189 results on '"Willis JH"'
Search Results
2. Speciation on a local geographic scale: The evolution of a rare rock outcrop specialist in Mimulus
- Author
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Ferris, KG, Sexton, JP, and Willis, JH
- Subjects
local speciation ,rock outcrops ,genetics ,Mimulus filicifolius ,Mimulus laciniatus ,Mimulus guttatus ,Evolutionary Biology ,Biological Sciences ,Medical and Health Sciences - Abstract
Speciation can occur on both large and small geographical scales. In plants, local speciation, where small populations split off from a large-ranged progenitor species, is thought to be the dominant mode, yet there are still few examples to verify speciation has occurred in this manner. A recently described morphological species in the yellow monkey flowers, Mimulus filicifolius, is an excellent candidate for local speciation because of its highly restricted geographical range. Mimulus filicifolius was formerly identified as a population of M. laciniatus due to similar lobed leaf morphology and rocky outcrop habitat. To investigatewhether M. filicifolius is genetically divergent and reproductively isolated from M. laciniatus, we examined patterns of genetic diversity in ten nuclear and eight microsatellite loci, and hybrid fertility in M. filicifolius and its purported close relatives: M. laciniatus, M. guttatus and M. nasutus. We found that M. filicifolius is genetically divergent from the other species and strongly reproductively isolated from M. laciniatus.We conclude that M. filicifolius is an independent rock outcrop specialist despite being morphologically and ecologically similar to M. laciniatus, and that its small geographical range nested within other wide-ranging members of the M. guttatus species complex is consistent with local speciation. © 2014 The Author(s) Published by the Royal Society. All rights reserved.
- Published
- 2014
3. Underinsurance and key health outcomes for children with special health care needs.
- Author
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Oswald DP, Bodurtha JN, Willis JH, and Moore MB
- Published
- 2007
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4. Widespread changes in gene expression accompany body size evolution in nematodes.
- Author
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Woodruff GC, Willis JH, Johnson E, and Phillips PC
- Subjects
- Animals, Caenorhabditis elegans genetics, Caenorhabditis elegans growth & development, Biological Evolution, Caenorhabditis genetics, Gene Expression Profiling, Transcriptome, Evolution, Molecular, Transforming Growth Factor beta metabolism, Transforming Growth Factor beta genetics, Body Size genetics, Gene Expression Regulation, Developmental
- Abstract
Body size is a fundamental trait that drives multiple evolutionary and ecological patterns. Caenorhabditis inopinata is a fig-associated nematode that is exceptionally large relative to other members of the genus, including Caenorhabditis elegans. We previously showed that C. inopinata is large primarily due to postembryonic cell size expansion that occurs during the larval-to-adult transition. Here, we describe gene expression patterns in C. elegans and C. inopinata throughout this developmental period to understand the transcriptional basis of body size change. We performed RNA-seq in both species across the L3, L4, and adult stages. Most genes are differentially expressed across all developmental stages, consistent with C. inopinata's divergent ecology and morphology. We also used a model comparison approach to identify orthologues with divergent dynamics across this developmental period between the 2 species. This included genes connected to neurons, behavior, stress response, developmental timing, and small RNA/chromatin regulation. Multiple hypodermal collagens were also observed to harbor divergent developmental dynamics across this period, and genes important for molting and body morphology were also detected. Genes associated with transforming growth factor β signaling revealed idiosyncratic and unexpected transcriptional patterns given their role in body size regulation in C. elegans. This widespread transcriptional divergence between these species is unexpected and maybe a signature of the ecological and morphological divergence of C. inopinata. Alternatively, transcriptional turnover may be the rule in the Caenorhabditis genus, indicative of widespread developmental system drift among species. This work lays the foundation for future functional genetic studies interrogating the bases of body size evolution in this group., Competing Interests: Conflicts of interest The author(s) declare no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)
- Published
- 2024
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5. Pervasive conservation of intron number and other genetic elements revealed by a chromosome-level genomic assembly of the hyper-polymorphic nematode Caenorhabditis brenneri .
- Author
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Teterina AA, Willis JH, Baer CF, and Phillips PC
- Abstract
With within-species genetic diversity estimates that span the gambit of that seen across the entirety of animals, the Caenorhabditis genus of nematodes holds unique potential to provide insights into how population size and reproductive strategies influence gene and genome organization and evolution. Our study focuses on Caenorhabditis brenneri , currently known as one of the most genetically diverse nematodes within its genus and metazoan phyla. Here, we present a high-quality gapless genome assembly and annotation for C. brenneri , revealing a common nematode chromosome arrangement characterized by gene-dense central regions and repeat rich peripheral parts. Comparison of C. brenneri with other nematodes from the 'Elegans' group revealed conserved macrosynteny but a lack of microsynteny, characterized by frequent rearrangements and low correlation iof orthogroup sizes, indicative of high rates of gene turnover. We also assessed genome organization within corresponding syntenic blocks in selfing and outcrossing species, affirming that selfing species predominantly experience loss of both genes and intergenic DNA. Comparison of gene structures revealed strikingly small number of shared introns across species, yet consistent distributions of intron number and length, regardless of population size or reproductive mode, suggesting that their evolutionary dynamics are primarily reflective of functional constraints. Our study provides valuable insights into genome evolution and expands the nematode genome resources with the highly genetically diverse C. brenneri , facilitating research into various aspects of nematode biology and evolutionary processes.
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- 2024
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6. Patterns of Genomic Diversity in a Fig-Associated Close Relative of Caenorhabditis elegans.
- Author
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Woodruff GC, Willis JH, and Phillips PC
- Subjects
- Animals, Caenorhabditis elegans genetics, Genetics, Population, Genomics, Ficus genetics, Caenorhabditis genetics
- Abstract
The evolution of reproductive mode is expected to have profound impacts on the genetic composition of populations. At the same time, ecological interactions can generate close associations among species, which can in turn generate a high degree of overlap in their spatial distributions. Caenorhabditis elegans is a hermaphroditic nematode that has enabled extensive advances in developmental genetics. Caenorhabditis inopinata, the sister species of C. elegans, is a gonochoristic nematode that thrives in figs and obligately disperses on fig wasps. Here, we describe patterns of genomic diversity in C. inopinata. We performed RAD-seq on individual worms isolated from the field across three Okinawan island populations. C. inopinata is about five times more diverse than C. elegans. Additionally, C. inopinata harbors greater differences in diversity among functional genomic regions (such as between genic and intergenic sequences) than C. elegans. Conversely, C. elegans harbors greater differences in diversity between high-recombining chromosome arms and low-recombining chromosome centers than C. inopinata. FST is low among island population pairs, and clear population structure could not be easily detected among islands, suggesting frequent migration of wasps between islands. These patterns of population differentiation appear comparable with those previously reported in its fig wasp vector. These results confirm many theoretical population genetic predictions regarding the evolution of reproductive mode and suggest C. inopinata population dynamics may be driven by wasp dispersal. This work sets the stage for future evolutionary genomic studies aimed at understanding the evolution of sex as well as the evolution of ecological interactions., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
- Published
- 2024
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7. The genetic basis of traits associated with the evolution of serpentine endemism in monkeyflowers.
