ResearchPad - indigenous-populations https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Integrating testing for chronic strongyloidiasis within the Indigenous adult preventive health assessment system in endemic communities in the Northern Territory, Australia: An intervention study]]> https://www.researchpad.co/article/elastic_article_13848 Strongyloidiasis is a neglected tropical disease that is endemic in some Aboriginal communities in the Northern Territory. This study asks if the number and proportion of persons tested for chronic strongyloidiasis can be increased by incorporating a Strongyloides serology test into the existing routine Indigenous adult preventive health assessment system in remote endemic communities. This study demonstrated that integrating Strongyloides serology test within the Indigenous adult preventive health assessment system does increase the number and proportion of people tested in endemic communities. This intervention means that life-threatening clinical complications of strongyloidiasis can be prevented by early detection and treatment. Primary health care services have an important role in increased testing in this high-risk population. Primary health care clinicians incorporated chronic strongyloidiasis with other preventable chronic and infectious diseases. The sustainable population health systems-based approach successfully increased coverage by integrating testing for chronic strongyloidiasis into the adult preventive health assessment in health services in remote Indigenous Australian endemic communities, utilising the electronic health record system. The Strongyloides report developed to measure the change in clinical practice would be replicable in other health services with high risk populations.

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<![CDATA[Promoting resilience in adolescents: A new social identity benefits those who need it most]]> https://www.researchpad.co/article/5c40f815d5eed0c484386fe5

The Social Identity Approach to Health holds that groups provide us with a sense of meaning and belonging, and that these identity processes have a significant positive impact on our health and wellbeing. Typically, research drawing from the social identity approach with adolescents has focused on the benefits of existing group memberships. Here, using a sail-training intervention, we investigated the impact of providing adolescents with a new group (i.e., a new social identity) on psychological resilience. Across two studies, we demonstrate the benefits of a new social identity, in terms of increases in psychological resilience, flow predominantly to those adolescents who report the lowest levels of resilience at the start of the voyage. We discuss our findings in relation to the social identity approach and adolescent identity development more generally.

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<![CDATA[On the Origin of Tibetans and Their Genetic Basis in Adapting High-Altitude Environments]]> https://www.researchpad.co/article/5989db3bab0ee8fa60bd4b87

Since their arrival in the Tibetan Plateau during the Neolithic Age, Tibetans have been well-adapted to extreme environmental conditions and possess genetic variation that reflect their living environment and migratory history. To investigate the origin of Tibetans and the genetic basis of adaptation in a rigorous environment, we genotyped 30 Tibetan individuals with more than one million SNP markers. Our findings suggested that Tibetans, together with the Yi people, were descendants of Tibeto-Burmans who diverged from ancient settlers of East Asia. The valleys of the Hengduan Mountain range may be a major migration route. We also identified a set of positively-selected genes that belong to functional classes of the embryonic, female gonad, and blood vessel developments, as well as response to hypoxia. Most of these genes were highly correlated with population-specific and beneficial phenotypes, such as high infant survival rate and the absence of chronic mountain sickness.

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<![CDATA[Ethnic and Racial Inequalities in Notified Cases of Tuberculosis in Brazil]]> https://www.researchpad.co/article/5989da04ab0ee8fa60b7555c

Objective

This study analysed clinical and sociodemographic aspects and follow-up for notified cases of tuberculosis (TB) and explored inequalities in incidence rates and outcome by colour or race and the geographic macro-regions of Brazil.

Methods

This paper reports the results of a population-based descriptive epidemiological study of all notified cases of TB in Brazil during the period from 01/01/2008 to 31/12/2011. We analysed sociodemographic and clinical variables according to colour or race (white, black, Asian, mixed, and indigenous) and geographic macro-regions of the country (North, Northeast, Central-West, South, and Southeast).

Results

During the study period, the average incidence of TB in Brazil was 36.7 cases per 100,000 inhabitants, with the highest rates occurring in the North and Southeast regions. The analysis of TB notifications by colour or race revealed that the indigenous population presented the highest incidence rates in all macro-regions except the South, where higher rates were reported in black patients. ‘Cured’ was the most frequently reported treatment outcome for all skin colour categories. The highest cure rate occurred among the indigenous population (76.8%), while the lowest cure rate occurred among the black population (70.7%). Rates of treatment default were highest among blacks (10.5%) and lowest among the indigenous population (6.9%). However, the fatality rate was similar across race categories, varying between 2.8% and 3.8% for whites and the indigenous population, respectively. The lowest cure rates were observed when follow-up was inadequate (58.3%), and the highest was observed when the follow-up was classified as excellent (96.8%).

