Climate Change and American Bullfrog Invasion: What Could We Expect in South America?

Background

Biological invasion and climate change pose challenges to biodiversity conservation in the 21^st century. Invasive species modify ecosystem structure and functioning and climatic changes are likely to produce invasive species'' range shifts pushing some populations into protected areas. The American Bullfrog (Lithobates catesbeianus) is one of the hundred worst invasive species in the world. Native from the southeast of USA, it has colonized more than 75% of South America where it has been reported as a highly effective predator, competitor and vector of amphibian diseases.

Methodology/Principal Findings

We modeled the potential distribution of the bullfrog in its native range based on different climate models and green-house gases emission scenarios, and projected the results onto South America for the years of 2050 and 2080. We also overlaid projected models onto the South American network of protected areas. Our results indicate a slight decrease in potential suitable area for bullfrog invasion, although protected areas will become more climatically suitable. Therefore, invasion of these sites is forecasted.

Conclusion/Significance

We provide new evidence supporting the vulnerability of the Atlantic Forest Biodiversity Hotspot to bullfrog invasion and call attention to optimal future climatic conditions of the Andean-Patagonian forest, eastern Paraguay, and northwestern Bolivia, where invasive populations have not been found yet. We recommend several management and policy strategies to control bullfrog invasion and argue that these would be possible if based on appropriate articulation among government agencies, NGOs, research institutions and civil society.     

Genetic Structure,Diversity and Long Term Viability of a Medicinal Plant,Nothapodytes nimmoniana Graham. (Icacinaceae), in Protected and Non-Protected Areas in the Western Ghats Biodiversity Hotspot

Background and Question

The harvesting of medicinal plants from wild sources is escalating in many parts of the world, compromising the long-term survival of natural populations of medicinally important plants and sustainability of sources of raw material to meet pharmaceutical industry needs. Although protected areas are considered to play a central role in conservation of plant genetic resources, the effectiveness of protected areas for maintaining medicinal plant populations subject to intense harvesting pressure remain largely unknown. We conducted genetic and demographic studies of Nothapodytes nimmoniana Graham, one of the extensively harvested medicinal plant species in the Western Ghats biodiversity hotspot, India to assess the effectiveness of protected areas in long-term maintenance of economically important plant species.

Methodology/Principal Findings

The analysis of adults and seedlings of N. nimmoniana in four protected and four non-protected areas using 7 nuclear microsatellite loci revealed that populations that are distributed within protected areas are subject to lower levels of harvesting and maintain higher genetic diversity (H_e = 0.816, H_o = 0.607, A = 18.857) than populations in adjoining non-protected areas (H_e = 0.781, H_o = 0.511, A = 15.571). Furthermore, seedlings in protected areas had significantly higher observed heterozygosity (H_o = 0.630) and private alleles as compared to seedlings in adjoining non-protected areas (H_o = 0.426). Most populations revealed signatures of recent genetic bottleneck. The prediction of long-term maintenance of genetic diversity using BOTTLESIM indicated that current population sizes of the species are not sufficient to maintain 90% of present genetic diversity for next 100 years.

Conclusions/Significance

Overall, these results highlight the need for establishing more protected areas encompassing a large number of adult plants in the Western Ghats to conserve genetic diversity of economically and medicinally important plant species.     

Evaluation of Outbreak Detection Performance Using Multi-Stream Syndromic Surveillance for Influenza-Like Illness in Rural Hubei Province,China: A Temporal Simulation Model Based on Healthcare-Seeking Behaviors

Background

Syndromic surveillance promotes the early detection of diseases outbreaks. Although syndromic surveillance has increased in developing countries, performance on outbreak detection, particularly in cases of multi-stream surveillance, has scarcely been evaluated in rural areas.

Objective

This study introduces a temporal simulation model based on healthcare-seeking behaviors to evaluate the performance of multi-stream syndromic surveillance for influenza-like illness.

