The Allelic Correlation Structure of Gainj- and Kalam-Speaking People. II. the Genetic Distance between Population Subdivisions

The patterning of allele frequency variability among 18 local groups of Gainj and Kalam speakers of highland Papua New Guinea is investigated using new genetic distance methods. The genetic distances proposed here are obtained by decomposing Sewall Wright's coefficient FST into a set of coefficients corresponding to all pairs of population subdivisions. Two statistical methods are given to estimate these quantities. One method provides estimates weighted by sample sizes, while the other method does not use sample size weighting. Both methods correct for the within-individual and between-individual-within-groups sums of squares. Genetic distances among the Gainj and Kalam subdivisions are analyzed with respect to demographic, geographic, and linguistic variables. We find that a demographic feature, group size, has the greatest demonstrable association with the patterning of genetic distances. The pattern of geographic distances among groups displays a weak congruence with the pattern of genetic distances, and the association of genetic and linguistic diversity is very low. An effect of differences in group size on genetic distances is not surprising, from basic theoretical considerations, but genetic distances have not often been analyzed with respect to these variables in the past. The lack of correspondence between genetic distances and linguistic and geographic differences is an unusual feature that distinguishes the Gainj and Kalam from most other tribal populations.     

The Allelic Correlation Structure of Gainj-and Kalam-Speaking People. I. the Estimation and Interpretation of Wright''s F-Statistics

The internal patterning of allelic correlations in the Gainj and Kalam swidden horticulturalists of highland Papua New Guinea is examined within the context of Sewall Wright's F-statistic model. A multiallelic extension of the model is given first, and multivariate variance-component estimators for the parameters are suggested. Then, it is shown that the expectation of the F-statistic set depends on the age structure of the population and that knowledge of the population and sample age structure is critical for meaningful analysis. The array of F-statistics estimated jointly over five polymorphic enzyme loci reveals the following features of Gainj and Kalam population structure: (1) significant departures from panmictic expectations and (2) characteristics of a continuously distributed breeding population, rather than those expected for populations subdivided into demes with discrete boundaries. Finally, the F-statistics estimated for the Gainj and Kalam are briefly compared to estimates obtained from other tribal populations. It is seen that the level of differentiation observed in the Gainj and Kalam is only about one-third that observed in South American swidden horticulturalists. Consequently, some conventional wisdom regarding the interrelationship of socioecological settings and genetic structures may require reevaluation.     

Female fecundity in highland Papua New Guinea

Demographers often assume that interpopulation variation in birth spacing is attributable primarily to behavioral differences (e.g., in breastfeeding, coital frequency, or contraceptive practice), and that the contribution of physiological factors is negligible. This assumption may be correct, but it should be tested, especially in light of recent evidence that there may be more variation in ovarian function among human populations than was previously believed. In this paper, we apply a stochastic model of the determinants of fecundability (the monthly probability of conception) to endocrinological data collected among the Gainj, a tribal population in highland Papua New Guinea. Based on previous research, the Gainj are known to have age patterns of ovarian function that differ markedly from the Western norms. When account is taken of the late menarche, early menopause, and long ovarian cycles that appear to characterize Gainj women, mean apparent fecundability across the female reproductive span is reduced by about 27 per cent (from 0.316 to 0.235), and the mean waiting time to next apparent conception is increased by just over one month. Thus, despite the fact that Gainj women differ from Western women with respect to reproductive physiology by as much as or more than any other known population, the demographic impact of these differences appears to be slight.     

Determinants of effective population size for loci with different modes of inheritance

Here we report an assessment of the determinants of effective population size (N(e)) in species with overlapping generations. Specifically, we used a stochastic demographic model to investigate the influence of different life-history variables on N(e)/N (where N = population census number) and the influence of sex differences in life-history variables on N(e) for loci with different modes of inheritance. We applied an individual-based modeling approach to two datasets: one from a natural population of savannah baboons (Papio cynocephalus) in the Amboseli basin of southern Kenya and one from a human tribal population (the Gainj of Papua New Guinea). Simulation-based estimates of N(e)/N averaged 0.329 for the Amboseli baboon population (SD = 0.116, 95% CI = 0.172 - 0.537) and 0.786 for the Gainj (SD = 0.184, 95% CI = 0.498 - 1.115). Although variance in male fitness had a substantial impact on N(e)/N in each of the two primate populations, ratios of N(e) values for autosomal and sex-linked loci exhibited no significant departures from Poisson-expected values. In each case, similarities in sex-specific N(e) values were attributable to the unexpectedly high variance in female fitness. Variance in male fitness resulted primarily from age-dependent variance in reproductive success, whereas variance in female fitness resulted primarily from stochastic variance in survival during the reproductive phase.     

