132 research outputs found
Reconstructing Colonization Dynamics of the Human Parasite Schistosoma mansoni following Anthropogenic Environmental Changes in Northwest Senegal
© 2015 Van den Broeck et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article
Covert deformed wing virus infections have long-term deleterious effects on honeybee foraging and survival
Several studies have suggested that covert stressors can contribute to bee colony declines. Here we
provide a novel case study and show using radio-frequency identification (RFID) tracking technology
that covert deformed wing virus (DWV) infections in adult honeybee workers seriously impact longterm
foraging and survival under natural foraging conditions. In particular, our experiments show
that adult workers injected with low doses of DWV experienced increased mortality rates, that DWV
caused workers to start foraging at a premature age, and that the virus reduced the workersâ total
activity span as foragers. Altogether, these results demonstrate that covert deformed wing virus
infections have strongly deleterious effects on honey bee foraging and survival. These results are
consistent with previous studies that suggested DWV to be an important contributor to the ongoing
bee declines in Europe and the US. Overall, our study underlines the strong impact that covert
pathogen infections can have on individual and group-level performance in bees
Spatially dense 3D facial heritability and modules of co-heritability in a father-offspring design
Introduction: The human face is a complex trait displaying a strong genetic component as illustrated by various studies on facial heritability. Most of these start from sparse descriptions of facial shape using a limited set of landmarks. Subsequently, facial features are preselected as univariate measurements or principal components and the heritability is estimated for each of these features separately. However, none of these studies investigated multivariate facial features, nor the co-heritability between different facial features. Here we report a spatially dense multivariate analysis of facial heritability and co-heritability starting from data from fathers and their children available within ALSPAC. Additionally, we provide an elaborate overview of related craniofacial heritability studies. Methods: In total, 3D facial images of 762 father-offspring pairs were retained after quality control. An anthropometric mask was applied to these images to establish spatially dense quasi-landmark configurations. Partial least squares regression was performed and the (co-)heritability for all quasi-landmarks (âŒ7160) was computed as twice the regression coefficient. Subsequently, these were used as input to a hierarchical facial segmentation, resulting in the definition of facial modules that are internally integrated through the biological mechanisms of inheritance. Finally, multivariate heritability estimates were obtained for each of the resulting modules. Results: Nearly all modular estimates reached statistical significance under 1,000,000 permutations and after multiple testing correction (p †1.3889 Ă 10-3), displaying low to high heritability scores. Particular facial areas showing the greatest heritability were similar for both sons and daughters. However, higher estimates were obtained in the former. These areas included the global face, upper facial part (encompassing the nasion, zygomas and forehead) and nose, with values reaching 82% in boys and 72% in girls. The lower parts of the face only showed low to moderate levels of heritability. Conclusion: In this work, we refrain from reducing facial variation to a series of individual measurements and analyze the heritability and co-heritability from spatially dense landmark configurations at multiple levels of organization. Finally, a multivariate estimation of heritability for global-to-local facial segments is reported. Knowledge of the genetic determination of facial shape is useful in the identification of genetic variants that underlie normal-range facial variation
Environmental variables, habitat discontinuity and life history shaping the genetic structure of Pomatoschistus marmoratus
Coastal lagoons are semi-isolated ecosystems
exposed to wide fluctuations of environmental conditions
and showing habitat fragmentation. These features may
play an important role in separating species into different
populations, even at small spatial scales. In this study, we
evaluate the concordance between mitochondrial (previous
published data) and nuclear data analyzing the genetic
variability of Pomatoschistus marmoratus in five localities,
inside and outside the Mar Menor coastal lagoon (SE
Spain) using eight microsatellites. High genetic diversity
and similar levels of allele richness were observed across
all loci and localities, although significant genic and
genotypic differentiation was found between populations
inside and outside the lagoon. In contrast to the FST values
obtained from previous mitochondrial DNA analyses
(control region), the microsatellite data exhibited significant
differentiation among samples inside the Mar Menor
and between lagoonal and marine samples. This pattern
was corroborated using Cavalli-Sforza genetic distances.
