Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish.

Despite deep evolutionary conservation, recombination rates vary greatly across the genome and among individuals, sexes and populations. Yet the impact of this variation on adaptively diverging populations is not well understood. Here we characterized fine-scale recombination landscapes in an adaptively divergent pair of marine and freshwater populations of threespine stickleback from River Tyne, Scotland. Through whole-genome sequencing of large nuclear families, we identified the genomic locations of almost 50,000 crossovers and built recombination maps for marine, freshwater and hybrid individuals at a resolution of 3.8 kb. We used these maps to quantify the factors driving variation in recombination rates. We found strong heterochiasmy between sexes but also differences in recombination rates among ecotypes. Hybrids showed evidence of significant recombination suppression in overall map length and in individual loci. Recombination rates were lower not only within individual marine-freshwater-adaptive loci, but also between loci on the same chromosome, suggesting selection on linked gene 'cassettes'. Through temporal sampling along a natural hybrid zone, we found that recombinants showed traits associated with reduced fitness. Our results support predictions that divergence in cis-acting recombination modifiers, whose functions are disrupted in hybrids, may play an important role in maintaining differences among adaptively diverging populations.

Effects of conflicting emotional cues on toddlers' emotion perception.

The communication of emotion is dynamic and occurs across multiple channels, such as facial expression and tone of voice. When cues are in conflict, interpreting emotion can become challenging. Here, we examined the effects of incongruent emotional cues on toddlers' interpretation of emotions. We presented 33 children (22-26 months, Mage = 23.8 months, 15 female) with side-by-side images of faces along with sentences spoken in a tone of voice that conflicted with semantic content. One of the two faces matched the emotional tone of the audio, whereas the other matched the semantic content. For both congruent and incongruent trials, toddlers showed no overall looking preference to either type of face stimuli. However, during the second exposure to the sentences of incongruent trials, older children tended to look longer to the face matching semantic content when listening to happy vs. angry content. Results inform our understanding of the early development of complex emotion understanding.

Who feels like they belong? Personality and belonging in college.

Having a secure sense of belonging at school supports students' academic achievement and well-being. However, little research has examined how students' personalities relate to their feelings of school belonging. We address this gap in the literature by leveraging data from a large sample of first-year college students (N = 4,753) from a diverse set of North American colleges and universities (N = 12). We found that both extraversion and agreeableness were positively associated with belonging, while neuroticism was negatively associated with belonging. In an exploratory analysis, we examined differences between large and small schools. Students who were more extraverted, less neurotic, and less open were more likely to attend large schools. Additionally, the association between extraversion and belonging was stronger for students at large schools. These findings advance our understanding of who comes to feel like they belong at college and how school context may influence these relationships. We emphasize the need for continued research on the relationship between personality and belonging. Additionally, we highlight the implications of these results for higher education institutions.

Yucatec Maya Children's Responding to Emotional Challenge.

While the field of affective science has seen increased interest in and representation of the role of culture in emotion, prior research has disproportionately centered on Western, English-speaking, industrialized, and/or economically developed nations. We investigated the extent to which emotional experiences and responding may be shaped by cultural display rule understanding among Yucatec Maya children, an indigenous population residing in small-scale communities in remote areas of Mexico's Yucatan peninsula. Data were collected from forty-two 6- and 10-year-old Yucatec children who completed a resting baseline and a structured disappointing gift task. Children were asked about whether specific emotions are better to show or to hide from others and self-reported the intensity of their discrete positive and negative emotional experiences. We observed and coded expressive positive and negative affective behavior during and after the disappointing gift task, and continuously acquired physiological measures of autonomic nervous system function. These multi-method indices of emotional responding enable us to provide a nuanced description of children's observable and unobservable affective experiences. Results generally indicated that children's understanding of and adherence to cultural display rules (i.e., to suppress negative emotions but openly show positive ones) was evidenced across indices of emotion, as predicted. The current study is a step toward the future of affective science, which lies in the pursuit of more diverse and equitable representation in study samples, increased use of concurrent multimethod approaches to studying emotion, and increased exploration of how emotional processes develop.

Where and with whom does a brief social-belonging intervention promote progress in college?