Conclusions

This study revealed that—apart from the heterogeneous distribution of TB among the Brazilian macro-regions—ethnic-racial inequalities exist in terms of clinical-epidemiological characteristics and incidence rates as well as follow-up for cases undergoing treatment. The highest rates of TB occurred among the indigenous people.

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<![CDATA[A Population-Based Cohort Study of Mycobacterium tuberculosis Beijing Strains: An Emerging Public Health Threat in an Immigrant-Receiving Country?]]> https://www.researchpad.co/article/5989da71ab0ee8fa60b94e24

Introduction

Mycobacterium tuberculosis Beijing strains are frequently associated with tuberculosis outbreaks and drug resistance. However, contradictory evidence and limited study generalizability make it difficult to foresee if the emergence of Beijing strains in high-income immigrant-receiving countries poses an increased public health threat. The purpose of this study was to determine if Beijing strains are associated with high risk disease presentations relative to other strains within Canada.

Methods

This was a retrospective population-based study of culture-confirmed active TB cases in a major immigrant-receiving province of Canada in 1991 through 2007. Of 1,852 eligible cases, 1,826 (99%) were successfully genotyped. Demographic, clinical, and mycobacteriologic surveillance data were combined with molecular diagnostic data. The main outcome measures were site of disease, lung cavitation, sputum smear positivity, bacillary load, and first-line antituberculosis drug resistance.

Results

A total of 350 (19%) patients had Beijing strains; 298 (85%) of these were born in the Western Pacific. Compared to non-Beijing strains, Beijing strains were significantly more likely to be associated with polyresistance (aOR 1.8; 95% CI 1.0–3.3; p = 0.046) and multidrug-resistance (aOR 3.4; 1.0–11.3; p = 0.049). Conversely, Beijing strains were no more likely than non-Beijing strains to be associated with respiratory disease (aOR 1.3; 1.0–1.8; p = 0.053), high bacillary load (aOR 1.2; 0.6–2.7), lung cavitation (aOR 1.0; 0.7–1.5), immediately life-threatening forms of tuberculosis (aOR 0.8; 0.5–1.6), and monoresistance (aOR 0.9; 0.6–1.3). In subgroup analyses, Beijing strains only had a significant association with multidrug-resistant tuberculosis (aOR 6.1; 1.2–30.4), and an association of borderline significance with polyresistant tuberculosis (aOR 1.8; 1.0–3.5; p = 0.062), among individuals born in the Western Pacific.

Conclusion

Other than an increased risk of polyresistant or multidrug-resistant tuberculosis, Beijing strains appear to pose no more of a public health threat than non-Beijing strains within a high-income immigrant-receiving country.

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<![CDATA[Bringing state-of-the-art diagnostics to vulnerable populations: The use of a mobile screening unit in active case finding for tuberculosis in Palawan, the Philippines]]> https://www.researchpad.co/article/5989db50ab0ee8fa60bdc1f5

Background

Globally, case detection of tuberculosis (TB) has stabilized in recent years. Active case finding (ACF) has regained an increased attention as a complementary strategy to fill the case detection gap. In the Philippines, the DetecTB project implemented an innovative ACF strategy that offered a one-stop diagnostic service with a mobile unit equipped with enhanced diagnostic tools including chest X-ray (CXR) and Xpert®MTB/RIF (Xpert). The project targeted the rural poor, the urban poor, prison inmates, indigenous population and high school students.

Methods

This is a retrospective review of TB screening data from 25,103 individuals. A descriptive analysis was carried out to compare screening and treatment outcomes across target populations. Univariate and multivariate analyses were performed to identify predictors of TB for each population. The composition of bacteriologically-confirmed cases by smear and symptom status was further investigated.

