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

The COVID States Project #43: COVID-19 vaccine rates and attitudes among Americans

Who has been most likely to be vaccinated? And who is most likely to be vaccine resistant? Among the early, eligible individuals, who has received the vaccine, and who has refused to be vaccinated? In this report we address these questions by examining the relationship between various sociodemographic categories and vaccination rates, vaccination resistance, vaccination hesitancy, vaccine accessibility, and vaccine refusal. We examine both the current state of these relationships, as well as changes in vaccine resistance over time. We find strong relationships between these vaccine outcomes at the individual level and age, education, income, race, partisanship, gender, and urbanicity. All of these relationships are statistically significant in a multivariable analysis; but education stands out as a particularly powerful predictor. The divergent vaccination rate likely partially reflects the complex distribution process for the vaccine that has hurt those with the least resources and knowledge to navigate that complexity. Further, the emphasis in many states on mass vaccination sites reduces the contact of vaccine skeptics with the person best able to discuss the benefits and risks of vaccination: their primary care physicians

The COVID States Project #47: Update on COVID-19 vaccine attitudes among healthcare workers

This report is an update of our February report on attitudes and vaccination rates of healthcare workers. The essential patterns are similar, with the obvious exception being the increased rates of vaccination. We focus on vaccination, vaccine resistance, vaccine hesitancy, vaccine access, and vaccine refusal

The COVID States Project #45: Vaccine hesitancy and resistance among parents

Are parents more skeptical of coronavirus vaccines than other adults? A 2017 study by the Pew Research Center found that parents—especially those with younger children—are generally more vaccine hesitant than non-parents. Moreover, in recent years, increasing numbers of parents have either delayed or forgone entirely having their children vaccinated against preventable diseases. The question thus arises as to whether this pattern applies to the COVID-19 vaccine. In a December 2020 report, we found that substantial majorities of parents supported prohibiting in-person teaching in K-12 schools, and requiring that children be vaccinated before returning to in-person classes. But does this translate into an intention among parents to vaccinate themselves? In a subsequent report (February 2021), we found stark divides in vaccine hesitancy by education, race, income, party, and other demographic factors. This raises the question of whether parents from all backgrounds are more skeptical than non-parents, or if vaccine skepticism among parents varies with party, race, or economic class. To address these questions, this report compares rates of vaccine hesitancy and resistance among respondents with or without children under age 18

The COVID States Project #41: Trajectory of health-related behaviors in New Jersey

New Jersey is similar to other states in the northeast, in that it had its initial spike in COVID-19 cases during March and April 2020, with a second wave that peaked in December 2020 and January 2021. This report presents an overview of key trends in the behavior of New Jersey residents since the first months of the pandemic, with respect to following health guidelines aimed at curbing the spread of COVID-19