Directed sequencing and annotation of three Dicentrarchus labrax L. chromosomes by applying Sanger- and pyrosequencing technologies on pooled DNA of comparatively mapped BAC clones

AbstractDicentrarchus labrax is one of the major marine aquaculture species in the European Union. In this study, we have developed a directed-sequencing strategy to sequence three sea bass chromosomes and compared results with other teleosts.Three BAC DNA pools were created from sea bass BAC clones that mapped to stickleback chromosomes/groups V, XVII and XXI. The pools were sequenced to 17–39x coverage by pyrosequencing. Data assembly was supported by Sanger reads and mate pair data and resulted in superscaffolds of 13.2Mb, 17.5Mb and 13.7Mb respectively. Annotation features of the superscaffolds include 1477 genes. We analyzed size change of exon, intron and intergenic sequence between teleost species and deduced a simple model for the evolution of genome composition in teleost lineage.Combination of second generation sequencing technologies, Sanger sequencing and genome partitioning strategies allows “high-quality draft assemblies” of chromosome-sized superscaffolds, which are crucial for the prediction and annotation of complete genes

Effects of biologically induced differential heating in an eddy-permitting coupled ocean-ecosystem model

On the basis of integrations of an eddy-permitting coupled physical-biological model of the tropical Pacific we explore changes in the simulated mean circulation as well as its intraseasonal to interannual variability driven by the biologically modulated vertical absorption profiles of solar radiation. Three sensitivity ocean hind-cast experiments, covering the period from 1948 to 2003, are performed. In the first one, simulated chlorophyll affects the attenuation of light in the water column, while in the second experiment, the chlorophyll concentration is kept constant in time by prescribing an empirically derived spatial pattern. The third experiment uses a spatially and temporally constant value for the attenuation depth. The biotically induced differential heating is generated by increased absorption of light in the surface layers, leading to a surface warming and subsurface cooling. The effect is largest in the eastern equatorial Pacific. However, the initial vertical redistribution of heat leads to considerable changes of the near-surface ocean circulation subsequently influencing the near-surface temperature structure. In general, including biophysical coupling improves the model performance in terms of temperature and ocean circulation patterns. In particular, the upwelling in the eastern equatorial Pacific is enhanced, the mixed layer becomes shallower, the warm bias in the eastern Pacific is reduced, and the zonal temperature gradient increases. This leads to stronger La Niña events and an associated increase in the variability of the Niño3 SSTA time series. Furthermore, the eddy kinetic energy (EKE) associated with mesoscale eddies in the eastern equatorial Pacific increases by almost 100% because of enhanced EKE production due to enhanced horizontal and vertical shear of the mean currents

Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity.

Some species responded successfully to prehistoric changes in climate [1, 2], while others failed to adapt and became extinct [3]. The factors that determine successful climate adaptation remain poorly understood. We constructed a reference genome and studied physiological adaptations in the Alpine marmot (Marmota marmota), a large ground-dwelling squirrel exquisitely adapted to the "ice-age" climate of the Pleistocene steppe [4, 5]. Since the disappearance of this habitat, the rodent persists in large numbers in the high-altitude Alpine meadow [6, 7]. Genome and metabolome showed evidence of adaptation consistent with cold climate, affecting white adipose tissue. Conversely, however, we found that the Alpine marmot has levels of genetic variation that are among the lowest for mammals, such that deleterious mutations are less effectively purged. Our data rule out typical explanations for low diversity, such as high levels of consanguineous mating, or a very recent bottleneck. Instead, ancient demographic reconstruction revealed that genetic diversity was lost during the climate shifts of the Pleistocene and has not recovered, despite the current high population size. We attribute this slow recovery to the marmot's adaptive life history. The case of the Alpine marmot reveals a complicated relationship between climatic changes, genetic diversity, and conservation status. It shows that species of extremely low genetic diversity can be very successful and persist over thousands of years, but also that climate-adapted life history can trap a species in a persistent state of low genetic diversity.This work was supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC001134), the UK Medical Research Council (FC001134), and the Wellcome Trust (FC001134). CB and AC are supported by the Agence Nationale de la Recherche (project ANR-13-JSV7-0005) and the Centre National de la Recherche Scientifique (CNRS), CB is supported by the Rhône-Alpes region (Grant 15.005146.01). LD is supported by Agence Nationale de la Recherche (project ANR-12-ADAP-0009). TIG is supported by a Leverhulme Early Career Fellowship (Grant ECF-2015-453) and a NERC grant (NE/N013832/1). JMG is supported by a Hertha Finberg Fellowship (FWF T703). LDR is supported by the Diabetes UK RD Lawrence Fellowship (16/0005382)

Brutalität ohne Grenzen? Befunde aus Dunkelfeldforschungen über die Entwicklung der Häufigkeit aggressiven Verhaltens Jugendlicher

Mansel J. Brutalität ohne Grenzen? Befunde aus Dunkelfeldforschungen über die Entwicklung der Häufigkeit aggressiven Verhaltens Jugendlicher. In: Timmermann H, Wessela E, eds. Jugendforschung in Deutschland. Eine Zwischenbilanz. Opladen: Leske + Budrich; 1999: 205-242

Data from: Characterization of the genome and transcriptome of the blue tit Cyanistes caeruleus: polymorphisms, sex-biased expression and selection signals

Decoding genomic sequences and determining their variation within populations has potential to reveal adaptive processes and unravel the genetic basis of ecologically relevant trait variation within a species. The blue tit Cyanistes caeruleus – a long-time ecological model species – has been used to investigate fitness consequences of variation in mating and reproductive behaviour. However, very little is known about the underlying genetic changes due to natural and sexual selection in the genome of this songbird. As a step to bridge this gap, we assembled the first draft genome of a single blue tit, mapped the transcriptome of five females and five males to this reference, identified genomewide variants and performed sex-differential expression analysis in the gonads, brain and other tissues. In the gonads, we found a high number of sex-biased genes, and of those, a similar proportion were sex-limited (genes only expressed in one sex) in males and females. However, in the brain, the proportion of female-limited genes within the female-biased gene category (82%) was substantially higher than the proportion of male-limited genes within the male-biased category (6%). This suggests a predominant on-off switching mechanism for the female-limited genes. In addition, most male-biased genes were located on the Z-chromosome, indicating incomplete dosage compensation for the male-biased genes. We called more than 500 000 SNPs from the RNA-seq data. Heterozygote detection in the single reference individual was highly congruent between DNA-seq and RNA-seq calling. Using information from these polymorphisms, we identified potential selection signals in the genome. We list candidate genes which can be used for further sequencing and detailed selection studies, including genes potentially related to meiotic drive evolution. A public genome browser of the blue tit with the described information is available at http://public-genomes-ngs.molgen.mpg.de

Tests for sex-differential expression in the brain

Cuffdiff results files; differential expression of all brain genes between 5 male and 5 female blue tits