The habitat fragmentation inside the coastal lagoon and
among lagoon and marine localities could be acting as a
barrier to gene flow and contributing to the observed
genetic structure. Our results from generalized additive
models point a significant link between extreme lagoonal
environmental conditions (mainly maximum salinity) and
P. marmoratus genetic composition. Thereby, these environmental
features could be also acting on genetic structure
of coastal lagoon populations of P. marmoratus favoring
their genetic divergence. The mating strategy of P. marmoratus
could be also influencing our results obtained from
mitochondrial and nuclear DNA. Therefore, a special
consideration must be done in the selection of the DNA
markers depending on the reproductive strategy of the
species
Genomic analyses of hair from Ludwig van Beethoven
Ludwig van Beethoven (1770â1827) remains among the most influential and popular classical music composers. Health problems significantly impacted his career as a composer and pianist, including progressive hearing loss, recurring gastrointestinal complaints, and liver disease. In 1802, Beethoven requested that following his death, his disease be described and made public. Medical biographers have since proposed numerous hypotheses, including many substantially heritable conditions. Here we attempt a genomic analysis of Beethoven in order to elucidate potential underlying genetic and infectious causes of his illnesses. We incorporated improvements in ancient DNA methods into existing protocols for ancient hair samples, enabling the sequencing of high-coverage genomes from small quantities of historical hair. We analyzed eight independently sourced locks of hair attributed to Beethoven, five of which originated from a single European male. We deemed these matching samples to be almost certainly authentic and sequenced Beethoven\u27s genome to 24-fold genomic coverage. Although we could not identify a genetic explanation for Beethoven\u27s hearing disorder or gastrointestinal problems, we found that Beethoven had a genetic predisposition for liver disease. Metagenomic analyses revealed furthermore that Beethoven had a hepatitis B infection during at least the months prior to his death. Together with the genetic predisposition and his broadly accepted alcohol consumption, these present plausible explanations for Beethoven\u27s severe liver disease, which culminated in his death. Unexpectedly, an analysis of Y chromosomes sequenced from five living members of the Van Beethoven patrilineage revealed the occurrence of an extra-pair paternity event in Ludwig van Beethoven\u27s patrilineal ancestry
Subdividing Y-chromosome haplogroup R1a1 reveals Norse Viking dispersal lineages in Britain
The inïŹuence of Viking-Age migrants to the British Isles is obvious in archaeological and place-names evidence, but their demographic impact has been unclear. Autosomal genetic analyses support Norse Viking contributions to parts of Britain, but show no signal corresponding to the Danelaw, the region under Scandinavian administrative control from the ninth to eleventh centuries. Y-chromosome haplogroup R1a1 has been considered as a possible marker for Viking migrations because of its high frequency in peninsular Scandinavia (Norway and Sweden). Here we select ten Y-SNPs to discriminate informatively among hg R1a1 sub-haplogroups in Europe, analyse these in 619 hg R1a1 Y chromosomes including 163 from the British Isles, and also type 23 short-tandem repeats (Y-STRs) to assess internal diversity. We ïŹnd three speciïŹcally Western-European sub-haplogroups, two of which predominate in Norway and Sweden, and are also found in Britain; starlike features in the STR networks of these lineages indicate histories of expansion. We ask whether geographical distributions of hg R1a1 overall, and of the two sub-lineages in particular, correlate with regions of Scandinavian inïŹuence within Britain. Neither shows any frequency difference between regions that have higher (â„10%) or lower autosomal contributions from Norway and Sweden, but both are signiïŹcantly overrepresented in the region corresponding to the Danelaw. These differences between autosomal and Y-chromosomal histories suggest either male-speciïŹc contribution, or the inïŹuence of patrilocality. Comparison of modern DNA with recently available ancient DNA data supports the interpretation that two sub-lineages of hg R1a1 spread with the Vikings from peninsular Scandinavia
Robustly Safe Compilation
