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

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

New JC virus (JCV) genotypes from papua new guinea and micronesia (type 8 and type 2E) and evolutionary analysis of 32 complete JCV genomes.

The JC virus (JCV) is a ubiquitous human polyomavirus that frequently resides in the kidneys of healthy individuals and is excreted in the urine of a large percentage of the population. Geographic-specific JCV variants, isolated from urine and from brain of progressive multifocal leukoencephalopathy (PML) patients, have been grouped into seven distinct genotypes based on whole genome analysis and by individual polymorphic nucleotides (typing sites) in the VP1 coding region. Mutations in the archetypal regulatory region, sometimes consisting of deletions and/or duplications, are also useful taxonomic characters for further characterizing and subdividing genotypes. Investigation of JCV variation in Papua New Guinea (PNG) revealed three distinct variants called PNG- 1, PNG-2, and PNG-3. These variants exhibited consistent coding region and regulatory region mutations. Evolutionary analysis of 32 complete JCV genomes including six new viral genomes from the western Pacific suggests that the new PNG JCV variants are closely associated with the broad group of Type 2 strains of JCV found throughout Asia, forming a monophyletic group with the Northeast Asian strains (Type 2A). Within the Type 2 clade, however, the PNG JCV variants cluster as two distinct groups and are therefore described here as new JCV genotypes designated Type 2E and Type 8.

Human polyomavirus JC variants in Papua New Guinea and Guam reflect ancient population settlement and viral evolution.

The peopling of the Pacific was a complex sequence of events that is best reconstructed by reconciling insights from various disciplines. Here we analyze the human polyomavirus JC (JCV) in Highlanders of Papua New Guinea (PNG), in Austronesian-speaking Tolai people on the island of New Britain, and in nearby non-Austronesian-speaking Baining people. We also characterize JCV from the Chamorro of Guam, a Micronesian population. All JCV strains from PNG and Guam fall within the broad Asian group previously defined in the VP1 gene as Type 2 or Type 7, but the PNG strains were distinct from both genotypes. Among the Chamorro JCV samples, 8 strains (Guam-1) were like the Type 7 strains found in Southeast Asia, while nine strains (Guam-2) were distinct from both the mainland strains and most PNG strains. We identified three JCV variants within Papua New Guinea (PNG-1, PNG-2 and PNG-3), but none of the Southeast Asian (Type 7) strains. PNG-1 strains were present in all three populations (Highlanders and the Baining and Tolai of New Britain), but PNG-2 strains were restricted to the Highlanders. Their relative lack of DNA sequence variation suggests that they arose comparatively recently. The single PNG-3 strain, identified in an Austronesian-speaking Tolai individual, was closely related to the Chamorro variants (Guam-2), consistent with a common Austronesian ancestor. In PNG-2 variants a complex regulatory region mutation inserts a duplication into a nearby deletion, a change reminiscent of those seen in the brains of progressive multifocal leukoencephalopathy patients. This is the first instance of a complex JCV rearrangement circulating in a human population.

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.

A novel JC virus variant found in the Highlands of Papua New Guinea has a 21-base pair deletion in the agnoprotein gene.

OBJECTIVES: This paper describes a unique JC virus (JCV) variant recovered from the Highlands of Papua New Guinea that contains an inframe 21-bp deletion in the agnoprotein gene. We characterize the mutation and suggest possible roles for the deletion in JCV evolution. STUDY DESIGN/METHODS: JCV DNA was extracted from urine and polymerase chain reaction (PCR) amplified using whole genome primers. PCR products were cloned, and multiple clones were sequenced. The JCV agnogene was PCR amplified to verify the presence of the agnogene deletion. RESULTS: This mutation creates a 21-bp deletion near the 3' end, which alters the predicted secondary structure of the messenger RNA and changes local codon usage at the 3' end of the agnogene. Protein secondary structure predictions suggest the deleted portion of the agnoprotein may be a flexible surface feature. CONCLUSIONS: We describe the first stable coding region deletion in JCV that presumably signifies a single evolutionary event that led to the split from other Highlands viral groups and occurred well after the human expansions that led to the peopling of the Southwest Pacific.

A common deletion polymorphism in the apolipoprotein A4 gene and its significance in lipid metabolism.

