The population genomic legacy of the second plague pandemic

SummaryHuman populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%–40%.1 It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).2 Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17th–19th century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics.Results and discussion STAR★Method

The population genomic legacy of the second plague pandemic

Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%-40%.1 It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).2 Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17th-19th century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics

Experimental design for determining quantitative structure activity relationship for antibacterial chitosan derivatives

To access publisher's full text version of this article click on the hyperlink at the bottom of the pageExperimental design approach was successfully used to guide the synthesis and determine the structure-activity relationship for antimicrobial derivatives of the biopolymer chitosan. Specialized software with D-optimal design capabilities was used to create a library of chitosan derivatives with optimal structural variation in order to conduct a detailed investigation of the structure-activity relationship. The derivatives contain three substituents: N,N,N-trimethylamine, N-acetyl and N-stearoyl at different degrees of substitution (DS) on the 2-amino group of chitosan. The design matrix consisted of 14 target materials that were synthesized in 'one-pot synthesis' using TBDMS-chitosan as the precursor to allow precise control of the DS. The antibacterial activity (MIC) towards the Gram positive bacteria Staphylococcus aureus and the Gram negative bacteria Escherichia coli, hemolytic activity (HC50) towards human red blood cells and solubility of the chitosan derivatives were used as the responses in the model. The response surface model was refined by removing the interaction terms to improve the statistical significance and predictive power of the model. The investigation showed that materials with DS for trimethylation in the range 0.45-0.65, acetylation in the range 0.08-0.33 and stearoylation in the range 0.22-0.29 were capable of showing high antimicrobial activity, high solubility and low hemolytic activity.Icelandic Research Fund/120443021 University of Iceland Research Fund Bergporu og Porsteins Schevings Thorsteinsso

New sequence variants associated with bone mineral density

In an extended genome-wide association study of bone mineral density among 6,865 Icelanders and a follow-up in 8,510 subjects of European descent, we identified four new genome-wide significant loci. These are near the SOST gene at 17q21, the MARK3 gene at 14q32, the SP7 gene at 12q13 and the TNFRSF11A (RANK) gene at 18q21. Furthermore, nonsynonymous SNPs in the C17orf53, LRP4, ADAM19 and IBSP genes were suggestively associated with bone density. © 2009 Nature America, Inc. All rights reserved

Ancient genomes from Iceland reveal the making of a human population

The genomes of ancient humans can reveal patterns of early human migration (see the Perspective by Achilli et al.). Iceland has a genetically distinct population, despite relatively recent settlement (∼1100 years ago). Ebenesersdóttir et al. examined the genomes of ancient Icelandic people, dating to near the colonization of Iceland, and compared them with modernday Icelandic populations. The ancient DNA revealed that the founders had Gaelic and Norse origins. Genetic drift since the initial settlement has left modern Icelanders with allele frequencies that are distinctive, although still skewed toward those of their Norse founders. Scheib et al. sequenced ancient genomes from the Channel Islands of California, USA, and Ontario, Canada. The ancient Ontario population was similar to other ancient North Americans, as well as to modern Algonquian-speaking Native Americans. In contrast, the California individuals were more like groups that now live in Mexico and South America. It appears that a genetic split and population isolation likely occurred during the Ice Age, but the peoples remixed at a later date