Changing household composition,labor patterns,and fertility in a highland New Guinea population

The European demographic transition of the nineteenth century is often proposed as a model for demographic change in twentieth century developing nations, and economic development is seen as leading to an inevitable reduction in total fertility in these nations. This paper examines data from the Gainj of Papua New Guinea, a natural fertility population with very low reproductive output, and suggests that the effects of development on fertility change are much more complex than a simple demographic transition model would suggest. Looking at two variables known to contribute significantly to low total fertility among the Gainj, late age at first birth for women and long interbirth intervals, the paper suggests that households, in their recruitment and allocation of labor, may exert a mediating influence in the relationship between economic development and fertility.     

Birth spacing patterns in humans and apes

Comparative studies of birth interval dynamics in wild primates suffer from several problems of analysis and interpretation: (1) the data are always right-censored, (2) sample sizes are usually small, (3) the distribution of birth intervals is expected to be non-normal, (4) early offspring mortality is a confounding variable, and (5) differences in life history (e.g., presence or absence of menopause) can complicate interpretation of the results. A survival analysis designed to minimize these problems is applied to published data on wild chimpanzees and gorillas from Gombe and Virunga Parks, respectively, and to new data on wild orangutans from Tanjung Puting National Park and on a human population, the Gainj of highland Papua New Guinea. According to this analysis, the estimated median birth interval (when the offspring whose birth opens the interval does not die within the interval) is 43.3 +/- 1.0 months for the Gainj, 45.5 +/- 1.2 months for gorillas, 66.6 +/- 1.3 months for chimpanzees, and 92.6 +/- 2.4 months for orangutans.     

Multilocus population genetic analysis of the Southwest Pacific malaria vector Anopheles punctulatus

The population structure and history of the cryptic malaria vector species, Anopheles punctulatus (Doenitz), was investigated throughout Papua New Guinea and the Solomon Islands with the aim of detailing genetic subdivisions and the potential for movement through this biogeographically complex region. We obtained larval collections from over 80 sites and utilised a diverse array of molecular markers that evolve through different processes. Individuals were initially identified to species and genotyped using the ribosomal DNA second internal transcribed spacer. DNA sequencing of a single copy nuclear ribosomal protein S9 and the mitochondrial cytochrome oxidase I loci were then investigated and 12 nuclear microsatellite markers were developed and analysed. Our data revealed three genetically distinct populations – one in Papua New Guinea, the second on Buka Island (Bougainville Province, Papua New Guinea), and the third on Guadalcanal Island (Solomon Islands). Genetic differentiation within Papua New Guinea was much lower than that found in studies of other closely related species in the region. The data does suggest that A. punctulatus has undergone a population bottleneck followed by a recent population and range expansion in Papua New Guinea. Humans and regional economic growth may be facilitating this population expansion, as A. punctulatus is able to rapidly occupy human modified landscapes and traverse unsealed roads. We therefore anticipate extensive movement of this species through New Guinea – particularly into the highlands, with a potential increase in malaria frequency in a warming climate – as well as relatively unrestricted gene flow of advantageous alleles that may confound vector control efforts.     

Independent histories of human Y chromosomes from Melanesia and Australia

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

Reduced Y-chromosome,but not mitochondrial DNA,diversity in human populations from West New Guinea