Apolipoprotein A-IV (apoA-IV, protein; APOA4, gene) is a major constituent of high-density lipoprotein (HDL) and triglyceride-rich lipoprotein particles, but its precise function in lipid metabolism is still uncertain. We have determined APOA4 genetic polymorphism in 285 randomly selected Melanesians from the Solomon Islands and have evaluated its significance in lipid metabolism. By using isoelectric focusing and immunoblotting techniques, a variant pattern, indistinguishable from the APOA4*2 allele uniquely found in white populations at a frequency of about 8%, was detected at a relatively high frequency (19%) in the Melanesian sample. Polymerase chain reaction (PCR) amplification and DNA sequencing of the 3' end of the APOA4 gene revealed that the Melanesian mutation is distinct from the known APOA4*2 mutation and that it involves a four-amino acid deletion in the evolutionarily conserved carboxyl-terminal region in the apoA-IV protein, which consists of four repeats of four amino acids each. After adjustment for concomitant variables, we investigated the impact of the deletion polymorphism on plasma levels of cholesterol, triglycerides, apoA-I, apoA-II, and apoE. A significant (P = .02) and gene-dosage effect was observed on the plasma levels of apoA-I and apoA-II: these levels were lowest in individuals homozygous for the deletion allele (D), intermediate in heterozygotes (ND), and highest in homozygous individuals for the normal allele (N). The average effect of the APOA4*D allele was to lower apoA-I and apoA-II by 8 mg/dL and 2 mg/dL, respectively, and the APOA4 polymorphism accounted for about 3% of the phenotypic variance in both cases.(ABSTRACT TRUNCATED AT 250 WORDS)

Lipid and apolipoprotein levels in six Solomon Island societies differ from those in a U.S. white population.

Levels of plasma cholesterol, triglycerides, and apolipoproteins (apo) AI, AII, and E in 560 males and 744 females from six Solomon Island societies were compared with levels in age- and sex-matched participants in the Rochester Family Heart Study (RFHS). The overall average cholesterol, triglyceride, apo AI, and apo AII levels for all the Solomon Island societies were significantly lower than levels for the RFHS (P less than 0.001). The mean level of apo E for these societies was significantly higher than levels in RFHS in spite of the fact that the levels of triglycerides were significantly lower. Normally, apo E is a major constituent of triglyceride-rich very-low-density lipoprotein (VLDL). For both sexes, none of the Solomon Island societies showed a significant correlation of plasma cholesterol levels with apo E. In the RFHS, this correlation was 0.50 in males and 0.43 in females. Mean apo E levels are estimated to be 4.15-6.0% of the high-density lipoprotein (HDL) protein in the different Solomon Island societies. This study establishes a distinctive Solomon Island lipid profile characterized by the high apo E levels, which appear to be associated primarily with the HDL particle, whereas, in normal Western populations, it is associated primarily with VLDL, and only small quantities are associated with HDL.

The Solomon Islands Project: an introduction.

The twin themes of the Solomon Islands Biomedical Project remain 1) the remarkable genetic heterogeneity of the groups in the Solomons; and 2) the differential responses to these groups to rapid modernization/acculturation over the past two decades of this long term study. This introduction summarizes the historical and ethnic relationships of the survey groups, their established genetic distances and their rankings with regard to acculturation at the times of their first survey, and changes occurring up to 1985-86. Relevant features of diet, life style, and epidemiology are described.

PIP: The first heterogenous humans arrived in the Solomon Islands by 28,000 B.C. Linguistically the inhabitants are divided into non-Austronesian (NAN) and Austronesian languages introduced by homogenous people 6000-7000 B.C. Through intermixing 7 distinct groups have evolved who are included in the survey, although they are divided into 3 language groups. The Bougainville groups are inland NAN speakers; the Malaita groups are Austronesian speakers, and the Ontong Javanese speak a Polynesian language. Genetic similarity was found between Malaita Island inhabitants and South Bougainville Island dwellers. North Bougainvillians were different in polymorphic traits, while the Ontong Javans clustered with the Malaitan groups. Population distance matrices were taken from male and female odontometrics, male and female dermatoglyphics, and male and female anthropometry. The Ontong Javans were removed from the rest. A ranking of population distance was devised using these matrices. The Malaita and South Bougainville groups were fairly close; the Aita of North Bougainville were close to South Bougainville groups; and the Ontong Java were closest to Malaita groups and most distant from Bougainville NAN speakers. Acculturation status caused by modernization was measured during 1966-72: the South Bougainville populations were most acculturated and the Aita of North Bougainville were the least. The Malaita and the Ontong Java were also less acculturated. The surveys of 1985-86 indicated that the populations of Bougainville, Malaita, and Ontong Java were affected by an open pit copper mine, road construction, and commerce. The traditional root crop staple, pork, and fish diet changed to imported white rice and bread, animal lard, sugar, salt, canned mutton, cookies, coffee, tea, and tobacco. The negative effects on serum cholesterol, glucose metabolism, blood pressure, and body weight because of less physical activity followed.