A promising way to mitigate inequality is by addressing students' worries about belonging. But where and with whom is this social-belonging intervention effective? Here we report a team-science randomized controlled experiment with 26,911 students at 22 diverse institutions. Results showed that the social-belonging intervention, administered online before college (in under 30 minutes), increased the rate at which students completed the first year as full-time students, especially among students in groups that had historically progressed at lower rates. The college context also mattered: The intervention was effective only when students' groups were afforded opportunities to belong. This study develops methods for understanding how student identities and contexts interact with interventions. It also shows that a low-cost, scalable intervention generalizes its effects to 749 4-year institutions in the United States.

Early antecedents of emotion differentiation and regulation: Experience tunes the appraisal thresholds of emotional development in infancy.

In this review, we synthesize evidence to highlight cognitive appraisal as an important developmental antecedent of individual differences in emotion differentiation and adept emotion regulation. Emotion differentiation is the degree to which emotions are experienced in a nuanced or "granular" way-as specific and separable phenomena. More extensive differentiation is related to positive wellbeing and has emerged as a correlate of emotion regulation skill among adults. We argue that the cognitive appraisal processes that underlie these facets of emotional development are instantiated early in the first year of life and tuned by environmental input and experience. Powerful socializing input in the form of caregivers' contingent and selective responding to infants' emotional signals carves and calibrates the infant's appraisal thresholds for what in their world ought to be noticed, deemed as important or personally meaningful, and responded to (whether and how). These appraisal thresholds are thus unique to the individual child despite the ubiquity of the appraisal process in emotional responding. This appraisal infrastructure, while plastic and continually informed by experience across the lifespan, likely tunes subsequent emotion differentiation, with implications for children's emotion regulatory choices and skills. We end with recommendations for future research in this area, including the urgent need for developmental emotion science to investigate the diverse sociocultural contexts in which children's cognitive appraisals, differentiation of emotions, and regulatory responses are being built across childhood.

Evolution of stickleback spines through independent cis-regulatory changes at HOXDB.

Understanding the mechanisms leading to new traits or additional features in organisms is a fundamental goal of evolutionary biology. We show that HOXDB regulatory changes have been used repeatedly in different fish genera to alter the length and number of the prominent dorsal spines used to classify stickleback species. In Gasterosteus aculeatus (typically 'three-spine sticklebacks'), a variant HOXDB allele is genetically linked to shortening an existing spine and adding an additional spine. In Apeltes quadracus (typically 'four-spine sticklebacks'), a variant HOXDB allele is associated with lengthening a spine and adding an additional spine in natural populations. The variant alleles alter the same non-coding enhancer region in the HOXDB locus but do so by diverse mechanisms, including single-nucleotide polymorphisms, deletions and transposable element insertions. The independent regulatory changes are linked to anterior expansion or contraction of HOXDB expression. We propose that associated changes in spine lengths and numbers are partial identity transformations in a repeating skeletal series that forms major defensive structures in fish. Our findings support the long-standing hypothesis that natural Hox gene variation underlies key patterning changes in wild populations and illustrate how different mutational mechanisms affecting the same region may produce opposite gene expression changes with similar phenotypic outcomes.

Single-cell Senseless protein analysis reveals metastable states during the transition to a sensory organ fate.

Cell fate decisions can be envisioned as bifurcating dynamical systems, and the decision that Drosophila cells make during sensory organ differentiation has been described as such. We extended these studies by focusing on the Senseless protein which orchestrates sensory cell fate transitions. Wing cells contain intermediate Senseless numbers before their fate transition, after which they express much greater numbers of Senseless molecules as they differentiate. However, the dynamics are inconsistent with it being a simple bistable system. Cells with intermediate Senseless are best modeled as residing in four discrete states, each with a distinct protein number and occupying a specific region of the tissue. Although the states are stable over time, the number of molecules in each state vary with time. The fold change in molecule number between adjacent states is invariant and robust to absolute protein number variation. Thus, cells transitioning to sensory fates exhibit metastability with relativistic properties.

Closeness to God, Spiritual Struggles, and Wellbeing in the First Year of College.

