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1. Population climatic history predicts phenotypic responses in novel environments for Arabidopsis thaliana in North America

   https://doi.org/10.1002/ajb2.1334  

   Samis, Karen E. ; Stinchcombe, John R. ; Murren, Courtney J. ( July 2019 , American Journal of Botany)

   Determining how species perform in novel climatic environments is essential for understanding (1) responses to climate change and (2) evolutionary consequences of biological invasions. For the vast majority of species, the number of population characteristics that will predict performance and patterns of natural selection in novel locations in the wild remains limited.

   We evaluated phenological, vegetative, architectural, and fitness‐related traits in experimental gardens in contrasting climates (Ontario, Canada, and South Carolina,USA) in the North American non‐native distribution ofArabidopsis thaliana. We assessed the effects of climatic distance, geographic distance, and genetic features of history on performance and patterns of natural selection in the novel garden settings.

   We found that plants had greater survivorship, flowered earlier, were larger, and produced more fruit in the south, and that genotype‐by‐environment interactions were significant between gardens. However, our analyses revealed similar patterns of natural selection between gardens in distinct climate zones. After accounting for genetic ancestry, we also detected that population climatic distance best predicted performance within gardens.

   These data suggest that colonization success in novel, non‐native environments is determined by a combination of climate and genetic history. When performance at novel sites was assessed with seed sources from geographically and genetically disparate, established non‐native populations, proximity to the garden alone was insufficient to predict performance. Our study highlights the need to evaluate seed sources from diverse origins to describe comprehensively phenotypic responses to novel environments, particularly for taxa in which many source populations may contribute to colonization.

    

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2. Diagnostic implications of genetic copy number variation in epilepsy plus

   https://doi.org/10.1111/epi.14683  

   Coppola, Antonietta ; Cellini, Elena ; Stamberger, Hannah ; Saarentaus, Elmo ; Cetica, Valentina ; Lal, Dennis ; Djémié, Tania ; Bartnik‐Glaska, Magdalena ; Ceulemans, Berten ; Helen Cross, J. ; et al ( March 2019 , Epilepsia)

   Copy number variations (CNVs) represent a significant genetic risk for several neurodevelopmental disorders including epilepsy. As knowledge increases, reanalysis of existing data is essential. Reliable estimates of the contribution ofCNVs to epilepsies from sizeable populations are not available.

   We assembled a cohort of 1255 patients with preexisting array comparative genomic hybridization or single nucleotide polymorphism array basedCNVdata. All patients had “epilepsy plus,” defined as epilepsy with comorbid features, including intellectual disability, psychiatric symptoms, and other neurological and nonneurological features.CNVclassification was conducted using a systematic filtering workflow adapted to epilepsy.

   Of 1097 patients remaining after genetic data quality control, 120 individuals (10.9%) carried at least one autosomalCNVclassified as pathogenic; 19 individuals (1.7%) carried at least one autosomalCNVclassified as possibly pathogenic. Eleven patients (1%) carried more than one (possibly) pathogenicCNV. We identifiedCNVs covering recently reported (HNRNPU)or emerging (RORB) epilepsy genes, and further delineated the phenotype associated with mutations of these genes. Additional novel epilepsy candidate genes emerge from our study. Comparing phenotypic features of pathogenicCNVcarriers to those of noncarriers of pathogenicCNVs, we show that patients with nonneurological comorbidities, especially dysmorphism, were more likely to carry pathogenicCNVs (odds ratio = 4.09, confidence interval = 2.51‐6.68;P = 2.34 × 10⁻⁹). Meta‐analysis including data from published control groups showed that the presence or absence of epilepsy did not affect the detected frequency ofCNVs.

   The use of a specifically adapted workflow enabled identification of pathogenic autosomalCNVs in 10.9% of patients with epilepsy plus, which rose to 12.7% when we also considered possibly pathogenicCNVs. Our data indicate that epilepsy with comorbid features should be considered an indication for patients to be selected for a diagnostic algorithm includingCNVdetection. Collaborative large‐scaleCNVreanalysis leads to novel declaration of pathogenicity in unexplained cases and can promote discovery of promising candidate epilepsy genes.

