Both congruent and incongruent trials drive the congruency sequence effect: Novel support for an episodic retrieval view of adaptive control in the prime-probe task.

The congruency effect in Stroop-like tasks-a popular measure of distraction-is smaller after incongruent relative to congruent trials. However, it is unclear whether this congruency sequence effect (CSE)-a popular index of coping with distraction-reflects adjustments of control after congruent trials, incongruent trials, or both. The episodic retrieval account of the CSE posits adjustments of control after both congruent and incongruent trials. In this account, retrieving a memory of the previous trial's congruency (i.e., congruent or incongruent) biases control processes to prepare for an upcoming trial with the same congruency (i.e., congruent or incongruent). In contrast, the default setting account posits adjustments of control after a single trial type. For example, control processes might increase inhibition of the response cued by the distractor after incongruent trials but make no adjustments after congruent trials. To distinguish between these accounts for the first time while (a) using long distractor-target intervals and (b) excluding prevalent feature integration and contingency learning confounds, we employed a confound-minimized prime-probe task with neutral trials. We usually observed adjustments of control after both trial types. Furthermore, whether the reduction of the congruency effect after incongruent trials indexed (a) inhibition of the distractor-congruent response or (b) activation of the distractor-incongruent response depended on whether the distractor and target were same-sized or different-sized, respectively. These findings favor the episodic retrieval account of the CSE over the default setting account. They also indicate that "low-level" stimulus properties may influence the nature of "high-level" control adjustments. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Proactive response preparation contributes to contingency learning: novel evidence from force-sensitive keyboards.

Contingency learning can involve learning that the identity of one stimulus in a sequence predicts the identity of the next stimulus. It remains unclear, however, whether such learning speeds responses to the next stimulus only by reducing the threshold for triggering the expected response after stimulus onset or also by preparing the expected response before stimulus onset. To distinguish between these competing accounts, we manipulated the probabilities with which each of two prime arrows (Left and Right) were followed by each of two probe arrows (Up and Down) in a prime-probe task while using force-sensitive keyboards to monitor sub-threshold finger force. Consistent with the response preparation account, two experiments revealed greater force just before probe onset on the response key corresponding to the direction in which the probe was more (versus less) likely to point (e.g., Up vs. Down). Furthermore, mirroring sequential contingency effects in behavior, this pre-probe force effect vanished after a single low-probability trial. These findings favor the response preparation account over the threshold only account. They also suggest the possibility that contingency learning in our tasks indexes trial-by-trial expectations regarding the utility of the prime for predicting the upcoming probe.

Average Nucleotide Identity based Staphylococcus aureus strain grouping allows identification of strain-specific genes in the pangenome.

Staphylococcus aureus causes both hospital and community acquired infections in humans worldwide. Due to the high incidence of infection S. aureus is also one of the most sampled and sequenced pathogens today, providing an outstanding resource to understand variation at the bacterial subspecies level. We processed and downsampled 83,383 public S. aureus Illumina whole genome shotgun sequences and 1,263 complete genomes to produce 7,954 representative substrains. Pairwise comparison of core gene Average Nucleotide Identity (ANI) revealed a natural boundary of 99.5% that could be used to define 145 distinct strains within the species. We found that intermediate frequency genes in the pangenome (present in 10-95% of genomes) could be divided into those closely linked to strain background ("strain-concentrated") and those highly variable within strains ("strain-diffuse"). Non-core genes had different patterns of chromosome location; notably, strain-diffuse associated with prophages, strain-concentrated with the vSaß genome island and rare genes (<10% frequency) concentrated near the origin of replication. Antibiotic genes were enriched in the strain-diffuse class, while virulence genes were distributed between strain-diffuse, strain-concentrated, core and rare classes. This study shows how different patterns of gene movement help create strains as distinct subspecies entities and provide insight into the diverse histories of important S. aureus functions.

Comparing partial repetition costs in two- and four-choice tasks: Evidence for abstract relational codes.