Methods

Data were obtained in six towns of rural Hubei Province, China, from April 2012 to June 2013. A Susceptible-Exposed-Infectious-Recovered model generated 27 scenarios of simulated influenza A (H1N1) outbreaks, which were converted into corresponding simulated syndromic datasets through the healthcare-behaviors model. We then superimposed converted syndromic datasets onto the baselines obtained to create the testing datasets. Outbreak performance of single-stream surveillance of clinic visit, frequency of over the counter drug purchases, school absenteeism, and multi-stream surveillance of their combinations were evaluated using receiver operating characteristic curves and activity monitoring operation curves.

Results

In the six towns examined, clinic visit surveillance and school absenteeism surveillance exhibited superior performances of outbreak detection than over the counter drug purchase frequency surveillance; the performance of multi-stream surveillance was preferable to signal-stream surveillance, particularly at low specificity (Sp <90%).

Conclusions

The temporal simulation model based on healthcare-seeking behaviors offers an accessible method for evaluating the performance of multi-stream surveillance.     

Representation of global and national conservation priorities by Colombia's Protected Area Network

Background

How do national-level actions overlap with global priorities for conservation? Answering this question is especially important in countries with high and unique biological diversity like Colombia. Global biodiversity schemes provide conservation guidance at a large scale, while national governments gazette land for protection based on a combination of criteria at regional or local scales. Information on how a protected area network represents global and national conservation priorities is crucial for finding gaps in coverage and for future expansion of the system.

Methodology/Principal Findings

We evaluated the agreement of Colombia''s protected area network with global conservation priorities, and the extent to which the network reflects the country''s biomes, species richness, and common environmental and physical conditions. We used this information to identify priority biomes for conservation. We find the dominant strategy in Colombia has been a proactive one, allocating the highest proportion of protected land on intact, difficult to access and species rich areas like the Amazon. Threatened and unique areas are disproportionately absent from Colombia''s protected lands. We highlight six biomes in Colombia as conservation priorities that should be considered in any future expansion of Colombia''s protected area network. Two of these biomes have less than 3% of their area protected and more than 70% of their area transformed for human use. One has less than 3% protected and high numbers of threatened vertebrates. Three biomes fall in both categories.

Conclusions

Expansion of Colombia''s Protected Area Network should consider the current representativeness of the network. We indicate six priority biomes that can contribute to improving the representation of threatened species and biomes in Colombia.     

Urbanization Increases Aedes albopictus Larval Habitats and Accelerates Mosquito Development and Survivorship

Introduction

Aedes albopictus is a very invasive and aggressive insect vector that causes outbreaks of dengue fever, chikungunya disease, and yellow fever in many countries. Vector ecology and disease epidemiology are strongly affected by environmental changes. Urbanization is a worldwide trend and is one of the most ecologically modifying phenomena. The purpose of this study is to determine how environmental changes due to urbanization affect the ecology of Aedes albopictus.

Methods

Aquatic habitats and Aedes albopictus larval population surveys were conducted from May to November 2013 in three areas representing rural, suburban, and urban settings in Guangzhou, China. Ae. albopictus adults were collected monthly using BG-Sentinel traps. Ae. albopictus larva and adult life-table experiments were conducted with 20 replicates in each of the three study areas.

Results

The urban area had the highest and the rural area had the lowest number of aquatic habitats that tested positive for Ae. albopictus larvae. Densities in the larval stages varied among the areas, but the urban area had almost two-fold higher densities in pupae and three-fold higher in adult populations compared with the suburban and rural areas. Larvae developed faster and the adult emergence rate was higher in the urban area than in suburban and rural areas. The survival time of adult mosquitoes was also longer in the urban area than it was in suburban and rural areas. Study regions, surface area, water depth, water clearance, surface type, and canopy coverage were important factors associated with the presence of Ae. albopictus larvae.

