JC virus genotypes in the western Pacific suggest Asian mainland relationships and virus association with early population movements

Distinct genotypes of human polyomavirus JC (JCV) have remained population associated possibly from the time of dispersal of modern humans from Africa. Seven major genotypes with additional subtypes serve as plausible markers for following early and more recent human migrations in all parts of the world. Phylogenetic trees of JCV sequences from the major continental population groups show a trifurcation at the base indicating early division into European, African, and Asian branches. Here, we have explored JCV relationships in the island populations of the western Pacific. Since these islands were settled from the Asian mainland and islands of Southeast Asia, we expected that their virus genotypes might show an Asian connection. We found that Type 2E (Austronesian) and Type 8 (non-Austronesian) are widely distributed in western Pacific populations. A few south China strains were found (Type 7A). A subtype of Type 8, Type 8A, was confined to Papua New Guinea. In keeping with these assignments we find that phylogenetic analysis by neighbor-joining and maximum parsimony methods places Type 2E in a closer relationship to east Asian mainland strains such as Type 2A and Type 7. Our findings support the Asian origins of the western Pacific JCV strains, and suggest three broad movements: an ancient one characterized by Type 8A, and then Type 8B, followed much later by migrations carrying Type 2E, which may correlate with the arrival of Austronesian-language speakers, the bearers of the "Lapita" cultural complex (approximately 3,500 to 5,000 years ago), and relatively recent movements carrying largely Type 7A (south China) strains directly from the West.     

Reproductive Isolation Among Geographical Populations of <Emphasis Type="Italic">Drosophila Bipectinata</Emphasis> Duda (Diptera,Drosophilidae) with Recognition of Three Subspecies

Among D. bipectinata Duda, 1923, three subspecies, bipectinata from Southeast Asia (SEA) and Okinawa (OKN), szentivanii stat. nov. from Papua New Guinea (PNG) (Mather & Dobzhansky, 1962) and pacificiae ssp. nov. from South Pacific Ocean (SPO), are recognized. The external morphology of the reproductive organs and the numbers of teeth per row in the sex combs are different between the three subspecies. Furthermore, the sterility of hybrid males between strains from the different regions confirms the subspecies status of each population from SEA, PNG and SPO, together with different gene arrangements in the geographical populations. Although males of the strains from OKN (Okinawa), the northernmost population, show significant differences in the number of teeth of sex combs from males of SEA (Southeast Asia) strains, hybrid males between them are fertile.     

Albumin — vitamin D-binding protein haplotypes in Asian-Pacific populations

Summary We have determined the various haplotypic combinations between alleles as well as restriction fragment length polymorphisms of two linked genetic markers, albumin and vitamin D-binding protein or group-specific component, in a number of Asian-Pacific populations. Using the partial maximum likelihood method, we constructed a phylogenetic network from the haplotype frequencies to assess relationships among the populations sampled. No systematic linkage disequilibrium was detected between most of the combinations, suggesting a lack of operation of any selection pressure at the two loci. The phylogenetic analysis confirmed the known interrelationships among various populations in the Asian-Pacific region. The Australian aborigines clustered closely with the non-Austronesian-speaking highlanders from Papua New Guinea, as expected. Similarly, the Austronesian-speaking Polynesians, Micronesians, and the Southeast Asians branched off together as a separate group. The position of the Austronesian-speaking Tolais from New Britain with respect to other populations from the Southwest Pacific was anomalous. The Tolais revealed a strong affinity with the Australian aborigines, which is inexplicable. The populations from China formed a tight cluster with other populations from the Asian-Pacific region. Genetic interrelationships of these populations with the white Australians were remote, which is in accordance with the known affinities of various human racial groups.     

Evolutionary insights on the origin of human T-cell lymphoma/leukemia virus type I (HTLV-I) derived from sequence analysis of a new HTLV-I variant from Papua New Guinea.

