Unraveling the Gut Microbiome of the Invasive Small Indian Mongoose (Urva auropunctata) in the Caribbean.

Small Indian mongooses (Urva auropunctata) are among the most pervasive predators to disrupt the native ecology on Caribbean islands and are strongly entrenched in their areas of introduction. Few studies, however, have considered the microbial ecology of such biological invasions. In this study, we investigated the gut microbiota of invasive small Indian mongooses in terms of taxonomic diversity and functional potential. To this end, we collected fecal samples from 60 free-roaming mongooses trapped in different vegetation zones on the island Saint Kitts. The core gut microbiome, assessed by 16S rRNA amplicon gene sequencing on the Ion S5TM XL platform, reflects a carnivore-like signature with a dominant abundance of Firmicutes (54.96%), followed by Proteobacteria (13.98%) and Fusobacteria (12.39%), and a relatively minor contribution of Actinobacteria (10.4%) and Bacteroidetes (6.40%). Mongooses trapped at coastal sites exhibited a higher relative abundance of Fusobacterium spp. whereas those trapped in scrubland areas were enriched in Bacteroidetes, but there was no site-specific difference in predicted metabolic properties. Between males and females, beta-diversity was not significantly different and no sex-specific strategies for energy production were observed. However, the relative abundance of Gammaproteobacteria, and more specifically, Enterobacteriaceae, was significantly higher in males. This first description of the microbial profile of small Indian mongooses provides new insights into their bioecology and can serve as a springboard to further elucidating this invasive predator's impact throughout the Caribbean.

Association between HLA-DR4 haplotypes and tuberculin skin test response in the Aché population.

The human leukocyte antigen (HLA) system has a major role in the regulation of the immune response as it is involved in the defense against pathogens. Evidence for association with tuberculosis (TB) is more consistent for class II than for class I HLA genes. TB is important among indigenous peoples in South America, not only because of its historical role in regional depopulation, but also because it is still widespread. The aim of this study was to evaluate the association of HLA class II alleles, haplotypes and genotypes and tuberculin skin test response (TST) in 76 individuals of the Aché population. Poisson Regression was employed to assess risk genotypes. DRB1*04, DQA1*03 and DQB1*03:02 were associated with TST response in this population.

Cytokine gene polymorphisms are associated with susceptibility to tuberculosis in an Amerindian population.

SETTING: Cytokines play an important role in anti-tuberculosis immune response, combined with antigen-presenting cells and lymphocytes. Immune response gene polymorphisms have been reported to be associated with tuberculosis (TB) susceptibility in some but not all studies. OBJECTIVE: To evaluate the association of immune response genes with susceptibility to tuberculin skin test (TST) reactivity and/or TB. DESIGN: Fourteen single nucleotide polymorphisms were genotyped in 96 individuals of the Aché, a native Paraguayan population, by allelic discrimination using real-time polymerase chain reaction. Univariate and multivariate Poisson regression were employed to assess risk genotypes. RESULTS: A higher prevalence of purified protein derivative reactivity was associated with the TNF-α CCA/TCG haplotype (PR 1.298, 95%CI 1.059-1.589) and with the IL-10 AT/CC diplotype (PR 1.181, 95% CI 1.024-1.362), and the presence of the IL-8 rs4073 T allele was associated with protection against TB (PR 0.482, 95%CI 0.273-0.851). CONCLUSIONS: These results suggest that polymorphisms in genes associated with immune response are involved in TST reactivity and susceptibility to TB in the Aché population.

Distribution patterns of variability for 18 immune system genes in Amerindians--relationship with history and epidemiology.