Conclusions

Urbanization substantially increased the density, larval development rate, and adult survival time of Ae. albopictus, which in turn potentially increased the vector capacity, and therefore, disease transmissibility. Mosquito ecology and its correlation with dengue virus transmission should be compared in different environmental settings.     

Informing species conservation at multiple scales using data collected for marine mammal stock assessments

Background

Conservation planning and the design of marine protected areas (MPAs) requires spatially explicit information on the distribution of ecological features. Most species of marine mammals range over large areas and across multiple planning regions. The spatial distributions of marine mammals are difficult to predict using habitat modelling at ecological scales because of insufficient understanding of their habitat needs, however, relevant information may be available from surveys conducted to inform mandatory stock assessments.

Methodology and Results

We use a 20-year time series of systematic aerial surveys of dugong (Dugong dugong) abundance to create spatially-explicit models of dugong distribution and relative density at the scale of the coastal waters of northeast Australia (∼136,000 km²). We interpolated the corrected data at the scale of 2 km * 2 km planning units using geostatistics. Planning units were classified as low, medium, high and very high dugong density on the basis of the relative density of dugongs estimated from the models and a frequency analysis. Torres Strait was identified as the most significant dugong habitat in northeast Australia and the most globally significant habitat known for any member of the Order Sirenia. The models are used by local, State and Federal agencies to inform management decisions related to the Indigenous harvest of dugongs, gill-net fisheries and Australia''s National Representative System of Marine Protected Areas.

Conclusion/Significance

In this paper we demonstrate that spatially-explicit population models add value to data collected for stock assessments, provide a robust alternative to predictive habitat distribution models, and inform species conservation at multiple scales.     

Projected Demographic Profile of People Living with HIV in Australia: Planning for an Older Generation

Background

Advances in HIV antiretroviral therapy (ART) has reduced mortality in people living with HIV (PLHIV), resulting in an ageing population of PLHIV. Knowledge of demographic details such as age, geographical location and sex, will aid in the planning of training and resource allocation to effectively care for the future complex health needs of PLHIV.

Methods

An agent-based, stochastic, geographical model was developed to determine the current and future demographic of PLHIV in Australia. Data and parameters were sourced from Australia''s National HIV Registry and peer reviewed literature. Processes that were simulated include progression to AIDS, mortality and internal migration.

Findings

The model estimates the mean age of PLHIV in Australia is increasing at a rate of 0.49 years each year. The expected proportion of PLHIV in over 55 years is estimated to increase from 25.3% in 2010 to 44.2% in 2020. Median age is lower in inner-city areas of the capital cities than in rural areas. The areas with the highest prevalence of HIV will continue to be capital cities; however, other areas will have greater percentage growth from 2010 to 2020.

Conclusions

The age of the population of people living with HIV is expected to increase considerably in the future. As the population of PLHIV ages, specialist clinical training and resource provision in the aged care sector will also need to be addressed.     

Identification of the Tyrosine-Protein Phosphatase Non-Receptor Type 2 as a Rheumatoid Arthritis Susceptibility Locus in Europeans

Objectives

Genome-wide association studies have facilitated the identification of over 30 susceptibility loci for rheumatoid arthritis (RA). However, evidence for a number of potential susceptibility genes have not so far reached genome-wide significance in studies of Caucasian RA.

Methods

A cohort of 4286 RA patients from across Europe and 5642 population matched controls were genotyped for 25 SNPs, then combined in a meta-analysis with previously published data.

Results

Significant evidence of association was detected for nine SNPs within the European samples. When meta-analysed with previously published data, 21 SNPs were associated with RA susceptibility. Although SNPs in the PTPN2 gene were previously reported to be associated with RA in both Japanese and European populations, we show genome-wide evidence for a different SNP within this gene associated with RA susceptibility in an independent European population (rs7234029, P = 4.4×10⁻⁹).

Conclusions

This study provides further genome-wide evidence for the association of the PTPN2 locus (encoding the T cell protein tyrosine phosphastase) with Caucasian RA susceptibility. This finding adds to the growing evidence for PTPN2 being a pan-autoimmune susceptibility gene.     

