Global Genetic Population Structure of Bacillus anthracis

Anthrax, caused by the bacterium Bacillus anthracis, is a disease of historical and current importance that is found throughout the world. The basis of its historical transmission is anecdotal and its true global population structure has remained largely cryptic. Seven diverse B. anthracis strains were whole-genome sequenced to identify rare single nucleotide polymorphisms (SNPs), followed by phylogenetic reconstruction of these characters onto an evolutionary model. This analysis identified SNPs that define the major clonal lineages within the species. These SNPs, in concert with 15 variable number tandem repeat (VNTR) markers, were used to subtype a collection of 1,033 B. anthracis isolates from 42 countries to create an extensive genotype data set. These analyses subdivided the isolates into three previously recognized major lineages (A, B, and C), with further subdivision into 12 clonal sub-lineages or sub-groups and, finally, 221 unique MLVA15 genotypes. This rare genomic variation was used to document the evolutionary progression of B. anthracis and to establish global patterns of diversity. Isolates in the A lineage are widely dispersed globally, whereas the B and C lineages occur on more restricted spatial scales. Molecular clock models based upon genome-wide synonymous substitutions indicate there was a massive radiation of the A lineage that occurred in the mid-Holocene (3,064–6,127 ybp). On more recent temporal scales, the global population structure of B. anthracis reflects colonial-era importation of specific genotypes from the Old World into the New World, as well as the repeated industrial importation of diverse genotypes into developed countries via spore-contaminated animal products. These findings indicate humans have played an important role in the evolution of anthrax by increasing the proliferation and dispersal of this now global disease. Finally, the value of global genotypic analysis for investigating bioterrorist-mediated outbreaks of anthrax is demonstrated

Detecting autozygosity through runs of homozygosity: A comparison of three autozygosity detection algorithms

<p>Abstract</p> <p>Background</p> <p>A central aim for studying runs of homozygosity (ROHs) in genome-wide SNP data is to detect the effects of autozygosity (stretches of the two homologous chromosomes within the same individual that are identical by descent) on phenotypes. However, it is unknown which current ROH detection program, and which set of parameters within a given program, is optimal for differentiating ROHs that are truly autozygous from ROHs that are homozygous at the marker level but vary at unmeasured variants between the markers.</p> <p>Method</p> <p>We simulated 120 Mb of sequence data in order to know the true state of autozygosity. We then extracted common variants from this sequence to mimic the properties of SNP platforms and performed ROH analyses using three popular ROH detection programs, PLINK, GERMLINE, and BEAGLE. We varied detection thresholds for each program (e.g., prior probabilities, lengths of ROHs) to understand their effects on detecting known autozygosity.</p> <p>Results</p> <p>Within the optimal thresholds for each program, PLINK outperformed GERMLINE and BEAGLE in detecting autozygosity from distant common ancestors. PLINK's sliding window algorithm worked best when using SNP data pruned for linkage disequilibrium (LD).</p> <p>Conclusion</p> <p>Our results provide both general and specific recommendations for maximizing autozygosity detection in genome-wide SNP data, and should apply equally well to research on whole-genome autozygosity burden or to research on whether specific autozygous regions are predictive using association mapping methods.</p

The effects of warming on the ecophysiology of two co-existing kelp species with contrasting distributions

The northeast Atlantic has warmed significantly since the early 1980s, leading to shifts in species distributions and changes in the structure and functioning of communities and ecosystems. This study investigated the effects of increased temperature on two co-existing habitat-forming kelps: Laminaria digitata, a northern boreal species, and Laminaria ochroleuca, a southern Lusitanian species, to shed light on mechanisms underpinning responses of trailing and leading edge populations to warming. Kelp sporophytes collected from southwest United Kingdom were maintained under 3 treatments: ambient temperature (12 °C), +3 °C (15 °C) and +6 °C (18 °C) for 16 days. At higher temperatures, L. digitata showed a decline in growth rates and Fv/Fm, an increase in chemical defence production and a decrease in palatability. In contrast, L. ochroleuca demonstrated superior growth and photosynthesis at temperatures higher than current ambient levels, and was more heavily grazed. Whilst the observed decreased palatability of L. digitata held at higher temperatures could reduce top-down pressure on marginal populations, field observations of grazer densities suggest that this may be unimportant within the study system. Overall, our study suggests that shifts in trailing edge populations will be primarily driven by ecophysiological responses to high temperatures experienced during current and predicted thermal maxima, and although compensatory mechanisms may reduce top-down pressure on marginal populations, this is unlikely to be important within the current biogeographical context. Better understanding of the mechanisms underpinning climate-driven range shifts is important for habitat-forming species like kelps, which provide organic matter, create biogenic structure and alter environmental conditions for associated communities

No Reliable Association between Runs of Homozygosity and Schizophrenia in a Well-Powered Replication Study