Responses are slower in two-choice tasks when either a previous stimulus feature or the previous response repeats than when all features repeat or all features change. Current views of action control posit that such partial repetition costs (PRCs) index the time to update a prior "binding" between a stimulus feature and the response or to resolve processing conflicts between retrieved and current features. However, violating a heuristic that stimulus feature repetitions and changes "signal" repetitions or changes of the previous response, respectively, may also contribute to such costs. To determine whether such relational codes affect performance, we compared PRCs in two- and four-choice tasks. While a stimulus feature repetition signals a response repetition in both tasks, a stimulus feature change signals a specific alternative response only in a two-choice task. Consistent with the signaling hypothesis, we observed similar complete repetition benefits in the two- and four-choice tasks but smaller complete change benefits in the four-choice task. We also investigated whether the smaller complete change benefit in the four-choice task-that is, the signaling effect-varies with the validity of the signal in the previous trial. In all four experiments, we observed a larger signaling effect after trials in which stimulus changes or repetitions corresponded to response changes or repetitions, respectively, than after trials in which stimulus changes did not correspond with response changes. We conclude that signaling contributes to PRCs, which indicates that bindings include relational codes. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

Effect-less? Event-files are not terminated by distal action effects.

Event-files that bind features of stimuli, responses, and action effects figure prominently in contemporary views of action control. When a previous feature repeats, a previous event-file is retrieved and can influence current performance. It is unclear, however, what terminates an event-file. A tacit assumption is that registering the distal (e.g., visual or auditory) sensory consequences of an action (i.e., the "action effect") terminates the event-file, thereby making it available for retrieval. We tested three different action-effect conditions (no distal action effect, visual action effect, or auditory action effect) in the same stimulus-response (S-R) binding task and observed no modulation of S-R binding effects. Instead, there were comparably large binding effects in all conditions. This suggests that proximal (e.g., somatosensory, proprioceptive) action effects terminate event-files independent of distal (e.g., visual, auditory) action effects or that the role event-file termination plays for S-R binding effects needs to be corrected. We conclude that current views of action control require further specification.

Fifty shades of greenbeard: robust evolution of altruism based on similarity of complex phenotypes.

We study the evolution of altruistic behaviour under a model where individuals choose to cooperate by comparing a set of continuous phenotype tags. Individuals play a donation game and only donate to other individuals that are sufficiently similar to themselves in a multidimensional phenotype space. We find the generic maintenance of robust altruism when phenotypes are multidimensional. Selection for altruism is driven by the coevolution of individual strategy and phenotype; altruism levels shape the distribution of individuals in phenotype space. Low donation rates induce a phenotype distribution that renders the population vulnerable to the invasion of altruists, whereas high donation rates prime a population for cheater invasion, resulting in cyclic dynamics that maintain substantial levels of altruism. Altruism is therefore robust to invasion by cheaters in the long term in this model. Furthermore, the shape of the phenotype distribution in high phenotypic dimension allows altruists to better resist the invasion by cheaters, and as a result the amount of donation increases with increasing phenotype dimension. We also generalize previous results in the regime of weak selection to two competing strategies in continuous phenotype space, and show that success under weak selection is crucial to success under strong selection in our model. Our results support the viability of a simple similarity-based mechanism for altruism in a well-mixed population.

Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes.

Bacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecting coevolving genes from large datasets of bacterial genomes based on pairwise comparisons of closely related individuals, analogous to a pedigree study in eukaryotic populations. We apply our method to pairs of genes from the Staphylococcus aureus accessory genome of over 75,000 annotated gene families using a database of over 40,000 whole genomes. We find many pairs of genes that appear to be gained or lost in a coordinated manner, as well as pairs where the gain of one gene is associated with the loss of the other. These pairs form networks of rapidly coevolving genes, primarily consisting of genes involved in virulence, mechanisms of horizontal gene transfer, and antibiotic resistance, particularly the SCCmec complex. While we focus on gene gain and loss, our method can also detect genes that tend to acquire substitutions in tandem, or genotype-phenotype or phenotype-phenotype coevolution. Finally, we present the R package DeCoTUR that allows for the computation of our method.

Modeling the evolution of recombination plasticity: A prospective review.

Meiotic recombination is one of the main sources of genetic variation, a fundamental factor in the evolutionary adaptation of sexual eukaryotes. Yet, the role of variation in recombination rate and other recombination features remains underexplored. In this review, we focus on the sensitivity of recombination rates to different extrinsic and intrinsic factors. We briefly present the empirical evidence for recombination plasticity in response to environmental perturbations and/or poor genetic background and discuss theoretical models developed to explain how such plasticity could have evolved and how it can affect important population characteristics. We highlight a gap between the evidence, which comes mostly from experiments with diploids, and theory, which typically assumes haploid selection. Finally, we formulate open questions whose solving would help to outline conditions favoring recombination plasticity. This will contribute to answering the long-standing question of why sexual recombination exists despite its costs, since plastic recombination may be evolutionary advantageous even in selection regimes rejecting any non-zero constant recombination.