- Author
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Toll K and Willis JH
- Subjects
- Quantitative Trait Loci, Phenotype, Chromosome Mapping, Soil chemistry, Flowers genetics, Mimulus genetics
- Abstract
The floras on chemically and physically challenging soils, such as gypsum, shale, and serpentine, are characterized by narrowly endemic species. The evolution of edaphic endemics may be facilitated or constrained by genetic correlations among traits contributing to adaptation and reproductive isolation across soil boundaries. The yellow monkeyflowers in the Mimulus guttatus species complex are an ideal system in which to examine these evolutionary patterns. To determine the genetic basis of adaptive and prezygotic isolating traits, we performed genetic mapping experiments with F2 hybrids derived from a cross between a serpentine endemic, M. nudatus, and its close relative M. guttatus. Few large effect and many small effect QTL contribute to interspecific divergence in life history, floral, and leaf traits, and a history of directional selection contributed to trait divergence. Loci contributing to adaptive traits and prezygotic reproductive isolation overlap, and their allelic effects are largely in the direction of species divergence. These loci contain promising candidate genes regulating flowering time and plant organ size. Together, our results suggest that genetic correlations among traits can facilitate the evolution of adaptation and speciation and may be a common feature of the genetic architecture of divergence between edaphic endemics and their widespread relatives., (© The Author(s) 2023. Published by Oxford University Press on behalf of The Society for the Study of Evolution (SSE). All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2024
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8. Widespread changes in gene expression accompany body size evolution in nematodes.
- Author
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Woodruff GC, Willis JH, Johnson E, and Phillips PC
- Abstract
Body size is a fundamental trait that drives multiple evolutionary and ecological patterns. Caenorhabditis inopinata is a fig-associated nematode that is exceptionally large relative to other members of the genus, including C. elegans . We previously showed that C. inopinata is large primarily due to postembryonic cell size expansion that occurs during the larval-to-adult transition. Here, we describe gene expression patterns in C. elegans and C. inopinata throughout this developmental period to understand the transcriptional basis of body size change. We performed RNA-seq in both species across the L3, L4, and adult stages. Most genes are differentially expressed across all developmental stages, consistent with C. inopinata 's divergent ecology and morphology. We also used a model comparison approach to identify orthologs with divergent dynamics across this developmental period between the two species. This included genes connected to neurons, behavior, stress response, developmental timing, and small RNA/chromatin regulation. Multiple hypodermal collagens were also observed to harbor divergent developmental dynamics across this period, and genes important for molting and body morphology were also detected. Genes associated with TGF-β signaling revealed idiosyncratic and unexpected transcriptional patterns given their role in body size regulation in C. elegans . Widespread transcriptional divergence between these species is unexpected and may be a signature of the ecological and morphological divergence of C. inopinata . Alternatively, transcriptional turnover may be the rule in the Caenorhabditis genus, indicative of widespread developmental system drift among species. This work lays the foundation for future functional genetic studies interrogating the bases of body size evolution in this group., Competing Interests: The authors declare no conflict of interest.
- Published
- 2023
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9. Epigenetic context predicts gene expression variation and reproductive traits across genetically identical individuals.
- Author
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Webster AK, Willis JH, Johnson E, Sarkies P, and Phillips PC
- Abstract
In recent decades, genome-wide association studies (GWAS) have been the major approach to understand the biological basis of individual differences in traits and diseases. However, GWAS approaches have proven to have limited predictive power to explain individual differences, particularly for complex traits and diseases in which environmental factors play a substantial role in their etiology. Indeed, individual differences persist even in genetically identical individuals, although fully separating genetic and environmental causation is difficult or impossible in most organisms. To understand the basis of individual differences in the absence of genetic differences, we measured two quantitative reproductive traits in 180 genetically identical young adult Caenorhabditis elegans roundworms in a shared environment and performed single-individual transcriptomics on each worm. We identified hundreds of genes for which expression variation was strongly associated with reproductive traits, some of which depended on prior environmental experience and some of which was random. Multiple small sets of genes together were highly predictive of reproductive traits across individuals, explaining on average over half and over a quarter of variation in the two traits. We manipulated mRNA levels of predictive genes using RNA interference to identify a set of causal genes, demonstrating the utility of this approach for both prediction and understanding underlying biology. Finally, we found that the chromatin environment of predictive genes was enriched for H3K27 trimethylation, suggesting that individual gene expression differences underlying critical traits may be driven in part by chromatin structure. Together, this work shows that individual differences in gene expression that arise independently of underlying genetic differences are both predictive and causal in shaping reproductive traits at levels that equal or exceed genetic variation.
- Published
- 2023
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10. Genomic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes.
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Teterina AA, Willis JH, Lukac M, Jovelin R, Cutter AD, and Phillips PC
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- Animals, Caenorhabditis elegans genetics, Polymorphism, Genetic, Biological Evolution, Genomics, Genetic Variation, Caenorhabditis genetics
- Abstract
Caenorhabditis nematodes form an excellent model for studying how the mode of reproduction affects genetic diversity, as some species reproduce via outcrossing whereas others can self-fertilize. Currently, chromosome-level patterns of diversity and recombination are only available for self-reproducing Caenorhabditis, making the generality of genomic patterns across the genus unclear given the profound potential influence of reproductive mode. Here we present a whole-genome diversity landscape, coupled with a new genetic map, for the outcrossing nematode C. remanei. We demonstrate that the genomic distribution of recombination in C. remanei, like the model nematode C. elegans, shows high recombination rates on chromosome arms and low rates toward the central regions. Patterns of genetic variation across the genome are also similar between these species, but differ dramatically in scale, being tenfold greater for C. remanei. Historical reconstructions of variation in effective population size over the past million generations echo this difference in polymorphism. Evolutionary simulations demonstrate how selection, recombination, mutation, and selfing shape variation along the genome, and that multiple drivers can produce patterns similar to those observed in natural populations. The results illustrate how genome organization and selection play a crucial role in shaping the genomic pattern of diversity whereas demographic processes scale the level of diversity across the genome as a whole., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Teterina et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
- Published
- 2023
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11. Post-insemination sexual selection in males indirectly masculinizes the female transcriptome.
