations from across the world. The ancient Y chromosome sequences are providing us the first exciting glimpses into the past variation of male-specific compartment of the genome and the opportunity to evaluate models based on previously made inferences from patterns of genetic variation in living populations. Analyses of the ancient Y chromosome sequences are challenging not only because of issues generally related to ancient DNA work, such as DNA damage-induced mutations and low content of endogenous DNA in most human remains, but also because of specific properties of the Y chromosome, such as its highly repetitive nature and high homology with the X chromosome. Shotgun sequencing of uniquely mapping regions of the Y chromosomes to sufficiently high coverage is still challenging and costly in poorly preserved samples. To increase the coverage of specific target SNPs capture-based methods have been developed and used in recent years to generate Y chromosome sequence data from hundreds of prehistoric skeletal remains. Besides the prospects of testing directly as how much genetic change in a given time period has accompanied changes in material culture the sequencing of ancient Y chromosomes allows us also to better understand the rate at which mutations accumulate and get fixed over time. This review considers genome-scale evidence on ancient Y chromosome diversity that has recently started to accumulate in geographic areas favourable to DNA preservation. More specifically the review focuses on examples of regional continuity and change of the Y chromosome haplogroups in North Eurasia and in the New World.

Lack of gene-language correlation due to reciprocal female but directional male admixture in Austronesians and non-Austronesians of East Timor

Nusa Tenggara, including East Timor, located at the crossroad between Island Southeast Asia, Near Oceania, and Australia, are characterized by a complex cultural structure harbouring speakers from two different major linguistic groups of different geographic origins (Austronesian (AN) and non-Austronesian (NAN)). This provides suitable possibilities to study gene-language relationship; however, previous studies from other parts of Nusa Tenggara reported conflicting evidence about gene-language correlation in this region. Aiming to investigate gene-language relationships including sex-mediated aspects in East Timor, we analysed the paternally inherited non-recombining part of the Y chromosome (NRY) and the maternally inherited mitochondrial (mt) DNA in a representative collection of AN- and NAN-speaking groups. Y-SNP (single-nucleotide polymorphism) data were newly generated for 273 samples and combined with previously established Y-STR (short tandem repeat) data of the same samples, and with previously established mtDNA data of 290 different samples with, however, very similar representation of geographic and linguistic coverage of the country. We found NRY and mtDNA haplogroups of previously described putative East/Southeast Asian (E/SEA) and Near Oceanian (NO) origins in both AN and NAN speakers of East Timor, albeit in different proportions, suggesting reciprocal genetic admixture between both linguistic groups for females, but directional admixture for males. Our data underline the dual genetic origin of East Timorese in E/SEA and NO, and highlight that substantial genetic admixture between the two major linguistic groups had occurred, more so via women than men. Our study therefore provides another example where languages and genes do not conform due to sex-biased genetic admixture across major linguistic groups.

Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia

Background

From a mtDNA dominant perspective, the exit from Africa of modern humans to colonize Eurasia occurred once, around 60 kya, following a southern coastal route across Arabia and India to reach Australia short after. These pioneers carried with them the currently dominant Eurasian lineages M and N. Based also on mtDNA phylogenetic and phylogeographic grounds, some authors have proposed the coeval existence of a northern route across the Levant that brought mtDNA macrohaplogroup N to Australia. To contrast both hypothesis, here we reanalyzed the phylogeography and respective ages of mtDNA haplogroups belonging to macrohaplogroup M in different regions of Eurasia and Australasia.

Results

The macrohaplogroup M has a historical implantation in West Eurasia, including the Arabian Peninsula. Founder ages of M lineages in India are significantly younger than those in East Asia, Southeast Asia and Near Oceania. Moreover, there is a significant positive correlation between the age of the M haplogroups and its longitudinal geographical distribution. These results point to a colonization of the Indian subcontinent by modern humans carrying M lineages from the east instead the west side.