Native American populations generally have a higher prevalence of infectious diseases than non-Native populations and this fact can induce different pressures in their immune system. We investigated the patterns of population differentiation (FST ) of 32 polymorphisms related to adaptive immune response in four Native American populations (Aché, Guarani-Kaiowá, Guarani-Ñandeva and Kaingang), and the results were compared with the three major world population data [Yoruba of Ibadan, Nigeria (YRI), Utah residents with northern and Western Europe ancestry (CEU) and Han Chinese of Beijing, China (CHB)] available in the HapMap database. The Aché clearly differentiated from the other Amerindians, but when all Native Americans were compared with the samples of other ethnic groups the lowest difference (0.08) was found with CHB (Asians), the second lowest (0.15) with YRI (Africans) and the most marked with CEU (European-derived). The considerable intra and interethnic differences found can be explained both in terms of diverse evolutionary distances and more recent environmental pathogen exposures; and they should be appropriately considered prior to any specific public health action.

Molecular variability of the 16p13.3 region in Amerindians and its anthropological significance.

A total of 1558 base pairs in the 16p13.3 region were investigated in 98 individuals of Mongolian, Northern Arctic and Amerindian affiliation, and the results compared with those obtained in a previous worldwide study of the same genomic region. Fifty-five polymorphic sites could be classified into thirty-five haplotypes from the total data. A median joining network based on the haplotypes revealed two distinct clusters: one with low diversity, with haplotypes found in all five geographic-ethnic categories; while the other, with the most divergent haplotypes, was composed mainly of Africans and a few Amerindians. Almost all neutrality parameters yielded significantly negative values. Demographic simulations with the exclusively Amerindian dataset rejected all scenarios, including a bottleneck beginning more than 12,000 years ago. The demographic scenarios tested considering population growth were similar among the Amerindian and worldwide or Eurasian data sets. The results suggest that Amerindians are a representative sample of Eurasian populations, preserving the signal of demographic growth from the out of Africa exodus and, together with data from uniparental markers, support a scenario of a bottleneck of moderate intensity during the peopling of the New World.

APOE polymorphism distribution among Native Americans and related populations.

BACKGROUND: Apolipoprotein E (apoE, protein; APOE, gene) plays a central role in lipid metabolism. Three common alleles, E*2, E*3 and E*4 have quantitative effects on lipid and lipoproteins levels, which are major risk determinants of cardiovascular diseases in several populations. Given their clinical significance, it is of interest to know the distribution of APOE variants in populations from diverse ethnic groups, as well as to determine if this polymorphism presents variations that might be associated with given evolutionary factors. AIM: We report the distribution of APOE polymorphisms in Native American populations from South America, comparing it with other native populations of the Americas and Siberia. SUBJECTS AND METHODS: The sample consisted of 315 individuals from nine Native American populations living at subtropical latitudes of Argentina, Brazil and Paraguay. The extended analysis included 50 populations across South and North America, Greenland and Siberia. The geographic patterns of the variation were investigated through correlation analysis, spatial autocorrelation and analysis molecular of variance (AMOVA). RESULTS: The incidence of the most common allele (APOE*3) in the sample analysed ranged from 0.78 to 0.98. The second allele in prevalence, APOE*4, varied from 0.00 to 0.17. The rare allele APOE*2 was found in five of the nine populations investigated. This variant was found in a male with both maternal and paternal Native American lineages, suggesting that this allele is present in Native Americans and hence should not be used as an indicator of admixture. APOE*3 and APOE*4 present, respectively, positive and negative associations with latitude, although the pattern is much more pronounced in the Northern Hemisphere than in South America. APOE*2 increases its frequency with latitude but this pattern is statistically significant only in South America. CONCLUSION: The overall APOE spatial pattern seems, in general, compatible with a directional demographic expansion which occurred in north-eastern Asia and much of the New World. The APOE*2 allele shows this pattern in South America but a random distribution in the Northern Hemisphere, suggesting that the possibility of selection should not be discarded.

Extremely limited mitochondrial DNA variability among the Aché Natives of Paraguay.

