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Herbivorous insects are exceptionally diverse, accounting for a quarter of all known eukaryotic species, but the genomic basis of adaptations that enabled this dietary transition remains poorly understood. Many studies have suggested that expansions and contractions of chemosensory and detoxification gene families-genes directly mediating interactions with plant chemical defenses-underlie successful plant colonization. However, this hypothesis has been challenging to test because the origins of herbivory in many insect lineages are ancient (>150 million years ago (mya)), obscuring genomic evolutionary patterns. Here, we characterized chemosensory and detoxification gene family evolution across Scaptomyza, a genus nested within Drosophila that includes a recently derived (

For agriculturally important plants, pollination and herbivory are two ecological factors that play into the success of crop yields. Each is also important in natural environments where invasive plants and their effect on species interactions may alter the native ecology. The California Wild Radish (Raphanus sativus x raphanistrum), a hybrid derived from an agriculturally important crop and a nonnative cultivar, is common in California. Remarkably, it has recently replaced wild populations of both progenitor species. Experiments on phenotypic variation for petal color and anti-herbivore defenses suggest both pairs of polymorphisms are maintained as a result of pollinator- and herbivore-mediated natural selection. This species provides an opportunity to understand how natural selection shapes the evolution of ecologically important traits when traits are constrained by two opposing forces. Here we provide the genome assembly of the California Wild Radish displaying improvement to currently existing genomes for agronomically important crucifers. This genome sequence provides the tools to dissect the genomic architecture of traits related to herbivory and pollination using natural variation in the wild as well as the ability to infer demographic and selective history in the context of hybridization. Study systems like these will improve our understanding and predictions of evolutionary change for correlated traits.

Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of genome assemblies for 101 lines of 93 drosophilid species encompassing 14 species groups and 35 sub-groups. The genomes are highly contiguous and complete, with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. We show that Nanopore-based assemblies are highly accurate in coding regions, particularly with respect to coding insertions and deletions. These assemblies, along with a detailed laboratory protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution at the scale of hundreds of species.

Identifying the genetic mechanisms of adaptation requires the elucidation of links between the evolution of DNA sequence, phenotype, and fitness1. Convergent evolution can be used as a guide to identify candidate mutations that underlie adaptive traits2-4, and new genome editing technology is facilitating functional validation of these mutations in whole organisms1,5. We combined these approaches to study a classic case of convergence in insects from six orders, including the monarch butterfly (Danaus plexippus), that have independently evolved to colonize plants that produce cardiac glycoside toxins6-11. Many of these insects evolved parallel amino acid substitutions in the α-subunit (ATPα) of the sodium pump (Na+/K+-ATPase)7-11, the physiological target of cardiac glycosides12. Here we describe mutational paths involving three repeatedly changing amino acid sites (111, 119 and 122) in ATPα that are associated with cardiac glycoside specialization13,14. We then performed CRISPR-Cas9 base editing on the native Atpα gene in Drosophila melanogaster flies and retraced the mutational path taken across the monarch lineage11,15. We show in vivo, in vitro and in silico that the path conferred resistance and target-site insensitivity to cardiac glycosides16, culminating in triple mutant 'monarch flies' that were as insensitive to cardiac glycosides as monarch butterflies. 'Monarch flies' retained small amounts of cardiac glycosides through metamorphosis, a trait that has been optimized in monarch butterflies to deter predators17-19. The order in which the substitutions evolved was explained by amelioration of antagonistic pleiotropy through epistasis13,14,20-22. Our study illuminates how the monarch butterfly evolved resistance to a class of plant toxins, eventually becoming unpalatable, and changing the nature of species interactions within ecological communities2,6-11,15,17-19.

