Detecting recent selective sweeps while controlling for mutation rate and background selection

A composite likelihood ratio test implemented in the program sweepfinder is a commonly used method for scanning a genome for recent selective sweeps. sweepfinder uses information on the spatial pattern (along the chromosome) of the site frequency spectrum around the selected locus. To avoid confounding effects of background selection and variation in the mutation process along the genome, the method is typically applied only to sites that are variable within species. However, the power to detect and localize selective sweeps can be greatly improved if invariable sites are also included in the analysis. In the spirit of a Hudson–Kreitman–Aguadé test, we suggest adding fixed differences relative to an out‐group to account for variation in mutation rate, thereby facilitating more robust and powerful analyses. We also develop a method for including background selection, modelled as a local reduction in the effective population size. Using simulations, we show that these advances lead to a gain in power while maintaining robustness to mutation rate variation. Furthermore, the new method also provides more precise localization of the causative mutation than methods using the spatial pattern of segregating sites alone.Christian D. Huber, Michael DeGiorgio, Ines Hellmann, Rasmus Nielse

Population Genomics on the Fly: Recent Advances in Drosophila

Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of genetic tools that allow to uncover mechanistic links between genotype and phenotype. Moreover, given its worldwide distribution in diverse habitats and its moderate genome-size, Drosophila has proven very powerful for population genetics inference and was one of the first eukaryotes whose genome was fully sequenced. In this book chapter, we provide a brief historical overview of research in Drosophila and then focus on recent advances during the genomic era. After describing different types and sources of genomic data, we discuss mechanisms of neutral evolution including the demographic history of Drosophila and the effects of recombination and biased gene conversion. Then, we review recent advances in detecting genome-wide signals of selection, such as soft and hard selective sweeps. We further provide a brief introduction to background selection, selection of noncoding DNA and codon usage and focus on the role of structural variants, such as transposable elements and chromosomal inversions, during the adaptive process. Finally, we discuss how genomic data helps to dissect neutral and adaptive evolutionary mechanisms that shape genetic and phenotypic variation in natural populations along environmental gradients. In summary, this book chapter serves as a starting point to Drosophila population genomics and provides an introduction to the system and an overview to data sources, important population genetic concepts and recent advances in the field

Efeito do ultra-som terapêutico contínuo em placas epifisárias de coelhos Efectos de la ultrasonografia terapéutica continua en placas epifisarias de conejos Effect of continuous therapeutic ultrasound in rabbit growth plates

Devido aos efeitos terapêuticos, o ultra-som tem se tornado ferramenta indispensável no tratamento fisioterapêutico de alterações causadas por lesões e em diversas doenças, porém seu uso em pacientes pediátricos é controverso por possíveis distúrbios e danos à placa epifisária. O objetivo deste estudo é verificar se o ultra-som contínuo apresenta efeitos de alteração na placa de crescimento da tíbia de coelhas. Oito coelhas da raça Nova Zelândia com dois meses de idade foram submetidas a um tratamento usando ultra-som terapêutico de forma contínua com dose de 1W/cm² na região lateral da articulação do joelho direito por 5min, durante 10 dias com dois dias de intervalo após a 5ª aplicação. A articulação do joelho esquerdo foi utilizada como controle. A análise histológica mostrou uma alteração na espessura da cartilagem epifisária, sendo que no lado tratado o tamanho foi 24,40% maior do que no controle (p < 0,0001), enquanto a análise radiológica não apresentou diferença entre os membros. Conclui-se que o ultra-som terapêutico na forma utilizada produz alterações histológicas significativas na espessura da cartilagem no lado tratado, sugerindo uma aceleração no metabolismo da placa.<br>Debido a los efectos terapéuticos, la ultrasonografía se ha convertido en una herramienta indispensable al tratamiento fisioterapéutico de las alteraciones causadas por lesiones y en diversas enfermedades, a pesar de esto su uso en pacientes pediátricos es controversial por los posibles disturbios y daños a la placa epifisaria. El objetivo de este estudio es verificar si la ultrasonografía continua presenta efectos de alteración en la placa de crecimiento de al tibia de conejas. Ocho conejas de la raza Nueva Zelanda con 2 meses de edad fueron sometidas a un tratamiento usando ultrasonografía terapéutica de forma continua con dosis de 1W/cm² en la región lateral de la articulación de la rodilla derecha por 5 min, durante 10 días con 2 días de intervalo después de la 5ª aplicación. La articulación de la rodilla izquierda fue utilizada como control. El análisis histológico reportó una alteración en la espesura del cartílago epifisario, en el lado tratado el tamaño fue de 24,40% mayor del que en el control (p < 0,0001); mientras que el análisis radiológico no presentó ninguna diferencia entre los miembros. Por tanto, se concluye que la ultrasonografía terapéutica en la forma utilizada produce alteraciones histológicas significativas en la espesura del cartílago en el lado tratado, lo que sugiere una aceleración en el metabolismo de la placa.<br>The therapeutic efficiency of ultrasound has become an indispensable tool of physical therapy treatment in cases of alteration by lesions and in many kinds of sickness. However, in pediatric cases the use of ultrasound is controversial due to possible disturbance and damage to the growth plate. The aim of this study is to find out if the continuous ultrasound presents alteration effects on the growth plate of female rabbits. Eight New Zealand female rabbits with two months of age were tested. They were treated by continuous therapeutic ultrasound with doses of 1 W/cm² in the lateral region of the right knee joint for five minutes, during 10 days, with an interval of two days after five applications. The left knee joint was used as a control. The histological analysis showed an alteration in the thickness of the growth plate on the treated side 24.40% bigger than in the left knee joint of the control (p < 0.0001). On other hand, the radiological analysis did not show any difference between the limbs. The conclusion was that the therapeutic ultrasound produced significant histological alterations in the cartilage thickness on the treated side according to the manner it was used in the experiment. Such fact suggests an acceleration in the growth plate metabolism