Conclusions

The existence of a northern route, previously proposed for the mtDNA macrohaplogroup N, is confirmed here for the macrohaplogroup M. Both mtDNA macrolineages seem to have differentiated in South East Asia from ancestral L3 lineages. Taking this genetic evidence and those reported by other disciplines we have constructed a new and more conciliatory model to explain the history of modern humans out of Africa.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0816-8) contains supplementary material, which is available to authorized users.

Genomic insights into the peopling of the Southwest Pacific

The appearance of people associated with the Lapita culture in the South Pacific around 3,000 years ago marked the beginning of the last major human dispersal to unpopulated lands. However, the relationship of these pioneers to the long-established Papuan people of the New Guinea region is unclear. Here we present genome-wide ancient DNA data from three individuals from Vanuatu (about 3,100-2,700 years before present) and one from Tonga (about 2,700-2,300 years before present), and analyse them with data from 778 present-day East Asians and Oceanians. Today, indigenous people of the South Pacific harbour a mixture of ancestry from Papuans and a population of East Asian origin that no longer exists in unmixed form, but is a match to the ancient individuals. Most analyses have interpreted the minimum of twenty-five per cent Papuan ancestry in the region today as evidence that the first humans to reach Remote Oceania, including Polynesia, were derived from population mixtures near New Guinea, before their further expansion into Remote Oceania. However, our finding that the ancient individuals had little to no Papuan ancestry implies that later human population movements spread Papuan ancestry through the South Pacific after the first peopling of the islands.

Rapid mortality transition of Pacific Islands in the 19th century

The depopulation of Pacific islands during the 16th to 19th centuries is a striking example of historical mass mortality due to infectious disease. Pacific Island populations have not been subject to such cataclysmic infectious disease mortality since. Here we explore the processes which could have given rise to this shift in infectious disease mortality patterns. We show, using mathematical models, that the population dynamics exhibited by Pacific Island populations are unlikely to be the result of Darwinian evolution. We propose that extreme mortality during first-contact epidemics is a function of epidemiological isolation, not a lack of previous selection. If, as pathogens become established in populations, extreme mortality is rapidly suppressed by herd immunity, Pacific Island population mortality patterns can be explained with no need to invoke genetic change. We discuss the mechanisms by which this could occur, including (i) a link between the proportion of the population transmitting infectious agents and case-fatality rates, and (ii) the course of infection with pathogens such as measles and smallpox being more severe in adults than in children. Overall, we consider the present-day risk of mass mortality from newly emerging infectious diseases is unlikely to be greater on Pacific islands than in other geographical areas.

Lethality of First Contact Dysentery Epidemics on Pacific Islands

Infectious diseases depopulated many isolated Pacific islands when they were first exposed to global pathogen circulation from the 18th century. Although the mortality was great, the lack of medical observers makes determination of what happened during these historical epidemics largely speculative. Bacillary dysentery caused by Shigella is the most likely infection causing some of the most lethal island epidemics. The fragmentary historical record is reviewed to gain insight into the possible causes of the extreme lethality that was observed during first-contact epidemics in the Pacific. Immune aspects of the early dysentery epidemics and postmeasles infection resulting in subacute inflammatory enteric disease suggest that epidemiologic isolation was the major lethality risk factor on Pacific islands in the 19th century. Other possible risk factors include human leukocyte antigen homogeneity from a founder effect and pathogen-induced derangement of immune tolerance to gut flora. If this analysis is correct, then Pacific islands are currently at no greater risk of emerging disease epidemics than other developing countries despite their dark history.

Fine-Scale Human Population Structure in Southern Africa Reflects Ecogeographic Boundaries

Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until ∼2000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about their population history. We examine new genome-wide polymorphism data and whole mitochondrial genomes for >100 South Africans from the ≠Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking ≠Khomani (formerly hunter-gatherers) share ancestry with other Khoe-speaking forager populations that form a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu speakers, ∼14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited genetic impact from eastern Africa.

Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families

The paternal haplogroup (hg) N is distributed from southeast Asia to eastern Europe. The demographic processes that have shaped the vast extent of this major Y chromosome lineage across numerous linguistically and autosomally divergent populations have previously been unresolved. On the basis of 94 high-coverage re-sequenced Y chromosomes, we establish and date a detailed hg N phylogeny. We evaluate geographic structure by using 16 distinguishing binary markers in 1,631 hg N Y chromosomes from a collection of 6,521 samples from 56 populations. The more southerly distributed sub-clade N4 emerged before N2a1 and N3, found mostly in the north, but the latter two display more elaborate branching patterns, indicative of regional contrasts in recent expansions. In particular, a number of prominent and well-defined clades with common N3a3'6 ancestry occur in regionally dissimilar northern Eurasian populations, indicating almost simultaneous regional diversification and expansion within the last 5,000 years. This patrilineal genetic affinity is decoupled from the associated higher degree of language diversity.

Exploring Ecosystems and Health by Shifting to a Regional Focus: Perspectives from the Oceania EcoHealth Chapter

This article highlights contributions that can be made to the public health field by incorporating "ecosystem approaches to health" to tackle future environmental and health challenges at a regional level. This qualitative research reviews attitudes and understandings of the relationship between public health and the environment and the priorities, aspirations and challenges of a newly established group (the Oceania EcoHealth Chapter) who are attempting to promote these principles. Ten semi-structured interviews with Oceania EcoHealth Chapter members highlighted the important role such groups can play in informing organisations working in the Oceania region to improve both public health and environmental outcomes simultaneously. Participants of this study emphasise the need to elevate Indigenous knowledge in Oceania and the role regional groups play in this regard. They also emphasis that regional advocacy and ecosystem approaches to health could bypass silos in knowledge and disciplinary divides, with groups like the Oceania EcoHealth Chapter acting as a mechanism for knowledge exchange, engagement, and action at a regional level with its ability to bridge the gap between environmental stewardship and public health.

Pacific Populations, Metabolic Disease and 'Just-So Stories': A Critique of the 'Thrifty Genotype' Hypothesis in Oceania

Pacific populations have long been observed to suffer a high burden of metabolic disease, including obesity, type 2 diabetes and gout. The 'Thrifty Genotype' hypothesis has frequently been used to explain this high prevalence of disease. Here, the 'Thrifty Genotype' hypothesis and the evolutionary background of Pacific populations are examined. We question its relevance not only in the Pacific region but more generally. Not only has the hypothesis not been explicitly tested, but most archaeological and anthropological data from the Pacific fundamentally do not support its application.

Maternal ancestry and population history from whole mitochondrial genomes

MtDNA has been a widely used tool in human evolutionary and population genetic studies over the past three decades. Its maternal inheritance and lack of recombination have offered the opportunity to explore genealogical relationships among individuals and to study the frequency differences of matrilineal clades among human populations at continental and regional scales. The whole mtDNA genome sequencing delivers molecular resolution that is sufficient to distinguish patterns that have arisen over thousands of years. However, mutation rate is highly variable among the functional and non-coding domains of mtDNA which makes it challenging to obtain accurate split dates of the mitochondrial clades. Due to the shallow coalescent time of mitochondrial TMRCA at approximately 100 to 200 thousand years (ky), mtDNA data have only limited power to inform us about the more distant past and the early stages of human evolutionary history. The variation shared by mitochondrial genomes of individuals drawn from different continents outside Africa has been used to illuminate the details of the colonization process of the Old World, whereas regional patterns of variation have been at the focus of studies addressing questions of a more recent time scale. In the era of whole nuclear genome sequencing, mitochondrial genomes are continuing to be informative as a unique tool for the assessment of female-specific aspects of the demographic history of human populations.

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.

Ancient DNA and the human settlement of the Pacific: a review

The Pacific region provides unique opportunities to study human evolution including through analyses of ancient DNA. While some of the earliest studies involving ancient DNA from skeletal remains focused on Pacific samples, in the following 25 years, several factors meant that little aDNA research, particularly research focused on human populations, has emerged. This paper briefly presents the genetic evidence for population origins, reviews what ancient DNA work has been undertaken to address human history and evolution in the Pacific region, and argues that the future is bright but research requires a collaborative approach between academic disciplines but also with local communities.

