Genetic ancestry of participants in the National Children’s Study

Background

The National Children’s Study (NCS) is a prospective epidemiological study in the USA tasked with identifying a nationally representative sample of 100,000 children, and following them from their gestation until they are 21 years of age. The objective of the study is to measure environmental and genetic influences on growth, development, and health. Determination of the ancestry of these NCS participants is important for assessing the diversity of study participants and for examining the effect of ancestry on various health outcomes.

Results

We estimated the genetic ancestry of a convenience sample of 641 parents enrolled at the 7 original NCS Vanguard sites, by analyzing 30,000 markers on exome arrays, using the 1000 Genomes Project superpopulations as reference populations, and compared this with the measures of self-reported ethnicity and race. For 99% of the individuals, self-reported ethnicity and race agreed with the predicted superpopulation. NCS individuals self-reporting as Asian had genetic ancestry of either South Asian or East Asian groups, while those reporting as either Hispanic White or Hispanic Other had similar genetic ancestry. Of the 33 individuals who self-reported as Multiracial or Non-Hispanic Other, 33% matched the South Asian or East Asian groups, while these groups represented only 4.4% of the other reported categories.

Conclusions

Our data suggest that self-reported ethnicity and race have some limitations in accurately capturing Hispanic and South Asian populations. Overall, however, our data indicate that despite the complexity of the US population, individuals know their ancestral origins, and that self-reported ethnicity and race is a reliable indicator of genetic ancestry.     

Towards practical privacy-preserving genome-wide association study

Background

The deployment of Genome-wide association studies (GWASs) requires genomic information of a large population to produce reliable results. This raises significant privacy concerns, making people hesitate to contribute their genetic information to such studies.

Results

We propose two provably secure solutions to address this challenge: (1) a somewhat homomorphic encryption (HE) approach, and (2) a secure multiparty computation (MPC) approach. Unlike previous work, our approach does not rely on adding noise to the input data, nor does it reveal any information about the patients. Our protocols aim to prevent data breaches by calculating the χ² statistic in a privacy-preserving manner, without revealing any information other than whether the statistic is significant or not. Specifically, our protocols compute the χ² statistic, but only return a yes/no answer, indicating significance. By not revealing the statistic value itself but only the significance, our approach thwarts attacks exploiting statistic values. We significantly increased the efficiency of our HE protocols by introducing a new masking technique to perform the secure comparison that is necessary for determining significance.

Conclusions

We show that full-scale privacy-preserving GWAS is practical, as long as the statistics can be computed by low degree polynomials. Our implementations demonstrated that both approaches are efficient. The secure multiparty computation technique completes its execution in approximately 2 ms for data contributed by one million subjects.

     

Variability in Size of the Nuclear Genome in Pygmy Wood Mouse <Emphasis Type="Italic">Sylvaemus uralensis</Emphasis> (Rodentia,Muridae)

Earlier, in an integral genetic study, the Asian and European races were distinguished within the species Sylvaemus uralensis (pygmy wood mouse) and the European race was divided into the East European and South European forms. Each of these groups differed from the others, in particular, in the quantity of the centromeric heterochromatin in karyotypes of the animals. To establish the pattern of its changes in S. uralensis, in the present study the DNA content in splenocyte nuclei in all races and forms of pygmy wood mice was assessed using DNA flow cytometry. The heterochromatin amount in karyotypes and genome size were shown to be correlated. The East European chromosomal race of S. uralensis (Central Chernozem and Non-Chernozem regions of Russia, Crimea Peninsula, Middle Volga region, and Southern Ural) and the Asian race of this species (East Kazakhstan, Uzbekistan, and East Turkmenistan), which have respectively the highest and the lowest amounts of centromeric heterochromatin in the karyotype, exhibit the greatest difference in the DNA content in the genome. On average, the difference is approximately 8% in males and 6.7% in females; in both cases, the ranges of variability were distinctly different. Against the general background of the trait variation, the Asian race, whose members have the smallest DNA amount in their cells, looks homogeneous. The genome of the South European chromosomal form of S. uralensis (Caucasus, Transcaucasia, Carpathians, and Balkan Peninsula), which exhibits an intermediate content of the centromeric heterochromatin in the karyotype, is smaller that the genome of the East European race (by 3.2% in the group of males and by 1.9%, in the group of females), but larger than that of the Asian race (by 5% in either sex). Thus, the variability of size of centromeric C-blocks in pygmy wood mouse is likely to be associated with elimination (or, conversely, an increase in the amount) of the genetically inert chromatin. It is suggested that a significant contribution to the variability of genome size in S. uralensis is made by heterochromosomes, or, more precisely, their variable regions, which seem to be largely heterochromatic.     