Results

The highest yield with lowest number needed to screen (NNS) was found in prison (6.2%, NNS: 16), followed by indigenous population (2.9%, NNS: 34), the rural poor (2.2%, NNS: 45), the urban poor (2.1%, NNS: 48), and high school (0.2%, NNS: 495). The treatment success rate for all populations was high with 89.5% in rifampicin-susceptible patients and 83.3% in rifampicin-resistant patients. A relatively higher loss to follow-up rate was observed in indigenous population (7.5%) and the rural poor (6.4%). Only cough more than two weeks showed a significant association with TB diagnosis in all target populations (Adjusted Odds Ratio ranging from 1.71 to 6.73) while other symptoms and demographic factors varied in their strength of association. The urban poor had the highest proportion of smear-positive patients with cough more than two weeks (72.0%). The proportion of smear-negative (Xpert-positive) patients without cough more than two weeks was the highest in indigenous population (39.3%), followed by prison inmates (27.7%), and the rural poor (22.8%).

Conclusions

The innovative ACF strategy using mobile unit yielded a substantial number of TB patients and achieved successful treatment outcomes. TB screening in prison, indigenous population, and urban and rural poor communities was found to be effective. The combined use of CXR and Xpert largely contributed to increased case detection.

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<![CDATA[The Influence of Natural Barriers in Shaping the Genetic Structure of Maharashtra Populations]]> https://www.researchpad.co/article/5989d9f1ab0ee8fa60b6ea53

Background

The geographical position of Maharashtra state makes it rather essential to study the dispersal of modern humans in South Asia. Several hypotheses have been proposed to explain the cultural, linguistic and geographical affinity of the populations living in Maharashtra state with other South Asian populations. The genetic origin of populations living in this state is poorly understood and hitherto been described at low molecular resolution level.

Methodology/Principal Findings

To address this issue, we have analyzed the mitochondrial DNA (mtDNA) of 185 individuals and NRY (non-recombining region of Y chromosome) of 98 individuals belonging to two major tribal populations of Maharashtra, and compared their molecular variations with that of 54 South Asian contemporary populations of adjacent states. Inter and intra population comparisons reveal that the maternal gene pool of Maharashtra state populations is composed of mainly South Asian haplogroups with traces of east and west Eurasian haplogroups, while the paternal haplogroups comprise the South Asian as well as signature of near eastern specific haplogroup J2a.

Conclusions/Significance

Our analysis suggests that Indian populations, including Maharashtra state, are largely derived from Paleolithic ancient settlers; however, a more recent (∼10 Ky older) detectable paternal gene flow from west Asia is well reflected in the present study. These findings reveal movement of populations to Maharashtra through the western coast rather than mainland where Western Ghats-Vindhya Mountains and Narmada-Tapti rivers might have acted as a natural barrier. Comparing the Maharastrian populations with other South Asian populations reveals that they have a closer affinity with the South Indian than with the Central Indian populations.

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<![CDATA[Are Isolated Indigenous Populations Headed toward Extinction?]]> https://www.researchpad.co/article/5989daebab0ee8fa60bbf619

At least 50 indigenous groups spread across lowland South America remain isolated and have only intermittent and mostly hostile interactions with the outside world. Except in emergency situations, the current policy of governments in Brazil, Colombia, and Peru towards isolated tribes is a “leave them alone” strategy, in which isolated groups are left uncontacted. However, these no-contact policies are based on the assumption that isolated populations are healthy and capable of persisting in the face of mounting external threats, and that they can maintain population viability in the long-term. Here, we test this assumption by tracking the sizes and movements of cleared horticultural areas made by 8 isolated groups over the last 10–14 years. We used deforestation data derived from remote sensing Landsat satellite sensors to identify clearings, and those were then validated and assessed with high-resolution imagery. We found only a single example of a relatively large and growing population (c. 50 cleared ha and 400 people), whereas all of the other 7 groups exhibited much smaller villages and gardens with no sizable growth through time. These results indicated that the smaller groups are critically endangered, and it prompts an urgent re-thinking of policies toward isolated populations, including plans for well-organized contacts that may help save lives and rescue isolated indigenous populations from imminent extinction.