Recent developments in the genetic history of East Asia and Oceania

Recent developments in our understanding of the genetic history of Asia and Oceania have been driven by technological advances. Specifically, our understanding of the past has been augmented by: genome sequences from ancient hominins and ancient modern humans; more comprehensive studies of existing populations (e.g., complete mtDNA genome sequences and genome-wide data) and the development of new statistics and analytical methods to interpret the abundance of new data. We review some of the new discoveries since we entered the age of archaic and modern genomics and how they have changed our understanding of the settlement and subsequent population dynamics in Asia and the Pacific.

Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia

The highly structured distribution of Y-chromosome haplogroups suggests that current patterns of variation may be informative of past population processes. However, limited phylogenetic resolution, particularly of subclades within haplogroup K, has obscured the relationships of lineages that are common across Eurasia. Here we genotype 13 new highly informative single-nucleotide polymorphisms in a worldwide sample of 4413 males that carry the derived allele at M526, and reconstruct an NRY haplogroup tree with significantly higher resolution for the major clade within haplogroup K, K-M526. Although K-M526 was previously characterized by a single polytomy of eight major branches, the phylogenetic structure of haplogroup K-M526 is now resolved into four major subclades (K2a-d). The largest of these subclades, K2b, is divided into two clusters: K2b1 and K2b2. K2b1 combines the previously known haplogroups M, S, K-P60 and K-P79, whereas K2b2 comprises haplogroups P and its subhaplogroups Q and R. Interestingly, the monophyletic group formed by haplogroups R and Q, which make up the majority of paternal lineages in Europe, Central Asia and the Americas, represents the only subclade with K2b that is not geographically restricted to Southeast Asia and Oceania. Estimates of the interval times for the branching events between M9 and P295 point to an initial rapid diversification process of K-M526 that likely occurred in Southeast Asia, with subsequent westward expansions of the ancestors of haplogroups R and Q.

Human genetics of the Kula Ring: Y-chromosome and mitochondrial DNA variation in the Massim of Papua New Guinea

The island region at the southeastern-most tip of New Guinea and its inhabitants known as Massim are well known for a unique traditional inter-island trading system, called Kula or Kula Ring. To characterize the Massim genetically, and to evaluate the influence of the Kula Ring on patterns of human genetic variation, we analyzed paternally inherited Y-chromosome (NRY) and maternally inherited mitochondrial (mt) DNA polymorphisms in >400 individuals from this region. We found that the nearly exclusively Austronesian-speaking Massim people harbor genetic ancestry components of both Asian (AS) and Near Oceanian (NO) origin, with a proportionally larger NO NRY component versus a larger AS mtDNA component. This is similar to previous observations in other Austronesian-speaking populations from Near and Remote Oceania and suggests sex-biased genetic admixture between Asians and Near Oceanians before the occupation of Remote Oceania, in line with the Slow Boat from Asia hypothesis on the expansion of Austronesians into the Pacific. Contrary to linguistic expectations, Rossel Islanders, the only Papuan speakers of the Massim, showed a lower amount of NO genetic ancestry than their Austronesian-speaking Massim neighbors. For the islands traditionally involved in the Kula Ring, a significant correlation between inter-island travelling distances and genetic distances was observed for mtDNA, but not for NRY, suggesting more male- than female-mediated gene flow. As traditionally only males take part in the Kula voyages, this finding may indicate a genetic signature of the Kula Ring, serving as another example of how cultural tradition has shaped human genetic diversity.

Hyperuricaemia in the Pacific: why the elevated serum urate levels?

Pacific Island populations, particularly those of Polynesian descent, have a high prevalence of hyperuricaemia and gout. This is due to an inherently higher urate level among these populations with a demonstrated genetic predisposition. While an excess of urate can cause pathology, urate is also important for human health. It has been implicated as an antioxidant, has a neuroprotective role and is involved in innate immune responses. This paper provides a brief review of urate levels worldwide, with a particular focus on island Southeast Asia and the Pacific. We then present possible evolutionary explanations for the elevated serum urate levels among Pacific populations in the context of the physiological importance of urate and of the settlement history of the region. Finally, we propose that ancestry may play a significant role in hyperuricaemia in these populations and that exposure to malaria prior to population expansion into the wider Pacific may have driven genetic selection for variants contributing to high serum urate.