Assessing the distribution and conservation status of a long-horned beetle with species distribution models

Data shortfalls on species distribution affect species differently, but it is frequent among insects. Species distribution models (SDMs) are important tools to fill biogeographic deficits and provide support for practical conservation actions, particularly for cryptic or hard to survey species. We employed SDMs to evaluate one such species, the long-horned beetle (Macrodontia cervicornis), listed as ‘vulnerable’ in the IUCN’s Red List of Threatened Species. Given new distributional data for this species, we applied three different SDMs to: (1) provide the first assessment of this species’ distribution and potential dispersal routes; (2) evaluate the effectiveness of the current South American protected areas system for its conservation; and (3) discuss its potential distribution, as well as historical, biogeographical, and taxonomic issues related to it. Our models reached fair True Skilled Statistics values (TSS > 0.5), with the core area for M. cervicornis located in the Amazon forest, although suitable areas were also predicted along the Atlantic forest. Areas in the dry diagonal South American corridor (dry biomes of Cerrado, Caatinga, and Pampas) in South America were not predicted as suitable. The preference of M. cervicornis for humid areas with high temperatures may guarantee a better physiological control for dehydration, considering that large insects are more affected by water loss. In general, approximately 15 % of the distribution of M. cervicornis is in humid protected areas. The disconnected distribution of the long-horned beetle may be an indication of the existence of cryptic species under the same classification. We suggest that similar studies with other insect groups (e.g. butterflies, bees) should be conducted to properly assess their distributions, conservation status, and responses to hot-humid gradients throughout South America.     

Southeastern U.S.A. continental shelf respiratory rates revisited

Respiratory rates on the U. S. southeastern continental shelf have been estimated several times by different investigators, most recently by Jiang et al. (Biogeochemistry 98:101–113, 2010) who report lower mean rates than were found in earlier work and attribute the differences to analytical error in all methods used in earlier studies. The differences are, instead, attributable to the differences in the geographical scope of the studies. The lower estimates of regional organic carbon flux of Jiang et al. (Biogeochemistry 98:101–113, 2010) are a consequence of their extrapolation of data from a small portion of the shelf to the entire South Atlantic Bight. This comment examines the methodologies used as well as the variability of respiratory rates in this region over space and time.     

Invasive <Emphasis Type="Italic">Tamarix</Emphasis> (Tamaricaceae) in South Africa: current research and the potential for biological control

Most species of Tamarix originate in Eurasia and at least five species have become invasive around the world, including South Africa. However, T. usneoides is indigenous to southern Africa, where the potential for biological control of the invasive species is being investigated. Recent research on the invasive species is reviewed here with particular reference to these South African biocontrol efforts. The successful biological control programme against invasive Tamarix in the USA, using several species of “Tamarisk beetle”, is being used as a guide for the South African research. The South African programme is complicated by firstly, the presence of the indigenous T. usneoides which raises the precision of host-specificity required, and secondly, the introduced and indigenous Tamarix have a high intrinsic value for phytoremediation of mine tailings dams in South Africa. The phylogenetic proximity of these Tamarix species to each other has contributed to this challenge, which has nevertheless been successfully addressed by molecular techniques used to separate the species. In addition, classical morphological techniques have been used to separate the Tamarisk beetles, so that now they can generally be matched to Tamarix tree species. Overall, it is concluded that given the broad knowledge now available on the ecology and identity of both the trees and their biocontrol agents, the prospects for successful biological control of Tamarix in South Africa are good.     