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<![CDATA[Genetic Divergence Disclosing a Rapid Prehistorical Dispersion of Native Americans in Central and South America]]> https://www.researchpad.co/article/5989dafeab0ee8fa60bc5b15

An accurate estimate of the divergence time between Native Americans is important for understanding the initial entry and early dispersion of human beings in the New World. Current methods for estimating the genetic divergence time of populations could seriously depart from a linear relationship with the true divergence for multiple populations of a different population size and significant population expansion. Here, to address this problem, we propose a novel measure to estimate the genetic divergence time of populations. Computer simulation revealed that the new measure maintained an excellent linear correlation with the population divergence time in complicated multi-population scenarios with population expansion. Utilizing the new measure and microsatellite data of 21 Native American populations, we investigated the genetic divergences of the Native American populations. The results indicated that genetic divergences between North American populations are greater than that between Central and South American populations. None of the divergences, however, were large enough to constitute convincing evidence supporting the two-wave or multi-wave migration model for the initial entry of human beings into America. The genetic affinity of the Native American populations was further explored using Neighbor-Net and the genetic divergences suggested that these populations could be categorized into four genetic groups living in four different ecologic zones. The divergence of the population groups suggests that the early dispersion of human beings in America was a multi-step procedure. Further, the divergences suggest the rapid dispersion of Native Americans in Central and South Americas after a long standstill period in North America.

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<![CDATA[Heterogeneity in Genetic Admixture across Different Regions of Argentina]]> https://www.researchpad.co/article/5989da7aab0ee8fa60b97fc8

The population of Argentina is the result of the intermixing between several groups, including Indigenous American, European and African populations. Despite the commonly held idea that the population of Argentina is of mostly European origin, multiple studies have shown that this process of admixture had an impact in the entire Argentine population. In the present study we characterized the distribution of Indigenous American, European and African ancestry among individuals from different regions of Argentina and evaluated the level of discrepancy between self-reported grandparental origin and genetic ancestry estimates. A set of 99 autosomal ancestry informative markers (AIMs) was genotyped in a sample of 441 Argentine individuals to estimate genetic ancestry. We used non-parametric tests to evaluate statistical significance. The average ancestry for the Argentine sample overall was 65% European (95%CI: 63–68%), 31% Indigenous American (28–33%) and 4% African (3–4%). We observed statistically significant differences in European ancestry across Argentine regions [Buenos Aires province (BA) 76%, 95%CI: 73–79%; Northeast (NEA) 54%, 95%CI: 49–58%; Northwest (NWA) 33%, 95%CI: 21–41%; South 54%, 95%CI: 49–59%; p<0.0001] as well as between the capital and immediate suburbs of Buenos Aires city compared to more distant suburbs [80% (95%CI: 75–86%) versus 68% (95%CI: 58–77%), p = 0.01]. European ancestry among individuals that declared all grandparents born in Europe was 91% (95%CI: 88–94%) compared to 54% (95%CI: 51–57%) among those with no European grandparents (p<0.001). Our results demonstrate the range of variation in genetic ancestry among Argentine individuals from different regions in the country, highlighting the importance of taking this variation into account in genetic association and admixture mapping studies in this population.

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<![CDATA[New Insights into the Lake Chad Basin Population Structure Revealed by High-Throughput Genotyping of Mitochondrial DNA Coding SNPs]]> https://www.researchpad.co/article/5989da10ab0ee8fa60b79630

Background

Located in the Sudan belt, the Chad Basin forms a remarkable ecosystem, where several unique agricultural and pastoral techniques have been developed. Both from an archaeological and a genetic point of view, this region has been interpreted to be the center of a bidirectional corridor connecting West and East Africa, as well as a meeting point for populations coming from North Africa through the Saharan desert.

Methodology/Principal Findings

Samples from twelve ethnic groups from the Chad Basin (n = 542) have been high-throughput genotyped for 230 coding region mitochondrial DNA (mtDNA) Single Nucleotide Polymorphisms (mtSNPs) using Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight (MALDI-TOF) mass spectrometry. This set of mtSNPs allowed for much better phylogenetic resolution than previous studies of this geographic region, enabling new insights into its population history. Notable haplogroup (hg) heterogeneity has been observed in the Chad Basin mirroring the different demographic histories of these ethnic groups. As estimated using a Bayesian framework, nomadic populations showed negative growth which was not always correlated to their estimated effective population sizes. Nomads also showed lower diversity values than sedentary groups.