Response-repetition costs in task switching do not index a simple response-switch bias: Evidence from manipulating the number of response alternatives.

Response repetitions aid performance when a task repeats but impair performance when a task switches. Although this interaction is robust, theoretical accounts remain controversial. Here, we used an un-cued, predictable task-switching paradigm with univalent targets to explore whether a simple bias to switch the response when the task switches can explain the interaction. In Experiment 1A (n = 40), we replicated the basic interaction in a two-choice task. In Experiment 1B (n = 60), we observed the same interaction in a three-choice task, wherein a bias to switch the response when the task switches cannot prime a specific alternative response because both remaining response alternatives are equally likely. Exploratory comparisons revealed a larger interaction between task repetition and response repetition in the three-choice task than in the two-choice task for mean response time (RT) and the opposite pattern for mean error rate (ER). Critically, in the three-choice task, response-repetition costs in task switches were significant in both RT and ER. Since a bias to switch the response cannot prime a specific response alternative in a three-choice task, we conclude that such a bias cannot account for response-repetition costs in task-switch trials.

Altruistic responses to the most vulnerable involve sensorimotor processes.

Introduction: Why do people help strangers? Prior research suggests that empathy motivates bystanders to respond to victims in distress. However, this work has revealed relatively little about the role of the motor system in human altruism, even though altruism is thought to have originated as an active, physical response to close others in immediate need. We therefore investigated whether a motor preparatory response contributes to costly helping. Methods: To accomplish this objective, we contrasted three charity conditions that were more versus less likely to elicit an active motor response, based on the Altruistic Response Model. These conditions described charities that (1) aided neonates versus adults, (2) aided victims requiring immediate versus preparatory support, and (3) provided heroic versus nurturant aid. We hypothesized that observing neonates in immediate need would elicit stronger brain activation in motor-preparatory regions. Results: Consistent with an evolutionary, caregiving-based theory of altruism, participants donated the most to charities that provided neonates with immediate, nurturant aid. Critically, this three-way donation interaction was associated with increased BOLD signal and gray matter volume in motor-preparatory regions, which we identified in an independent motor retrieval task. Discussion: These findings advance the field of altruism by shifting the spotlight from passive emotional states toward action processes that evolved to protect the most vulnerable members of our group.

Isolation by distance in populations with power-law dispersal.

Limited dispersal of individuals between generations results in isolation by distance, in which individuals further apart in space tend to be less related. Classic models of isolation by distance assume that dispersal distances are drawn from a thin-tailed distribution and predict that the proportion of the genome that is identical by descent between a pair of individuals should decrease exponentially with the spatial separation between them. However, in many natural populations, individuals occasionally disperse over very long distances. In this work, we use mathematical analysis and coalescent simulations to study the effect of long-range (power-law) dispersal on patterns of isolation by distance. We find that it leads to power-law decay of identity-by-descent at large distances with the same exponent as dispersal. We also find that broad power-law dispersal produces another, shallow power-law decay of identity-by-descent at short distances. These results suggest that the distribution of long-range dispersal events could be estimated from sequencing large population samples taken from a wide range of spatial scales.

Partial repetition costs index a mixture of binding and signaling.

People respond more slowly in two-choice tasks when either a previous stimulus feature or the previous response repeats in partial repetition trials than when (a) both repeat in complete repetition trials or (b) both alternate in complete alternation trials. The binding account posits that such partial repetition costs index a memory-retrieval conflict, which occurs because partial repetition trials trigger the retrieval of a previous stimulus feature or response that conflicts with a current stimulus feature or response. However, such costs may additionally reflect a simple decision-making heuristic that uses the repetition or alternation of a previous stimulus feature as a "signal" to bias response selection toward a repetition or an alternation of the previous response. To determine whether signaling contributes to partial repetition costs, we employed a four-choice task. Here, a stimulus feature repetition still signals a response repetition, but a stimulus feature alternation does not signal which of the three remaining responses to make. Consistent with an influence of signaling, we sometimes observed complete repetition advantages without complete alternation advantages. Exploratory analyses further revealed that partial repetition costs measured more broadly were smaller in the four-choice task than in a matched two-choice task. These findings suggest that partial repetition costs index a mixture of binding and signaling.

The binary structure of event files generalizes to abstract features: A nonhierarchical explanation of task set boundaries for the congruency sequence effect.