In stark contrast to widespread declines along the Scotia Arc,a survey of the South Sandwich Islands finds a robust seabird community

The South Sandwich Islands, in the South Atlantic Ocean, are a major biological hot spot for penguins and other seabirds, but their remoteness and challenging coastlines preclude regular biological censuses. Here we report on an extensive survey of the South Sandwich Islands, the first since the late 1990s, which was completed through a combination of direct counting, GPS mapping, and interpretation of high-resolution commercial satellite imagery. We find that the South Sandwich Islands host nearly half of the world’s Chinstrap Penguin (Pygoscelis antarctica) population (1.3 million breeding pairs), as well as c. 95,000 breeding pairs of Macaroni Penguins (Eudyptes chrysolophus), and several thousand breeding pairs of Gentoo Penguins (Pygoscelis papua). Despite being at the northern edge of their breeding range, we found an unexpectedly large (≥125,000 breeding pairs) population of Adélie Penguins (Pygoscelis adeliae). Additionally, we report that nearly 1900 pairs of Southern Giant Petrels (Macronectes giganteus) breed in the South Sandwich Islands, 4 % of the global population, almost all of which are found on Candlemas Island. We find that the South Sandwich Islands have not experienced the same changes in penguin abundance and distribution as the rest of the Scotia Arc and associated portions of the western Antarctic Peninsula. This discovery adds important context to the larger conversation regarding changes to penguin populations in the Southern Ocean.     

Used for ill; used for good: a century of collecting data on race in South Africa

Abstract

Data on race have been collected in South African censuses for a century. We examine the role played by the census in solidifying race as a social statistic and show that, in contrast to the majority of situations, operational and legislative factors rendered the census largely unimportant as a vehicle for doing this. Since 1994, race has been entirely self-reported and not subject to state reinterpretation. We examine the implications of this for future data collection exercises and caution against reifying race as a predictor of social outcomes in post-apartheid South Africa, and argue for its gradual phasing out.     

Ecogeographical Variation in Skull Shape of South-American Canids: Abiotic or Biotic Processes?

Species morphological changes can be mutually influenced by environmental or biotic factors, such as competition. South American canids represent a quite recent radiation of taxa that evolved forms very disparate in phenotype, ecology and behaviour. Today, in the central part of South America there is one dominant large species (the maned wolf, Chrysocyon brachyurus) that directly influence sympatric smaller taxa via interspecific killing. Further south, three species of similar sized foxes (Lycalopex spp.) share the same habitats. Such unique combination of taxa and geographic distribution makes South American dogs an ideal group to test for the simultaneous impact of climate and competition on phenotypic variation. Using geometric morphometrics, we quantified skull size and shape of 431 specimens belonging to the eight extant South American canid species: Atelocynus microtis, Cerdocyon thous, Ch. brachyurus, Lycalopex culpaeus, L. griseus, L. gymnocercus, L. vetulus and Speothos venaticus. South American canids are significantly different in both skull size and shape. The hypercarnivorous bush dog is mostly distinct in shape from all the other taxa while a degree of overlap in shape—but not size—occurs between species of the genus Lycalopex. Both climate and competition impacts interspecific morphological variation. We identified climatic adaptations as the main driving force of diversification for the South American canids. Competition has a lower degree of impact on their skull morphology although it might have played a role in the past, when canid community was richer in morphotypes.     

Evaluating the efficacy of <Emphasis Type="Italic">Hypogeococcus</Emphasis> sp. as a biological control agent of the cactaceous weed <Emphasis Type="Italic">Cereus jamacaru</Emphasis> in South Africa

We evaluated the efficacy of Hypogeococcus sp. (Hemiptera: Pseudococcidae) as a biological control agent of the cactaceous weed Cereus jamacaru De Candolle (Queen of the Night cactus) in South Africa. This weed has been described as being under complete biological control due to the action of Hypogeococcus sp., although no formal post-release evaluation had been conducted prior to this study. Biological control was associated with significant reductions in fruiting, plant survival and plant densities, while plant population age structures were negatively affected. Weed populations infected by Hypogeococcus sp. were typified by low or non-existent recruitment and are expected to diminish with time. Populations where Hypogeococcus sp. was absent displayed extensive recruitment, and are predicted to expand or self-replace, if left unchecked. These data indicate that Hypogeococcus sp. has a significant negative effect on C. jamacaru at the individual plant and population level, and given sufficient time provides complete biological control over this weed in South Africa.     