Conclusions/Significance

Compared to sedentary population, nomads showed signals of stronger genetic drift occurring in their ancestral populations. These populations, however, retained more haplotype diversity in their hypervariable segments I (HVS-I), but not their mtSNPs, suggesting a more ancestral ethnogenesis. Whereas the nomadic population showed a higher Mediterranean influence signaled mainly by sub-lineages of M1, R0, U6, and U5, the other populations showed a more consistent sub-Saharan pattern. Although lifestyle may have an influence on diversity patterns and hg composition, analysis of molecular variance has not identified these differences. The present study indicates that analysis of mtSNPs at high resolution could be a fast and extensive approach for screening variation in population studies where labor-intensive techniques such as entire genome sequencing remain unfeasible.

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<![CDATA[The Q2 Mitochondrial Haplogroup in Oceania]]> https://www.researchpad.co/article/5989da86ab0ee8fa60b9c33e

Many details surrounding the origins of the peoples of Oceania remain to be resolved, and as a step towards this we report seven new complete mitochondrial genomes from the Q2a haplogroup, from Papua New Guinea, Fiji and Kiribati. This brings the total to eleven Q2 genomes now available. The Q haplogroup (that includes Q2) is an old and diverse lineage in Near Oceania, and is reasonably common; within our sample set of 430, 97 are of the Q haplogroup. However, only 8 are Q2, and we report 7 here. The tree with all complete Q genomes is proven to be minimal. The dating estimate for the origin of Q2 (around 35 Kya) reinforces the understanding that humans have been in Near Oceania for tens of thousands of years; nevertheless the Polynesian maternal haplogroups remain distinctive. A major focus now, with regard to Polynesian ancestry, is to address the differences and timing of the ‘Melanesian’ contribution to the maternal and paternal lineages as people moved further and further into Remote Oceania. Input from other fields such as anthropology, history and linguistics is required for a better understanding and interpretation of the genetic data.

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<![CDATA[A Longitudinal Analysis of Mosquito Net Ownership and Use in an Indigenous Batwa Population after a Targeted Distribution]]> https://www.researchpad.co/article/5989da47ab0ee8fa60b8bfec

Major efforts for malaria prevention programs have gone into scaling up ownership and use of insecticidal mosquito nets, particularly in sub-Saharan Africa where the malaria burden is high. Socioeconomic inequities in access to long lasting insecticidal nets (LLINs) are reduced with free distributions of nets. However, the relationship between social factors and retention of nets after a free distribution has been less studied, particularly using a longitudinal approach. Our research aimed to estimate the ownership and use of LLINs, and examine the determinants of LLIN retention, within an Indigenous Batwa population after a free LLIN distribution. Two LLINs were given free of charge to each Batwa household in Kanungu District, Uganda in November 2012. Surveyors collected data on LLIN ownership and use through six cross-sectional surveys pre- and post-distribution. Household retention, within household access, and individual use of LLINs were assessed over an 18-month period. Socioeconomic determinants of household retention of LLINs post-distribution were modelled longitudinally using logistic regression with random effects. Direct house-to-house distribution of free LLINs did not result in sustainable increases in the ownership and use of LLINs. Three months post-distribution, only 73% of households owned at least one LLIN and this period also saw the greatest reduction in ownership compared to other study periods. Eighteen-months post distribution, only a third of households still owned a LLIN. Self-reported age-specific use of LLINs was generally higher for children under five, declined for children aged 6–12, and was highest for older adults aged over 35. In the model, household wealth was a significant predictor of LLIN retention, controlling for time and other variables. This research highlights on-going socioeconomic inequities in access to malaria prevention measures among the Batwa in southwestern Uganda, even after free distribution of LLINs, and provides critical information to inform local malaria programs on possible intervention entry-points to increase access and use among this marginalized population.

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<![CDATA[Cultural Diffusion Was the Main Driving Mechanism of the Neolithic Transition in Southern Africa]]> https://www.researchpad.co/article/5989da61ab0ee8fa60b90f06