Bioactive endophytes warrant intensified exploration and conservation

Background

A key argument in favor of conserving biodiversity is that as yet undiscovered biodiversity will yield products of great use to humans. However, the link between undiscovered biodiversity and useful products is largely conjectural. Here we provide direct evidence from bioassays of endophytes isolated from tropical plants and bioinformatic analyses that novel biology will indeed yield novel chemistry of potential value.

Methodology/Principal Findings

We isolated and cultured 135 endophytic fungi and bacteria from plants collected in Peru. nrDNAs were compared to samples deposited in GenBank to ascertain the genetic novelty of cultured specimens. Ten endophytes were found to be as much as 15–30% different than any sequence in GenBank. Phylogenetic trees, using the most similar sequences in GenBank, were constructed for each endophyte to measure phylogenetic distance. Assays were also conducted on each cultured endophyte to record bioactivity, of which 65 were found to be bioactive.

Conclusions/Significance

The novelty of our contribution is that we have combined bioinformatic analyses that document the diversity found in environmental samples with culturing and bioassays. These results highlight the hidden hyperdiversity of endophytic fungi and the urgent need to explore and conserve hidden microbial diversity. This study also showcases how undergraduate students can obtain data of great scientific significance.     

Phylogeography sheds light on the central–marginal hypothesis in a Mediterranean narrow endemic plant

Background and Aims

Understanding the factors that shape variation in genetic diversity across the geographic ranges of species is an important challenge in the effort to conserve evolutionary processes sustaining biodiversity. The historical influences leading to a central–marginal organization of genetic diversity have been explored for species whose range is known to have expanded from refugia after glacial events. However, this question has rarely been addressed for Mediterranean endemic plants of azonal habitats such as rocky slopes or screes. In this context, this comprehensive study examined molecular and field data from Arenaria provincialis (Caryophyllaceae), a narrow endemic plant of south-eastern France.

Methods

Across the whole geographic range, an investigation was made of whether high levels of abundance and genetic diversity (estimated from amplified fragment length polymorphism markers) are centrally distributed, to evaluate the relevance of the central–marginal hypothesis. Phylogeographic patterns inferred from chloroplast DNA (cpDNA) were used, applying Bayesian methods to test the influence of past biogeographic events. Multivariate analysis combining phylogeographic and ecological data was used to reveal the historical and ecological distinctiveness of populations.

Key Results

Despite the narrow distribution of A. provincialis, a high level of nucleotide variation is found within cpDNA loci, supporting its persistence throughout the Pleistocene period. The area characterized by the highest genetic diversity is centrally located. Structured phylogeography and Bayesian factor analysis supported the hypothesis that the central area of the distribution was the source of both westward and eastward migrations, probably during arid periods of the Pleistocene, and more recently was a crossroads of backward migrations. By contrast, the two areas located today at the range limits are younger, have reduced genetic diversity and are marginal in the ecological gradients.

Conclusions

This study highlights a case of strong population distinctiveness within a narrow range. Phylogeography sheds light on the historical role of the areas centrally situated in the distribution. The current range size and abundance patterns are not sufficient to predict the organization of genetic diversity.     

Conveniently Pre-Tagged and Pre-Packaged: Extended Molecular Identification and Metagenomics Using Complete Metazoan Mitochondrial Genomes

Background

Researchers sorely need markers and approaches for biodiversity exploration (both specimen linked and metagenomics) using the full potential of next generation sequencing technologies (NGST). Currently, most studies rely on expensive multiple tagging, PCR primer universality and/or the use of few markers, sometimes with insufficient variability.