Prevalence of antibodies interactive with HTLV-I antigens in selected Solomon Islands populations.

Serum samples obtained in 1986 from healthy individuals in three distinct Solomon Islands populations were screened for antibodies to human lymphotropic virus type I (HTLV-I). One of the populations tested lives on the remote Polynesian outlier atoll, Ontong Java. The other two groups, the Baegu and the Lau, are Melanesians living on Malaita, the most populous of the larger Solomon Islands. Eighty-eight of a total of 601 (14.6%) sera tested were repeatably reactive in an enzyme-linked immunosorbent assay (ELISA) that uses as antigen a lysate of HTLV-I viral particles. The prevalence of antibodies interactive with HTLV-I viral particles. The prevalence of antibodies interactive with HTLV-I antigens varied among the three groups, ranging from 8.5% (16/188) in the Baegu, through 13% (7/54) in the Lau, to 18.1% (65/359) among the Ontong Java population. The specificity of the screening ELISA was confirmed by protein immunoblot. No serum samples were obtained from children under 9 years of age. Although 121 of the 601 sera came from children between the ages of 9 and 19, none of these were reactive in the HTLV-I ELISA. Starting in the third decade, the prevalence of HTLV-I seropositivity increased with age, from 8.8% (10/113) between the ages of 20 and 29 to a peak of 25.9% (15/58) and 25% (15/60) in the sixth and seventh decade, respectively. This age-specific prevalence pattern is strikingly similar to that which is seen in populations where HTLV-I infection is endemic.

Heterogeneity of the blood pressure distribution among Solomon Islands societies with increasing acculturation.

This study illustrates the very complex nature of gene by environmental interactions influencing the blood pressure (BP) distribution in a series of genetically distinctive populations undergoing rapid acculturation. We report the results of two BP and anthropometric surveys on Solomon Islands societies separated by an interval of 14 to 19 years. While differences in acculturation existed at the time of the initial survey, the interval between surveys was marked by rapid acculturation in almost all societies. Seven of the eight societies originally covered were included in the resurvey, and a large but variable proportion of the original sample subjects was recovered in the follow-up. Because the genetic relationships of the societies have been described, we were able to establish the following points concerning the role of genetic differences in determining the distribution of BP among these populations and, more important, the interaction of these genetic differences with changes associated with increasing acculturation: 1) In the initial survey, mean adjusted systolic and diastolic BPs were significantly heterogeneous among societies within and among genetically related clusters of societies (genetic clusters) and sexes. At the same time, rank differences in these means were not associated with rank differences in acculturation status among societies ignoring cluster membership. 2) Importantly, in the follow-up survey increasing acculturation resulted in the disappearance of significant differences in mean systolic and diastolic BP among genetic clusters in males, despite continued significant heterogeneity among societies within genetic clusters. In females, differences among genetic clusters persisted, but the degree of significance was substantially less with increasing acculturation. We interpret these changes as evidence for genotype by environment interaction. 3) There were significant differences in interindividual variances of both systolic and diastolic BPs among genetic clusters in the first survey. Ranks of these variances were not significantly associated with acculturation rank. In the follow-up survey, however, most societies showed striking increases in the variance of both systolic and diastolic BPs with increased acculturation. These increases in variance of both systolic and diastolic BPs may be related to a) shifts in demography and/or anthropometry of some societies; b) increased range and intensity of environmental factors affecting BP and associated with increased acculturation; and/or c) genotype by environmental interactions. 4) The correlation between systolic and diastolic BP decreased over the interval for all societies within and among genetic clusters. This trend was partly the result of larger changes in variances for systolic than diastolic BP in the resurveys.(ABSTRACT TRUNCATED AT 400 WORDS)

Study of 47 DNA markers in five populations from four continents.