Current views posit that forming and retrieving memories of ongoing events influences action control. However, the organizational structure of these memories, or event files, remains unclear. The hierarchical coding view posits a hierarchical structure, wherein task sets occupy a high level of the hierarchy. Here, the contents of an event file can be retrieved only if the task set repeats. In contrast, the binary coding view posits a nonhierarchical structure, which consists of a collection of independent, binary bindings between different feature pairs. In this view, repeating an abstract feature from a previous event (e.g., the previous trial's S-R mapping) triggers the retrieval of the associated feature from the same binding (e.g., the previous trial's congruency) even if the task set changes. To distinguish between these views, we investigated the nature of task set boundaries for the congruency sequence effect (CSE), an index of adaptive control that reflects event file formation and retrieval. Specifically, we investigated whether or not a CSE appears when the task set changes but the previous trial's S-R mapping repeats. Three experiments involving a cross-modal prime-probe task yielded a CSE under these conditions and ruled out alternative explanations. These findings show that the typical binary structure of event files generalizes from concrete features (e.g., colors and locations) to abstract features (e.g., S-R mappings and task sets). Therefore, contrary to the hierarchical coding view, they provide a nonhierarchical explanation of task set boundaries for the CSE. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

Spatial structure alters the site frequency spectrum produced by hitchhiking.

The reduction of genetic diversity due to genetic hitchhiking is widely used to find past selective sweeps from sequencing data, but very little is known about how spatial structure affects hitchhiking. We use mathematical modeling and simulations to find the unfolded site frequency spectrum left by hitchhiking in the genomic region of a sweep in a population occupying a 1D range. For such populations, sweeps spread as Fisher waves, rather than logistically. We find that this leaves a characteristic 3-part site frequency spectrum at loci very close to the swept locus. Very low frequencies are dominated by recent mutations that occurred after the sweep and are unaffected by hitchhiking. At moderately low frequencies, there is a transition zone primarily composed of alleles that briefly "surfed" on the wave of the sweep before falling out of the wavefront, leaving a spectrum close to that expected in well-mixed populations. However, for moderate-to-high frequencies, there is a distinctive scaling regime of the site frequency spectrum produced by alleles that drifted to fixation in the wavefront and then were carried throughout the population. For loci slightly farther away from the swept locus on the genome, recombination is much more effective at restoring diversity in 1D populations than it is in well-mixed ones. We find that these signatures of space can be strong even in apparently well-mixed populations with negligible spatial genetic differentiation, suggesting that spatial structure may frequently distort the signatures of hitchhiking in natural populations.

Heterogeneity in viral populations increases the rate of deleterious mutation accumulation.

RNA viruses have high mutation rates, with the majority of mutations being deleterious. We examine patterns of deleterious mutation accumulation over multiple rounds of viral replication, with a focus on how cellular coinfection and heterogeneity in viral output affect these patterns. Specifically, using agent-based intercellular simulations we find, in agreement with previous studies, that coinfection of cells by viruses relaxes the strength of purifying selection and thereby increases the rate of deleterious mutation accumulation. We further find that cellular heterogeneity in viral output exacerbates the rate of deleterious mutation accumulation, regardless of whether this heterogeneity in viral output is stochastic or is due to variation in the cellular multiplicity of infection. These results highlight the need to consider the unique life histories of viruses and their population structure to better understand observed patterns of viral evolution.

Rethinking attentional reset: Task sets determine the boundaries of adaptive control.

Adaptive control processes that minimise distraction often operate in a context-specific manner. For example, they may minimise distraction from irrelevant conversations during a lecture but not in the hallway afterwards. It remains unclear, however, whether (a) salient perceptual features or (b) task sets based on such features serve as contextual boundaries for adaptive control in standard distractor-interference tasks. To distinguish between these possibilities, we manipulated whether the structure of a standard, visual distractor-interference task allowed (Experiment 1) or did not allow (Experiment 2) participants to associate salient visual features (i.e., colour patches and colour words) with different task sets. We found that changing salient visual features across consecutive trials reduced a popular measure of adaptive control in distractor-interference tasks-the congruency sequence effect (CSE)-only when the task structure allowed participants to associate these visual features with different task sets. These findings extend prior support for the task set hypothesis from somewhat atypical cross-modal tasks to a standard unimodal task. In contrast, they pose a challenge to an alternative "attentional reset" hypothesis, and related views, wherein changing salient perceptual features always results in a contextual boundary for the CSE.