It is well known that the Neolithic transition spread across Europe at a speed of about 1 km/yr. This result has been previously interpreted as a range expansion of the Neolithic driven mainly by demic diffusion (whereas cultural diffusion played a secondary role). However, a long-standing problem is whether this value (1 km/yr) and its interpretation (mainly demic diffusion) are characteristic only of Europe or universal (i.e. intrinsic features of Neolithic transitions all over the world). So far Neolithic spread rates outside Europe have been barely measured, and Neolithic spread rates substantially faster than 1 km/yr have not been previously reported. Here we show that the transition from hunting and gathering into herding in southern Africa spread at a rate of about 2.4 km/yr, i.e. about twice faster than the European Neolithic transition. Thus the value 1 km/yr is not a universal feature of Neolithic transitions in the world. Resorting to a recent demic-cultural wave-of-advance model, we also find that the main mechanism at work in the southern African Neolithic spread was cultural diffusion (whereas demic diffusion played a secondary role). This is in sharp contrast to the European Neolithic. Our results further suggest that Neolithic spread rates could be mainly driven by cultural diffusion in cases where the final state of this transition is herding/pastoralism (such as in southern Africa) rather than farming and stockbreeding (as in Europe).

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<![CDATA[Population Genetic Structure and Origins of Native Hawaiians in the Multiethnic Cohort Study]]> https://www.researchpad.co/article/5989d9d6ab0ee8fa60b66071

The population genetic structure of Native Hawaiians has yet to be comprehensively studied, and the ancestral origins of Polynesians remain in question. In this study, we utilized high-resolution genome-wide SNP data and mitochondrial genomes of 148 and 160 Native Hawaiians, respectively, to characterize their population structure of the nuclear and mitochondrial genomes, ancestral origins, and population expansion. Native Hawaiians, who self-reported full Native Hawaiian heritage, demonstrated 78% Native Hawaiian, 11.5% European, and 7.8% Asian ancestry with 99% belonging to the B4 mitochondrial haplogroup. The estimated proportions of Native Hawaiian ancestry for those who reported mixed ancestry (i.e. 75% and 50% Native Hawaiian heritage) were found to be consistent with their self-reported heritage. A significant proportion of Melanesian ancestry (mean = 32%) was estimated in 100% self-reported Native Hawaiians in an ADMIXTURE analysis of Asian, Melanesian, and Native Hawaiian populations of K = 2, where K denotes the number of ancestral populations. This notable proportion of Melanesian admixture supports the “Slow-Boat” model of migration of ancestral Polynesian populations from East Asia to the Pacific Islands. In addition, approximately 1,300 years ago a single, strong expansion of the Native Hawaiian population was estimated. By providing important insight into the underlying population structure of Native Hawaiians, this study lays the foundation for future genetic association studies of this U.S. minority population.

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<![CDATA[Patterns of Admixture and Population Structure in Native Populations of Northwest North America]]> https://www.researchpad.co/article/5989dae1ab0ee8fa60bbc094

The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas.

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<![CDATA[Swedish Population Substructure Revealed by Genome-Wide Single Nucleotide Polymorphism Data]]> https://www.researchpad.co/article/5989dac9ab0ee8fa60bb36b1

The use of genome-wide single nucleotide polymorphism (SNP) data has recently proven useful in the study of human population structure. We have studied the internal genetic structure of the Swedish population using more than 350,000 SNPs from 1525 Swedes from all over the country genotyped on the Illumina HumanHap550 array. We have also compared them to 3212 worldwide reference samples, including Finns, northern Germans, British and Russians, based on the more than 29,000 SNPs that overlap between the Illumina and Affymetrix 250K Sty arrays. The Swedes - especially southern Swedes - were genetically close to the Germans and British, while their genetic distance to Finns was substantially longer. The overall structure within Sweden appeared clinal, and the substructure in the southern and middle parts was subtle. In contrast, the northern part of Sweden, Norrland, exhibited pronounced genetic differences both within the area and relative to the rest of the country. These distinctive genetic features of Norrland probably result mainly from isolation by distance and genetic drift caused by low population density. The internal structure within Sweden (FST = 0.0005 between provinces) was stronger than that in many Central European populations, although smaller than what has been observed for instance in Finland; importantly, it is of the magnitude that may hamper association studies with a moderate number of markers if cases and controls are not properly matched geographically. Overall, our results underline the potential of genome-wide data in analyzing substructure in populations that might otherwise appear relatively homogeneous, such as the Swedes.

