A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics.

The increasing availability of genomic resequencing data sets and high-quality reference genomes across the tree of life present exciting opportunities for comparative population genomic studies. However, substantial challenges prevent the simple reuse of data across different studies and species, arising from variability in variant calling pipelines, data quality, and the need for computationally intensive reanalysis. Here, we present snpArcher, a flexible and highly efficient workflow designed for the analysis of genomic resequencing data in nonmodel organisms. snpArcher provides a standardized variant calling pipeline and includes modules for variant quality control, data visualization, variant filtering, and other downstream analyses. Implemented in Snakemake, snpArcher is user-friendly, reproducible, and designed to be compatible with high-performance computing clusters and cloud environments. To demonstrate the flexibility of this pipeline, we applied snpArcher to 26 public resequencing data sets from nonmammalian vertebrates. These variant data sets are hosted publicly to enable future comparative population genomic analyses. With its extensibility and the availability of public data sets, snpArcher will contribute to a broader understanding of genetic variation across species by facilitating the rapid use and reuse of large genomic data sets.

Comparative study highlights how gene flow shapes adaptive genomic architecture.

Adaptation to environmental conditions, and the mechanisms underlying these adaptations, can vary greatly among species. This variation can be attributed to a variety of factors including the strength of evolutionary processes like selection, gene flow, time since divergence, and/or genetic drift, as well as the interactions between these processes. A number of simulation and theoretical studies have helped elucidate the role of these processes on the genomic basis of adaptation (Schaal et al., 2022; Yeaman et al., 2016). However, complementary empirical studies to test these theoretical expectations for within-species adaptation have been limited due to the challenging nature of evaluating these processes in a comparative framework. To do this effectively, it is necessary to have systems where the range of environmental variation is similar between species, but where one or more of these evolutionary processes vary. In a From the Cover article in this issue of Molecular Ecology, Shi et al. (2022) provide an excellent example of a freshwater system where rates of gene flow differ between populations of six riverine species due to variation in spawning strategies (i.e., broadcast spawners = high gene flow, nest spawners = low gene flow), but all experience the same variation in environmental conditions across their distributions. The authors take a multivariate approach to evaluate the genomic basis of adaptation by using a combination of differentiation-based and genotype-environment association (GEA) methods. By comparing the amount of gene flow between species and the resulting genomic basis of local adaptation, they are able to infer how genomic architecture may be shaped by rates of gene flow. Their results identify a general pattern of increased genomic clustering in species with increasing levels of gene flow. However, two of six species did not follow this pattern, which could be due to additional factors not assessed. Additionally, they provide convincing evidence that the underlying evolutionary mechanisms that formed genomic clusters within each species vary. These deviations from a general pattern highlight how difficult evaluating these processes in natural populations are, particularly because species-specific responses can vary dramatically. Taken together, their comparative framework for assessing the genomic architecture of adaptation is unique, sheds important light on how evolutionary processes can impact adaptation, and provides robust empirical support of foundational theoretical and simulation studies.

Evolution of thermal physiology alters the projected range of threespine stickleback under climate change.

Species distribution models (SDMs) are widely used to predict range shifts but could be unreliable under climate change scenarios because they do not account for evolution. The thermal physiology of a species is a key determinant of its range and thus incorporating thermal trait evolution into SDMs might be expected to alter projected ranges. We identified a genetic basis for physiological and behavioural traits that evolve in response to temperature change in natural populations of threespine stickleback (Gasterosteus aculeatus). Using these data, we created geographical range projections using a mechanistic niche area approach under two climate change scenarios. Under both scenarios, trait data were either static ("no evolution" models), allowed to evolve at observed evolutionary rates ("evolution" models) or allowed to evolve at a rate of evolution scaled by the trait variance that is explained by quantitative trait loci (QTL; "scaled evolution" models). We show that incorporating these traits and their evolution substantially altered the projected ranges for a widespread panmictic marine population, with over 7-fold increases in area under climate change projections when traits are allowed to evolve. Evolution-informed SDMs should improve the precision of forecasting range dynamics under climate change, and aid in their application to management and the protection of biodiversity.

Species- and site-specific genome editing in complex bacterial communities.

Understanding microbial gene functions relies on the application of experimental genetics in cultured microorganisms. However, the vast majority of bacteria and archaea remain uncultured, precluding the application of traditional genetic methods to these organisms and their interactions. Here, we characterize and validate a generalizable strategy for editing the genomes of specific organisms in microbial communities. We apply environmental transformation sequencing (ET-seq), in which nontargeted transposon insertions are mapped and quantified following delivery to a microbial community, to identify genetically tractable constituents. Next, DNA-editing all-in-one RNA-guided CRISPR-Cas transposase (DART) systems for targeted DNA insertion into organisms identified as tractable by ET-seq are used to enable organism- and locus-specific genetic manipulation in a community context. Using a combination of ET-seq and DART in soil and infant gut microbiota, we conduct species- and site-specific edits in several bacteria, measure gene fitness in a nonmodel bacterium and enrich targeted species. These tools enable editing of microbial communities for understanding and control.

Mitochondrial volume density and evidence for its role in adaptive divergence in response to thermal tolerance in threespine stickleback.