Genetic diversity of four Filipino negrito populations from Luzon: comparison of male and female effective population sizes and differential integration of immigrants into Aeta and Agta communities

Genetic data corresponding to four negrito populations (two Aeta and two Agta; n = 120) from the Luzon region of the Philippines have been analyzed. These data comprise mitochondrial DNA (mtDNA) hypervariable segment 1 haplotypes and haplogroups, Y-chromosome haplogroups and short tandem repeats (STRs), autosomal STRs, and X-chromosome STRs. The genetic diversity and structure of the populations were investigated at a local, regional, and interregional level. We found a high level of autosomal differentiation, combined with no significant reduction in diversity, consistent with long-term settlement of the Luzon region by the ancestors of the Agta and Aeta followed by reduced gene flow between these two ethnolinguistic groups. Collectively, the Aeta have a much higher ratio of female:male effective population size than do the Agta, a finding that supports phylogenetic analysis of their mtDNA and Y-chromosome haplogroups, which suggests different genetic sex-biased contributions from putative Austronesian source populations. We propose that factors of social organization that led to the reduction in Agta female effective population size may also be linked to the limited incorporation of female lineages associated with the settlement of the Philippines by Austronesian speakers; conversely, the reduction in Aeta male effective population size, relative to females, could be indicative of a limited incorporation of male lineages associated with this demographic process.

Global patterns of diversity and selection in human tyrosinase gene

Global variation in skin pigmentation is one of the most striking examples of environmental adaptation in humans. More than two hundred loci have been identified as candidate genes in model organisms and a few tens of these have been found to be significantly associated with human skin pigmentation in genome-wide association studies. However, the evolutionary history of different pigmentation genes is rather complex: some loci have been subjected to strong positive selection, while others evolved under the relaxation of functional constraints in low UV environment. Here we report the results of a global study of the human tyrosinase gene, which is one of the key enzymes in melanin production, to assess the role of its variation in the evolution of skin pigmentation differences among human populations. We observe a higher rate of non-synonymous polymorphisms in the European sample consistent with the relaxation of selective constraints. A similar pattern was previously observed in the MC1R gene and concurs with UV radiation-driven model of skin color evolution by which mutations leading to lower melanin levels and decreased photoprotection are subject to purifying selection at low latitudes while being tolerated or even favored at higher latitudes because they facilitate UV-dependent vitamin D production. Our coalescent date estimates suggest that the non-synonymous variants, which are frequent in Europe and North Africa, are recent and have emerged after the separation of East and West Eurasian populations.

Human platelet antigens frequencies in Maori and Polynesian populations

BACKGROUND

Allele frequencies of human platelet antigens (HPA) reflect population history and possibility of platelet-specific alloimmunization. Here, we report on screening of variants at HPA loci for Polynesian and Maori subjects.

OBJECTIVES

Our aims are to evaluate new HPA genotyping methods, compile and analyse new HPA datasets for these subjects, use HPA data for tracing ancestry, migration patterns, genetic admixture and its potential influence on health.

MATERIALS AND METHODS

A total of 75 Maori and 25 Polynesian DNA samples were genotyped using commercial BAGene HPA-TYPE DNA-SSP kits, BLOODchip hybridization SNP assays and DNA sequence based typing.

RESULTS

Genotyping was successful and cross validation of PCR-SSP and BLOODchip gave 100% agreement. Among the HPA loci tested, only six are dimorphic (HPA-1 to -3, -5, -6 and -15) and all others are monomorphic. The Polynesians and Maori have the 'a' allele form as the most common for all loci except HPA-15.