- Author
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Kasimatis KR, Willis JH, and Phillips PC
- Abstract
Sex-specific regulation of gene expression is the most plausible way for generating sexually differentiated phenotypes from an essentially shared genome. However, since genetic material is shared, sex-specific selection in one sex can have an indirect response in the other sex. From a gene expression perspective, this tethered response can move one sex away from their wildtype expression state and impact potentially many gene regulatory networks. Here, using experimental evolution in the model nematode Caenorhabditis elegans , we explore the coupling of direct sexual selection on males with the transcriptomic response in females over microevolutionary timescales to uncover the extent to which post-insemination reproductive traits share a genetic basis between the sexes. We find that differential gene expression is driven by female ancestral or evolved generation alone and that male generation has no impact on changes in gene expression. Almost all differentially expressed genes were downregulated in evolved females. Moreover, 80% of these gene were located on the X chromosome and have wildtype female-biased expression profiles. Changes in gene expression profiles were likely driven through trans -acting pathways that are shared between the sexes. We found no evidence that the core dosage compensation machinery was impacted by experimental evolution. Together these data suggest masculinization of the female transcriptome driven by direct selection on male sperm competitive ability. Our results indicate that on short evolutionary timescales sexual selection can generate sexual conflict in expression space., Lay Summary: Sexual selection drives the evolution of some of the most dramatic phenotypic differences between the sexes. Such sexual dimorphism is so common across multicellular organisms that we often overlook how remarkable it is for shared genetic material to create numerous and complex sex differences. At an evolutionary level, sexual dimorphism furthers the opportunity for sex-specific selection to optimize the fitness of a given sex. As a consequence, sex-specific selection, such as sexual selection, can have an indirect evolutionary response in the other sex due to genetic associations created by the sexes sharing the same genome. This correlated evolutionary response can create sexual conflict by shifting a sex away from their fitness optimum. At the functional level, sexual dimorphism is generated is through sex-specific regulation of gene expression. Bridging the evolutionary response to sexual selection with the evolution of sex-specific gene regulation during post-mating interactions has proved challenging. We previously used experimental evolution to increase male fertility by directly selecting for increased sperm competitive ability. In this study, we examined the effect of this direct selection on males on gene expression patterns in females. Differential gene expression was determined by whether a female was ancestral or evolved generation, indicating that gene expression changes were an evolved response due to indirect selection on females. Significantly differentially expressed genes were downregulated in evolved females. These genes tended to be female-biased in wildtype individuals and located on the X chromosome. The downregulation of X-linked genes suggests expression levels in females equal to or lower than that in males. Together these results indicate a less female-like transcriptome after experimental evolution. This supports a sexual conflict scenario by which direct sexual selection on males indirectly masculinizes the female transcriptome over short evolutionary timescales.
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- 2023
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12. Long-term Outcomes Following Temperature-Controlled Radiofrequency Neurolysis for the Treatment of Chronic Rhinitis.
- Author
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Ehmer D, McDuffie CM, McIntyre JB, Davis BM, Mehendale NH, Willis JH, Watkins JP, and Kakarlapudi VV
- Abstract
Background: Temperature-controlled radiofrequency neurolysis of the posterior nasal nerve has been shown to reduce the symptom burden of patients with chronic rhinitis., Objectives: To evaluate the long-term safety and effectiveness of temperature-controlled radiofrequency neurolysis of the posterior nasal nerve for the treatment of chronic rhinitis., Methods: A prospective extension of a 12-month single-arm study, where reflective total nasal symptom score (rTNSS) and the responses to a study-specific quality of life questionnaire and patient satisfaction survey were collected at 24 months., Results: Forty-seven patients completed initial 12-month follow-up after treatment with the study device, of which 34 patients were reconsented and completed 24-month follow-up. The mean rTNSS of the long-term follow-up patients improved from 8.4 (95% confidence interval (CI), 7.7 to 9.0) at baseline to 2.9 (95% CI, 2.1 to 3.6), P < .001 at 24 months, a 65.5% improvement. On a 6-point scale (0-5), postnasal drip improved from a mean of 4.1 (95% CI, 3.6 to 4.6) to 2.1 (95% CI, 1.7 to 2.5) and chronic cough improved from 3.2 (95% CI, 2.7 to 3.6) to 0.9 (95% CI, 0.5 to 1.3) from baseline through 24 months; P < .001 for both measures. The proportion of patients achieving a minimal clinically important difference of 30% improvement from baseline at 24 months was 88.2% (95% CI, 73.4%-95.3%). At 24 months, 24% of patients were taking overall fewer and 15% taking overall more rhinitis medication classes than at baseline. Patients reported a higher quality of life in terms of sleep, well-being, and lower oral medication/nasal spray use at 24 months. There were no serious adverse events considered related to the procedure in the 12-24-month period., Conclusion: Temperature-controlled radiofrequency neurolysis results in a significant and durable reduction in the symptom burden of chronic rhinitis and patients reported improved quality of life through 24 months postprocedure., Competing Interests: Declaration of Conflicting Interests: The author(s) declared the following potential conflicts of interest with respect to the research, authorship, and/or publication of this article: Xxxxxxx. Dale Ehmer and V. Vasu Kakarlapudi are consultants for Aerin Medical. The authors have no other funding, financial relationships, or conflicts of interest to disclose., (© The Author(s) 2022.)
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- 2022
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13. Post-insemination selection dominates pre-insemination selection in driving rapid evolution of male competitive ability.
- Author
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Kasimatis KR, Moerdyk-Schauwecker MJ, Lancaster R, Smith A, Willis JH, and Phillips PC
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- Animals, Caenorhabditis elegans genetics, Female, Male, Reproduction genetics, Selection, Genetic, Sexual Behavior, Animal physiology, Insemination, Spermatozoa physiology
- Abstract
Sexual reproduction is a complex process that contributes to differences between the sexes and divergence between species. From a male's perspective, sexual selection can optimize reproductive success by acting on the variance in mating success (pre-insemination selection) as well as the variance in fertilization success (post-insemination selection). The balance between pre- and post-insemination selection has not yet been investigated using a strong hypothesis-testing framework that directly quantifies the effects of post-insemination selection on the evolution of reproductive success. Here we use experimental evolution of a uniquely engineered genetic system that allows sperm production to be turned off and on in obligate male-female populations of Caenorhabditis elegans. We show that enhanced post-insemination competition increases the efficacy of selection and surpasses pre-insemination sexual selection in driving a polygenic response in male reproductive success. We find that after 10 selective events occurring over 30 generations post-insemination selection increased male reproductive success by an average of 5- to 7-fold. Contrary to expectation, enhanced pre-insemination competition hindered selection and slowed the rate of evolution. Furthermore, we found that post-insemination selection resulted in a strong polygenic response at the whole-genome level. Our results demonstrate that post-insemination sexual selection plays a critical role in the rapid optimization of male reproductive fitness. Therefore, explicit consideration should be given to post-insemination dynamics when considering the population effects of sexual selection., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2022
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14. Genetic diversity estimates for the Caenorhabditis Intervention Testing Program screening panel.
