Evolution and connectivity in the world-wide migration system of the mallard: Inferences from mitochondrial DNA

<p>Abstract</p> <p>Background</p> <p>Main waterfowl migration systems are well understood through ringing activities. However, in mallards (<it>Anas platyrhynchos</it>) ringing studies suggest deviations from general migratory trends and traditions in waterfowl. Furthermore, surprisingly little is known about the population genetic structure of mallards, and studying it may yield insight into the spread of diseases such as Avian Influenza, and in management and conservation of wetlands. The study of evolution of genetic diversity and subsequent partitioning thereof during the last glaciation adds to ongoing discussions on the general evolution of waterfowl populations and flyway evolution. Hypothesised mallard flyways are tested explicitly by analysing mitochondrial mallard DNA from the whole northern hemisphere.</p> <p>Results</p> <p>Phylogenetic analyses confirm two mitochondrial mallard clades. Genetic differentiation within Eurasia and North-America is low, on a continental scale, but large differences occur between these two land masses (<it>F</it>_ST= 0.51). Half the genetic variance lies within sampling locations, and a negligible portion between currently recognised waterfowl flyways, within Eurasia and North-America. Analysis of molecular variance (AMOVA) at continent scale, incorporating sampling localities as smallest units, also shows the absence of population structure on the flyway level. Finally, demographic modelling by coalescence simulation proposes a split between Eurasia and North-America 43,000 to 74,000 years ago and strong population growth (~100fold) since then and little migration (not statistically different from zero).</p> <p>Conclusions</p> <p>Based on this first complete assessment of the mallard's world-wide population genetic structure we confirm that no more than two mtDNA clades exist. Clade A is characteristic for Eurasia, and clade B for North-America although some representatives of clade A are also found in North-America. We explain this pattern by evaluating competing hypotheses and conclude that a complex mix of historical, recent and anthropogenic factors shaped the current mallard populations. We refute population classification based on flyways proposed by ornithologists and managers, because they seem to have little biological meaning. Our results have implications for wetland management and conservation, with special regard to the release of farmed mallards for hunting, as well as for the possible transmission of Avian Influenza by mallards due to migration.</p

Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos)

<p>Abstract</p> <p>Background</p> <p>Next generation sequencing technologies allow to obtain at low cost the genomic sequence information that currently lacks for most economically and ecologically important organisms. For the mallard duck genomic data is limited. The mallard is, besides a species of large agricultural and societal importance, also the focal species when it comes to long distance dispersal of Avian Influenza. For large scale identification of SNPs we performed Illumina sequencing of wild mallard DNA and compared our data with ongoing genome and EST sequencing of domesticated conspecifics. This is the first study of its kind for waterfowl.</p> <p>Results</p> <p>More than one billion base pairs of sequence information were generated resulting in a 16× coverage of a reduced representation library of the mallard genome. Sequence reads were aligned to a draft domesticated duck reference genome and allowed for the detection of over 122,000 SNPs within our mallard sequence dataset. In addition, almost 62,000 nucleotide positions on the domesticated duck reference showed a different nucleotide compared to wild mallard. Approximately 20,000 SNPs identified within our data were shared with SNPs identified in the sequenced domestic duck or in EST sequencing projects. The shared SNPs were considered to be highly reliable and were used to benchmark non-shared SNPs for quality. Genotyping of a representative sample of 364 SNPs resulted in a SNP conversion rate of 99.7%. The correlation of the minor allele count and observed minor allele frequency in the SNP discovery pool was 0.72.</p> <p>Conclusion</p> <p>We identified almost 150,000 SNPs in wild mallards that will likely yield good results in genotyping. Of these, ~101,000 SNPs were detected within our wild mallard sequences and ~49,000 were detected between wild and domesticated duck data. In the ~101,000 SNPs we found a subset of ~20,000 SNPs shared between wild mallards and the sequenced domesticated duck suggesting a low genetic divergence. Comparison of quality metrics between the total SNP set (122,000 + 62,000 = 184,000 SNPs) and the validated subset shows similar characteristics for both sets. This indicates that we have detected a large amount (~150,000) of accurately inferred mallard SNPs, which will benefit bird evolutionary studies, ecological studies (e.g. disentangling migratory connectivity) and industrial breeding programs.</p

Treatment options for patients with triple-negative breast cancer

Breast cancer is a heterogeneous disease composed of different subtypes, characterized by their different clinicopathological characteristics, prognoses and responses to treatment. In the past decade, significant advances have been made in the treatment of breast cancer sensitive to hormonal treatments, as well as in patients whose malignant cells overexpress or amplify HER2. In contrast, mainly due to the lack of molecular targets, little progress has been made in the treatment of patients with triple-negative breast cancer. Recent improved understanding of the natural history, pathophysiology, and molecular features of triple-negative breast cancers have provided new insights into management and therapeutic strategies for women affected with this entity. Ongoing and planned translational clinical trials are likely to optimize and improve treatment of women with this disease

ICAR: endoscopic skull‐base surgery

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Comparative Genomics of the Waterfowl Innate Immune System.