Purpose: Variability in the input plays an important role in language learning. The current study examined the role of object variability for new word learning by preschoolers with specific language impairment (SLI). Method: Eighteen 4- and 5-year-old children with SLI were taught 8 new words in 3 short activities over the course of 3 sessions. Half of the children saw 3 identical objects corresponding to each new word during training (No Variability group); the other half of the children saw 3 different objects corresponding to each new word during training (High Variability group). Children completed vocabulary learning tests for objects seen during training and for new within-category objects that were never seen during training as a test of category generalization. Learning was assessed the day after each training activity, and retention was assessed 3 weeks after the last training session. Results: There were no group differences on trained or generalization items immediately following training sessions. However, children in the High Variability group demonstrated significantly better retention 3 weeks after experimental training. Conclusion: These findings demonstrate that object variability facilitates retention of new word learning by children with SLI. Supplemental Material: https://doi.org/10.23641/asha.5583979

Purpose: Two studies examined learning of grammar-like visual sequences to determine whether a general deficit in statistical learning characterizes this population. Furthermore, we tested the hypothesis that difficulty in sustaining attention during the learning task might account for differences in statistical learning. Method: In Study 1, adults with normal language (NL) or language-learning disability (LLD) were familiarized with the visual artificial grammar and then tested using items that conformed or deviated from the grammar. In Study 2, a 2nd sample of adults with NL and LLD were presented auditory word pairs with weak semantic associations (e.g., "groom" + "clean") along with the visual learning task. Participants were instructed to attend to visual sequences and to ignore the auditory stimuli. Incidental encoding of these words would indicate reduced attention to the primary task. Results: In Studies 1 and 2, both groups demonstrated learning and generalization of the artificial grammar. In Study 2, neither the NL nor the LLD group appeared to encode the words presented during the learning phase. Conclusion: The results argue against a general deficit in statistical learning for individuals with LLD and demonstrate that both NL and LLD learners can ignore extraneous auditory stimuli during visual learning.

Purpose: Even without explicit instruction, learners are able to extract information about the form of a language simply by attending to input that reflects the underlying grammar. In this study, the authors explored the role of variability in this learning by asking whether varying the number of unique exemplars heard by the learner affects learning of an artificial syntactic form. Method: Learners with normal language ("n" = 16) and language-based learning disability (LLD; "n"= 16) were exposed to strings of nonwords that represented an underlying grammar. Half of the learners heard 3 exemplars 16 times each (low variability group), and the other half of the learners heard 24 exemplars twice each (high variability group). Learners were then tested for recognition of items heard and generalization of the grammar with new nonword strings. Results: Only those learners with LLD who were in the high variability group were able to demonstrate generalization of the underlying grammar. For learners with normal language, both those in the high and the low variability groups showed generalization of the grammar, but relative effect sizes suggested a larger learning effect in the high variability group. Conclusion: The results demonstrate that the structure of the learning context can determine the ability to generalize from specific training items to novel cases. (Contains 2 tables and 2 figures.)

Previous language learning research reveals that the statistical properties of the input offer sufficient information to allow listeners to segment words from fluent speech in an artificial language. The current pair of studies uses a natural language to test the ecological validity of these findings and to determine whether a listener's language background influences this process. In Study 1, the "guessibility" of potential test words from the Norwegian language was presented to 22 listeners who were asked to differentiate between true words and nonwords. In Study 2, 22 adults who spoke one of 12 different primary languages learned to segment words from continuous speech in an implicit language learning paradigm. The task consisted of two sessions, approximately three weeks apart, each requiring participants to listen to 7.2 minutes of Norwegian sentences followed by a series of bisyllabic test items presented in isolation. The participants differentially accepted the Norwegian words and Norwegian-like nonwords in both test sessions, demonstrating the capability to segment true words from running speech. The results were consistent across three broadly-defined language groups, despite differences in participants' language background.

Purpose: Two studies examined learning of grammar-like visual sequences to determine whether a general deficit in statistical learning characterizes this population. Furthermore, we tested the hypothesis that difficulty in sustaining attention during the learning task might account for differences in statistical learning. Method: In Study 1, adults with normal language (NL) or language-learning disability (LLD) were familiarized with the visual artificial grammar and then tested using items that conformed or deviated from the grammar. In Study 2, a 2nd sample of adults with NL and LLD were presented auditory word pairs with weak semantic associations (e.g., groom + clean) along with the visual learning task. Participants were instructed to attend to visual sequences and to ignore the auditory stimuli. Incidental encoding of these words would indicate reduced attention to the primary task. Results: In Studies 1 and 2, both groups demonstrated learning and generalization of the artificial grammar. In Study 2, neither the NL nor the LLD group appeared to encode the words presented during the learning phase. Conclusion: The results argue against a general deficit in statistical learning for individuals with LLD and demonstrate that both NL and LLD learners can ignore extraneous auditory stimuli during visual learning. Key Words: adults, language, language disorders, procedural learning, statistical learning, An individual's ability to detect statistical regularities in their environment plays an important role in perceptual and cognitive learning, including language acquisition, skill learning, and object recognition. Recognition of statistical [...]