- Author
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Teterina AA, Coleman-Hulbert AL, Banse SA, Willis JH, Perez VI, Lithgow GJ, Driscoll M, and Phillips PC
- Abstract
The Caenorhabditis Intervention Testing Program (CITP) was founded on the principle that compounds with positive effects across a genetically diverse test-set should have an increased probability of engaging conserved biochemical pathways with mammalian translational potential. To fulfill its mandate, the CITP uses a genetic diversity panel of Caenorhabditis strains for assaying longevity effects of candidate compounds. The panel comprises 22 strains from three different species, collected globally, to achieve inter-population genetic diversity. The three represented species, C. elegans , C. briggsae , and C. tropicalis , are all sequential hermaphrodites, which simplifies experimental procedures while maximizing intra-population homogeneity. Here, we present estimates of the genetic diversity encapsulated by the constituent strains in the panel based on their most recently published and publicly available whole-genome sequences, as well as two newly generated genomic data sets. We observed average genome-wide nucleotide diversity (π) within the C. elegans (1.2e-3), C. briggsae (7.5e-3), and C. tropicalis strains (2.6e-3) greater than estimates for human populations, and comparable to that found in mouse populations. Our analysis supports the assumption that the CITP screening panel encompasses broad genetic diversity, suggesting that lifespan-extending chemicals with efficacy across the panel should be enriched for interventions that function on conserved processes that are shared across genetic backgrounds. While the diversity panel was established by the CITP for studying longevity interventions, the panel may prove useful for the broader research community when seeking broadly efficacious interventions for any phenotype with potential genetic background effects., (Copyright: © 2022 by the authors.)
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- 2022
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15. Slow Recovery from Inbreeding Depression Generated by the Complex Genetic Architecture of Segregating Deleterious Mutations.
- Author
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Adams PE, Crist AB, Young EM, Willis JH, Phillips PC, and Fierst JL
- Subjects
- Alleles, Animals, Caenorhabditis elegans genetics, Inbreeding, Male, Mutation, Inbreeding Depression
- Abstract
The deleterious effects of inbreeding have been of extreme importance to evolutionary biology, but it has been difficult to characterize the complex interactions between genetic constraints and selection that lead to fitness loss and recovery after inbreeding. Haploid organisms and selfing organisms like the nematode Caenorhabditis elegans are capable of rapid recovery from the fixation of novel deleterious mutation; however, the potential for recovery and genomic consequences of inbreeding in diploid, outcrossing organisms are not well understood. We sought to answer two questions: 1) Can a diploid, outcrossing population recover from inbreeding via standing genetic variation and new mutation? and 2) How does allelic diversity change during recovery? We inbred C. remanei, an outcrossing relative of C. elegans, through brother-sister mating for 30 generations followed by recovery at large population size. Inbreeding reduced fitness but, surprisingly, recovery from inbreeding at large populations sizes generated only very moderate fitness recovery after 300 generations. We found that 65% of ancestral single nucleotide polymorphisms (SNPs) were fixed in the inbred population, far fewer than the theoretical expectation of ∼99%. Under recovery, 36 SNPs across 30 genes involved in alimentary, muscular, nervous, and reproductive systems changed reproducibly across replicates, indicating that strong selection for fitness recovery does exist. Our results indicate that recovery from inbreeding depression via standing genetic variation and mutation is likely to be constrained by the large number of segregating deleterious variants present in natural populations, limiting the capacity for recovery of small populations., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
- Published
- 2022
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16. Temperature-Controlled Radiofrequency Neurolysis for the Treatment of Rhinitis.
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Ehmer D, McDuffie CM, Scurry WC Jr, McIntyre JB, Mehendale NH, Willis JH, Shealy RB, Watkins JP, and Kakarlapudi VV
- Subjects
- Administration, Intranasal, Adult, Aged, Female, Humans, Male, Middle Aged, Prospective Studies, Quality of Life, Temperature, Treatment Outcome, Rhinitis surgery
- Abstract
Background: Chronic rhinitis is a prevalent condition with a significant impact on quality of life. Posterior nasal nerve and vidian neurectomy are surgical options for treating the symptoms of chronic rhinitis but are invasive procedures., Objective: To determine the outcomes of patients diagnosed with refractory chronic rhinitis and treated with temperature-controlled radiofrequency neurolysis of the posterior nasal nerve area in a minimally invasive procedure., Methods: A prospective, single-arm multicenter study with follow-up through 52 weeks. Eligible adult patients had chronic rhinitis symptoms of at least 6 months duration with inadequate response to at least 4 weeks usage of intranasal steroids and an overall 12-h reflective total nasal symptom score (rTNSS) ≥ 6 with subscores 2 to 3 for rhinorrhea, 1 to 3 for nasal congestion, and 0 to 3 for each of nasal itching and sneezing. Temperature-controlled radiofrequency energy was delivered to the nasal cavity mucosa overlying the posterior nasal nerve region with a novel single-use, disposable, handheld device., Results: A total of 50 patients were treated (42.0% male; mean age 57.9 ± 11.9 years), and 47 completed the study through 52 weeks. Mean rTNSS significantly improved from 8.5 (95% CI 8.0, 9.0) at baseline to 3.6 (95% CI 3.0, 4.3) at 52 weeks ( P < .001), a 57.6% improvement. Similar trends in improvement were noted for rTNSS subscores (rhinorrhea, nasal congestion, itching, sneezing), postnasal drip scores, and chronic cough scores. Subgroup analysis demonstrated the treatment was effective regardless of rhinitis classification (allergic or nonallergic). No serious adverse events with a relationship to the device/procedure occurred., Conclusions: Temperature-controlled radiofrequency neurolysis of the posterior nasal nerve area for the treatment of chronic rhinitis is safe and resulted in a durable improvement in the symptoms of chronic rhinitis through a 52-week follow-up. Data suggest that this novel device could be considered a minimally invasive option in the otolaryngologist's armamentarium for the treatment of chronic rhinitis.
- Published
- 2022
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17. Lepidopteran wing scales contain abundant cross-linked film-forming histidine-rich cuticular proteins.
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Liu J, Chen Z, Xiao Y, Asano T, Li S, Peng L, Chen E, Zhang J, Li W, Zhang Y, Tong X, Kadono-Okuda K, Zhao P, He N, Arunkumar KP, Gopinathan KP, Xia Q, Willis JH, Goldsmith MR, and Mita K
- Subjects
- Animal Scales drug effects, Animals, Bombyx drug effects, Chromatography, Liquid, Tandem Mass Spectrometry, Wings, Animal drug effects, Animal Scales chemistry, Bombyx chemistry, Insect Proteins chemistry, Proteins chemistry, Wings, Animal chemistry
- Abstract
Scales are symbolic characteristic of Lepidoptera; however, nothing is known about the contribution of cuticular proteins (CPs) to the complex patterning of lepidopteran scales. This is because scales are resistant to solubilization, thus hindering molecular studies. Here we succeeded in dissolving developing wing scales from Bombyx mori, allowing analysis of their protein composition. We identified a distinctive class of histidine rich (His-rich) CPs (6%-45%) from developing lepidopteran scales by LC-MS/MS. Functional studies using RNAi revealed CPs with different histidine content play distinct and critical roles in constructing the microstructure of the scale surface. Moreover, we successfully synthesized films in vitro by crosslinking a 45% His-rich CP (BmorCPR152) with laccase2 using N-acetyl- dopamine or N-β-alanyl-dopamine as the substrate. This molecular study of scales provides fundamental information about how such a fine microstructure is constructed and insights into the potential application of CPs as new biomaterials.