BACKGROUND: The Aché Natives are an especially interesting group of people, due to their distinctive morphological aspect and the fact that only in the last three decades have they established more permanent contact with outside populations. The objectives of the present study were: (a) to verify their distinctiveness in relation to mitochondrial DNA (mtDNA) variability; (b) to ascertain whether the pattern observed was congruent with other genetic studies performed among them; and (c) to establish historical inferences that would explain the eventual similarities or differences. SUBJECTS AND METHODS: Sample collection was made at two localities in eastern Paraguay. DNA from 64 maternally unrelated subjects were tested in relation to the mtDNA hypervariable segment 1 (HVS-1) by automatic sequencing. RESULTS: Fifty-six individuals presented exactly the same haplogroup B founder haplotype; another differed from it by a single transition polymorphism at site 16362, while six other subjects showed an identical haplogroup A founding haplotype. An A/G heteroplasmy at the 16269 site was seen in one haplogroup B individual, probably due to a somatic mutation. CONCLUSIONS: The Aché present distinctive differences and reduced mtDNA HVS-1 variability compared to other South American Natives. Similar differences were observed for other genetic systems. At present it is not clear whether their peculiarities already existed in their founding populations or whether they were secondarily acquired due to a long period of isolation in the humid, subtropical forest.

HLA class II diversity in seven Amerindian populations. Clues about the origins of the Aché.

The study of the HLA variability of Native American populations revealed several alleles specific to one or more of the Latin American indigenous populations. The analysis of Amerindian groups distributed all over the continent might inform about the area of origin and the dispersal of these alleles and shed light on the evolution of this remarkable polymorphism. Moreover, HLA alleles and haplotypes are excellent markers to understand the genetic relationships between populations. For these reasons, we characterized the HLA class II polymorphism in seven South American Amerindian populations and compared the results with those previously reported for other Amerindian groups. The Guarani-Kaiowá (n = 160) and Guarani-Nandeva (n = 87) were from the Brazilian state of Mato Grosso do Sul, the Guarani-M'byá (n = 93) and Kaingang (n = 235) from Paraná state, the Aché (n = 89) from eastern Paraguay, the Quechua (n = 44) from Andean Peru. From Amazonia, a heterogeneous group was analyzed (n = 45). The most frequent alleles and haplotypes are common also in other Amerindian populations. Each HLA-DRB1 allele was typically found in combination with just one DQA1-DQB1 haplotype, most likely as a result of some form of random genetic drift and reduced gene flow from non-Amerindians. The frequency distribution differed significantly among all populations, although differences were less pronounced between the Guarani subgroups. Marker alleles allowed an estimate of European and sub-Saharan African gene flow into these populations: Quechua 23%, Guarani-Nandeva 14%, Kaingang 7%, Guarani-M'byá 4%, Guarani-Kaiowá, Amazonia, and Aché 0%. Interestingly, the DRB1*1413 allele, previously found only among the Guarani-M'byá (frequency 15%), appeared in the Aché (8%). The relationship of the Aché to other Amerindian populations is unclear, and this finding reveals a link with the Guarani. On the basis of genetic distance and the HLA allele/haplotype set, we propose that the Aché are differentiated Tupi-Guarani group, most closely related to the Guarani-M'byá.

Methylenetetrahydrofolate reductase (MTHFR) allele frequencies in Amerindians.

Neural tube defects (NTDs) have been associated with abnormalities of folate metabolism. Methylenetetrahydrofolate reductase (MTHFR) is the regulatory enzyme for the conversion of homocysteine to methionine. The C677T mutation in the MTHFR gene affects folate distribution, and homozygosity for the T allele may be associated with an increased risk of NTDs. A second mutation, an A1298C transversion in this same gene, is also associated with an increased risk for NTDs but only in conjunction with the 677T allele. A low incidence of NTDs has been observed in high-altitude populations; however, these studies did not provide information about the allele distribution of genes involved in folate metabolism. This investigation compares allele frequencies of the C677T and A1298C polymorphisms between Quechua people living at 3200-4200 m in the Peruvian Central Andes and an Aché group living at low altitude. Allele frequencies at both loci were not significantly different between the two populations. The absence of the 677T/677T genotypes and of the 677T/1298C arrangement in both groups may indicate a genetic contribution to reduced risk for NTDs; however, factors other than altitude are likely responsible for the low variant allele frequencies in these populations.