To investigate the paternal population history of New Guinea, 183 individuals from 11 regional populations of West New Guinea (WNG) and 131 individuals from Papua New Guinea (PNG) were analyzed at 26 binary markers and seven short-tandem-repeat loci from the nonrecombining part of the human Y chromosome and were compared with 14 populations of eastern and southeastern Asia, Polynesia, and Australia. Y-chromosomal diversity was low in WNG compared with PNG and with most other populations from Asia/Oceania; a single haplogroup (M-M4) accounts for 75% of WNG Y chromosomes, and many WNG populations have just one Y haplogroup. Four Y-chromosomal lineages (haplogroups M-M4, C-M208, C-M38, and K-M230) account for 94% of WNG Y chromosomes and 78% of all Melanesian Y chromosomes and were identified to have most likely arisen in Melanesia. Haplogroup C-M208, which in WNG is restricted to the Dani and Lani, two linguistically closely related populations from the central and western highlands of WNG, was identified as the major Polynesian Y-chromosome lineage. A network analysis of associated Y-chromosomal short-tandem-repeat haplotypes suggests two distinct population expansions involving C-M208--one in New Guinea and one in Polynesia. The observed low levels of Y-chromosome diversity in WNG contrast with high levels of mtDNA diversity reported for the same populations. This most likely reflects extreme patrilocality and/or biased male reproductive success (polygyny). Our data further provide evidence for primarily female-mediated gene flow within the highlands of New Guinea but primarily male-mediated gene flow between highland and lowland/coastal regions.     

Genetic affinities of AB0 and Rh blood groups among populations of Andhra Pradesh, India: 2. Tribes

Genetic affinities of 21 tribal populations of Andhra Pradesh are reported in terms of genetic distance analysis with regard to AB0 and Rh loci. These tribal populations show a high degree of differentiation in the distribution of AB0 blood groups. Some tribes exhibit the monomorphism for Rh (D) locus. The genetic distance analysis reveals that the 21 tribes included in this study are genetically distant from one another and the genetic clustering pattern correlates with linguistic/ethnic affiliation and geographical propinquity of these tribal populations to a certain extent. The possible reasons for different cluster formations are discussed.     

Genetic distances among the five tribal populations of Andhra, Pradesh, South India.

In this paper, data on genetic distances among five tribal populations ae given. Among the five tribes, Koya Dora, Raj Gond and Naikpod are autochthonous populations of the Deccan plateau whereas the other two groups, Pardhan and Lambadi are migrants. Kova Doras were sampled from five distant localities. Genetic markers typed are: A1A2B0, Rho(D) blood group systems glucose-6-phosphate dehydrogenase deficiency, transferrin, haptoglobin, groupspecific component, haemoglobin, colour-vision deficiency and tastability to P. T. C. Using frequency data for the above nine genetic loci, genetic distances between the five endogamous tribes, and between the five groups of Koya Dora are calculated by adopting the statistical method of Edwards (1971). While genetic distances between Koya Dora, Raj Gond and Lambadi are minimal, the genetic distance between Pardhans and other tribal groups is maximum. Naikpods occupy an intermediate position. The closeness of Lambadi with Koya Dora and RAJ Gond can be regarded as coincidental. Interestingly, the differences in the genetic distance values between five Koya Dora groups are as great as the differences between the five endogamous tribal populations tested for the same loci. Genetic affinities of these tribal populations are discussed in relation to their ethnic origin migration and geographical isolation.     

A population genetic study of six VNTR loci in three ethnically defined populations.

To investigate the population genetic characteristics of VNTR polymorphisms in human populations, we have studied the allele frequency distribution of six VNTR loci (D1S57, RB1, D1S77, D1S61, alpha-globin 5'HVR, D1S76) in three well-defined populations (Kachari of Northeast India; Dogrib Indian of Canada; and New Guinea Highlander of Papua New Guinea). Even though the number of alleles sampled is limited, 48 to 92 alleles per locus per population, significant variation is noticed in the number of alleles per locus for all the populations. Using alternate summary measures, we have observed that genotype distributions at the six VNTR loci apparently conform to their respective Hardy-Weinberg predictions. Multilocus genotype profiles of the individuals in each of the three populations suggest that the VNTR alleles are independently segregating with the exception of the two linked loci D1S76 and D1S77. Lack of fit of all VNTR loci to one particular model of mutational change, either the Infinite Allele Model or the Stepwise Mutation Model, suggests more than one mechanism for production of new VNTR alleles. This study also indicates that increased heterozygosity at VNTR loci in comparison to protein and blood group loci may lead to more accurate estimates of genetic distance.     