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- 2021
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18. The genetic architecture and evolution of life-history divergence among perennials in the Mimulus guttatus species complex.
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Coughlan JM, Brown MW, and Willis JH
- Subjects
- Adaptation, Physiological, Phenotype, Quantitative Trait Loci, Mimulus genetics
- Abstract
Ecological divergence is a fundamental source of phenotypic diversity between closely related species, yet the genetic architecture of most ecologically relevant traits is poorly understood. Differences in elevation can impose substantial divergent selection on both complex, correlated suites of traits (such as life-history), as well as novel adaptations. We use the Mimulus guttatus species complex to assess if the divergence in elevation is accompanied by trait divergence in a group of closely related perennials and determine the genetic architecture of this divergence. We find that divergence in elevation is associated with differences in life-history, as well as a unique trait, the production of rhizomes. The divergence between two perennials is largely explained by few mid-to-large effect quantitative trait loci (QTLs). However, the presence of QTLs with correlated, but opposing effects on multiple traits leads to some hybrids with transgressive trait combinations. Lastly, we find that the genetic architecture of the ability to produce rhizomes changes through development, wherein most hybrids produce rhizomes, but only later in development. Our results suggest that elevational differences may shape life-history divergence between perennials, but aspects of the genetic architecture of divergence may have implications for hybrid fitness in nature.
- Published
- 2021
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19. Populations Are Differentiated in Biological Rhythms without Explicit Elevational Clines in the Plant Mimulus laciniatus .
- Author
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Leinonen PH, Salmela MJ, Greenham K, McClung CR, and Willis JH
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- Acclimatization, California, Seasons, Altitude, Circadian Clocks, Mimulus, Photoperiod
- Abstract
Environmental variation along an elevational gradient can yield phenotypic differentiation resulting from varying selection pressures on plant traits related to seasonal responses. Thus, genetic clines can evolve in a suite of traits, including the circadian clock, that drives daily cycling in varied traits and that shares its genetic background with adaptation to seasonality. We used populations of annual Mimulus laciniatus from different elevations in the Sierra Nevada in California to explore among-population differentiation in the circadian clock, flowering responses to photoperiod, and phenological traits (days to cotyledon emergence, days to flowering, and days to seed ripening) in controlled common-garden conditions. Further, we examined correlations of these traits with environmental variables related to temperature and precipitation. We observed that the circadian period in leaf movement was differentiated among populations sampled within about 100 km, with population means varying by 1.6 h. Significant local genetic variation occurred within 2 populations in which circadian period among families varied by up to 1.8 h. Replicated treatments with variable ecologically relevant photoperiods revealed marked population differentiation in critical day length for flowering that ranged from 11.0 to 14.1 h, corresponding to the time period between late February and mid-May in the wild. Flowering time varied among populations in a 14-h photoperiod. Regardless of this substantial population-level diversity, obvious linear clinality in trait variability across elevations could not be determined based on our genotypic sample; it is possible that more complex spatial patterns of variation arise in complex terrains such as those in the Sierra Nevada. Moreover, we did not find statistically significant bivariate correlations between population means of different traits. Our research contributes to the understanding of genetic variation in the circadian clock and in seasonal responses in natural populations, highlighting the need for more comprehensive investigations on the association between the clock and other adaptive traits in plants.
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- 2020
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20. Chromosome-Level Assembly of the Caenorhabditis remanei Genome Reveals Conserved Patterns of Nematode Genome Organization.
- Author
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Teterina AA, Willis JH, and Phillips PC
- Subjects
- Animals, Caenorhabditis classification, Chromatin chemistry, Chromatin genetics, Chromosomes genetics, Contig Mapping, Evolution, Molecular, Repetitive Sequences, Nucleic Acid, Caenorhabditis genetics, Conserved Sequence, Genome, Helminth, Phylogeny
- Abstract
The nematode Caenorhabditis elegans is one of the key model systems in biology, including possessing the first fully assembled animal genome. Whereas C. elegans is a self-reproducing hermaphrodite with fairly limited within-population variation, its relative C. remanei is an outcrossing species with much more extensive genetic variation, making it an ideal parallel model system for evolutionary genetic investigations. Here, we greatly improve on previous assemblies by generating a chromosome-level assembly of the entire C. remanei genome (124.8 Mb of total size) using long-read sequencing and chromatin conformation capture data. Like other fully assembled genomes in the genus, we find that the C. remanei genome displays a high degree of synteny with C. elegans despite multiple within-chromosome rearrangements. Both genomes have high gene density in central regions of chromosomes relative to chromosome ends and the opposite pattern for the accumulation of repetitive elements. C. elegans and C. remanei also show similar patterns of interchromosome interactions, with the central regions of chromosomes appearing to interact with one another more than the distal ends. The new C. remanei genome presented here greatly augments the use of the Caenorhabditis as a platform for comparative genomics and serves as a basis for molecular population genetics within this highly diverse species., (Copyright © 2020 by the Genetics Society of America.)
- Published
- 2020
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21. Patterns of Hybrid Seed Inviability in the Mimulus guttatus sp. Complex Reveal a Potential Role of Parental Conflict in Reproductive Isolation.
- Author
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Coughlan JM, Wilson Brown M, and Willis JH
- Subjects
- Longevity, Mimulus genetics, Sympatry, Hybridization, Genetic, Mimulus physiology, Reproductive Isolation, Seeds physiology
- Abstract
Genomic conflicts may play a central role in the evolution of reproductive barriers. Theory predicts that early-onset hybrid inviability may stem from conflict between parents for resource allocation to offspring. Here, we describe M. decorus: a group of cryptic species within the M. guttatus species complex that are largely reproductively isolated by hybrid seed inviability (HSI). HSI between M. guttatus and M. decorus is common and strong, but populations of M. decorus vary in the magnitude and directionality of HSI with M. guttatus. Patterns of HSI between M. guttatus and M. decorus, as well as within M. decorus, conform to the predictions of parental conflict: first, reciprocal F1s exhibit size differences and parent-of-origin-specific endosperm defects; second, the extent of asymmetry between reciprocal F1 seed size is correlated with asymmetry in HSI; and third, inferred differences in the extent of conflict predict the extent of HSI between populations. We also find that HSI is rapidly evolving, as populations that exhibit the most HSI are each others' closest relative. Lastly, although all populations appear largely outcrossing, we find that the differences in the inferred strength of conflict scale positively with π, suggesting that demographic or life history factors other than transitions to self-fertilization may influence the rate of parental-conflict-driven evolution. Overall, these patterns suggest the rapid evolution of parent-of-origin-specific resource allocation alleles coincident with HSI within and between M. guttatus and M. decorus. Parental conflict may therefore be an important evolutionary driver of reproductive isolation., (Copyright © 2019 Elsevier Ltd. All rights reserved.)