Spirituality is an important, but oft-overlooked, aspect of the self that may affect college students' wellbeing and belonging. Few studies have systematically examined closeness to God and spiritual struggles as predictors of college student wellbeing during early college, which is a critical window for identity development. Moreover, research exploring interactions between spiritual struggles and closeness to God in predicting wellbeing outcomes is scarce. We address these gaps in the literature with an analytic sample comprised of 839 first-year college participants who identify as religious. The results of correlational analyses and linear mixed effect models are presented. Closeness to God was associated with greater wellbeing and belonging, and spiritual struggles were associated with lower wellbeing and belonging. In exploratory analyses, a moderating effect of closeness to God on the relation between spiritual struggles and negative outcomes was observed. Implications for higher education and college student development are discussed.

Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution.

Similar forms often evolve repeatedly in nature, raising long-standing questions about the underlying mechanisms. Here, we use repeated evolution in stickleback to identify a large set of genomic loci that change recurrently during colonization of freshwater habitats by marine fish. The same loci used repeatedly in extant populations also show rapid allele frequency changes when new freshwater populations are experimentally established from marine ancestors. Marked genotypic and phenotypic changes arise within 5 years, facilitated by standing genetic variation and linkage between adaptive regions. Both the speed and location of changes can be predicted using empirical observations of recurrence in natural populations or fundamental genomic features like allelic age, recombination rates, density of divergent loci, and overlap with mapped traits. A composite model trained on these stickleback features can also predict the location of key evolutionary loci in Darwin's finches, suggesting that similar features are important for evolution across diverse taxa.

Rule learning transfer across linguistic and visual modalities in 7-month-old infants.

Rule learning (RL) refers to infants' ability to extract high-order, repetition-based rules from a sequence of elements and to generalize them to new items. RL has been demonstrated in both the auditory and the visual modality, but no studies have investigated infants' transfer of learning across these two modalities, a process that is fundamental for the development of many complex cognitive skills. Using a visual habituation procedure within a cross-modal RL task, we tested 7-month-old infants' transfer of learning both from speech to vision (auditory-visual-AV-condition) and from vision to speech (visual-auditory-VA-condition). Results showed a transfer of learning in the AV condition, but only for those infants who were able to efficiently extract the rule during the learning (habituation) phase. In contrast, in the VA condition infants provided no evidence of RL. Overall, this study indicates that 7-month-old infants can transfers high-order rules across modalities with an advantage for transferring from speech to vision, and that this ability is constrained by infants' individual differences in the way they process the to-be-learned rules.

Two novel loci underlie natural differences in Caenorhabditis elegans abamectin responses.

Parasitic nematodes cause a massive worldwide burden on human health along with a loss of livestock and agriculture productivity. Anthelmintics have been widely successful in treating parasitic nematodes. However, resistance is increasing, and little is known about the molecular and genetic causes of resistance for most of these drugs. The free-living roundworm Caenorhabditis elegans provides a tractable model to identify genes that underlie resistance. Unlike parasitic nematodes, C. elegans is easy to maintain in the laboratory, has a complete and well annotated genome, and has many genetic tools. Using a combination of wild isolates and a panel of recombinant inbred lines constructed from crosses of two genetically and phenotypically divergent strains, we identified three genomic regions on chromosome V that underlie natural differences in response to the macrocyclic lactone (ML) abamectin. One locus was identified previously and encodes an alpha subunit of a glutamate-gated chloride channel (glc-1). Here, we validate and narrow two novel loci using near-isogenic lines. Additionally, we generate a list of prioritized candidate genes identified in C. elegans and in the parasite Haemonchus contortus by comparison of ML resistance loci. These genes could represent previously unidentified resistance genes shared across nematode species and should be evaluated in the future. Our work highlights the advantages of using C. elegans as a model to better understand ML resistance in parasitic nematodes.

Fitness maps to a large-effect locus in introduced stickleback populations.