Identification and genetic diversity of two invasive <Emphasis Type="Italic">Pissodes</Emphasis> spp. Germar (Coleoptera: Curculionidae) in their introduced range in the southern hemisphere

During the first half of the twentieth century, two accidental cases of introduction of Pissodes weevils were recorded from the southern hemisphere. The weevils in South Africa were identified as the deodar weevil (Pissodes nemorensis) and those in South America as the small banded pine weevil (Pissodes castaneus). Wide distribution of the two species in their invasive range, general difficulty in identifying some Pissodes spp., and the varying feeding and breeding behaviours of the species in South Africa has necessitated better evidence of species identity and genetic diversity of both species and population structure of the species in South Africa. Barcoding and the Jerry-to-Pat region of the COI gene were investigated. Morphometric data of the South African species was analysed. Our results confirmed the introduction of only one Pissodes species of North American origin to South Africa. However, this species is not P. nemorensis, but an unrecognized species of the P. strobi complex or a hybrid between P. strobi and P. nemorensis. Only P. castaneus, of European origin, was identified from South America. We identified ten mitochondrial DNA haplotypes from South Africa with evidence of moderate genetic structure among geographic populations. Terminal leader and bole-feeding weevils did not differ at the COI locus. A single haplotype was identified from populations of P. castaneus in South America. Results of the present study will have implications on quarantine, research and management of these insect species.     

Long-term variability of meiobenthos: value,synopsis, hypothesis generation and predictive modelling

Few long-term data sets exist for meiofauna. Such data sets are expensive to collect, sort and identify; continuous meiofauna data for a period of greater than two years are limited to one site in Belgium (7 yrs) and two sites (one mud, one sand) in South Carolina, USA (11 yrs). The Belgian study concentrates on benthic copepod abundances whereas data from South Carolina includes major taxa and benthic copepods as well as 4 years of concurrent macrofauna abundance and 3 years of nematode species abundances. In South Carolina, the variance associated with meiofaunal abundance had 6 or 12 month recurrent cycles. Similar analyses on 4 years of macrofauna from the same 2 sites indicated the same cyclicity: one year. Seasonality of the South Carolina major taxa and the 6 most abundant mud copepod species was pronounced at the mud site, but absent or less pronounced at the sand site. Similar results were also found for the nematode species over three years. Variability in meiofaunal abundance was greater year-to-year than within a year. Many such long-term data sets are analysed and abandoned. Herewith, I use our long-term results to hypothesize the causes of the high temporal variance in mud and the lower temporal variance in sand. Is it because the mud fauna is controlled by seasonal inputs of natant predators while at the hydrodynamically active sand site temporal variability is homogenized by constant physical activity? By appropriate statistical modelling long-term data sets can also be used to assess the appropriateness of the sampling schedule (spatial and temporal) and as a predictor of future trends.     

<Emphasis Type="Italic">Tamarix</Emphasis> (Tamaricaceae) hybrids: the dominant invasive genotype in southern Africa

Hybridization is regarded as a rapid mechanism for increasing genetic variation that can potentially enhance invasiveness. Tamarix hybrids appear to be the dominant genotypes in their invasions. Exotic Tamarix are declared invasive in South Africa and the exotic T. chinensis and T. ramosissima are known to hybridize between themselves, and with the indigenous T. usneoides. However, until now, it was not known which species or hybrid is the most prevalent in the invasion. With a biocontrol programme being considered as a way of suppressing the alien Tamarix populations, it is important to document the population genetic dynamics of all species in the region. This investigation sought to identify Tamarix species in southern Africa and their hybrids, describe their population structure, and reveal the geographic origin of the invasive species. To achieve this, nuclear Internal Transcribed Spacer (ITS) sequence data and the multilocus Amplified Fragment Length Polymorphisms (AFLPs) markers were used. Phylogenetic analysis and population genetic structure confirmed the presence of three species in South Africa (T. chinensis, T. ramosissima and T. usneoides) with their hybrids. The indigenous T. usneoides is clearly genetically distant from the alien species T. chinensis and T. ramosissima. Interestingly, the Tamarix infestation in South Africa is dominated (64.7 %) by hybrids between T. chinensis and T. ramosissima. The exotic species match their counterparts from their places of origin in Eurasia, as well as those forming part of the invasion in the US.     