- Published
- 2020
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22. Dissecting the role of a large chromosomal inversion in life history divergence throughout the Mimulus guttatus species complex.
- Author
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Coughlan JM and Willis JH
- Subjects
- Ecotype, Genetics, Population, Mimulus growth & development, Quantitative Trait Loci genetics, Recombination, Genetic, Reproductive Isolation, Adaptation, Physiological genetics, Chromosome Inversion genetics, Genetic Speciation, Mimulus genetics
- Abstract
Chromosomal inversions can play an important role in adaptation, but the mechanism of their action in many natural populations remains unclear. An inversion could suppress recombination between locally beneficial alleles, thereby preventing maladaptive reshuffling with less-fit, migrant alleles. The recombination suppression hypothesis has gained much theoretical support but empirical tests are lacking. Here, we evaluated the evolutionary history and phenotypic effects of a chromosomal inversion which differentiates annual and perennial forms of Mimulus guttatus. We found that perennials likely possess the derived orientation of the inversion. In addition, this perennial orientation occurs in a second perennial species, M. decorus, where it is strongly associated with life history differences between co-occurring M. decorus and annual M. guttatus. One prediction of the recombination suppression hypothesis is that loci contributing to local adaptation will predate the inversion. To test whether the loci influencing perenniality pre-date this inversion, we mapped QTLs for life history traits that differ between annual M. guttatus and a more distantly related, collinear perennial species, M. tilingii. Consistent with the recombination suppression hypothesis, we found that this region is associated with life history in the absence of the inversion, and this association can be broken into at least two QTLs. However, the absolute phenotypic effect of the LG8 inversion region on life history is weaker in M. tilingii than in perennials which possess the inversion. Thus, while we find support for the recombination suppression hypothesis, the contribution of this inversion to life history divergence in this group is likely complex., (© 2018 John Wiley & Sons Ltd.)
- Published
- 2019
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23. Proteomics reveals localization of cuticular proteins in Anopheles gambiae.
- Author
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Zhou Y, Badgett MJ, Orlando R, and Willis JH
- Subjects
- Animals, Anopheles anatomy & histology, Larva anatomy & histology, Larva metabolism, Pupa anatomy & histology, Pupa metabolism, Anopheles metabolism, Insect Proteins metabolism, Molting physiology, Proteomics
- Abstract
Anopheles gambiae devotes over 2% of its protein coding genes to its 298 structural cuticular proteins (CPs). This paper provides new LC-MS/MS data on two adult structures, proboscises and palps, as well as three larval samples - 4th instar larvae, just their terminal segment, and a preparation enriched in their tracheae. These data were combined with our previously published results of proteins from five other adult structures, whole adults, and two preparations chosen for their relatively clean cuticle, the larval head capsules left behind after ecdysis and the pupal cuticles left behind after adult eclosion. Peptides from 28 CPs were recovered in all adult structures; 24 CPs were identified for the first time, 6 of these were members of the TWDL family. Most newly identified proteins came from the larval sources. Based solely on peptide recovery, from our data and from other investigators, most available on VectorBase, there were only 4 CPs that were restricted to a single adult structure. More were restricted to a single metamorphic stage, 14 in larvae, 0 in pupae and 32 in adults. Expression data from our earlier RT-qPCR studies reduces these numbers. Charting restriction of CPs to stage or structure is a step forward in establishing their specific roles., (Copyright © 2018 Elsevier Ltd. All rights reserved.)
- Published
- 2019
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24. Major QTL controls adaptation to serpentine soils in Mimulus guttatus.
- Author
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Selby JP and Willis JH
- Subjects
- Chromosome Mapping, Genetics, Population, Mimulus physiology, Selection, Genetic, Adaptation, Physiological genetics, Ecosystem, Mimulus genetics, Quantitative Trait Loci, Soil chemistry
- Abstract
Spatially varying selection is a critical driver of adaptive differentiation. Yet, there are few examples where the fitness effects of naturally segregating variants that contribute to local adaptation have been measured in the field. Plant adaptation to harsh soil habitats provides an ideal study system for investigating the genetic basis of local adaptation. The work presented here identifies a major locus underlying adaptation to serpentine soils in Mimulus guttatus and estimates the strength of selection on this locus in native field sites. Reciprocal transplant and common-garden studies show that serpentine and nonserpentine populations of M. guttatus differ in their ability to survive on serpentine soils. We directly mapped these field survival differences by performing a bulk segregant analysis with F2 survivors from a field transplant study and identify a single QTL where individuals that are homozygous for the nonserpentine allele do not survive on serpentine soils. Genotyping the survivors from an independent mapping population reveals that this same QTL controls serpentine tolerance in a second, geographically distant population. Finally, we show that this QTL controls tolerance to soil properties, as opposed to some other aspect of the field sites that may differ, by performing a laboratory-based common-garden experiment in native serpentine soils that replicates the survival differences observed in the field. These results indicate that despite the myriad chemical and physical challenges plants face in serpentine habitats, adaptation to these soils in M. guttatus has a simple genetic basis., (© 2018 John Wiley & Sons Ltd.)
- Published
- 2018
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25. Hybrid inviability and differential submergence tolerance drive habitat segregation between two congeneric monkeyflowers.
- Author
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Toll K and Willis JH
- Subjects
- California, Ecosystem, Hybridization, Genetic, Sympatry, Mimulus
- Abstract
Closely related, ecologically similar species are often separated at small geographic scales while being broadly sympatric. Both adaptation to abiotic environmental conditions and a variety of biotic interactions may determine small-scale allopatry. In Northern California's coast range, two monkeyflower species, Mimulus guttatus and Mimulus nudatus, can co-occur within local sites but rarely overlap at fine spatial scales, even though they are often separated by less than 1 m. M. guttatus naturally grows in wetter areas and is often submerged for up to four months of the year, while M. nudatus naturally occupies drier sites. We used a combination of observational data, reciprocal transplant, and laboratory experiments to test a series of biotic and abiotic hypotheses for the observed distribution pattern. Although M. guttatus can tolerate dry hillside conditions like those in which M. nudatus occurs, M. nudatus is unable to survive submerged for more than a week, limiting its distribution from seasonal streams inundated for months and dominated by M. guttatus. While herbivores did not differentially damage species, transplants were more likely to be damaged in M. guttatus' seep habitat and M. nudatus was less tolerant to herbivory. Individuals of each species transplanted into populations of heterospecific congeners produced large proportions (up to 80%) of inviable seeds resulting from increased hybridization rates in close sympatry. Mimulus nudatus' inability to tolerate submergence and herbivory establishes some degree of habitat association, and then, hybrid seed inviability reduces the ability of the locally rarer species to persist within the congener's microhabitat and maintains habitat segregation. Together these data show that both environmental filtering and biotic interactions shape the fine-scale distribution of close relatives., (© 2018 by the Ecological Society of America.)