Recent studies have established the presence of human T-cell lymphoma/leukemia virus type I (HTLV-I) in Melanesia. An HTLV-I strain, PNG-1, has now been isolated from a healthy member of the Hagahai, a remote, recently contacted group in Papua New Guinea. To further characterize PNG-1, we employed polymerase chain reaction amplification with subsequent cloning and sequencing of amplified products. Sequence analyses of amplified regions of pol, env, and pX genes of this variant indicate marked heterogeneity (approximately 7%) from prototype HTLV-I. Based on available sequence data, PNG-1 is distinct from all other known HTLV-I strains and diverges from the common ancestor of HTLV-I prior to prototype isolates. The data also suggest, therefore, that HTLV-I originated in the Indo-Malay region rather than Africa.     

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.     

Trypanosoma evansi control and containment in Australasia

Animal trypanosomosis caused by Trypanosoma evansi is endemic throughout Southeast Asia, where it is an important constraint on the productivity of smallholder livestock. In the past decade, T. evansi has emerged as a serious threat to the viability of smallholder livestock industries in the Philippines and causes severe disease outbreaks with high mortality. Trypanosoma evansi also poses a threat to livestock and native fauna in Australia and Papua New Guinea (PNG) where it is absent, but the risk of it spreading from Indonesia is high. Surveillance for T. evansi in PNG and Australia, and its control in the Philippines is restricted by the poor sensitivity and inadequate validation of existing diagnostic tests and lack of information on the determinants of infection.     

Analysis of HLA-DRB1 polymorphism in the Gidra of Papua New Guinea

The genetic structure of the Gidra-speaking population inhabiting 13 villages in Papua New Guinea was investigated, based on the analysis of HLA-DRB1 polymorphism. Nei's fixation indices (F(IS), F(IT), and F(ST)) showed that the Gidra villages were genetically differentiated. The genetic distances significantly correlated with the geographic distances among the 13 villages. Thus, it is likely that a low intervillage migration rate has been maintained since the Gidra community was established. Correspondence analysis revealed that the Gidra, who belong to non-Austronesian-speaking groups, are genetically located at the intermediate point between the Aboriginal Australian groups and the Austronesian-speaking groups. Moreover, the HLA-DRB1*0802 allele, which has been observed in only two Polynesian groups (Austronesian-speaking groups) of Oceanian populations, was also found in the Gidra. These results suggest that the admixture of Austronesian and indigenous non-Austronesian groups beyond the linguistic boundary occurred partly in Papua New Guinea before Austronesian groups spread to the Pacific.     

Population genetics of Anopheles koliensis through Papua New Guinea: New cryptic species and landscape topography effects on genetic connectivity

New Guinea is a topographically and biogeographically complex region that supports unique endemic fauna. Studies describing the population connectivity of species through this region are scarce. We present a population and landscape genetic study on the endemic malaria‐transmitting mosquito, Anopheles koliensis (Owen). Using mitochondrial and nuclear sequence data, as well as microsatellites, we show the evidence of geographically discrete population structure within Papua New Guinea (PNG). We also confirm the existence of three rDNA ITS2 genotypes within this mosquito and assess reproductive isolation between individuals carrying different genotypes. Microsatellites reveal the clearest population structure and show four clear population units. Microsatellite markers also reveal probable reproductive isolation between sympatric populations in northern PNG with different ITS2 genotypes, suggesting that these populations may represent distinct cryptic species. Excluding individuals belonging to the newly identified putative cryptic species (ITS2 genotype 3), we modeled the genetic differences between A. koliensis populations through PNG as a function of terrain and find that dispersal is most likely along routes with low topographic relief. Overall, these results show that A. koliensis is made up of geographically and genetically discrete populations in Papua New Guinea with landscape topography being important in restricting dispersal.     