Empirical approaches to household organization

This issue of Human Ecologyis devoted to studies of household organization, originally presented at an invited session of the American Anthropological Association annual meetings in New Orleans in 1990. These papers share an empirical orientation and an interest in demographic processes and economic change, particularly in rural and non-Western societies, including !Kung foragers and Herero agro-pastoralists of Botswana, Ariaal and Rendille pastoralists of Kenya, Gainj horticulturalists of highland New Guinea, and a Euro-Caribbean populaiton of St. Barthélemy, West Indies. These papers demonstrate both the vitality of household studies and the utility of empirical approaches in understanding household formation, continuity, and adaptation to social, economic, and political change.     

Women and development: A highland New Guinea example

This paper presents an analysis of household variables and their relationship to success in cash cropping among the Gainj of Madang Province, Papua New Guinea. Censuses and household surveys from 1978, the year in which cash cropping began, and 1983 provide data that show different patterns of change in household structure for more and less commercially successful households. The results illustrate the importance of women's labor in economic development and the dynamic nature of the relationship between household structure and economic development.     

Population structure, mitochondrial polyphyly and the repeated loss of human biting ability in anopheline mosquitoes from the southwest Pacific

Australia and New Guinea contain high levels of endemism and biodiversity, yet there have been few evaluations of population‐level genetic diversity in fauna occurring throughout the Australo‐Papuan region. Using extensive geographical sampling, we examined and compared the phylogenetic relationships, phylogeography and population structure of Anopheles farauti, An. hinesorum and An. irenicus throughout their ranges in the southwest Pacific using mitochondrial (mtDNA COI) and nuclear (ribosomal protein S9 and ribosomal DNA ITS2) loci. Phylogenetic analyses suggest that the ability to utilize humans as hosts has been lost repeatedly, coincident with independent colonizations of the Solomon Islands. As some of the species under investigation transmit malaria in the region, this is a medically important finding. Maximum likelihood and Bayesian phylogenetic analyses of nuclear loci also showed that the three species are monophyletic. However, putative introgression of An. hinesorum mtDNA onto a nuclear background of An. farauti was evident in populations from Queensland, Torres Strait and southern New Guinea. Haplotype networks and pairwise F_ST values show that there is significant genetic structure within New Guinea and Australia in both An. farauti and An. hinesorum, consistent with a long‐term history of low gene flow among populations.     

Population structure and genetic heterogeneity in the Upper Markham Valley of New Guinea.

An analysis is presented of the standardized Wahlund's variances (f) in gene frequencies of the ABO, Rh and MNS blood group systems among 19 villages of the Atsera isolate of the upper Markham Valley, Papua New Guinea. In the past, there has been some disagreement over the relative importance of population structure and natural selection in the determination of these variances. The Lewontin-Krakauer test is presented as a means of resolving this disagreement. According to this test, selectively neutral variation in gene frequencies should generate essentially homogeneous values of f for all loci, a homogeneity which can be tested by comparing the value of (formula: see text) to a theoretical (formula: see text) expected when variations in (formula: see text) are due solely to sampling error. The observed value of (formula: see text) for the Atsera isolate is 2.9 x 10(-5), which is not significantly different from the expected values that range from 1.23 x 10(-5) to 2.46 x 10(-5) depending on the constant used in calculating (formula: see text). Therefore it appears that nonselective aspects of population structure such as genetic drift and intervillage migration are responsible for the recorded genetic variation in this isolate.     

Genetic distance analysis of twenty-two South American Indian populations.

Extent of genic variability among 22 tribal groups of South American Indians in terms of net codon differences per locus has been studied on the basis of determinations on ten genetic systems. The possibility of more than one (other than the north-south route, considered by others) migrational pattern is discussed in the light of the existing genetic variability among the Andean highland and the jungle populations. Genic similarities (as measured by gene identity) are related with geographic proximities which reflect the importance of random genetic drift in creating the present genic divergence among these population groups. Although the materials used in this paper form probably only a non-random sample of structural genome, intralocus variance (sampling) is found to contribute only a little in the variabilities of heterozygosity or genetic distance.     

Mitochondrial and nuclear genetic relationships among Pacific Island and Asian populations.