- Published
- 2018
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26. Selective trade-offs maintain alleles underpinning complex trait variation in plants.
- Author
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Troth A, Puzey JR, Kim RS, Willis JH, and Kelly JK
- Subjects
- Alleles, Evolution, Molecular, Gene Frequency, Genetic Fitness, Polymorphism, Genetic, Mimulus genetics, Multifactorial Inheritance, Plants genetics, Selection, Genetic
- Abstract
To understand evolutionary factors that maintain complex trait variation, we sequenced genomes from a single population of the plant Mimulus guttatus , identifying hundreds of nucleotide variants associated with morphological and life history traits. Alleles that delayed flowering also increased size at reproduction, which suggests pervasive antagonistic pleiotropy in this annual plant. The "large and slow" alleles, which were less common in small, rapidly flowering populations, became more abundant in populations with greater plant size. Furthermore, natural selection within the field population favored alternative alleles from year to year. Our results suggest that environmental fluctuations and selective trade-offs maintain polygenic trait variation within populations and also contribute to the geographic divergence in this wildflower species., (Copyright © 2018, American Association for the Advancement of Science.)
- Published
- 2018
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27. Dramatic evolution of body length due to postembryonic changes in cell size in a newly discovered close relative of Caenorhabditis elegans .
- Author
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Woodruff GC, Willis JH, and Phillips PC
- Abstract
Understanding morphological diversity-and morphological constraint-has been a central question in evolutionary biology since its inception. Nematodes of the genus Caenorhabditis , which contains the well-studied model organism C. elegans , display remarkable morphological consistency in the face of extensive genetic divergence. Here, we provide a description of the broad developmental patterns of a newly discovered species, C . sp. 34, which was isolated from fresh figs in Okinawa and which is among the closest known relatives of C. elegans . C . sp. 34 displays an extremely large body size; it can grow to be nearly twice as long as C. elegans and all other known members of the genus. Observations of the timing of developmental milestones reveal that C . sp. 34 develops about twice as slowly as C. elegans . Measurements of embryonic and larval size show that the size difference between C . sp. 34 and C. elegans is largely due to postembryonic events, particularly during the transition from larval to adult stages. This difference in size is not attributable to differences in germ line chromosome number or the number of somatic cells. The overall difference in body size is therefore largely attributable to changes in cell size via increased cytoplasmic volume. Because of its close relationship to C. elegans , the distinctness of C . sp. 34 provides an ideal system for the detailed analysis of evolutionary diversification. The context of over 40 years of C. elegans developmental genetics also reveals clues into how natural selection and developmental constraint act jointly to promote patterns of morphological stasis and divergence in this group.
- Published
- 2018
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28. Differential adaptation to a harsh granite outcrop habitat between sympatric Mimulus species.
- Author
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Ferris KG and Willis JH
- Subjects
- Animals, Herbivory, Hybridization, Genetic, Mimulus physiology, Selection, Genetic, Species Specificity, Water, Adaptation, Physiological genetics, Biological Evolution, Ecosystem, Mimulus genetics, Sympatry
- Abstract
Understanding which environmental variables and traits underlie adaptation to harsh environments is difficult because many traits evolve simultaneously as populations or species diverge. Here, we investigate the ecological variables and traits that underlie Mimulus laciniatus' adaptation to granite outcrops compared to its sympatric, mesic-adapted progenitor, Mimulus guttatus. We use fine-scale measurements of soil moisture and herbivory to examine differences in selective forces between the species' habitats, and measure selection on flowering time, flower size, plant height, and leaf shape in a reciprocal transplant using M. laciniatus × M. guttatus F
4 hybrids. We find that differences in drought and herbivory drive survival differences between habitats, that M. laciniatus and M. guttatus are each better adapted to their native habitat, and differential habitat selection on flowering time, plant stature, and leaf shape. Although early flowering time, small stature, and lobed leaf shape underlie plant fitness in M. laciniatus' seasonally dry environment, increased plant size is advantageous in a competitive mesic environment replete with herbivores like M. guttatus'. Given that we observed divergent selection between habitats in the direction of species differences, we conclude that adaptation to different microhabitats is an important component of reproductive isolation in this sympatric species pair., (© 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.)- Published
- 2018
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29. Plastic breeding system response to day length in the California wildflower Mimulus douglasii.
- Author
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Barnett LL, Troth A, and Willis JH
- Subjects
- Adaptation, Physiological physiology, California, Flowers growth & development, Flowers physiology, Reproduction, Temperature, Mimulus physiology, Photoperiod
- Abstract
Premise of the Study: Angiosperms have evolved multiple breeding systems that allow reproductive success under varied conditions. Striking among these are cleistogamous breeding systems, where individuals can produce alternative flower types specialized for distinct mating strategies. Cleistogamy is thought to be environmentally-dependent, but little is known about environmental triggers. If production of alternate flowers is environmentally induced, populations may evolve locally adapted responses. Mimulus douglasii, exhibits a cleistogamous breeding system, and ranges across temperature and day-length gradients, providing an ideal system to investigate environmental parameters that control cleistogamy., Methods: We compared flowering responses across Mimulus douglasii population accessions that produce distinct outcrossing and self-pollinating flower morphs. Under controlled conditions, we determined time to flower, and number and type of flowers produced under different temperatures and day lengths., Key Results: Temperature and day length both affect onset of flowering. Long days shift flower type from predominantly chasmogamous to cleistogamous. The strength of the response to day length varies across accessions whether temperature varies or is held constant., Conclusions: Cleistogamy is an environmentally sensitive polyphenism in Mimulus douglasii, allowing transition from one mating strategy to another. Longer days induce flowering and production of cleistogamous flowers. Shorter days induce chasmogamous flowers. Population origin has a small effect on response to environmental cues., (© 2018 Botanical Society of America.)
- Published
- 2018
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30. The Evolution and Metamorphosis of Arthropod Proteomics and Genomics.