Taxonomy and First Records of Two <Emphasis Type="Italic">Megaselia</Emphasis> Rondani Species (Diptera: Phoridae) Preying upon Eggs of <Emphasis Type="Italic">Phyllomedusa iheringii</Emphasis> Boulenger (Anura: Phyllomedusidae)

Non-aquatic reproductive modes have evolved among frogs possibly favored by some advantages such as the avoidance of aquatic predators. These reproductive modes, however, make the egg clutches susceptible to terrestrial predators, among which Diptera larvae are some of the most harmful. The present work reports the predation by phorid flies of 22 egg clutches of Phyllomedusa iheringii Boulenger in the South of Brazil. Phorid specimens were identified as Megaselia bruchiana (Borgmeier & Schmitz) and Megaselia necrophaga (Enderlein), species that were reported previously to be associated with ants and dead beetles, respectively. Frog-feeding in these species is hypothesized to be use of an alternative seasonal food source. We amend the diagnoses of both Megaselia species and provide new illustrations to facilitate their identification. We also describe the male of M. bruchiana for the first time and associate males with females of both species.     

Physical violence against intimate partners and related exposures to violence among South African men

Background

Despite high rates of intimate partner violence in South Africa, there have been no national studies of men''s perpetration of violence against female partners.

Methods

We analyzed data from the South Africa Stress and Health Study, a cross-sectional, nationally representative study, specifically examining data for men who had ever been married or had ever cohabited with a female partner. We calculated the prevalence of physical violence against intimate female partners and used logistic regression to examine associations with physical abuse during childhood and exposure to parental and community violence.

Results

A total of 834 male participants in the South Africa Stress and Health Study met the study criteria. Of these, 27.5% reported using physical violence against their current or most recent female partner during their current or most recent marriage or cohabiting relationship. Crude odds ratios (ORs) and 95% confidence intervals (CIs) indicated significant associations between perpetration of violence against an intimate partner and witnessing parental violence (OR 3.91, 95% CI 2.66–5.73) or experiencing physical abuse during childhood (OR 3.24, 95% CI 2.27–4.63), but not exposure to community violence (OR 1.29, 95% CI 0.88–1.88). The 2 significant associations persisted in adjusted analyses: OR 3.22 (95% CI 1.94–5.33) for witnessing parental violence and OR 1.73 (95% CI 1.07–2.79) for experiencing physical abuse during childhood.

Interpretation

We found a high prevalence of physical violence perpetrated by men against their intimate partners. Men who experienced physical abuse during childhood or were exposed to parental violence were at the greatest risk.Most research about men''s perpetration of violence against female intimate partners has concentrated on elucidating the factors that put women at risk for experiencing such violence and identifying the related service needs. Less work has been done to investigate the factors affecting men''s risk of perpetrating violence against women. Such work is needed to inform development of empirically based public health programs to reduce men''s use of such violence. Intimate partner violence is of pandemic proportions, with global estimates indicating that 15% to 75% of women have experienced such abuse.^1,2 Such violence may confer grave health consequences, including transmission of HIV/AIDS.³The overwhelming majority of research on violence against intimate partners perpetrated by men has been conducted in Western countries, with the focus on men at high risk for such activity (e.g., prisoners, people enrolled in intervention programs for batterers).^4,5 This work has highlighted the importance of exposure to violence early in life (e.g., witnessing parental violence, experiencing child abuse) in predicting perpetration of violence against a partner during adulthood.⁶ Recently, the potential relations between community violence and men''s perpetration of violence against intimate partners have also been examined.⁷Fewer studies have been done in developing nations, but several notable investigations have recently assessed men''s perpetration of violence against intimate partners in South Africa, specifically in Eastern Cape and Cape Town. Two of these studies have indicated high rates of violence against intimate partners: 31.8% in Eastern Cape⁸ and 42.3% in Cape Town.⁹ The extent to which these findings reflect national rates is unknown. Furthermore, work with both men and women in South Africa has demonstrated strong relations between violence (men''s perpetration and women''s victimization) and higher rates of sexually risky behaviours.^3,8 Associations between women''s experience as victims of intimate partner violence and HIV infection have also been documented.³ These data strongly suggest that men''s perpetration of violence against intimate partners is common in South Africa and that it may play an important role in this nation''s HIV epidemic,^3,8 which currently ranks highest in the world with respect to the number of people living with HIV.¹⁰In the study reported here, we sought to build upon prior work by using a national sample of South African men to examine the prevalence of physical violence perpetrated by men against their female intimate partners and potential violence-related risk factors (i.e., exposure to parental violence, experience of abuse in childhood and exposure to community violence).     