A new biological function of Shiitake mushroom,Lentinula edodes, in a myco-heterotrophic orchid,Erythrorchis ochobiensis

The biological function ofLentinula edodes in a myco-heterotrophic orchid,Erythrorchis ochobiensis was examined, using one local variant each from Japan (JPN), Papua New Guinea (PNG) and New Zealand (NZ). All variants induced seed germination: PNG and NZ isolates were effective at 25°C and JPN isolate showed the highest germination rate at 30°C. Germinated seeds developed into plants and formed normal endomycorrhizas. Hence, it is concluded thatL. edodes has a perfect symbiotic potential withE. ochobiensis, though it has not been observed in the root of the orchid in the field.     

Whole-Genome Sequences and Comparative Genomics of Salmonella enterica Serovar Typhi Isolates from Patients with Fatal and Nonfatal Typhoid Fever in Papua New Guinea

Many of the developing countries of the Southeast Asian region are significantly affected by endemic typhoid fever, possibly as a result of marginal living standards. It is an important public health problem in countries such as Papua New Guinea, which is geographically close to some of the foci of endemicity in Asia. The severity of the disease varies in different regions, and this may be attributable to genetic diversity among the native strains. Genome sequence data on strains from different countries are needed to clearly understand their genetic makeup and virulence potential. We describe the genomes of two Salmonella Typhi isolates from patients with fatal and nonfatal cases of typhoid fever in Papua New Guinea. We discuss in brief the underlying sequencing methodology, assembly, genome statistics, and important features of the two draft genomes, which form an essential step in our functional molecular infection epidemiology program centering on typhoid fever. The comparative genomics of these and other isolates would enable us to identify genetic rearrangements and mechanisms responsible for endemicity and the differential severity of pathogenic salmonellae in Papua New Guinea and elsewhere.     

Emergence of artemisinin-resistant Plasmodium falciparum with kelch13 C580Y mutations on the island of New Guinea

The rapid and aggressive spread of artemisinin-resistant Plasmodium falciparum carrying the C580Y mutation in the kelch13 gene is a growing threat to malaria elimination in Southeast Asia, but there is no evidence of their spread to other regions. We conducted cross-sectional surveys in 2016 and 2017 at two clinics in Wewak, Papua New Guinea (PNG) where we identified three infections caused by C580Y mutants among 239 genotyped clinical samples. One of these mutants exhibited the highest survival rate (6.8%) among all parasites surveyed in ring-stage survival assays (RSA) for artemisinin. Analyses of kelch13 flanking regions, and comparisons of deep sequencing data from 389 clinical samples from PNG, Indonesian Papua and Western Cambodia, suggested an independent origin of the Wewak C580Y mutation, showing that the mutants possess several distinctive genetic features. Identity by descent (IBD) showed that multiple portions of the mutants’ genomes share a common origin with parasites found in Indonesian Papua, comprising several mutations within genes previously associated with drug resistance, such as mdr1, ferredoxin, atg18 and pnp. These findings suggest that a P. falciparum lineage circulating on the island of New Guinea has gradually acquired a complex ensemble of variants, including kelch13 C580Y, which have affected the parasites’ drug sensitivity. This worrying development reinforces the need for increased surveillance of the evolving parasite populations on the island, to contain the spread of resistance.     

A 9.1-kb insertion/deletion polymorphism suggests a common pattern of genetic diversity in Island Melanesia

Earlier reports suggest a distinct pattern of genetic variation linked to both language and geographic distance in Island Melanesia. Inland Papuan-speaking populations from different islands tend to share one allelic profile, while shore-based or more cosmopolitan populations share another, related to Southeast Asian influence over the past 3000 years. In the present paper, we report the genotypes and allele frequencies of an informative 9.1-thousand-base-pairs (kb) insertion/deletion polymorphism in 19 populations living in Island Melanesia. The populations studied inhabit the islands of New Britain, New Ireland, New Hanover, and Mussau in the Bismarck Archipelago, and speak either Austronesian or Papuan languages. We also include for reference a collection from New Guinea and Bougainville. The data show a marked fluctuation in the allele frequency among the different isolates, with the 9.1-kb(-) allele frequency ranging from 0.67 to 0.98. The deletion allele reaches fixation in some Papuan-speaking interior populations of New Britain, as well as in the interiors of New Guinea and Bougainville. However, certain inland Austronesian-speaking populations also share a similar high frequency of the deletion. Our data suggest that language distinctions are generally, but not invariably, indicative of diverse allelic patterns in this complex region, where inland groups on large islands tend to be often distinctive from shore-based populations.     