Forty seven DNA markers from 30 genes or chromosomal regions were investigated in five populations (Biaka and Mbuti Pygmies, Melanesians, Chinese and Caucasoids). Both the variation between populations (measured by FST) and between markers is highly significant. The average heterozygosity for all markers is .284 and the average FST is .145. There was no significant difference in the FST values, or in the average heterozygosity between known genes and random segments. The FST distance between all populations considered in pairs, and averaged over all loci favours a primary split between Eurasia and Africa, but this conclusion is neither statistically significant nor uncomplicated. Condensing the 47 markers into 30 "genes" where 10 were treated as haplotypes, it was found that the haplotypes always give higher FST's than the separate markers, although similar conclusions can be drawn.

Partial correlation of distance matrices in studies of population structure.

Anthropological studies of human population structure commonly compare various monogenic and polygenic (metric) distance matrices to distance matrices obtained from measures of geographical dispersion, linguistic differences, and migration patterns in an attempt to infer something about the effects of evolutionary factors (drift and differential selection, in particular). It is, though, commonly recognized that geography, language, and migration patterns may be intercorrelated due to the common effects of historical and social processes. Previous attempts to deal with the problems of assessing relative effects among such sets of intercorrelated factors using partial correlations have resulted in coefficients that are either not well defined or have no known sampling distribution or both. Here, we outline a general approach to partialling distance matrices that results in well-defined coefficients and valid significance testing procedures. Application of the matrix partialling methods to a variety of distance matrices obtained for a sample of eight ethnolinguistic groups from the Harvard Solomon Islands Expedition (Friedlaender et al., 1986) reveals a close association between language dissimilarity and dermatoglyphics controlling for geography, thus reinforcing earlier suggestions that dermatoglyphics, properly used, reflect historical relationships of groups in this region better than do anthropometry, odontometrics, or small batteries of blood polymorphisms.

Patterns of adult weight and fat change in six Solomon Islands societies: a semi-longitudinal study.

Semi-longitudinal changes with aging in weight, height, arm circumference, and subscapular and triceps skinfold circumference are presented for adult males and females in 6 different populations in the Solomon Islands and Papua New Guinea, which have differed dramatically in their exposure to modern industrialized societies over the past decade. Those groups who remain less acculturated show little or no evidence of a secular trend in adult body size and women in these groups lose weight through their childbearing years and into old age. Men lose less. In the more acculturated groups, weight gain due to increases in fatness have already become the norm for all female cohorts, and most male cohorts. In most groups there are significant losses in muscle mass after age 40 in men, regardless of acculturation status, which were not detected in women. Because changes in diet have been more extreme for men than women in the more acculturated groups, and childbearing and nursing patterns have not changed, the more consistent and significant shift in female fat changes with age is most likely due to a sharp change in activity pattern, in addition to dietary change.

Linkage disequilibrium in Bougainville Island.

Linkage disequilibria are estimated for three 2-locus systems in 18 samples from Bougainville Island, Solomon Islands. The systems are haptoglobin, acid phosphatase and MN blood group. The disequilibria are estimated two ways: by maximum likelihood (ML) and by the covariance between the non-alleles. Though seven of the 52 ML estimates are statistically different than zero, none of the covariance estimates are significant. We conclude that because linkage disequilibrium for loosely linked loci is a small quantity and because the sample sizes for most populations studied by anthropologists are small, linkage disequilibrium will not be a useful parameter for the study of natural selection in these populations.

Language boundaries and biological differentiation of Bougainville: multivariate analysis of variance.

Blood genetic and antropometric data on Melanesians from Bougainville, Papus New Guinea, are analyzed by random-effects analysis of variance to partition the observed variation into components for the individuals, village, and language group level. Both clinial and unpatterned group differences exist. The differences between language groups appear to be substantial, even when the results are corrected for clinal effects. The amounts of variation of each level correspond roughly to a similar analysis of heterozygosity in blood polymorphisms. Observed current migration figures suggest that language and village constitute a 2-fold hierarchical subdivision of the breeding system, and this analysis shows probable random drift effects between groups at both the village and language level. Both language and genetic constitution of these villages are the result of differentiation in place.