    

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3. Genetic architecture, biochemical underpinnings and ecological impact of floral UV patterning

   https://doi.org/10.1111/mec.13542  

   Brock, Marcus T. ; Lucas, Lauren K. ; Anderson, Nickolas A. ; Rubin, Matthew J. ; Cody Markelz, R. J. ; Covington, Michael F. ; Devisetty, Upendra K. ; Chapple, Clint ; Maloof, Julin N. ; Weinig, Cynthia ( February 2016 , Molecular Ecology)

   Floral attraction traits can significantly affect pollinator visitation patterns, but adaptive evolution of these traits may be constrained by correlations with other traits. In some cases, molecular pathways contributing to floral attraction are well characterized, offering the opportunity to explore loci potentially underlying variation among individuals. Here, we quantify the range of variation in floralUVpatterning (i.e.UV‘bulls‐eye nectar guides) among crop and wild accessions ofBrassica rapa. We then use experimental crosses to examine the genetic architecture, candidate loci and biochemical underpinnings of this patterning as well as phenotypic manipulations to test the ecological impact. We find qualitative variation inUVpatterning between wild (commonly lackingUVpatterns) and crop (commonly exhibitingUVpatterns) accessions. Similar to the majority of crops, recombinant inbred lines (RILs) derived from an oilseed crop × WIfast‐plant^®cross exhibitUVpatterns, the size of which varies extensively among genotypes. InRILs, we further observe strong statistical‐genetic andQTLcorrelations within petal morphological traits and within measurements of petalUVpatterning; however, correlations between morphology andUVpatterning are weak or nonsignificant, suggesting thatUVpatterning is regulated and may evolve independently of overall petal size.HPLCanalyses reveal a high concentration of sinapoyl glucose inUV‐absorbing petal regions, which, in concert with physical locations ofUV‐traitQTLs, suggest a regulatory and structural gene as candidates underlying observed quantitative variation. Finally, insects prefer flowers withUVbulls‐eye patterns over those that lack patterns, validating the importance ofUVpatterning in pollen‐limited populations ofB. rapa.

    

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4. Distributed phenomics with the un PAK project reveals the effects of mutations

   https://doi.org/10.1111/tpj.14427  

   Rutter, Matthew T. ; Murren, Courtney J. ; Callahan, Hilary S. ; Bisner, April M. ; Leebens‐Mack, Jim ; Wolyniak, Michael J. ; Strand, Allan E. ( July 2019 , The Plant Journal)

   Determining how genes are associated with traits in plants and other organisms is a major challenge in modern biology. The unPAKproject – undergraduates phenotyping Arabidopsis knockouts – has generated phenotype data for thousands of non‐lethal insertion mutation lines within a singleArabidopsis thalianagenomic background. The focal phenotypes examined by unPAKare complex macroscopic fitness‐related traits, which have ecological, evolutionary and agricultural importance. These phenotypes are placed in the context of the wild‐type and also natural accessions (phytometers), and standardized for environmental differences between assays. Data from the unPAKproject are used to describe broad patterns in the phenotypic consequences of insertion mutation, and to identify individual mutant lines with distinct phenotypes as candidates for further study. Inclusion of undergraduate researchers is at the core of unPAKactivities, and an important broader impact of the project is providing students an opportunity to obtain research experience.

    

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5. Evidence for divergence of response in Indica , Japonica , and wild rice to high CO 2 × temperature interaction

   https://doi.org/10.1111/gcb.13279  

   Wang, Diane R. ; Bunce, James A. ; Tomecek, Martha B. ; Gealy, David ; McClung, Anna ; McCouch, Susan R. ; Ziska, Lewis H. ( April 2016 , Global Change Biology)

   HighCO₂and high temperature have an antagonistic interaction effect on rice yield potential and present a unique challenge to adapting rice to projected future climates. Understanding how the differences in response to these two abiotic variables are partitioned across rice germplasm accessions may be key to identifying potentially useful sources of resilient alleles for adapting rice to climate change. In this study, we evaluated eleven globally diverse rice accessions under controlled conditions at two carbon dioxide concentrations (400 and 600 ppm) and four temperature environments (29 °C day/21 °C night; 29 °C day/21 °C night with additional heat stress at anthesis; 34 °C day/26 °C night; and 34 °C day/26 °C night with additional heat stress at anthesis) for a suite of traits including five yield components, five growth characteristics, one phenological trait, and four photosynthesis‐related measurements. Multivariate analyses of mean trait data from these eight treatments divide our rice panel into two primary groups consistent with the genetic classification ofINDICA/INDICA‐like andJAPONICApopulations. Overall, we find that the productivity of plants grown under elevated [CO₂] was more sensitive (negative response) to high temperature stress compared with that of plants grown under ambient [CO₂] across this diversity panel. We report differential response toCO₂× temperature interaction forINDICA/INDICA‐like andJAPONICArice accessions and find preliminary evidence for the beneficial introduction of exotic alleles into cultivated rice genomic background. Overall, these results support the idea of using wild or currently unadapted gene pools in rice to enhance breeding efforts to secure future climate change adaptation.

    

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