Phenotypic plasticity is predicted to permit persistence in new environments, and may subsequently evolve to enhance fitness. Colonizing environments with lower winter temperatures can lead to the evolution of lower critical thermal minima; the corresponding physiological traits associated with temperature tolerance are predicted to involve mitochondrial function. Threespine stickleback (Gasterosteus aculeatus) have colonized freshwater lakes along the Pacific Northwest. These freshwater populations are known to exhibit cold-induced increases in mitochondrial volume density in pectoral muscle, but whether such plasticity evolved before or after colonization is uncertain. Here, we measure critical thermal minima (CTmin) in one marine and one freshwater population of threespine stickleback, and mitochondrial volume density in pectoral and cardiac tissue of both populations acclimated to different temperature treatments (6.2, 14.5 and 20.6 â„ƒ). Mitochondrial volume density increased with cold acclimation in pectoral muscle; cardiac muscle was non-plastic but had elevated mitochondrial volume densities compared to pectoral muscle across all temperature treatments. There were no differences in the levels of plasticity between marine and freshwater stickleback, but neither were there differences in CTmin. Importantly, marine stickleback exhibited plasticity under low-salinity conditions, suggesting that marine stickleback had at least one necessary phenotype for persistence in freshwater environments before colonization occurred.

The ontogenetic scaling of form and function in the spotted ratfish, Hydrolagus colliei (Chondrichthyes: Chimaeriformes): Fins, muscles, and locomotion.

The alteration of form and function through the life of a fish can have profound impacts on the ability to move through water. Although several studies have examined morphology and function in relation to body size, there is a paucity of data for chondrichthyans, an ancient group of fishes. Ratfishes are interesting in that they utilize flapping pectoral fins to drive movement, and they diverged from elasmobranchs early in the gnathostome phylogeny. Using the spotted ratfish, Hydrolagus colliei, we quantified the scaling of traits relevant for locomotion, including median and paired fin external anatomy, the musculature of the pectoral and pelvic fins, and the kinematics of the pectoral fins. Whereas pelvic fins scaled with either positive allometry (fin span and area) or isometry (fin chord length at the base of the fin), pectoral fin measurements either scaled with negative allometry (fin span and aspect ratio) or isometry (fin area and chord length). Correspondingly, all pelvic fin muscles exhibited positive allometry, whereas pectoral muscles exhibited a mix of isometric and positively allometric growth. Caudal fin area and body frontal area both scaled with positive allometry, whereas dorsal fin area and span scale with isometry. Pectoral fin amplitude during swimming exhibited isometry, and fin beat frequency decreased with body size. Our results highlight the complex changes in form and function throughout ontogeny. Finally, we highlight that hierarchical differentiation in morphology can occur during growth, potentially leading to complex changes in performance of a functional system.

Rape Myth Consistency and Gender Differences in Perceiving Rape Victims: A Meta-Analysis.

An overview discusses feminist analyses of oppression, attitudes toward rape victims, and previously studied predictors of individuals' attitudes toward rape victims. To better understand such attitudes, this meta-analysis examines the moderating influences of various rape victim, perpetrator, and crime characteristics' rape myth consistency on gender differences in individuals' perceptions of rape victims (i.e., victim responsibility and blame attributions and rape minimizing attitudes). Consistent with feminist theoretical predictions, results indicated that, overall, men perceived rape victims more negatively than women did. However, this sex difference was moderated by the rape myth consistency within the rape vignettes. Implications for research are discussed.

Individuals' beliefs about the etiology of same-sex sexual orientation.

We examined the relationships between beliefs about the etiology of having a same-sex sexual orientation, sexual prejudice, and support for gay-relevant legislation using the justification-suppression model of prejudice as our theoretical foundation. Results indicated that more belief that a same-sex sexual orientation was due to nurture factors predicted less support for gay-relevant legislation, and that this relationship was mediated by levels of sexual prejudice. The opposite pattern was found for belief that a same-sex sexual orientation was due to nature factors. This suggests that beliefs about the etiology of sexual orientation may serve as justification (or suppression) factors in the expression of prejudice toward gay men and lesbians.

Oppression through acceptance?: predicting rape myth acceptance and attitudes toward rape victims.

Feminist theories of rape motivation are based on research suggesting a relationship between dominance and sexual aggression. However, the relationship between dominance and rape myth acceptance (RMA), a predictor of rape proclivity and sexual aggression and a key component in feminist theory, is understudied. The current study tests the hypotheses that individuals' scores on sex-based oppression and intergroup dominance measures will improve the predictive models for RMA and attitudes toward rape and rape victims. The hypotheses are supported. Individuals' general intergroup dominance and sex-based oppression attitudes provide significant unique prediction beyond previously studied predictors of attitudes about rape and rape victims.

The interference effect of men's handling of muscular action figures on a lexical decision task.

It has been shown in previous work [Action figures and men. Sex Roles 53, 877-885] that male participants who handled extremely muscular action figures had lower body esteem than those who did not handle action figures or a Ken doll. However, the internal mechanisms that dictated this effect are unclear. Therefore, the current study extended this previous work by having male participants handle action figures of varying muscularity and completing a lexical decision task with target words that consisted of both positive and negative body words and feeling words in order to determine if males would be primed to think negatively about their bodies and self or if positive thoughts about their bodies and self would be interfered with. The results show that those participants who handled the extremely muscular action figures responded significantly more slowly to feeling positive words (e.g., content, confident) and marginally more slowly to body positive words (e.g., muscle, bicep) than those who did not handle any action figures. Overall, this suggests that the interference of positive words, not the priming of negative words, is the internal mechanism that produces the decreased body image satisfaction after exposure to muscular stimuli. Implications and future research are discussed.