CONCLUSIONS

The newly observed HPA data as well as principal coordinate analysis clearly indicate genetic contributions from both, Asia and Australasia in Maori and Polynesian populations together with recent admixture with Europeans. In addition, different prevalences of HPA alleles among Polynesian, Maori and European populations contribute towards different risk profiles for platelet-specific alloimmunization. This is the first report for these populations and our findings are of direct practical relevance for blood transfusion centres, the management of pregnancies, assessment of neonatal alloimmune thrombocytopenia and management of multi-transfused patients.

Genome-wide data substantiate Holocene gene flow from India to Australia

The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early "southern route" migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India.

The Indonesian archipelago: an ancient genetic highway linking Asia and the Pacific

Indonesia, an island nation linking mainland Asia with the Pacific world, hosts a wide range of linguistic, ethnic and genetic diversity. Despite the complexity of this cultural environment, genetic studies in Indonesia remain surprisingly sparse. Here, we report mitochondrial DNA (mtDNA) and associated Y-chromosome diversity for the largest cohort of Indonesians examined to date-2740 individuals from 70 communities spanning 12 islands across the breadth of the Indonesian archipelago. We reconstruct 50 000 years of population movements, from mitochondrial lineages reflecting the very earliest settlers in island southeast Asia, to Neolithic population dispersals. Historic contacts from Chinese, Indians, Arabs and Europeans comprise a noticeable fraction of Y-chromosome variation, but are not reflected in the maternally inherited mtDNA. While this historic immigration favored men, patterns of genetic diversity show that women moved more widely in earlier times. However, measures of population differentiation signal that Indonesian communities are trending away from the matri- or ambilocality of early Austronesian societies toward the more common practice of patrilocal residence today. Such sex-specific dispersal patterns remain even after correcting for the different mutation rates of mtDNA and the Y chromosome. This detailed palimpsest of Indonesian genetic diversity is a direct outcome of the region's complex history of immigration, transitory migrants and populations that have endured in situ since the region's first settlement.

Historical collections reveal patterns of diffusion of sweet potato in Oceania obscured by modern plant movements and recombination

The history of sweet potato in the Pacific has long been an enigma. Archaeological, linguistic, and ethnobotanical data suggest that prehistoric human-mediated dispersal events contributed to the distribution in Oceania of this American domesticate. According to the "tripartite hypothesis," sweet potato was introduced into Oceania from South America in pre-Columbian times and was then later newly introduced, and diffused widely across the Pacific, by Europeans via two historically documented routes from Mexico and the Caribbean. Although sweet potato is the most convincing example of putative pre-Columbian connections between human occupants of Polynesia and South America, the search for genetic evidence of pre-Columbian dispersal of sweet potato into Oceania has been inconclusive. Our study attempts to fill this gap. Using complementary sets of markers (chloroplast and nuclear microsatellites) and both modern and herbarium samples, we test the tripartite hypothesis. Our results provide strong support for prehistoric transfer(s) of sweet potato from South America (Peru-Ecuador region) into Polynesia. Our results also document a temporal shift in the pattern of distribution of genetic variation in sweet potato in Oceania. Later reintroductions, accompanied by recombination between distinct sweet potato gene pools, have reshuffled the crop's initial genetic base, obscuring primary patterns of diffusion and, at the same time, giving rise to an impressive number of local variants. Moreover, our study shows that phenotypes, names, and neutral genes do not necessarily share completely parallel evolutionary histories. Multidisciplinary approaches, thus, appear necessary for accurate reconstruction of the intertwined histories of plants and humans.