Secure compilers generate compiled code that withstands many target-level attacks such as alteration of control flow, data leaks or memory corruption. Many existing secure compilers are proven to be fully abstract, meaning that they reflect and preserve observational equivalence. Fully abstract compilation is strong and useful but, in certain cases, comes at the cost of requiring expensive runtime constructs in compiled code. These constructs may have no relevance for security, but are needed to accommodate differences between the source and target languages that fully abstract compilation necessarily needs
Whatâs in a surname? Physique, aptitude, and sports type comparisons between Tailors and Smiths
Combined heredity of surnames and physique, coupled with past marriage patterns and trade-specific physical aptitude and selection factors, may have led to differential assortment of bodily characteristics among present-day men with specific trade-reflecting surnames (Tailor vs. Smith). Two studies reported here were partially consistent with this genetic-social hypothesis, first proposed by BĂ€umler (1980). Study 1 (N = 224) indicated significantly higher self-rated physical aptitude for prototypically strength-related activities (professions, sports, hobbies) in a random sample of Smiths. The counterpart effect (higher aptitude for dexterity-related activities among Tailors) was directionally correct, but not significant, and Tailor-Smith differences in basic physique variables were not significant. Study 2 examined two large datasets (Austria/Germany combined, and UK: N = 7001 and 20532) of menâs national high-score lists for track-and-field events requiring different physiques. In both datasets, proportions of Smiths significantly increased from light-stature over medium-stature to heavy-stature sports categories. The predicted counterpart effect (decreasing prevalences of Tailors along these categories) was not supported. Related prior findings, implicit egotism as an alternative interpretation of the evidence, and directions for further inquiry are discussed in conclusion
Methodology for Y Chromosome Capture: A complete genome sequence of Y chromosome using flow cytometry, laser microdissection and magnetic streptavidin-beads
This study is a comparison of the efficiency of three technologies used for Y chromosome capture and
the next-generation sequencing (NGS) technologies applied for determining its whole sequence. Our
main findings disclose that streptavidinâbiotin magnetic particle-based capture methodology offers
better and a deeper sequence coverage for Y chromosome capture, compared to chromosome sorting
and microdissection procedures. Moreover, this methodology is less time consuming and the most
selective for capturing only Y chromosomal material, in contrast with other methodologies that result
in considerable background material from other, non-targeted chromosomes. NGS results compared
between two platforms, NextSeq 500 and SOLID 5500xl, produce the same coverage results. This is the
first study to explore a methodological comparison of Y chromosome capture and genetic analysis. Our
results indicate an improved strategy for Y chromosome research with applications in several scientific
fields where this chromosome plays an important role, such as forensics, medical sciences, molecular
anthropology and cancer sciences.Spanish Alfonso Martin Escudero Foundation for the financial support to one of the
authors of the present work (MJ Alvarez âCubero)
3D facial phenotyping by biometric sibling matching used in contemporary genomic methodologies
The analysis of contemporary genomic data typically operates on one-dimensional phenotypic measurements (e.g. standing height). Here we report on a data-driven, family-informed strategy to facial phenotyping that searches for biologically relevant traits and reduces multivariate 3D facial shape variability into amendable univariate measurements, while preserving its structurally complex nature. We performed a biometric identification of siblings in a sample of 424 children, defining 1,048 sib-shared facial traits. Subsequent quantification and analyses in an independent European cohort (n = 8,246) demonstrated significant heritability for a subset of traits (0.17â0.53) and highlighted 218 genome-wide significant loci (38 also study-wide) associated with facial variation shared by siblings. These loci showed preferential enrichment for active chromatin marks in cranial neural crest cells and embryonic craniofacial tissues and several regions harbor putative craniofacial genes, thereby enhancing our knowledge on the genetic architecture of normal-range facial variation
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