Objective Pediatric traumatic brain injury (TBI) is associated with long-term cognitive and behavioral deficits. Social communication impairments are common and impact functional outcomes, such as social engagement and academic performance. There are many barriers to identifying social communication deficits following TBI, including the absence of a standardized parent-reported communication measure for use in this population. The Children's Communication Checklist—Second Edition (CCC-2) has demonstrated utility in identifying communication deficits in diagnoses other than TBI. This study investigated the clinical utility of the CCC-2's social communication scales in children with TBI. Method: 203 children who sustained TBI or orthopedic injuries between the ages of 36 and 83 months were recruited as part of a larger, longitudinal study. We analyzed social communication subscale scores from the CCC-2 an average of 3.5 years postinjury. We used binary logistic regression analyses to examine the measure's accuracy in classifying children with and without social communication deficits on other measures of pragmatic language and social competence. Correlation analyses and linear mixed models were used to examine the construct validity of the CCC-2. Results: The CCC-2 was able to accurately classify those with and without pragmatic language impairments on the Comprehensive Assessment of Spoken Language 92% of the time (sensitivity = 55%) and 96% of the time on the Home and Community Social Behavior scale (sensitivity = 72%). The CCC-2 demonstrated strong correlations with and predictive validity for measures of social communication and competence. Conclusions: The findings offer support for the clinical utility of the CCC-2 in the pediatric TBI population. [ABSTRACT FROM AUTHOR]

Purpose: Even without explicit instruction, learners are able to extract information about the form of a language simply by attending to input that reflects the underlying grammar. In this study, the authors explored the role of variability in this learning by asking whether varying the number of unique exemplars heard by the learner affects learning of an artificial syntactic form. Method: Learners with normal language (n = 16) and language-based learning disability (LLD; n = 16) were exposed to strings of nonwords that represented an underlying grammar. Half of the learners heard 3 exemplars 16 times each (low variability group), and the other half of the learners heard 24 exemplars twice each (high variability group). Learners were then tested for recognition of items heard and generalization of the grammar with new nonword strings. Results: Only those learners with LLD who were in the high variability group were able to demonstrate generalization of the underlying grammar. For learners with normal language, both those in the high and the low variability groups showed generalization of the grammar, but relative effect sizes suggested a larger learning effect in the high variability group. Conclusion: The results demonstrate that the structure of the learning context can determine the ability to generalize from specific training items to novel cases. Key Words: language, learning, language disorder, Although language form can certainly be learned through direct instruction, most frequently it is learned without explicit explanation of the rules for combining words into phrases or sentences. This is [...]

For agriculturally important plants, pollination and herbivory are 2 ecological factors that play into the success of crop yields. Each is also important in natural environments where invasive plants and their effect on species interactions may alter the native ecology. The California Wild Radish (Raphanus sativus × raphanistrum), a hybrid derived from an agriculturally important crop and a nonnative cultivar, is common in California. Remarkably, it has recently replaced wild populations of both progenitor species. Experiments on phenotypic variation for petal color and antiherbivore defenses suggest both pairs of polymorphisms are maintained as a result of pollinator- and herbivore-mediated natural selection. This species provides an opportunity to understand how natural selection shapes the evolution of ecologically important traits when traits are constrained by 2 opposing forces. Here we provide the genome assembly of the California Wild Radish displaying improvement to currently existing genomes for agronomically important crucifers. This genome sequence provides the tools to dissect the genomic architecture of traits related to herbivory and pollination using natural variation in the wild as well as the ability to infer demographic and selective history in the context of hybridization. Study systems like these will improve our understanding and predictions of evolutionary change for correlated traits. [ABSTRACT FROM AUTHOR]