Mutations of small effect underlie most adaptation to new environments, but beneficial variants with large fitness effects are expected to contribute under certain conditions. Genes and genomic regions having large effects on phenotypic differences between populations are known from numerous taxa, but fitness effect sizes have rarely been estimated. We mapped fitness over a generation in an F2 intercross between a marine and a lake stickleback population introduced to a freshwater pond. A quantitative trait locus map of the number of surviving offspring per F2 female detected a single, large-effect locus near Ectodysplasin (Eda), a gene having an ancient freshwater allele causing reduced bony armor and other changes. F2 females homozygous for the freshwater allele had twice the number of surviving offspring as homozygotes for the marine allele, producing a large selection coefficient, s = 0.50 ± 0.09 SE. Correspondingly, the frequency of the freshwater allele increased from 0.50 in F2 mothers to 0.58 in surviving offspring. We compare these results to allele frequency changes at the Eda gene in an Alaskan lake population colonized by marine stickleback in the 1980s. The frequency of the freshwater Eda allele rose steadily over multiple generations and reached 95% within 20 y, yielding a similar estimate of selection, s = 0.49 ± 0.05, but a different degree of dominance. These findings are consistent with other studies suggesting strong selection on this gene (and/or linked genes) in fresh water. Selection on ancient genetic variants carried by colonizing ancestors is likely to increase the prevalence of large-effect fitness variants in adaptive evolution.

Infants' learning of non-adjacent regularities from visual sequences.

Tracking adjacent (AD) and non-adjacent (NAD) dependencies in a sequence of elements is critical for the development of many complex abilities, such as language acquisition and social interaction. While learning of AD in infancy is a domain-general ability that is functioning across different domains, infants' processing of NAD has been reported only for speech sequences. Here, we tested 9- to 12- and 13- to 15-month-olds' ability to extract AxB grammars in visual sequences of unfamiliar elements. Infants were habituated to a series of 3-visual arrays following an AxB grammar in which the first element (A) predicted the third element (B), while intervening X elements changed continuously. Following habituation, infants were tested with 3-item arrays in which initial and final positions were switched (novel) or kept consistent with the habituation phase (familiar). Older infants successfully recognized the familiar AxB grammar at test, whereas the younger group showed some sensitivity to extract to NAD, albeit in a less robust form. This finding provides the first evidence that the ability to track NAD is a domain-general ability that is present also in the visual domain and that the sensitivity to such dependencies is related to developmental changes, as demonstrated in the auditory domain.

Am I a Science Person? A Strong Science Identity Bolsters Minority Students' Sense of Belonging and Performance in College.

Identifying as a "science person" is predictive of science success, but the mechanisms involved are not well-understood. We hypothesized that science identity predicts success because it fosters a sense of belonging in science classrooms. Thus, science identity should be particularly important for first-generation and racial-minority students, who may harbor doubts about belonging in science. Two field studies in college Introductory Biology classes (Ns = 368, 639) supported these hypotheses. A strong science identity predicted higher grades, particularly for minority students. Also consistent with hypotheses, Study 2 found that self-reported belonging in college mediated the relationship between science identity and performance. Furthermore, a social belonging manipulation eliminated the relationship between science identity and performance among minority students. These results support the idea that a strong science identity is particularly beneficial for minority students because it bolsters belonging in science courses. Practical and theoretical implications are discussed.

Increased ecological resource variability during a critical transition in hominin evolution.

Although climate change is considered to have been a large-scale driver of African human evolution, landscape-scale shifts in ecological resources that may have shaped novel hominin adaptations are rarely investigated. We use well-dated, high-resolution, drill-core datasets to understand ecological dynamics associated with a major adaptive transition in the archeological record ~24 km from the coring site. Outcrops preserve evidence of the replacement of Acheulean by Middle Stone Age (MSA) technological, cognitive, and social innovations between 500 and 300 thousand years (ka) ago, contemporaneous with large-scale taxonomic and adaptive turnover in mammal herbivores. Beginning ~400 ka ago, tectonic, hydrological, and ecological changes combined to disrupt a relatively stable resource base, prompting fluctuations of increasing magnitude in freshwater availability, grassland communities, and woody plant cover. Interaction of these factors offers a resource-oriented hypothesis for the evolutionary success of MSA adaptations, which likely contributed to the ecological flexibility typical of Homo sapiens foragers.

A brief social-belonging intervention in college improves adult outcomes for black Americans.