Methodology/Principal Findings

We propose a novel approach for the isolation and sequencing of a universal, useful and popular marker across distant, non-model metazoans: the complete mitochondrial genome. It relies on the properties of metazoan mitogenomes for enrichment, on careful choice of the organisms to multiplex, as well as on the wide collection of accumulated mitochondrial reference datasets for post-sequencing sorting and identification instead of individual tagging. Multiple divergent organisms can be sequenced simultaneously, and their complete mitogenome obtained at a very low cost. We provide in silico testing of dataset assembly for a selected set of example datasets.

Conclusions/Significance

This approach generates large mitogenome datasets. These sequences are useful for phylogenetics, molecular identification and molecular ecology studies, and are compatible with all existing projects or available datasets based on mitochondrial sequences, such as the Barcode of Life project. Our method can yield sequences both from identified samples and metagenomic samples. The use of the same datasets for both kinds of studies makes for a powerful approach, especially since the datasets have a high variability even at species level, and would be a useful complement to the less variable 18S rDNA currently prevailing in metagenomic studies.     

Selecting Biological Meaningful Environmental Dimensions of Low Discrepancy among Ranges to Predict Potential Distribution of Bean Plataspid Invasion

Background

The Bean plataspid (Megacopta cribraria) (Hemiptera: Pentatomidae), native to Asia, is becoming an invasive species in North America; its potential spread to soybean producing areas in the US is of great concern. Ecological niche modelling (ENM) has been used increasingly in predicting invasive species'' potential distribution; however, poor niche model transferability was sometimes reported, leading to the artifactual conclusion of niche differentiation during species'' invasion.

Methodology/Principals

We aim to improve the geographical transferability of ENM via environmental variable selection to predict the potential distribution of Bean plataspid invasion. Sixteen environmental dimensions between native and introduced Bean plataspid populations were compared, and classified into two datasets with different degrees of discrepancy by the interquartile range (IQR) overlap in boxplot. Niche models based on these two datasets were compared in native model prediction and invading model projection. Classical niche model approaches (i.e., model calibrated on native range and transferred outside) were used to anticipate the potential distribution of Bean plataspid invasion.

Conclusions/Significance

Niche models based on the two datasets showed little difference in native model predictions; however, when projecting onto the introduced area, models based on the environmental datasets showing low discrepancy among ranges recovered good model transferability in predicting the newly established population of Bean plataspid in the US. Recommendations were made for selecting biological meaningful environmental dimensions of low discrepancy among ranges to improve niche model transferability among these geographically separated areas. Outside of its native range, areas with invasion potential include the southeastern US in North America, southwestern Europe, southeastern South America, southern Africa, and the eastern coastal Australia.     

Bacterial distribution in the rhizosphere of wild barley under contrasting microclimates

Background

All plants in nature harbor a diverse community of rhizosphere bacteria which can affect the plant growth. Our samples are isolated from the rhizosphere of wild barley Hordeum spontaneum at the Evolution Canyon (‘EC’), Israel. The bacteria which have been living in close relationship with the plant root under the stressful conditions over millennia are likely to have developed strategies to alleviate plant stress.

Methodology/Principal Findings

We studied distribution of culturable bacteria in the rhizosphere of H. spontaneum and characterized the bacterial 1-aminocyclopropane-1-carboxylate deaminase (ACCd) production, biofilm production, phosphorus solubilization and halophilic behavior. We have shown that the H. spontaneum rhizosphere at the stressful South Facing Slope (SFS) harbors significantly higher population of ACCd producing biofilm forming phosphorus solubilizing osmotic stress tolerant bacteria.

Conclusions/Significance

The long-lived natural laboratory ‘EC’ facilitates the generation of theoretical testable and predictable models of biodiversity and genome evolution on the area of plant microbe interactions. It is likely that the bacteria isolated at the stressful SFS offer new opportunities for the biotechnological applications in our agro-ecological systems.     

Population density, water supply, and the risk of dengue fever in Vietnam: cohort study and spatial analysis

Background

Aedes aegypti, the major vector of dengue viruses, often breeds in water storage containers used by households without tap water supply, and occurs in high numbers even in dense urban areas. We analysed the interaction between human population density and lack of tap water as a cause of dengue fever outbreaks with the aim of identifying geographic areas at highest risk.