Socially responsible genetic research with descendants of the First Australians

Aboriginal Australians, one of the world’s indigenous peoples now outnumbered through colonization, are the most under-represented in genetic research because they feel that the benefits do not outweigh the social cost of involvement. Descendants of the First Australians have survived a period of European occupation during which time they were dispossessed of land, language and cultural identity resulting in inequities in health, education, and employment opportunities. Compared to Maori and Native American peoples, the ability to form organizations that help to control their affairs is very recent. The desire to control is understandably strong yet the ‘gate-keeping’ role of some organizations risks shifting the control away from smaller communities and has become increasingly politicized. In the past, research practices by Western scientists were poorly presented and have resulted in resistance to proposals that are perceived to have no beneficial outcomes for participants. In this age of advanced technological expertise in genetics, benefits to all humanity are clear to those carrying out research projects, yet not always to those being asked to participate, presenting extra challenges. Excellent guidelines for ethical conduct in research are available to assist researchers, prospective participants, and ethics committees or review boards that approve and monitor procedures. The essence of these guidelines are that research should be carried out with a spirit of integrity, respect, reciprocity, parity, recognition of survival and protection of social and cultural values, a need for control and shared responsibility. Specific Aboriginal organizations, with which researchers need to work to negotiate partnerships, vary within and between Australian states and will always expect Aboriginal personnel to be involved. People experienced in the consultation process are necessary as part of a team. By working patiently through lengthy negotiations with Aboriginal Australians, scientists can achieve valuable results, but failure to do so with respect and understanding will not yield hoped for outcomes. My own experience working with communities in the Darling River region of western New South Wales has been an enriching and rewarding one, with a long period of successful research lately delayed by increased expectation of monitoring and involvement at state level.

Craniofacial evolution in Polynesia: a geometric morphometric study of population diversity

OBJECTIVES

This study tests differences in craniofacial size and shape attributed to demographic history and plastic responses to differing environments in the islands of Polynesia. The dispersal of modern humans into Polynesia provides a useful scenario to investigate the impact of migration on human craniofacial diversity.

METHODS

Three dimensional geometric morphometric techniques are used to examine morphological diversity within Oceanic population samples. The importance of geographic and climatic variables is quantified by partial linear regression.

RESULTS

The results show a homogeneous Polynesian morphology grouping in relation to neighboring regions. There is, however, considerable diversity within the Polynesian samples themselves. Natural selection due to environmental differences is not an important factor in the patterns of craniofacial diversity found in the samples.

CONCLUSIONS

Historical patterns such as migration and population isolation influence patterns of craniofacial morphology within Polynesia, and our results demonstrate that morphological diversity can evolve in populations isolated for a relatively short period of time.

MLVA based classification of Mycobacterium tuberculosis complex lineages for a robust phylogeographic snapshot of its worldwide molecular diversity

Multiple-locus variable-number tandem repeat analysis (MLVA) is useful to establish transmission routes and sources of infections for various microorganisms including Mycobacterium tuberculosis complex (MTC). The recently released SITVITWEB database contains 12-loci Mycobacterial Interspersed Repetitive Units – Variable Number of Tandem DNA Repeats (MIRU-VNTR) profiles and spoligotype patterns for thousands of MTC strains; it uses MIRU International Types (MIT) and Spoligotype International Types (SIT) to designate clustered patterns worldwide. Considering existing doubts on the ability of spoligotyping alone to reveal exact phylogenetic relationships between MTC strains, we developed a MLVA based classification for MTC genotypic lineages. We studied 6 different subsets of MTC isolates encompassing 7793 strains worldwide. Minimum spanning trees (MST) were constructed to identify major lineages, and the most common representative located as a central node was taken as the prototype defining different phylogenetic groups. A total of 7 major lineages with their respective prototypes were identified: Indo-Oceanic/MIT57, East Asian and African Indian/MIT17, Euro American/MIT116, West African-I/MIT934, West African-II/MIT664, M. bovis/MIT49, M.canettii/MIT60. Further MST subdivision identified an additional 34 sublineage MIT prototypes. The phylogenetic relationships among the 37 newly defined MIRU-VNTR lineages were inferred using a classification algorithm based on a bayesian approach. This information was used to construct an updated phylogenetic and phylogeographic snapshot of worldwide MTC diversity studied both at the regional, sub-regional, and country level according to the United Nations specifications. We also looked for IS6110 insertional events that are known to modify the results of the spoligotyping in specific circumstances, and showed that a fair portion of convergence leading to the currently observed bias in phylogenetic classification of strains may be traced back to the presence of IS6110. These results shed new light on the evolutionary history of the pathogen in relation to the history of peopling and human migration.