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Abstract The Context-dependent Mutation Analysis Package and Visualization Software (CDMAP/CDVIS) is an automated, modular toolkit used for the analysis and visualization of context-dependent mutation patterns (site-specific variation in mutation rate from neighboring-nucleotide effects). The CDMAP computes context-dependent mutation rates using a Variant Call File (VCF), Genbank file, and reference genome and can generate high-resolution figures to analyze variation in mutation rate across spatiotemporal scales. This algorithm has been benchmarked against mutation accumulation data but can also be used to calculate context-dependent mutation rates for polymorphism or closely related species as long as the input requirements are met. Output from CDMAP can be integrated into CDVIS, an interactive database for visualizing mutation patterns across multiple taxa simultaneously. 

Abstract Low-mass galaxy pair fractions are understudied, and it is unclear whether low-mass pair fractions evolve in the same way as more massive systems over cosmic time. In the era of JWST, Roman, and Rubin, selecting galaxy pairs in a self-consistent way will be critical to connect observed pair fractions to cosmological merger rates across all mass scales and redshifts. Utilizing the Illustris TNG100 simulation, we create a sample of physically associated low-mass (10⁸<M_*< 5 × 10⁹M_⊙) and high-mass (5 × 10⁹<M_*< 10¹¹M_⊙) pairs betweenz= 0 and 4.2. The low-mass pair fraction increases fromz= 0 to 2.5, while the high-mass pair fraction peaks atz= 0 and is constant or slightly decreasing atz> 1. Atz= 0 the low-mass major (1:4 mass ratio) pair fraction is 4× lower than high-mass pairs, consistent with findings for cosmological merger rates. We show that separation limits that vary with the mass and redshift of the system, such as scaling by the virial radius of the host halo (r_sep< 1R_vir), are critical for recovering pair fraction differences between low-mass and high-mass systems. Alternatively, static physical separation limits applied equivalently to all galaxy pairs do not recover the differences between low- and high-mass pair fractions, even up to separations of 300 kpc. Finally, we place isolated mass analogs of Local Group galaxy pairs, i.e., Milky Way (MW)–M31, MW–LMC, LMC–SMC, in a cosmological context, showing that isolated analogs of LMC–SMC-mass pairs and low-separation (<50 kpc) MW–LMC-mass pairs are 2–3× more common atz≳ 2–3. 

Abstract Understanding how mutations affect survivability is a key component to knowing how organisms and complex traits evolve. However, most mutations have a minor effect on fitness and these effects are difficult to resolve using traditional molecular techniques. Therefore, there is a dire need for more accurate and precise fitness measurements methods. Here, we measured the fitness effects in Burkholderia cenocepacia HI2424 mutation accumulation (MA) lines using droplet-digital polymerase chain reaction (ddPCR). Overall, the fitness measurements from ddPCR-MA are correlated positively with fitness measurements derived from traditional phenotypic marker assays (r = 0.297, P = 0.05), but showed some differences. First, ddPCR had significantly lower measurement variance in fitness (F = 3.78, P < 2.6 × 10−13) in control experiments. Second, the mean fitness from ddPCR-MA measurements were significantly lower than phenotypic marker assays (−0.0041 vs −0.0071, P = 0.006). Consistent with phenotypic marker assays, ddPCR-MA measurements observed multiple (27/43) lineages that significantly deviated from mean fitness, suggesting that a majority of the mutations are neutral or slightly deleterious and intermixed with a few mutations that have extremely large effects. Of these mutations, we found a significant excess of mutations within DNA excinuclease and Lys R transcriptional regulators that have extreme deleterious and beneficial effects, indicating that modifications to transcription and replication may have a strong effect on organismal fitness. This study demonstrates the power of ddPCR as a ubiquitous method for high-throughput fitness measurements in both DNA- and RNA-based organisms regardless of cell type or physiology. 