A Holocene record of savanna vegetation dynamics in southern lowland Papua New Guinea

Vegetation History and Archaeobotany - The southern lowlands of Papua New Guinea (PNG) are biogeographically distinct. Vast tracts of savanna vegetation occur there and yet most palaeoecological...     

Evolutionary origins of taro (Colocasia esculenta) in Southeast Asia

As an ancient clonal root and leaf crop, taro (Colocasia esculenta, Araceae) is highly polymorphic with uncertain genetic and geographic origins. We explored chloroplast DNA diversity in cultivated and wild taros, and closely related wild taxa, and found cultivated taro to be polyphyletic, with tropical and temperate clades that appear to originate in Southeast Asia sensu lato. A third clade was found exclusively in wild populations from Southeast Asia to Australia and Papua New Guinea. Our findings do not support the hypothesis of taro domestication in Papua New Guinea, despite archaeological evidence for early use or cultivation there, and the presence of apparently natural wild populations in the region (Australia and Papua New Guinea).     

Intersterility between populations of <Emphasis Type="Italic">Lentinula edodes</Emphasis> from Papua New Guinea

Mating tests among strains of Lentinula edodes distributed in Asia-Australasia were conducted. As a result, 26 strains were classified into three groups: 2 strains from Mt. Wilhelm in Papua New Guinea (PN1 group) showed intersterility with 7 strains from Mt. Albert Edward and Mt. Kaisenik in Papua New Guinea (PN2 group) and semicompatibility (clamp formation restricted to contact zone between paired monokaryons) with 17 strains from Asia-Australasia (AA group), whereas the strains of the PN2 group showed compatibility with the AA group. These results suggest that the shiitake populations distributed in Asia-Australasia including Papua New Guinea are in the process of speciation. Contribution no. 391 from the Tottori Mycological Institute     

Genetic variation at 9 autosomal microsatellite loci in Asian and Pacific populations.

Genetic variation at 9 autosomal microsatellite loci (CFS1R, TH01, PLA2A, F13A1, CYP19, LPL, D20S481, D20S473, and D20S604) has been characterized in 16 Asian and Oceanic populations, mostly from mainland and insular Southeast Asia. The neighbor-joining tree and the principal coordinates analysis of the genetic relationships of these populations show a clear separation of Papua New Guinea Highlanders and, to a lesser extent, Malayan aborigines (Orang Asli or Semai) from the rest of the populations. Although the number of markers used in this study appears to be inadequate for clarifying the patterns of genetic relationships among the studied populations, in the principal coordinates analysis a geographic trend is observed in the mainland and insular Southeast Asian populations. Furthermore, in an attempt to contrast the extent of variation between autosomal and Y-chromosome-specific microsatellite loci and to reveal potential differences in the patterns of male and female migrations, we have also compared genetic variation at these 9 autosomal loci with variation observed at 5 Y-chromosome-specific microsatellites in a common set of 14 Asian populations.     

Health research in Papua New Guinea

The Papua New Guinea Institute of Medical Research (PNGIMR) is one of the most respected health research institutions in the developing world, and its studies of the local health problems of PNG have consistently had international relevance. This article examines the structural and philosophical factors that have enabled the success of the PNGIMR, and presents the PNGIMR approach to research as a potential model for other disease-endemic countries. An overview of PNGIMR research into malaria and filariasis is given with selected examples as an introduction to a Trends in Parasitology series on health research in Papua New Guinea.     

