Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations

Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and the sophistication of inference and simulation software. However, implementing these simulations still requires substantial time and specialized knowledge. These challenges are especially pronounced for simulating genomes for species that are not well-studied, since it is not always clear what information is required to produce simulations with a level of realism sufficient to confidently answer a given question. The community-developed framework stdpopsim seeks to lower this barrier by facilitating the simulation of complex population genetic models using up-to-date information. The initial version of stdpopsim focused on establishing this framework using six well-characterized model species (Adrion et al., 2020). Here, we report on major improvements made in the new release of stdpopsim (version 0.2), which includes a significant expansion of the species catalog and substantial additions to simulation capabilities. Features added to improve the realism of the simulated genomes include non-crossover recombination and provision of species-specific genomic annotations. Through community-driven efforts, we expanded the number of species in the catalog more than threefold and broadened coverage across the tree of life. During the process of expanding the catalog, we have identified common sticking points and developed the best practices for setting up genome-scale simulations. We describe the input data required for generating a realistic simulation, suggest good practices for obtaining the relevant information from the literature, and discuss common pitfalls and major considerations. These improvements to stdpopsim aim to further promote the use of realistic whole-genome population genetic simulations, especially in non-model organisms, making them available, transparent, and accessible to everyone

CpG-creating mutations are costly in many human viruses.

Mutations can occur throughout the virus genome and may be beneficial, neutral or deleterious. We are interested in mutations that yield a C next to a G, producing CpG sites. CpG sites are rare in eukaryotic and viral genomes. For the eukaryotes, it is thought that CpG sites are rare because they are prone to mutation when methylated. In viruses, we know less about why CpG sites are rare. A previous study in HIV suggested that CpG-creating transition mutations are more costly than similar non-CpG-creating mutations. To determine if this is the case in other viruses, we analyzed the allele frequencies of CpG-creating and non-CpG-creating mutations across various strains, subtypes, and genes of viruses using existing data obtained from Genbank, HIV Databases, and Virus Pathogen Resource. Our results suggest that CpG sites are indeed costly for most viruses. By understanding the cost of CpG sites, we can obtain further insights into the evolution and adaptation of viruses

Ultralight vector dark matter search using data from the KAGRA O3GK run

Among the various candidates for dark matter (DM), ultralight vector DM can be probed by laser interferometric gravitational wave detectors through the measurement of oscillating length changes in the arm cavities. In this context, KAGRA has a unique feature due to differing compositions of its mirrors, enhancing the signal of vector DM in the length change in the auxiliary channels. Here we present the result of a search for U(1)B−L gauge boson DM using the KAGRA data from auxiliary length channels during the first joint observation run together with GEO600. By applying our search pipeline, which takes into account the stochastic nature of ultralight DM, upper bounds on the coupling strength between the U(1)B−L gauge boson and ordinary matter are obtained for a range of DM masses. While our constraints are less stringent than those derived from previous experiments, this study demonstrates the applicability of our method to the lower-mass vector DM search, which is made difficult in this measurement by the short observation time compared to the auto-correlation time scale of DM

Search for eccentric black hole coalescences during the third observing run of LIGO and Virgo

Despite the growing number of confident binary black hole coalescences observed through gravitational waves so far, the astrophysical origin of these binaries remains uncertain. Orbital eccentricity is one of the clearest tracers of binary formation channels. Identifying binary eccentricity, however, remains challenging due to the limited availability of gravitational waveforms that include effects of eccentricity. Here, we present observational results for a waveform-independent search sensitive to eccentric black hole coalescences, covering the third observing run (O3) of the LIGO and Virgo detectors. We identified no new high-significance candidates beyond those that were already identified with searches focusing on quasi-circular binaries. We determine the sensitivity of our search to high-mass (total mass M>70 M⊙) binaries covering eccentricities up to 0.3 at 15 Hz orbital frequency, and use this to compare model predictions to search results. Assuming all detections are indeed quasi-circular, for our fiducial population model, we place an upper limit for the merger rate density of high-mass binaries with eccentricities 0<e≤0.3 at 0.33 Gpc−3 yr−1 at 90\% confidence level

