Population Genomics Reveals the Underlying Structure of the Small Pelagic European Sardine and Suggests Low Connectivity within Macaronesia.

The European sardine (Sardina pilchardus, Walbaum 1792) is indisputably a commercially important species. Previous studies using uneven sampling or a limited number of makers have presented sometimes conflicting evidence of the genetic structure of S. pilchardus populations. Here, we show that whole genome data from 108 individuals from 16 sampling areas across 5000 km of the species' distribution range (from the Eastern Mediterranean to the archipelago of Azores) support at least three genetic clusters. One includes individuals from Azores and Madeira, with evidence of substructure separating these two archipelagos in the Atlantic. Another cluster broadly corresponds to the center of the distribution, including the sampling sites around Iberia, separated by the Almeria-Oran front from the third cluster that includes all of the Mediterranean samples, except those from the Alboran Sea. Individuals from the Canary Islands appear to belong to the Mediterranean cluster. This suggests at least two important geographical barriers to gene flow, even though these do not seem complete, with many individuals from around Iberia and the Mediterranean showing some patterns compatible with admixture with other genetic clusters. Genomic regions corresponding to the top outliers of genetic differentiation are located in areas of low recombination indicative that genetic architecture also has a role in shaping population structure. These regions include genes related to otolith formation, a calcium carbonate structure in the inner ear previously used to distinguish S. pilchardus populations. Our results provide a baseline for further characterization of physical and genetic barriers that divide European sardine populations, and information for transnational stock management of this highly exploited species towards sustainable fisheries.

A comparison of tablet-based and paper-based venous insufficiency epidemiologic and economic study quality of life/symptom questionnaire for assessment of chronic venous disease.

OBJECTIVE: To comparatively evaluate performances of tablet-based versus paper-based Venous Insufficiency Epidemiologic and Economic Study-Quality of Life/Symptom (VEINES-QOL/Sym) questionnaire. METHODS: We prospectively evaluated 78 consecutive patients who completed tablet-based and paper-based VEINES-QOL/Sym questionnaires and compared their scores, completion time, data entry time, and ease of use. We used Student's t-test and Wilcoxon test for quantitative variables, Bland-Altman test and kappa coefficient for agreement between questionnaires and patients, respectively. Spearman's correlation coefficient was used to assess correlations. RESULTS: Most participants (83.3%) found it easier to use the tablet device. Less time was needed to complete the tablet-based (median, 4.75; IQR, 3-7 min) than the paper-based (median, 8.3; IQR, 6.3-11.3 min) questionnaire (p < .001). Better educated patients took less time to complete paper-based (p = .003) and tablet-based (p = .001) questionnaires and considered the latter easier to use (p = .010). CONCLUSIONS: The tablet-based VEINES-QOL/Sym proved to be an easy-to-use and time-saving tool.

Inferring the mode and strength of ongoing selection.

Genome sequence data are no longer scarce. The UK Biobank alone comprises 200,000 individual genomes, with more on the way, leading the field of human genetics toward sequencing entire populations. Within the next decades, other model organisms will follow suit, especially domesticated species such as crops and livestock. Having sequences from most individuals in a population will present new challenges for using these data to improve health and agriculture in the pursuit of a sustainable future. Existing population genetic methods are designed to model hundreds of randomly sampled sequences but are not optimized for extracting the information contained in the larger and richer data sets that are beginning to emerge, with thousands of closely related individuals. Here we develop a new method called trio-based inference of dominance and selection (TIDES) that uses data from tens of thousands of family trios to make inferences about natural selection acting in a single generation. TIDES further improves on the state of the art by making no assumptions regarding demography, linkage, or dominance. We discuss how our method paves the way for studying natural selection from new angles.

Measuring muscle activation using electromyography during neurodevelopmental treatment in individuals with severe cerebral palsy.