Methods and Findings

We conducted an individual-level cohort study in a population of 75,000 geo-referenced households in Vietnam over the course of two epidemics, on the basis of dengue hospital admissions (n = 3,013). We applied space-time scan statistics and mathematical models to confirm the findings. We identified a surprisingly narrow range of critical human population densities between around 3,000 to 7,000 people/km² prone to dengue outbreaks. In the study area, this population density was typical of villages and some peri-urban areas. Scan statistics showed that areas with a high population density or adequate water supply did not experience severe outbreaks. The risk of dengue was higher in rural than in urban areas, largely explained by lack of piped water supply, and in human population densities more often falling within the critical range. Mathematical modeling suggests that simple assumptions regarding area-level vector/host ratios may explain the occurrence of outbreaks.

Conclusions

Rural areas may contribute at least as much to the dissemination of dengue fever as cities. Improving water supply and vector control in areas with a human population density critical for dengue transmission could increase the efficiency of control efforts. Please see later in the article for the Editors'' Summary     

A Pleistocene Clone of Palmer's Oak Persisting in Southern California

Background

The distribution of Palmer''s oak (Quercus palmeri Engelm.) includes numerous isolated populations that are presumably relicts of a formerly larger range that has contracted due to spreading aridity following the end of the Pleistocene.

Principal Findings

We investigated a recently discovered disjunct population of Palmer''s oak in the Jurupa Mountains of Riverside County, California. Patterns of allozyme polymorphism, morphological homogeneity, widespread fruit abortion, and evidence of fire resprouting all strongly support the hypothesis that the population is a single clone. The size of the clone and estimates of annual growth from multiple populations lead us to conclude that the clone is in excess of 13,000 years old.

Conclusions

The ancient age of the clone implies it originated during the Pleistocene and is a relict of a vanished vegetation community. Range contraction after climate change best explains the modern disjunct distribution of Q. palmeri and perhaps other plants in California.     

Protecting biodiversity when money matters: maximizing return on investment

Background

Conventional wisdom identifies biodiversity hotspots as priorities for conservation investment because they capture dense concentrations of species. However, density of species does not necessarily imply conservation ‘efficiency’. Here we explicitly consider conservation efficiency in terms of species protected per dollar invested.

Methodology/Principal Findings

We apply a dynamic return on investment approach to a global biome and compare it with three alternate priority setting approaches and a random allocation of funding. After twenty years of acquiring habitat, the return on investment approach protects between 32% and 69% more species compared to the other priority setting approaches. To correct for potential inefficiencies of protecting the same species multiple times we account for the complementarity of species, protecting up to three times more distinct vertebrate species than alternate approaches.

Conclusions/Significance

Incorporating costs in a return on investment framework expands priorities to include areas not traditionally highlighted as priorities based on conventional irreplaceability and vulnerability approaches.     

Exercise related ventricular arrhythmias are related to cardiac fibrosis in hypertrophic cardiomyopathy mutation carriers

Aims

Hypertrophic cardiomyopathy (HCM) is a frequent cause of sudden cardiac death (SCD) due to exercise-related ventricular arrhythmias (ERVA); however the pathological substrate is uncertain. The aim was to determine the prevalence of ERVA and their relation with fibrosis as determined by cardiac magnetic resonance imaging (CMR) in carriers of an HCM causing mutation.

Methods

We studied the prevalence and origin of ERVA and related these with fibrosis on CMR in a population of 31 HCM mutation carriers.

Results

ERVA occurred in seven patients (23%) who all showed evidence of fibrosis (100% ERVA(+) vs. 58% ERVA(-), p = 0.04). No ventricular tachycardia or ventricular fibrillation occurred. In patients with ERVA, the extent of fibrosis was significantly larger (8 ± 4% vs. 3 ± 4%, p = 0.02). ERVA originated from areas with a high extent of fibrosis or regions directly adjacent to these areas.