CpG-creating mutations are costly in many human viruses

Mutations can occur throughout the virus genome and may be beneficial, neutral or deleterious. We are interested in mutations that yield a C next to a G, producing CpG sites. CpG sites are rare in eukaryotic and viral genomes. For the eukaryotes, it is thought that CpG sites are rare because they are prone to mutation when methylated. In viruses, we know less about why CpG sites are rare. A previous study in HIV suggested that CpG-creating transition mutations are more costly than similar non-CpG-creating mutations. To determine if this is the case in other viruses, we analyzed the allele frequencies of CpG-creating and non-CpG-creating mutations across various strains, subtypes, and genes of viruses using existing data obtained from Genbank, HIV Databases, and Virus Pathogen Resource. Our results suggest that CpG sites are indeed costly for most viruses. By understanding the cost of CpG sites, we can obtain further insights into the evolution and adaptation of viruses.ISSN:0269-7653ISSN:1573-847

Ten simple rules for an inclusive summer coding program for non-computer-science undergraduates.

Since 2015, we have run a free 9-week summer program that provides non-computer science (CS) undergraduates at San Francisco State University (SFSU) with experience in coding and doing research. Undergraduate research experiences remain very limited at SFSU and elsewhere, so the summer program provides opportunities for many more students beyond the mentoring capacity of our university laboratories. In addition, we were concerned that many students from historically underrepresented (HU) groups may be unable to take advantage of traditional summer research programs because these programs require students to relocate or be available full time, which is not feasible for students who have family, work, or housing commitments. Our program, which is local and part-time, serves about 5 times as many students as a typical National Science Foundation (NSF) Research Experiences for Undergraduates (REU) program, on a smaller budget. Based on our experiences, we present 10 simple rules for busy faculty who want to create similar programs to engage non-CS HU undergraduates in computational research. Note that while some of the strategies we implement are based on evidence-based publications in the social sciences or education research literature, the original suggestions we make here are based on our trial-and-error experiences, rather than formal hypothesis testing

CanMars mission Science Team operational results: implications for operations and the sample selection process for Mars Sample Return (MSR)

The CanMars Mars sample return (MSR) analogue mission was conducted as a field and operational test for the Mars 2020 sample cache rover mission and was the most realistic known MSR rover analogue mission to-date. A rover — similar in scale to that of rover planned for NASA's Mars 2020 mission — was deployed to a scientifically relevant Mars-analogue sedimentary field site with remote mission operations conducted at the University of Western Ontario, Canada; the mission aim was to inform on best practices and optimal approaches for sample acquisition modeled on the Mars 2020 rover mission. The daily operational procedures of the CanMars Science Team were modeled on those of current missions (i.e., Mars Science Laboratory tactical operations), serving as a study of known operational workflows and as a testbed for new approaches. This paper reports on the operational results of CanMars with best-practice recommendations. CanMars was designed as a Mars 2020 mock mission and thus carried similar science objectives; these included (1) advancing the understanding of the habitability potential of a subaqueous sedimentary environment through identifying, characterizing, and caching drilled samples containing high organic carbon (as a proxy for preserved ancient biosignatures) and (2) advancing the understanding of the history of water at the site. The in situ science investigations needed to address these science objectives were guided by the Mars Exploration Program Analysis Group goals. Effective and efficient Science Team operational procedures were developed – and many lessons were documented – through daily tactical planning and science investigations employed to meet the sample acquisition goals. In addition to the documentation of the CanMars operational procedures, this paper provides a brief summary of the science results from CanMars with a focus on recommendations for future analogue missions and planetary sample return flight missions, providing specific value to operational procedures for the Mars 2020 rover mission

Institutional Reforms to Enhance Urban Water Infrastructure with Climate Change Uncertainty

Climate change adds another layer of uncertainty to the complex issue of urban water infrastructure provision. Current institutional configurations surrounding infrastructure investments are deemed inflexible and ill-equipped to deal with climate uncertainty. This paper evaluates the regulatory and planning frameworks surrounding the urban water infrastructure provision in Victoria. Regulatory inflexibility, lack of clarity in the objectives of the water agencies and opaque supply augmentation policies constrain water businesses from making flexible infrastructure decisions. Future reforms need to focus on clarifying roles and objectives of water agencies, removing barriers to supply augmentation options including inter-sectoral transfers and a regulatory model that embeds flexibility in infrastructure decision processes