BACKGROUND: In the motor rehabilitation of individuals with neurological disorders, including cerebral palsy (CP), Neurodevelopmental treatment (NDT) one of the most used approaches worldwide. OBJECTIVE: To verify muscle activation in NDT handling in individuals with severe CP using electromyography. METHODS: This was a controlled, cross-sectional, quantitative clinical trial. The individuals were evaluated using electromyography to analyze the muscular activation of the spinal erector, gluteus medius, rectus abdominis and multifidus during different NDT handling. We evaluated 59 individuals: 39 with spastic quadriparesis CP (Gross Motor Function Classification System, level IV-V) and 20 typically-developing individuals (control group). These groups were homogeneous with respect to age and gender. RESULTS: There was a significant difference in muscle activation of the spinal erector, gluteus medius, rectus abdominis and multifidus in the six NDT handling used in this study: side-sitting for kneeling; supine for lateral decubitus, prone position for lateral decubitus, "sitting on horseback", sitting on the roll, and proprioceptive stimulation sitting on the ball. CONCLUSION: The results show that all NDT handling analyzed in this study were effective for muscle activation of the spinal erector, gluteus medius, rectus abdominis and multifidus in individuals with severe spastic quadriparetic CP.

Population Genomics of the Maize Pathogen Ustilago maydis: Demographic History and Role of Virulence Clusters in Adaptation.

The tight interaction between pathogens and their hosts results in reciprocal selective forces that impact the genetic diversity of the interacting species. The footprints of this selection differ between pathosystems because of distinct life-history traits, demographic histories, or genome architectures. Here, we studied the genome-wide patterns of genetic diversity of 22 isolates of the causative agent of the corn smut disease, Ustilago maydis, originating from five locations in Mexico, the presumed center of origin of this species. In this species, many genes encoding secreted effector proteins reside in so-called virulence clusters in the genome, an arrangement that is so far not found in other filamentous plant pathogens. Using a combination of population genomic statistical analyses, we assessed the geographical, historical, and genome-wide variation of genetic diversity in this fungal pathogen. We report evidence of two partially admixed subpopulations that are only loosely associated with geographic origin. Using the multiple sequentially Markov coalescent model, we inferred the demographic history of the two pathogen subpopulations over the last 0.5 Myr. We show that both populations experienced a recent strong bottleneck starting around 10,000 years ago, coinciding with the assumed time of maize domestication. Although the genome average genetic diversity is low compared with other fungal pathogens, we estimated that the rate of nonsynonymous adaptive substitutions is three times higher in genes located within virulence clusters compared with nonclustered genes, including nonclustered effector genes. These results highlight the role that these singular genomic regions play in the evolution of this pathogen.

A Population Genomics Lexicon.

Population genomics is a growing field stemming from soon a 100 years of developments in population genetics. Here, we summarize the main concepts and terminology underlying both theoretical and empirical statistical population genomics studies. We provide the reader with pointers toward the original literature as well as methodological and historical reviews.

Inference of recombination maps from a single pair of genomes and its application to ancient samples.

Understanding the causes and consequences of recombination landscape evolution is a fundamental goal in genetics that requires recombination maps from across the tree of life. Such maps can be obtained from population genomic datasets, but require large sample sizes. Alternative methods are therefore necessary to research organisms where such datasets cannot be generated easily, such as non-model or ancient species. Here we extend the sequentially Markovian coalescent model to jointly infer demography and the spatial variation in recombination rate. Using extensive simulations and sequence data from humans, fruit-flies and a fungal pathogen, we demonstrate that iSMC accurately infers recombination maps under a wide range of scenarios-remarkably, even from a single pair of unphased genomes. We exploit this possibility and reconstruct the recombination maps of ancient hominins. We report that the ancient and modern maps are correlated in a manner that reflects the established phylogeny of Neanderthals, Denisovans, and modern human populations.

The Evolution of Gene-Specific Transcriptional Noise Is Driven by Selection at the Pathway Level.