Mitochondrial and autosomal short tandem-repeat (STR) genetic distances among 28 Pacific Island and Asian populations are significantly correlated (r=.25, P<.01) but describe distinct patterns of relationships. Maternally inherited-mtDNA data suggest that Remote Oceanic Islanders originated in island Southeast Asia. In contrast, biparental STR data reveal substantial genetic affinities between Remote Oceanic Islanders and Near Oceanic populations from highland Papua New Guinea and Australia. The low correlation between maternal and biparental genetic markers from the same individuals may reflect differences in genome-effective population sizes or in sex-biased gene flow. To explore these possibilities, we have examined genetic diversity, gene flow, and correlations among genetic, linguistic, and geographic distances within four sets of populations representing potential geographic and cultural spheres of interaction. GST estimates (a measure of genetic differentiation inversely proportional to gene flow) from mtDNA sequences vary between 0.13 and 0.39 and are typically five times greater than GST estimates from STR loci (0.05-0.08). Significant correlations (r>.5, P<.05) between maternal genetic and linguistic distances are coincident with high mtDNA GST estimates (>0.38). Thus, genetic and linguistic distances may coevolve, and their correspondence may be preserved under conditions of genetic isolation. A significant correlation (r=.65, P<.01) between biparental genetic and geographic distances is coincident with a low STR GST estimate (0.05), indicating that isolation by distance is observed under conditions of high nuclear-gene flow. These results are consistent with an initial settlement of Remote Oceania from island Southeast Asia and with extensive postcolonization male-biased gene flow with Near Oceania.     

Demographic and endocrinological aspects of low natural fertility in Highland New Guinea

The Gainj of highland Papua New Guinea do not use contraception but have a total fertility rate of only 4.3 live births/woman, 1 of the lowest ever recorded in a natural fertility setting. Reproductive and marital histories were obtained from 305 females and 206 males aged 10+. Each subject was asked about: number of live born offspring ever produced; number of stillbirths ever produced; number and names of offspring currently being nursed; number of current and past spouses; and the cause of dissolution of all past marriages. Blood samples were drawn from 172 volunteer female subjects aged 10-60 years and ovarian function was classified by concentration of progesterone. From an analysis of these cross-sectional demographic and endocrinological data, the causes of low reproductive output have been identified in women of this population as: late menarche and marriage, a long interval between marriage and 1st birth, a high probability of widowhood at later reproductive ages, low effective fecundability and prolonged lactational amenorrhea. These are combined with near-universal marriage, and a low prevalence of primary sterility similar to that found in other populations. Of all the factors limiting fertility, by far the most important are those involved in birth spacing, especially lactational amenorrhea. The effects of widowhood on Gainj fertility are negligible. Factors acting to lower fertility fall into 2 categories: those that determine the age of onset of reproduction and those that act to space births. Given the observed pattern of birth spacing, however, the delay in commencement of reproduction represents on average no more than 1 or 2 live births averted/woman. In contrast, were age at 1st reproduction held constant while reducing birth intervals to a mean of 2.0-2.5 years, total fertility would increase to about 7 or 8. Future research on natural fertility should focus on specific behavioral and physiological mechanisms governing the reproductive process.     

Conservation genetics of Boelen’s python (Morelia boeleni) from New Guinea: reduced genetic diversity and divergence of captive and wild animals

Boelen’s python (Morelia boeleni) is a montane New Guinea endemic found in highlands above 1000 m and below the tree line. The ecology, natural history, distribution, population size, and conservation status of this species are largely unknown. It has a protected status in Papua New Guinea but not in Indonesian Papua and several US and European zoos have active captive breeding programs that have been largely unsuccessful. To understand the degree of genetic diversity in wild and captive animals we undertook a genetic analysis of 90 M. boeleni for which we sequenced two mtDNA loci and one nuclear locus for a total of 1,418 bp of sequence data per individual. All 16 wild-caught M. boeleni from Indonesia and all captive M. boeleni are genetically uniform for all three loci. The single wild-caught animal from Papua New Guinea showed extremely low levels of genetic divergence and diversity from the Indonesian and captive samples. Data from two congeners, M. amethistina and M. viridis, suggests that M. boeleni have reduced genetic variation with a small effective population size possibly due to historical bottlenecks. These data demonstrate the need for further studies of genetic diversity of M. boeleni from across its range and raise particular concern for the limited genetic diversity of M. boeleni used captive breeding programs in zoological parks.