The Highly Virulent 2006 Norwegian EHEC O103:H25 Outbreak Strain Is Related to the 2011 German O104:H4 Outbreak Strain

In 2006, a severe foodborne EHEC outbreak occured in Norway. Seventeen cases were recorded and the HUS frequency was 60%. The causative strain, Esherichia coli O103:H25, is considered to be particularly virulent. Sequencing of the outbreak strain revealed resemblance to the 2011 German outbreak strain E. coli O104:H4, both in genome and Shiga toxin 2-encoding (Stx2) phage sequence. The nucleotide identity between the Stx2 phages from the Norwegian and German outbreak strains was 90%. During the 2006 outbreak, stx2-positive O103:H25 E. coli was isolated from two patients. All the other outbreak associated isolates, including all food isolates, were stx-negative, and carried a different phage replacing the Stx2 phage. This phage was of similar size to the Stx2 phage, but had a distinctive early phage region and no stx gene. The sequence of the early region of this phage was not retrieved from the bacterial host genome, and the origin of the phage is unknown. The contaminated food most likely contained a mixture of E. coli O103:H25 cells with either one of the phages

The great tit HapMap project: a continental‐scale analysis of genomic variation in a songbird

A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude – almost the entire geographical range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear ‘islands of differentiation’, even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics

Hierarchical genetic structure in an evolving species complex: insights from genome wide ddRAD data in Sebastes mentella

This is the dataset used in Saha et al study "Hierarchical genetic structure in an evolving species complex: insights from genome wide ddRAD data in Sebastes mentella", published in Plos one. File Contents F1 This file includes biological data for fish used in the study F2 This file includes SNP data from 42,228 SNPs (from 277 fish) and it also shows filtration leading to a lower number of loci and fish F3 This file includes ddRAD sequence data for the study F4 Final SNP panels (and their genotypes) used in the study (also see F5) F5 Genotypes of fish for final SNP panels when fish were not clustered as per DAPC F6 SNP allele code

Hierarchical genetic structure in an evolving species complex: insights from genome wide ddRAD data in Sebastes mentella

This is the dataset used in Saha et al study "Hierarchical genetic structure in an evolving species complex: insights from genome wide ddRAD data in Sebastes mentella", published in Plos one. File Contents F1 This file includes biological data for fish used in the study F2 This file includes SNP data from 42,228 SNPs (from 277 fish) and it also shows filtration leading to a lower number of loci and fish F3 This file includes ddRAD sequence data for the study F4 Final SNP panels (and their genotypes) used in the study (also see F5) F5 Genotypes of fish for final SNP panels when fish were not clustered as per DAPC F6 SNP allele code

Hierarchical genetic structure in an evolving species complex: Insights from genome wide ddRAD data in Sebastes mentella.

The diverse biology and ecology of marine organisms may lead to complex patterns of intraspecific diversity for both neutral and adaptive genetic variation. Sebastes mentella displays a particular life-history as livebearers, for which existence of multiple ecotypes has been suspected to complicate the genetic population structure of the species. Double digest restriction-site associated DNA was used to investigate genetic population structure in S. mentella and to scan for evidence of selection. In total, 42,288 SNPs were detected in 277 fish, and 1,943 neutral and 97 tentatively adaptive loci were selected following stringent filtration. Unprecedented levels of genetic differentiation were found among the previously defined 'shallow pelagic', 'deep pelagic' and 'demersal slope' ecotypes, with overall mean FST = 0.05 and 0.24 in neutral and outlier SNPs, respectively. Bayesian computation estimated a concurrent and historical divergence among these three ecotypes and evidence of local adaptation was found in the S. mentella genome. Overall, these findings imply that the depth-defined habitat divergence of S. mentella has led to reproductive isolation and possibly adaptive radiation among these ecotypes. Additional sub-structuring was detected within the 'shallow' and 'deep' pelagic ecotypes. Population assignment of individual fish showed more than 94% agreement between results based on SNP and previously generated microsatellite data, but the SNP data provided a lower estimate of hybridization among the ecotypes than that by microsatellite data. We identified a SNP panel with only 21 loci to discriminate populations in mixed samples based on a machine-learning algorithm. This first SNP based investigation clarifies the population structure of S. mentella, and provides novel and high-resolution genomic tools for future investigations. The insights and tools provided here can readily be incorporated into the management of S. mentella and serve as a template for other exploited marine species exhibiting similar complex life history traits

From Watsons Bay, New South Wales, ca. 1880 [picture] /

Part of collection: Collection of photographs of New South Wales, ca. 1876-1897.; Title devised by cataloguer based on inscription on image.; "C. Bayliss Photo Sydney" -- photographer's blind stamp lower left.; Inscriptions: "P.S. 'Captain Cook' I"--In pen on verso.; Condition: Edge tear upper left.; Also available in an electronic version via the Internet at: http://nla.gov.au/nla.pic-vn4193075