Biochemical reactions within individual cells result from the interactions of molecules, typically in small numbers. Consequently, the inherent stochasticity of binding and diffusion processes generates noise along the cascade that leads to the synthesis of a protein from its encoding gene. As a result, isogenic cell populations display phenotypic variability even in homogeneous environments. The extent and consequences of this stochastic gene expression have only recently been assessed on a genome-wide scale, owing, in particular, to the advent of single-cell transcriptomics. However, the evolutionary forces shaping this stochasticity have yet to be unraveled. Here, we take advantage of two recently published data sets for the single-cell transcriptome of the domestic mouse Mus musculus to characterize the effect of natural selection on gene-specific transcriptional stochasticity. We show that noise levels in the mRNA distributions (also known as transcriptional noise) significantly correlate with three-dimensional nuclear domain organization, evolutionary constraints on the encoded protein, and gene age. However, the position of the encoded protein in a biological pathway is the main factor that explains observed levels of transcriptional noise, in agreement with models of noise propagation within gene networks. Because transcriptional noise is under widespread selection, we argue that it constitutes an important component of the phenotype and that variance of expression is a potential target of adaptation. Stochastic gene expression should therefore be considered together with the mean expression level in functional and evolutionary studies of gene expression.

On the limits of complexity in living forms.

In a recent book chapter, Morris, S.C., 2013. Life: the final frontier for complexity? In: Lineweaver, C.H., Davies, P.C.W., Ruse, M. (Eds.), Complexity and the Arrow of Time. pp. 135-161. argues that there are limits to the complexity of life forms and that with the exception of human beings these limits have already been reached. We recommend seeing human use of technology as a natural, evolutionary process. We then proceed to claim that biological engineering other species to increase their complexity can be an efficient way to delay the heat death locally. Whenever, wherever in the universe living things become intelligent enough to perform these kinds of operations, they will be able to increase complexity around them as long as a gradient of energy is available. This conclusion has deep impact on both science and philosophy.

Reproductive ability and level of infestation of the Varroa destructor mite in Apis mellifera apiaries in Blumenau, State of Santa Catarina, Brazil / Habilidade reprodutiva e níveis de infestação do ácaro Varroa destructor em colmeias de Apis mellifera no município de Blumenau, Estado de Santa Catarina, Brasil

Varroa destructor mite causes mortality of Apis mellifera bees throughout the world. Its greatest damage to these colonies has been reported in European countries and North America. The impact of the mite is related to the climate and the bee race on each region in which the plague has been established. Varroa causes little damage to the colonies of africanized honeybees in Brazil and the levels of infestation are relatively small and stable. The reproductive ability of Varroa females was evaluated in pupae of workers of 17-18 days of age, obtained from eight beehives of africanized bees for twelve months. The average number of offspring (deutonymphs, protonymphs and eggs) each Varroa produced was 3.18 ± 0.19. The average total number of deutonymph and protonymph was, respectively, 1.57 ± 0.15 and 1.61 ± 0.14. The levels of infestation demonstrated that the plague continue reaching low levels, the average was 4.11 ± 3.42.

O ácaro Varroa destructor é causador da mortalidade de abelhas Apis mellifera em várias partes do mundo. Seus principais danos foram relatados nos países da Europa e América do Norte. O impacto desse ácaro está relacionado às condições climáticas e à raça de abelhas em cada região onde a praga se estabeleceu. A Varroa causa poucos danos nas colônias de abelhas africanizadas no Brasil e os níveis de infestação são relativamente baixos e estáveis em crias e adultos. A habilidade reprodutiva das fêmeas do ácaro, foi avaliada em pupas de operárias de 17-18 idade, obtidas de oito colmeias de abelhas africanizadas, durante 12 meses. O numero médio total de descendentes (deutoninfas, protoninfas e ovos) que cada varroa produziu foi de 3.18 ± 0.19. Para o numero médio total de deutoninfas e protoninfas foi, respectivamente, 1.57 ± 0.15 e 1.61 ± 0.14. Os índices de infestação demonstram que a praga continua alcançando baixos níveis; a média foi de 4.11 ± 3.42.