ABSTRACT Powerful outflows are thought to play a critical role in galaxy evolution and black hole growth. We present the first large-scale systematic study of ionized outflows in paired galaxies and post-mergers compared to a robust control sample of isolated galaxies. We isolate the impact of the merger environment to determine if outflow properties depend on merger stage. Our sample contains ∼4000 paired galaxies and ∼250 post-mergers in the local universe (0.02 ≤ z ≤ 0.2) from the Sloan Digital Sky Survey Data Release 7 (SDSS DR 7) matched in stellar mass, redshift, local density of galaxies, and [O iii] λ5007 luminosity to a control sample of isolated galaxies. By fitting the [O iii] λ5007 line, we find ionized outflows in ∼15 per cent of our entire sample. Outflows are much rarer in star-forming galaxies compared to active galactic nuclei (AGNs), and outflow incidence and velocity increase with [O iii] λ5007 luminosity. Outflow incidence is significantly elevated in the optical + mid-infrared selected AGN compared to purely optical AGN; over 60 per cent show outflows at the highest luminosities ($$L_{\mathrm{[OIII]~\lambda 5007}}\, \gtrsim$$ 1042 erg s−1), suggesting mid-infrared AGN selection favours galaxies with powerful outflows, at least for higher [O iii] λ5007 luminosities. However, we find no statistically significant difference in outflow incidence, velocity, and luminosity in mergers compared to isolated galaxies, and there is no dependence on merger stage. Therefore, while interactions are predicted to drive gas inflows and subsequently trigger nuclear star formation and accretion activity, when the power source of the outflow is controlled for, the merging environment has no further impact on the large-scale ionized outflows as traced by [O iii] λ5007. 

ABSTRACT We investigate the spatial structure and evolution of star formation and the interstellar medium (ISM) in interacting galaxies. We use an extensive suite of parsec-scale galaxy-merger simulations (stellar mass ratio = 2.5:1), which employs the ‘Feedback In Realistic Environments-2’ model (fire-2). This framework resolves star formation, feedback processes, and the multiphase structure of the ISM. We focus on the galaxy-pair stages of interaction. We find that close encounters substantially augment cool (H i) and cold-dense (H2) gas budgets, elevating the formation of new stars as a result. This enhancement is centrally concentrated for the secondary galaxy, and more radially extended for the primary. This behaviour is weakly dependent on orbital geometry. We also find that galaxies with elevated global star formation rate (SFR) experience intense nuclear SFR enhancement, driven by high levels of either star formation efficiency (SFE) or available cold-dense gas fuel. Galaxies with suppressed global SFR also contain a nuclear cold-dense gas reservoir, but low SFE levels diminish SFR in the central region. Concretely, in the majority of cases, SFR enhancement in the central kiloparsec is fuel-driven (55 per cent for the secondary, 71 per cent for the primary) – while central SFR suppression is efficiency-driven (91 per cent for the secondary, 97 per cent for the primary). Our numerical predictions underscore the need of substantially larger, and/or merger-dedicated, spatially resolved galaxy surveys – capable of examining vast and diverse samples of interacting systems – coupled with multiwavelength campaigns aimed to capture their internal ISM structure. 

We quantify the frequency of companions of low-redshift (0.013 < z < 0.0252) dwarf galaxies (2 × 108 M⊙ < Mstar < 5 × 109 M⊙) that are isolated from more massive galaxies in SDSS and compare against cosmological expectations using mock observations of the Illustris simulation. Dwarf multiples are defined as two or more dwarfs that have angular separations >55 arcsec, projected separations rp < 150 kpc, and relative line-of-sight velocities ΔVLOS < 150 km s-1. While the mock catalogues predict a factor of two more isolated dwarfs than observed in SDSS, the mean number of observed companions per dwarf is Nc ˜ 0.04, in good agreement with Illustris when accounting for SDSS sensitivity limits. Removing these limits in the mock catalogues predicts Nc ˜ 0.06 for future surveys (LSST, DESI), which will be complete to Mstar = 2 × 108 M⊙. The 3D separations of mock dwarf multiples reveal a contamination fraction of ˜40 per cent in observations from projection effects. Most isolated multiples are pairs; triples are rare and it is cosmologically improbable that bound groups of dwarfs with more than three members exist within the parameter range probed in this study. We find that <1 per cent of LMC-analogues in the field have an SMC-analogue companion. The fraction of dwarf "Major Pairs" (stellar mass ratio >1:4) steadily increases with decreasing Primary stellar mass, whereas the cosmological "Major Merger rate" (per Gyr) has the opposite behaviour. We conclude that cosmological simulations can be reliably used to constrain the fraction of dwarf mergers across cosmic time.