The buttressing coalition of the PNGIMR: an example of international collaborative research

Good partnerships are based on mutual benefit. This also applies to international partnerships in medical research. The Papua New Guinea Institute of Medical Research (PNGIMR) has had many successful research collaborations, from which an interactive coalition has been built that is committed to supporting the PNGIMR without jeopardizing its integrity. This coalition also involves policy-makers from the Department of Health, teachers at the Medical School of Papua New Guinea and the Medical Research Advisory Committee of PNG. The PNGIMR's Buttressing Coalition supports research and training, but also assists the process of transferring research results into policy. The concept of "buttressing" is explored and the activities of the Buttressing Coalition are briefly described here. The idea of the Buttressing Coalition is a response from the international medical research community to globalization, and could be applied elsewhere, following the model developed in PNG.     

Patterns of Y-chromosome diversity intersect with the Trans-New Guinea hypothesis

The island of New Guinea received part of the first human expansion out of Africa (>40,000 years ago), but its human genetic history remains poorly understood. In this study, we examined Y-chromosome diversity in 162 samples from the Bird's Head region of northwest New Guinea (NWNG) and compared the results with previously obtained data from other parts of the island. NWNG harbors a high level of cultural and linguistic diversity and is inhabited by non-Austronesian (i.e., Papuan)-speaking groups as well as harboring most of West New Guinea's (WNG) Austronesian-speaking groups. However, 97.5% of its Y-chromosomes belong to 5 haplogroups that originated in Melanesia; hence, the Y-chromosome diversity of NWNG (and, according to available data, of New Guinea as a whole) essentially reflects a local history. The remaining 2.5% belong to 2 haplogroups (O-M119 and O-M122) of East Asian origin, which were brought to New Guinea by Austronesian-speaking migrants around 3,500 years ago. Thus, the Austronesian expansion had only a small impact on shaping Y-chromosome diversity in NWNG, although the linguistic impact of this expansion to this region was much higher. In contrast, the expansion of Trans-New Guinea (TNG) speakers (non-Austronesian) starting about 6,000-10,000 years ago from the central highlands of what is now Papua New Guinea, presumably in combination with the expansion of agriculture, played a more important role in determining the Y-chromosome diversity of New Guinea. In particular, we identified 2 haplogroups (M-P34 and K-M254) as suggestive markers for the TNG expansion, whereas 2 other haplogroups (C-M38 and K-M9) most likely reflect the earlier local Y-chromosome diversity. We propose that sex-biased differences in the social structure and cultural heritage of the people involved in the Austronesian and the TNG expansions played an important role (among other factors) in shaping the New Guinean Y-chromosome landscape.     

Patterns of molecular diversity in wild stocks of the redclaw crayfish (Cherax quadricarinatus) from northern Australia and Papua New Guinea: impacts of Plio-Pleistocene landscape evolution

1. Analysis of mitochondrial and nuclear DNA (microsatellites) in 379 individuals, collected from 15 localities in northern Australia and Papua New Guinea (PNG), demonstrated that wild redclaw crayfish ( Cherax quadricarinatus ) populations consist of two highly divergent Australian lineages and two PNG lineages.
2. The disjunction between the two Australian lineages occurs over a distance of approximately 200 km in the south-western corner of the Gulf of Carpenteria. These data conflict with an earlier study that detected no significant differentiation in 23 variable allozyme loci in redclaw sampled from northern Australia, but concur broadly with the previous recognition of two morphologically distinct species ( C. quadricarinatus and C. bicarinatus ) across northern Australia, and a third species in PNG ( C. albertsii ).
3. The inferred timing and patterns of divergence evident in the molecular data presented here closely align with a similar pattern reported in a co-distributed freshwater decapod crustacean, and broadly reflect patterns in some vertebrate taxa with similar distributions across northern Australia and PNG.
4. These congruent patterns most probably reflect periodic Plio-Pleistocene land and freshwater connections between Australia and New Guinea.