Conclusions

ERVA in HCM mutation carriers arose from the area of fibrosis detected by CMR; ERVA seems closely related to cardiac fibrosis. Fibrosis as detected by CMR should be evaluated as an additional risk factor to further delineate risk of SCD in carriers of an HCM causing mutation.     

Two decades of demography reveals that seed and seedling transitions limit population persistence in a translocated shrub

Background and Aims

Olearia flocktoniae is an endangered shrub that was passively translocated from its natural ecosystem, where it has since gone extinct. This study aimed to determine sensitivities vital to populations persisting in human-created areas.

Methods

Population colonization, longevity and extinction were investigated over 20 years using 133 populations. Seed-bank longevity was determined from germination trials of seeds exhumed from extinct and extant sites via a 10-year glasshouse trial and by in situ sowing experiments. From 27 populations, 98 cohorts were followed and matrix models of transitions from seeds to adults were used to evaluate the intrinsic rate of population growth against disturbance histories. Ten populations (38 cohorts) with different disturbance histories were used to evaluate sensitivities in vital rates.

Key Results

Most populations had few individuals (∼30) and were transient (<5 years above ground). The intrinsic population growth rate was rarely >1 and all but two populations were extinct at year 20. Seeds were short-lived in situ. Although >1000 seeds per plant were produced annually in most populations, sensitivity analysis showed that the transition to the seed bank and the transition from the seed bank to seedlings are key vulnerabilities in the life-cycle.

Conclusions

Seedling establishment is promoted by recent disturbance. Increasing the number of disturbance events in populations, even severe disturbances that almost extirpate populations, significantly increases longer-term population persistence. Only populations that were disturbed annually survived the full 20 years of the study. The results show that translocated populations of O. flocktoniae will fail to persist without active management.     

Intriguing balancing selection on the intron 5 region of LMBR1 in human population

Background

The intron 5 of gene LMBR1 is the cis-acting regulatory module for the sonic hedgehog (SHH) gene. Mutation in this non-coding region is associated with preaxial polydactyly, and may play crucial roles in the evolution of limb and skeletal system.

Methodology/Principal Findings

We sequenced a region of the LMBR1 gene intron 5 in East Asian human population, and found a significant deviation of Tajima''s D statistics from neutrality taking human population growth into account. Data from HapMap also demonstrated extended linkage disequilibrium in the region in East Asian and European population, and significantly low degree of genetic differentiation among human populations.

Conclusion/Significance

We proposed that the intron 5 of LMBR1 was presumably subject to balancing selection during the evolution of modern human.     

RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets

Background

Fuelled by the advent and subsequent development of next generation sequencing technologies, metagenomics became a powerful tool for the analysis of microbial communities both scientifically and diagnostically. The biggest challenge is the extraction of relevant information from the huge sequence datasets generated for metagenomics studies. Although a plethora of tools are available, data analysis is still a bottleneck.

Results

To overcome the bottleneck of data analysis, we developed an automated computational workflow called RIEMS – Reliable Information Extraction from Metagenomic Sequence datasets. RIEMS assigns every individual read sequence within a dataset taxonomically by cascading different sequence analyses with decreasing stringency of the assignments using various software applications. After completion of the analyses, the results are summarised in a clearly structured result protocol organised taxonomically. The high accuracy and performance of RIEMS analyses were proven in comparison with other tools for metagenomics data analysis using simulated sequencing read datasets.

Conclusions

RIEMS has the potential to fill the gap that still exists with regard to data analysis for metagenomics studies. The usefulness and power of RIEMS for the analysis of genuine sequencing datasets was demonstrated with an early version of RIEMS in 2011 when it was used to detect the orthobunyavirus sequences leading to the discovery of Schmallenberg virus.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0503-6) contains supplementary material, which is available to authorized users.