Funder: International Max Planck Research School of Organismal BiologyFunder: Universities of the State of Baden-WürttembergAnimal species differ considerably in their ability to fight off infections. Finding the genetic basis of these differences is not easy, as the immune response is comprised of a complex network of proteins that interact with one another to defend the body against infection. Here, we used population- and comparative genomics to study the evolutionary forces acting on the innate immune system in natural hosts of the avian influenza virus (AIV). For this purpose, we used a combination of hybrid capture, next- generation sequencing and published genomes to examine genetic diversity, divergence, and signatures of selection in 127 innate immune genes at a micro- and macroevolutionary time scale in 26 species of waterfowl. We show across multiple immune pathways (AIV-, toll-like-, and RIG-I -like receptors signalling pathways) that genes involved genes in pathogen detection (i.e., toll-like receptors) and direct pathogen inhibition (i.e., antimicrobial peptides and interferon-stimulated genes), as well as host proteins targeted by viral antagonist proteins (i.e., mitochondrial antiviral-signaling protein, [MAVS]) are more likely to be polymorphic, genetically divergent, and under positive selection than other innate immune genes. Our results demonstrate that selective forces vary across innate immune signaling signalling pathways in waterfowl, and we present candidate genes that may contribute to differences in susceptibility and resistance to infectious diseases in wild birds, and that may be manipulated by viruses. Our findings improve our understanding of the interplay between host genetics and pathogens, and offer the opportunity for new insights into pathogenesis and potential drug targets

Private Bag X54001

other individuals familiar from earlier in life when foraging, but select for partners that are 38 unfamiliar during mate choice. We found no effect of either personality or dominance on 39 foraging associations or mate choice. Our study shows how using social network analysis can 40 increase our understanding of the drivers behind population structure (in our case kin 41 selection and inbreeding avoidance). Moreover, our study demonstrates that social networks 42 can be largely determined by long-term processes, in particular early-life familiarity. Flack et al. 2006; Lusseau et al. 2011; Hirsch et al. 2012; Madden et al. 2012 based on earlier findings in this species (Choudhury &amp; Black 1994; Black &amp; Owen 1995). 90 We had no a priori expectations in respect of dominance or boldness (Schuett et al. 2010). and Sons, &apos;t Zand, the Netherlands) and after the experiments geese were returned to the 115 breeding farm. were circa two years of age. Two weeks before, the geese were separated into two single-sex 120 flocks, allowing the study of sex-specific factors that may contribute to association 121 preferences while avoiding any confounding inter-sexual interactions. We thus performed our 122 observations on one group consisting of all males, and one group consisting of all females. were seen together out of the total number of times those individuals were observed, thereby 141 controlling for inter-individual differences in the total number of sightings. SRI tends to be a and males similarly from 1 to 23. From these ranks, we derived a dominance distance matrix, RESULTS 274 Genetic relatedness 275 The average pairwise relatedness among all of the dyads was 0.035 ± 0.094 SD (range: 0 - females having relatively few strong and many weak connections 286 Female geese associated significantly more with individuals from the same familiarity group 287 (MRMPA: P &lt; 0.0001, 292 Average SRI within the male group was 0.034 ± 0.057 SD (range 0 -0.50), with most 293 individuals again having relatively few strong association

Final reading outcomes of the national randomized field trial of Success for All

Using a cluster randomization design, schools were randomly assigned to implement Success for All, a comprehensive reading reform model, or control methods. This article reports final literacy outcomes for a 3-year longitudinal sample of children who participated in the treatment or control condition from kindergarten through second grade and a combined longitudinal and in-mover student sample, both of which were nested within 35 schools. Hierarchical linear model analyses of all three outcomes for both samples revealed statistically significant school-level effects of treatment assignment as large as one third of a standard deviation. The results correspond with the Success for All program theory, which emphasizes both comprehensive school-level reform and targeted student-level achievement effects through a multi-year sequencing of literacy instruction