Purpose: To examine the long-term consequences of early childhood traumatic brain injury (TBI), approximately 6.8 years post-injury, on cognitive communication competency within a complex interplay of individual, contextual, and psychosocial factors. Additionally, we were interested in looking at the association of communication competence with social competence and overall functioning. Methods: 64 children with orthopedic injury, 40 children with moderate traumatic brain injury, and 14 children with severe traumatic brain injury who were between 3 years and 6 years 11 months at injury completed a narrative discourse task and clinical measures in a single visit at a longer term follow up in early adolescence, an average of 6.8 years post injury. Analyses of covariance were conducted to compare groups on the discourse task, and hierarchical linear regressions were conducted to examine the association of discourse measures with clinical measures of cognitive and psychosocial functioning. Results: Children with severe traumatic brain injury performed worse than children with moderate traumatic brain injury and orthopedic injury on all discourse indices and clinical measures. Injury severity, pragmatic skills, and socioeconomic status were associated with discourse gist. Discourse gist was the most sensitive measure of communication competence, and it was significantly associated with psychosocial outcomes independent of group. Conclusion: Children who sustain a severe traumatic brain injury in early childhood are at risk for long-term cognitive communication impairments that may be related to a complex interplay of injury, individual, and social factors. The assessment and treatment of cognitive communication impairments after traumatic brain injury are complex and require consideration of individual, contextual, and psychosocial factors. Discourse, in general, and gist reasoning specifically, is a sensitive measure for detecting cognitive communication competence several years after pediatric traumatic brain injury. Treatments to address gist reasoning deficits may support improvements in global and social functioning. [ABSTRACT FROM AUTHOR]

Herbivorous insects are exceptionally diverse, accounting for a quarter of all known eukaryotic species, but the genomic basis of adaptations that enabled this dietary transition remains poorly understood. Many studies have suggested that expansions and contractions of chemosensory and detoxification gene families-genes directly mediating interactions with plant chemical defenses-underlie successful plant colonization. However, this hypothesis has been challenging to test because the origins of herbivory in many insect lineages are ancient (>150 million years ago (mya)), obscuring genomic evolutionary patterns. Here, we characterized chemosensory and detoxification gene family evolution across Scaptomyza, a genus nested within Drosophila that includes a recently derived (<15 mya) herbivore lineage of mustard (Brassicales) specialists and carnation (Caryophyllaceae) specialists, and several nonherbivorous species. Comparative genomic analyses revealed that herbivorous Scaptomyza has among the smallest chemosensory and detoxification gene repertoires across 12 drosophilid species surveyed. Rates of gene turnover averaged across the herbivore clade were significantly higher than background rates in over half of the surveyed gene families. However, gene turnover was more limited along the ancestral herbivore branch, with only gustatory receptors and odorant-binding proteins experiencing strong losses. The genes most significantly impacted by gene loss, duplication, or changes in selective constraint were those involved in detecting compounds associated with feeding on living plants (bitter or electrophilic phytotoxins) or their ancestral diet (fermenting plant volatiles). These results provide insight into the molecular and evolutionary mechanisms of plant-feeding adaptations and highlight gene candidates that have also been linked to other dietary transitions in Drosophila., Competing Interests: Conflicts of interest statement The author(s) declare no conflict of interest., (© The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.)

Previous language learning research reveals that the statistical properties of the input offer sufficient information to allow listeners to segment words from fluent speech in an artificial language. The current pair of studies uses a natural language to test the ecological validity of these findings and to determine whether a listener's language background influences this process. In Study 1, the "guessibility" of potential test words from the Norwegian language was presented to 22 listeners who were asked to differentiate between true words and nonwords. In Study 2, 22 adults who spoke one of 12 different primary languages learned to segment words from continuous speech in an implicit language learning paradigm. The task consisted of two sessions, approximately three weeks apart, each requiring participants to listen to 7.2 minutes of Norwegian sentences followed by a series of bisyllabic test items presented in isolation. The participants differentially accepted the Norwegian words and Norwegian-like nonwords in both test sessions, demonstrating the capability to segment true words from running speech. The results were consistent across three broadly-defined language groups, despite differences in participants' language background.