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<![CDATA[Helicobacter pylori Genotyping from American Indigenous Groups Shows Novel Amerindian vacA and cagA Alleles and Asian, African and European Admixture]]> https://www.researchpad.co/article/5989db00ab0ee8fa60bc668f

It is valuable to extend genotyping studies of Helicobacter pylori to strains from indigenous communities across the world to better define adaption, evolution, and associated diseases. We aimed to genetically characterize both human individuals and their infecting H. pylori from indigenous communities of Mexico, and to compare them with those from other human groups. We studied individuals from three indigenous groups, Tarahumaras from the North, Huichols from the West and Nahuas from the center of Mexico. Volunteers were sampled at their community site, DNA was isolated from white blood cells and mtDNA, Y-chromosome, and STR alleles were studied. H. pylori was cultured from gastric juice, and DNA extracted for genotyping of virulence and housekeeping genes. We found Amerindian mtDNA haplogroups (A, B, C, and D), Y-chromosome DYS19T, and Amerindian STRs alleles frequent in the three groups, confirming Amerindian ancestry in these Mexican groups. Concerning H.pylori cagA phylogenetic analyses, although most isolates were of the Western type, a new Amerindian cluster neither Western nor Asian, was formed by some indigenous Mexican, Colombian, Peruvian and Venezuelan isolates. Similarly, vacA phylogenetic analyses showed the existence of a novel Amerindian type in isolates from Alaska, Mexico and Colombia. With hspA strains from Mexico and other American groups clustered within the three major groups, Asian, African or European. Genotyping of housekeeping genes confirmed that Mexican strains formed a novel Asian-related Amerindian group together with strains from remote Amazon Aborigines. This study shows that Mexican indigenous people with Amerindian markers are colonized with H. pylori showing admixture of Asian, European and African strains in genes known to interact with the gastric mucosa. We present evidence of novel Amerindian cagA and vacA alleles in indigenous groups of North and South America.

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<![CDATA[Why Don't We Ask? A Complementary Method for Assessing the Status of Great Apes]]> https://www.researchpad.co/article/5989daddab0ee8fa60bbaa03

Species conservation is difficult. Threats to species are typically high and immediate. Effective solutions for counteracting these threats, however, require synthesis of high quality evidence, appropriately targeted activities, typically costly implementation, and rapid re-evaluation and adaptation. Conservation management can be ineffective if there is insufficient understanding of the complex ecological, political, socio-cultural, and economic factors that underlie conservation threats. When information about these factors is incomplete, conservation managers may be unaware of the most urgent threats or unable to envision all consequences of potential management strategies. Conservation research aims to address the gap between what is known and what knowledge is needed for effective conservation. Such research, however, generally addresses a subset of the factors that underlie conservation threats, producing a limited, simplistic, and often biased view of complex, real world situations. A combination of approaches is required to provide the complete picture necessary to engage in effective conservation. Orangutan conservation (Pongo spp.) offers an example: standard conservation assessments employ survey methods that focus on ecological variables, but do not usually address the socio-cultural factors that underlie threats. Here, we evaluate a complementary survey method based on interviews of nearly 7,000 people in 687 villages in Kalimantan, Indonesia. We address areas of potential methodological weakness in such surveys, including sampling and questionnaire design, respondent biases, statistical analyses, and sensitivity of resultant inferences. We show that interview-based surveys can provide cost-effective and statistically robust methods to better understand poorly known populations of species that are relatively easily identified by local people. Such surveys provide reasonably reliable estimates of relative presence and relative encounter rates of such species, as well as quantifying the main factors that threaten them. We recommend more extensive use of carefully designed and implemented interview surveys, in conjunction with more traditional field methods.

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<![CDATA[The Economic Value of Environmental Services on Indigenous-Held Lands in Australia]]> https://www.researchpad.co/article/5989da34ab0ee8fa60b859e6

Australians could be willing to pay from $878m to $2b per year for Indigenous people to provide environmental services. This is up to 50 times the amount currently invested by government. This result was derived from a nationwide survey that included a choice experiment in which 70% of the 927 respondents were willing to contribute to a conservation fund that directly pays Indigenous people to carry out conservation activities. Of these the highest values were found for benefits that are likely to improve biodiversity outcomes, carbon emission reductions and improved recreational values. Of the activities that could be undertaken to provide the services, feral animal control attracted the highest level of support followed by coastal surveillance, weed control and fire management. Respondents' decisions to pay were not greatly influenced by the additional social benefits that can arise for Indigenous people spending time on country and providing the services, although there was approval for reduced welfare payments that might arise.

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