Y-chromosome biallelic polymorphisms and Native American population structure.

It has been proposed that women had a higher migration rate than men throughout human evolutionary history. However, in a recent study of South American natives using mtDNA restriction fragment polymorphisms and Y-chromosome microsatellites we failed to detect a significant difference in estimates of migration rates between the sexes. As the high mutation rate of microsatellites might affect estimates of population structure, we now examine biallelic polymorphisms in both mtDNA and the Y-chromosome. Analyses of these markers in Amerinds from North, Central and South America agree with our previous findings in not supporting a higher migration rate for women in these populations. Furthermore, they underline the importance of genetic drift in the evolution of Amerinds and suggest the existence of a North to South gradient of increasing drift in the Americas.

Alu insertions versus blood group plus protein genetic variability in four Amerindian populations.

BACKGROUND: Do the population relationships obtained using DNA or blood group plus protein markers remain the same or do they reveal different patterns, indicating that the factors which influence genetic variation at these two levels of analysis are diverse? Can these markers shed light on the biological classification of the Aché, a Paraguayan tribe which only recently established more permanent contacts with non-Indians? SUBJECTS AND METHODS: To consider these questions we typed 193 individuals from four Amerindian tribes in relation to 12 Alu polymorphisms (five of them never studied in these populations), while 22 blood group plus protein systems were studied among the Aché. These data were then integrated with those previously available (blood groups plus proteins) for the three other populations. DNA extraction and amplification, as well as the other laboratory procedures, were performed using standard methods currently in use in our laboratory. The genetic relationships were obtained using the D(A) distance, and the trees were constructed by the neighbour-joining method, both developed by M. Nei and collaborators. Reliability of the trees was tested by bootstrap replications. Other population variability values were also determined using Nei's methods. RESULTS: Alu polymorphism was observed in all populations and for most of the loci; in the seven systems from which we could compare our results with those of other Amerindian groups agreement was satisfactory. Unusual findings on the blood group plus protein systems of the Aché were a very low (5%) HP*1 frequency and the presence of the C(W) phenotype in the Rh blood group. The intertribal patterns of relationship and other aspects of their variation were remarkably congruent in the two sets (Alu; blood group plus protein) of systems. CONCLUSIONS: The answer to the first question posed above is affirmative. However, the problem of whether the Aché derived from a Gê group that preceded the Guarani colonization of Paraguay, or are just a differentiated Guarani group, could not be answered with the genetic information available; the second hypothesis seems more likely at present, but the point to be emphasized is the striking genetic distinctiveness of the Aché as compared to other Amerindians.

Reservation food sharing among the Ache of Paraguay.

We describe food transfer patterns among Ache Indians living on a permanent reservation. The social atmosphere at the reservation is characterized by a larger group size, a more predictable diet, and more privacy than the Ache typically experience in the forest while on temporary foraging treks. Although sharing patterns vary by resource type and package size, much of the food available at the reservation is given to members of just a few other families. We find significant positive correlations between amounts transferred among pairs of families, a measure of the "contingency" component required of reciprocal altruism models. These preferred sharing partners are usually close kin. We explore implications of these results in light of predictions from current sharing models.

"It's a Wonderful Life". signaling generosity among the Ache of Paraguay.

Intensive food sharing among foragers and horticulturists is commonly explained as a means of reducing the risk of daily shortfalls, ensuring adequate daily consumption for all group members who actively pool resources. Consistently high food producers who give more than they receive, however, gain the least risk-reduction benefit from this daily pooling because they are the least likely to go without food on any given day. Why then do some high producers consistently share food, and why do some average producers share proportionally more food than others? We propose that although these individuals may not receive the same amounts they give (i.e., strict Tit-for-Tat), one explanation for their generosity is that they receive additional food during hard times. These include brief episodes of sickness, disease, injury, or accidents-fairly common events in traditional societies that can render individuals incapable of producing food, thereby having long-term effects on morbidity and fecundity and ultimately on lifetime reproductive success. Data collected among the Ache, a group of South American forager-horticulturists, indicate that those who shared and produced more than average (signaling cooperative intent and/or ability to produce) were rewarded with more food from more people when injured or sick than those who shared and produced below average. These results, framed within the context of tradeoffs between short-term and long-term fitness, may provide insight into motivations behind costly expenditures for establishing and reinforcing status and reputation.