It is well known that inbreeding increases the risk of recessive monogenic diseases, but it is less certain whether it contributes to the etiology of complex diseases such as schizophrenia. One way to estimate the effects of inbreeding is to examine the association between disease diagnosis and genome-wide autozygosity estimated using runs of homozygosity (ROH) in genome-wide single nucleotide polymorphism arrays. Using data for schizophrenia from the Psychiatric Genomics Consortium (n = 21,868), Keller et al. (2012) estimated that the odds of developing schizophrenia increased by approximately 17% for every additional percent of the genome that is autozygous (β = 16.1, CI(β) = [6.93, 25.7], Z = 3.44, p = 0.0006). Here we describe replication results from 22 independent schizophrenia case-control datasets from the Psychiatric Genomics Consortium (n = 39,830). Using the same ROH calling thresholds and procedures as Keller et al. (2012), we were unable to replicate the significant association between ROH burden and schizophrenia in the independent PGC phase II data, although the effect was in the predicted direction, and the combined (original + replication) dataset yielded an attenuated but significant relationship between Froh and schizophrenia (β = 4.86,CI(β) = [0.90,8.83],Z = 2.40,p = 0.02). Since Keller et al. (2012), several studies reported inconsistent association of ROH burden with complex traits, particularly in case-control data. These conflicting results might suggest that the effects of autozygosity are confounded by various factors, such as socioeconomic status, education, urbanicity, and religiosity, which may be associated with both real inbreeding and the outcome measures of interest

Democracy on the Steppe: A Search for Active Local Citizenship in Rural Mongolia

This study seeks to understand how engaged Mongolia’s nomadic herders and other rural citizens are in local decision-making. To do so, we conducted over sixty interviews with rural citizens, local officials, and political experts. We also carried out two page-long written surveys which were filled out by nearly two hundred rural citizens in four provinces. Though many Mongolian political experts tend to dismiss local government as powerless and treat rural citizens as homogenous entity, our research has uncovered a remarkable diversity of opinion and activism at the local level. Through their participation in bag meetings and conversations with local officials, many rural herders and planters are frequently engaged in politics even if they do not regard it as such. Despite their lack of formal budgetary control, many local governors have taken on a variety of projects with the help of international donors, often taking herder’s ideas into account. In order to strengthen Mongolia’s democracy, therefore, we recommend that foreign donors focus their support on local governments and rural civil society organizations. In addition, the Mongolian national government and organization concerned with promoting democracy should give more emphasis to citizen education in the countryside and to fostering communication amongst herders groups and local governments nationwide

What I Saw on the Road to Insurrection: Internal Political Efficacy, Conspiracy Beliefs and the Effect of Depression on Support for the January 6th Storming of the Capitol

Depression can affect individuals’ attitudes by enhancing cognitive biases and altering perceptions of risk. Some evidence suggests an association between depression and endorsing mass violence. This linkage, however, is undertheorized by social science, tentatively empirically supported, with little attention to conditions impacting the relationship. We investigate whether and how mental health during the COVID-19 pandemic influenced Americans’ attitudes regarding domestic extremist violence surrounding the 2020 election and the January 6th US Capitol riot. We develop a theory regarding the circumstances under which depression will be positively associated with supporting extremist violence. We posit that it depends on internal political efficacy, conspiracy beliefs, and their combination. We test our theory using a two-wave national survey, from November 2020, and January 2021. We find that among efficacious individuals holding conspiracy beliefs, depression is positively associated with support for the Capitol stormers and for violence in response if the respondent believed the election was decided unfairly

The COVID States Project #10: The pandemic and the protests

A multi-wave 50-state COVID-19 survey: https://covidstates.org/ From: The COVID-19 Consortium for Understanding the Public’s Policy Preferences Across States. A joint project of: Northeastern University, Harvard University, Rutgers University, and Northwestern University

The COVID States Project #11: Perceptions of school reopening safety in the US

An increasing number of school districts across the United States have announced that they will provide entirely remote learning when school resumes this fall. Others, like New York City, continue to consider alternatives, including hybrid models in which students attend school part-time. While many other countries have succeeded in reopening schools without a resurgence of cases (with some notable exceptions), they reopened in a very different context, with rates of infection in the community far lower than in many places in the United States. On the other hand, the federal government, and some state governments, continue to focus on the importance of reopening. Another complication is the role of teachers’ unions, who have expressed discomfort about their teachers’ safety and their ability to provide a safe environment for students. And among schools already reopening, some students have already tested positive for COVID-19. Parents of school-age children thus confront difficult decisions about their children’s education - decisions that will hinge on whether they believe schools can be made safe. We surveyed 19,058 adults in the 50 U.S. states and the District of Columbia for 2 weeks beginning July 10 and ending July 26, asking about their perception of the safety of returning to school. We also asked a subset of respondents whether they support reopening schools for in-person classes in the fall. We further aimed to understand whether these comfort levels vary depending on rates of infection in their community, and on other attitudes about COVID-19