Impact of participant and interventionist race concordance on weight loss outcomes

Objective:

We have previously shown that racial composition of behavioral intervention groups does not affect achieved weight loss. However, it is unclear if the race of the interventionist affects intervention outcomes. The objective of this analysis is to estimate the impact of race concordance between participant and interventionist on weight change in the initial weight loss phase (phase I) of the Weight Loss Maintenance trial (WLM).

Design and Methods:

A total of 1,685 overweight or obese adults (BMI 25‐45 kg/m²) who were taking medication for hypertension and/or dyslipidemia participated in phase I of the WLM trial. All participants received a 6‐month intensive behavioral intervention in groups of 15‐20 facilitated by a trained interventionist. The main outcome is change in weight at 6 months.

Results:

Participants were on average 55 years of age, 67% female and 44% African American (AA). Three of seventeen interventionists were AA, 14 were non‐AA. Seventy‐three percent of participants shared race concordance with the interventionist. There was a small but statistically significant difference in weight change of participants who were the same race as the interventionist (?5.84 kg, s.e. 0.17) as compared with those who were not race concordant (?5.04 kg, s.e. 0.33), a difference of 0.8 kg, (P = 0.04). The impact of concordance on weight change differed by race (i.e., interaction of race and concordance was significant, P = 0.02).

Conclusions:

In a post hoc analysis of a group‐based behavioral intervention, race concordance for non‐AA participants was associated with slightly greater weight loss. Race concordance was not associated with weight loss for AA participants.

     

A review of the palm genus <Emphasis Type="Italic">Acrocomia</Emphasis>: Neotropical green gold

The genus Acrocomia, popularly known as macaw palm or macaúba, occurs in savanna areas and open forests of tropical America, with distribution from Central to southern South America. They are important oleaginous palm trees, due to their role in ecosystems and local economies and their potential for biofuel production and vegetable oil. Although the taxonomy of the genus is not resolved because of observed phenotypic diversity in A. aculeata (Jacq.) Lodd. ex Mart., there are several conflicting treatments. Some authors recognize three caulescent spp. occurring in South America: A. aculeata, A. intumescens Drude, and A. totai Mart, although a new one was described recently—Acrocomia corumbaensis. Because some Latin American governments want to expand production of macaw palm in their territory as raw material for agro-energy, several groups have been encouraged to study this genus, focusing on the production of biodiesel, seed germination, phenotypic aspects, and genetic diversity. The goal of this review is to compile key information available in the literature and herbarium data, focusing on South American populations of the genus.     

Racial/ethnic differences in the prevalence of gestational diabetes mellitus and maternal overweight and obesity,by Nativity,Florida, 2004‐2007

Objective:

We examined the risk of gestational diabetes mellitus (GDM) among foreign‐born and U.S.‐born mothers by race/ethnicity and BMI category.

Design and Method:

We used 2004‐2007 linked birth certificate and maternal hospital discharge data of live, singleton deliveries in Florida to compare GDM risk among foreign‐born and U.S.‐born mothers by race/ethnicity and BMI category. We examined maternal BMI and controlled for maternal age, parity, and height.

Results:

Overall, 22.4% of the women in our study were foreign born. The relative risk (RR) of GDM among women who were overweight or obese (BMI ≥ 25.0 kg m^?2) was higher than among women with normal BMI (18.5‐24.9 kg m^?2) regardless of nativity, ranging from 1.3 (95% confidence interval (CI) = 1.0, 1.9) to 3.8 (95% CI = 2.1, 7.2).Foreign‐born women also had a higher GDM risk than U.S.‐born women, with RR ranging from 1.1 (95% CI = 1.1, 1.2) to 2.1 (95% CI = 1.4, 3.1). This finding was independent of BMI, age, parity, and height for all racial/ethnicity groups.

Conclusions:

Although we found differences in age, parity, and height by nativity, these differences did not substantially reduce the increased risk of GDM among foreign‐born mothers. Health practitioners should be aware of and have a better understanding of how race/ethnicity and nativity can affect women with a high risk of GDM. Although BMI is a major risk factor for GDM, it does not appear to be associated with race/ethnicity or nativity.