Could mitigating persistent worries about belonging in the transition to college improve adult life for black Americans? To examine this question, we conducted a long-term follow-up of a randomized social-belonging intervention delivered in the first year of college. This 1-hour exercise represented social and academic adversity early in college as common and temporary. As previously reported in Science, the exercise improved black students' grades and well-being in college. The present study assessed the adult outcomes of these same participants. Examining adult life at an average age of 27, black adults who had received the treatment (versus control) exercise 7 to 11 years earlier reported significantly greater career satisfaction and success, psychological well-being, and community involvement and leadership. Gains were statistically mediated by greater college mentorship. The results suggest that addressing persistent social-psychological concerns via psychological intervention can shape the life course, partly by changing people's social realities.

A spontaneous complex structural variant in rcan-1 increases exploratory behavior and laboratory fitness of Caenorhabditis elegans.

Over long evolutionary timescales, major changes to the copy number, function, and genomic organization of genes occur, however, our understanding of the individual mutational events responsible for these changes is lacking. In this report, we study the genetic basis of adaptation of two strains of C. elegans to laboratory food sources using competition experiments on a panel of 89 recombinant inbred lines (RIL). Unexpectedly, we identified a single RIL with higher relative fitness than either of the parental strains. This strain also displayed a novel behavioral phenotype, resulting in higher propensity to explore bacterial lawns. Using bulk-segregant analysis and short-read resequencing of this RIL, we mapped the change in exploration behavior to a spontaneous, complex rearrangement of the rcan-1 gene that occurred during construction of the RIL panel. We resolved this rearrangement into five unique tandem inversion/duplications using Oxford Nanopore long-read sequencing. rcan-1 encodes an ortholog to human RCAN1/DSCR1 calcipressin gene, which has been implicated as a causal gene for Down syndrome. The genomic rearrangement in rcan-1 creates two complete and two truncated versions of the rcan-1 coding region, with a variety of modified 5' and 3' non-coding regions. While most copy-number variations (CNVs) are thought to act by increasing expression of duplicated genes, these changes to rcan-1 ultimately result in the reduction of its whole-body expression due to changes in the upstream regions. By backcrossing this rearrangement into a common genetic background to create a near isogenic line (NIL), we demonstrate that both the competitive advantage and exploration behavioral changes are linked to this complex genetic variant. This NIL strain does not phenocopy a strain containing an rcan-1 loss-of-function allele, which suggests that the residual expression of rcan-1 is necessary for its fitness effects. Our results demonstrate how colonization of new environments, such as those encountered in the laboratory, can create evolutionary pressure to modify gene function. This evolutionary mismatch can be resolved by an unexpectedly complex genetic change that simultaneously duplicates and diversifies a gene into two uniquely regulated genes. Our work shows how complex rearrangements can act to modify gene expression in ways besides increased gene dosage.

College Students' Sense of Belonging: A National Perspective.

In a nationally representative sample, first-year US college students "somewhat agree", on average, that they feel like they belong at their school. However, belonging varies by key institutional and student characteristics; of note, racial-ethnic minority and first-generation students report lower belonging than peers at four-year schools, while the opposite is true at two-year schools. Further, at four-year schools, belonging predicts better persistence, engagement, and mental health, even after extensive covariate adjustment. Although descriptive, these patterns highlight the need to better measure and understand belonging and related psychological factors that may promote college students' success and well-being.

Deep sampling of Hawaiian Caenorhabditis elegans reveals high genetic diversity and admixture with global populations.

Hawaiian isolates of the nematode species Caenorhabditis elegans have long been known to harbor genetic diversity greater than the rest of the worldwide population, but this observation was supported by only a small number of wild strains. To better characterize the niche and genetic diversity of Hawaiian C. elegans and other Caenorhabditis species, we sampled different substrates and niches across the Hawaiian islands. We identified hundreds of new Caenorhabditis strains from known species and a new species, Caenorhabditis oiwi. Hawaiian C. elegans are found in cooler climates at high elevations but are not associated with any specific substrate, as compared to other Caenorhabditis species. Surprisingly, admixture analysis revealed evidence of shared ancestry between some Hawaiian and non-Hawaiian C. elegans strains. We suggest that the deep diversity we observed in Hawaii might represent patterns of ancestral genetic diversity in the C. elegans species before human influence.