Fitness dependence preserves selection for recombination across diverse mixed mating strategies.

Meiotic recombination and the factors affecting its rate and fate in nature have inspired many studies in theoretical evolutionary biology. Classical theoretical models have inferred that recombination can be favored under a rather restricted parameter range. Thus, the ubiquity of recombination in nature remains an open question. However, these models assumed constant recombination with an equal rate across all individuals within the population, whereas empirical evidence suggests that recombination may display certain sensitivity to ecological stressors and/or genotype fitness. Models assuming condition-dependent recombination show that such a strategy can often be favored over constant recombination. Moreover, in our recent model with panmictic populations subjected to purifying selection, fitness-dependent recombination was quite often favored even when any constant recombination was rejected. By using numerical modeling, we test whether such a 'recombination-rescuing potential' of fitness dependence holds also beyond panmixia, given the recognized effect of mating strategy on the evolution of recombination. We show that deviations from panmixia generally increase the recombination-rescuing potential of fitness dependence, with the strongest effect under intermediate selfing or high clonality. We find that under partial clonality, the evolutionary advantage of fitness-dependent recombination is determined mostly by selection against heterozygotes and additive-by-additive epistasis, while under partial selfing, additive-by-dominance epistasis is also a driver.

Balancing task sensitivity with reliability for multimodal language assessments.

OBJECTIVE: Intraoperative tasks for awake language mapping are typically selected based on the language tracts that will likely be encountered during tumor resection. However, diminished attention and arousal secondary to perioperative sedatives may reduce a task's usefulness for identifying eloquent cortex. For instance, accuracy in performing select language tasks may be high preoperatively but decline in the operating room. In the present study, the authors sought to identify language tasks that can be performed with high accuracy in both situational contexts so the neurosurgical team can be confident that speech errors committed during awake language mapping result from direct cortical stimulation to eloquent cortex, rather than from poor performance in general. METHODS: We administered five language tasks to 44 patients: picture naming (PN), text reading (TR), auditory object naming (AN), repetition of 4-syllable words (4SYL), and production of syntactically intact sentences (SYNTAX). Performance was assessed using the 4-point scale of the quick aphasia battery 24 hours preoperatively and intraoperatively. We next determined whether or not accuracy on each task was higher preoperatively than intraoperatively. We also determined whether 1) intraoperative accuracy on a given task predicted intraoperative performance on the other tasks and 2) low preoperative accuracy on a task predicted a decrease in accuracy intraoperatively. RESULTS: Relative to preoperative accuracy, intraoperative accuracy declined on PN (3.90 vs 3.82, p = 0.0001), 4SYL (3.96 vs 3.91, p = 0.0006), and SYNTAX (3.85 vs 3.67, p = 0.0001) but not on TR (3.96 vs 3.94, p = 0.13) or AN (3.70 vs 3.58, p = 0.058). Intraoperative accuracy on PN and AN independently predicted intraoperative accuracy on the remaining language tasks (p < 0.001 and p < 0.01, respectively). Finally, low preoperative accuracy on SYNTAX predicted a decrease in accuracy on this task intraoperatively (R2 = 0.36, p = 0.00002). CONCLUSIONS: While TR lacks sensitivity in identifying language deficits at baseline, accuracy on TR is stable across testing settings. Baseline accuracy on the other four of our five language tasks was not predictive of intraoperative performance, signifying the need to repeat language tests prior to stimulation mapping to confirm reliability.

GABA levels in ventral visual cortex decline with age and are associated with neural distinctiveness.

Age-related neural dedifferentiation-a decline in the distinctiveness of neural representations in the aging brain-has been associated with age-related declines in cognitive abilities. But why does neural distinctiveness decline with age? Based on prior work in nonhuman primates and more recent work in humans, we hypothesized that the inhibitory neurotransmitter gamma-aminobutyric acid (GABA) declines with age and is associated with neural dedifferentiation in older adults. To test this hypothesis, we used magnetic resonance spectroscopy (MRS) to measure GABA and functional MRI (fMRI) to measure neural distinctiveness in the ventral visual cortex in a set of older and younger participants. Relative to younger adults, older adults exhibited lower GABA levels and less distinct activation patterns for faces and houses in the ventral visual cortex. Furthermore, individual differences in GABA within older adults positively predicted individual differences in neural distinctiveness. These results provide novel support for the view that age-related reductions of GABA contribute to age-related reductions in neural distinctiveness (i.e., neural dedifferentiation) in the human ventral visual cortex.