Apolipoprotein B signal peptide polymorphism distribution among south Amerindian populations.

We report the distribution of the APOB signal peptide polymorphism in 5 native populations of South America: 2 samples of Mataco and 1 sample each of Pilagá and Toba from the Argentinian Chaco and 1 sample of Ache from the Paraguay forest. A randomly selected subsample of a previously studied sample from the Cayapa of Ecuador (Scacchi et al. 1997) was reanalyzed to investigate probable differences attributable to sampling, laboratory techniques, or interobserver error. The polymorphism observed in the signal peptide region of the APOB gene among native populations of South America exhibits the same range of variation found among geographic continental populations, confirming the high genetic heterogeneity of South Amerindians. Extremes in the allele prevalences were found among the Mataco and Ache, populations not far apart geographically. The small differences in genotype and allele frequencies between the subsample of the Cayapa analyzed here and the original Cayapa sample and between the 2 Mataco samples were not statistically significant and most likely were due to sampling error.

The evolutionary context of chronic allergic conditions : The Hiwi of Venezuela.

The question of why populations with ecologies that resemble our evolutionary past rarely experience allergic conditions such as asthma has intrigued many biomedical scientists. Here we present descriptive data on the ecological context of allergic sensitization among the Hiwi of southwestern Venezuela and suggest reasons for why this and other lowland South American Indian groups do not express the allergic response at levels seen in industrialized contexts. Allergic sensitization among the Hiwi appears to be negligible. This absence occurs in the context of high exposure to macroparasites (mainly hookworm), nutritional stress, frequent and prolonged breastfeeding, low indoor allergen deposition, and few hours spent per day indoors. We conclude that seeking unidimensional answers to the question of why isolated human groups generally experience few allergic conditions is potentially flawed because allergies are produced by a multifaceted immunoglobulin E (IgE) system that responds in complex ways to the environmental and behavioral exposures we examined. Instead, we propose a general model of physiological trade-offs in energy allocation between production of IgE of undefined specificity and production of allergen-specific IgE. In addition, we consider the simultaneous effects that exposures such as nutritional stress, allergen exposure, and breastfeeding may have on these trade-offs.

[Report on the Seminar on Procedures of Demographic Estimation with Age-Specific Growth Rates, organized by the Latin American Center of Demography (CELADE) and the International Union for the Scientific Study of Population (IUSSP), Santiago, Chile, November 26-29, 1984]. / Informe del "Seminario sobre Procedimientos de Estimaciones Demograficas con Tasas de Crecimiento por Edad", organizado por el Centro Latinoamericano de Demografia (CELADE) y la Union Internacional para el Estudio Cientifico de la Poblacion (UIECP), Santiago de Chile, 26-29 de noviembre de 1984

PIP: This is a report on a seminar on the use of age-specific growth rates for demographic measurement in Latin America, held in Santiago, Chile, in November 1984. The seminar was jointly sponsored by the International Union for the Scientific Study of Population (IUSSP) and the Latin American Center of Demography (CELADE). (summary in ENG)^ieng

[A note on the use of information concerning the residence of surviving siblings to estimate emigration]. / Nota sobre la utilizacion de informacion sobre la residencia de los hermanos sobrevivientes para estimar la emigracion

"Two improvements are presented in the previously developed method for measuring international emigration based on information provided by surviving siblings. The first is a simplification of the procedure for estimating surviving siblings when the information does not exist because they all live abroad. The second...is a procedure for estimating the distribution by age of the surviving emigrant siblings using models." The improved procedures are applied to data for Barbados. (summary in ENG)