- Author
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Willis JH
- Subjects
- Animals, History, 20th Century, History, 21st Century, Insect Proteins genetics, Insect Proteins metabolism, Insecta genetics, Entomology history, Insect Proteins analysis, Insecta metabolism, Metamorphosis, Biological, Proteomics history
- Abstract
This article presents an overview of the development of techniques for analyzing cuticular proteins (CPs), their transcripts, and their genes over the past 50 years based primarily on experience in the laboratory of J.H. Willis. It emphasizes changes in the kind of data that can be gathered and how such data provided insights into the molecular underpinnings of insect metamorphosis and cuticle structure. It describes the techniques that allowed visualization of the location of CPs at both the anatomical and intracuticular levels and measurement of the appearance and deployment of transcripts from CP genes as well as what was learned from genomic and transcriptomic data. Most of the early work was done with the cecropia silkmoth, Hyalophora cecropia, and later work was with Anopheles gambiae.
- Published
- 2018
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31. Population-genomic inference of the strength and timing of selection against gene flow.
- Author
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Aeschbacher S, Selby JP, Willis JH, and Coop G
- Subjects
- Biological Evolution, California, Genetic Speciation, Genomics, Geography, Models, Genetic, Phylogeny, Recombination, Genetic, Reproductive Isolation, Selection, Genetic, Species Specificity, Gene Flow, Genetics, Population, Mimulus genetics, Polymorphism, Genetic
- Abstract
The interplay of divergent selection and gene flow is key to understanding how populations adapt to local environments and how new species form. Here, we use DNA polymorphism data and genome-wide variation in recombination rate to jointly infer the strength and timing of selection, as well as the baseline level of gene flow under various demographic scenarios. We model how divergent selection leads to a genome-wide negative correlation between recombination rate and genetic differentiation among populations. Our theory shows that the selection density (i.e., the selection coefficient per base pair) is a key parameter underlying this relationship. We then develop a procedure for parameter estimation that accounts for the confounding effect of background selection. Applying this method to two datasets from Mimulus guttatus , we infer a strong signal of adaptive divergence in the face of gene flow between populations growing on and off phytotoxic serpentine soils. However, the genome-wide intensity of this selection is not exceptional compared with what M. guttatus populations may typically experience when adapting to local conditions. We also find that selection against genome-wide introgression from the selfing sister species M. nasutus has acted to maintain a barrier between these two species over at least the last 250 ky. Our study provides a theoretical framework for linking genome-wide patterns of divergence and recombination with the underlying evolutionary mechanisms that drive this differentiation., Competing Interests: The authors declare no conflict of interest.
- Published
- 2017
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32. Properties of the cuticular proteins of Anopheles gambiae as revealed by serial extraction of adults.
- Author
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Zhou Y, Badgett MJ, Billard L, Bowen JH, Orlando R, and Willis JH
- Subjects
- Amino Acid Motifs genetics, Amino Acid Sequence, Animals, Anopheles genetics, Chromatography, Liquid, Insect Proteins genetics, Isoelectric Point, Multigene Family, Protein Binding, Solubility, Tandem Mass Spectrometry, Anopheles metabolism, Chitin metabolism, Insect Proteins isolation & purification, Insect Proteins metabolism
- Abstract
How cuticular proteins (CPs) interact with chitin and with each other in the cuticle remains unresolved. We employed LC-MS/MS to identify CPs from 5-6 day-old adults of Anopheles gambiae released after serial extraction with PBS, EDTA, 2-8M urea, and SDS as well as those that remained unextracted. Results were compared to published data on time of transcript abundance, localization of proteins within structures and within the cuticle, as well as properties of individual proteins, length, pI, percent histidine, tyrosine, glutamine, and number of AAP[A/V/L] repeats. Thirteen proteins were solubilized completely, all were CPRs, most belonging to the RR-1 group. Eleven CPs were identified in both soluble fractions and the final pellet, including 5 from other CP families. Forty-three were only detected from the final pellet. These included CPRs and members of the CPAP1, CPF, CPFL, CPLCA, CPLCG, CPLCP, and TWDL families, as well as several low complexity CPs, not assigned to families and named CPLX. For a given protein, many histidines or tyrosines or glutamines appear to be potential participants in cross-linking since we could not identify any peptide bearing these residues that was consistently absent. We failed to recover peptides from the amino-terminus of any CP. Whether this implicates that location in sclerotization or some modification that prevents detection is not known. Soluble CPRs had lower isoelectric points than those that remained in the final pellet; most members of other CP families had isoelectric points of 8 or higher. Obviously, techniques beyond analysis of differential solubility will be needed to learn how CPs interact with each other and with chitin.
- Published
- 2017
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33. Impact of genetic background and experimental reproducibility on identifying chemical compounds with robust longevity effects.
- Author
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Lucanic M, Plummer WT, Chen E, Harke J, Foulger AC, Onken B, Coleman-Hulbert AL, Dumas KJ, Guo S, Johnson E, Bhaumik D, Xue J, Crist AB, Presley MP, Harinath G, Sedore CA, Chamoli M, Kamat S, Chen MK, Angeli S, Chang C, Willis JH, Edgar D, Royal MA, Chao EA, Patel S, Garrett T, Ibanez-Ventoso C, Hope J, Kish JL, Guo M, Lithgow GJ, Driscoll M, and Phillips PC
- Subjects
- Animals, Benzothiazoles, Caenorhabditis classification, Caenorhabditis genetics, Caenorhabditis elegans drug effects, Caenorhabditis elegans genetics, Dose-Response Relationship, Drug, Fertility drug effects, Fertility genetics, Longevity genetics, Reproducibility of Results, Species Specificity, Thiazoles pharmacology, Caenorhabditis drug effects, Genetic Background, Longevity drug effects, Organic Chemicals pharmacology
- Abstract
Limiting the debilitating consequences of ageing is a major medical challenge of our time. Robust pharmacological interventions that promote healthy ageing across diverse genetic backgrounds may engage conserved longevity pathways. Here we report results from the Caenorhabditis Intervention Testing Program in assessing longevity variation across 22 Caenorhabditis strains spanning 3 species, using multiple replicates collected across three independent laboratories. Reproducibility between test sites is high, whereas individual trial reproducibility is relatively low. Of ten pro-longevity chemicals tested, six significantly extend lifespan in at least one strain. Three reported dietary restriction mimetics are mainly effective across C. elegans strains, indicating species and strain-specific responses. In contrast, the amyloid dye ThioflavinT is both potent and robust across the strains. Our results highlight promising pharmacological leads and demonstrate the importance of assessing lifespans of discrete cohorts across repeat studies to capture biological variation in the search for reproducible ageing interventions.
- Published
- 2017
- Full Text
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34. Metagenome-Assembled Draft Genome Sequence of a Novel Microbial Stenotrophomonas maltophilia Strain Isolated from Caenorhabditis remanei Tissue.
- Author
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Fierst JL, Murdock DA, Thanthiriwatte C, Willis JH, and Phillips PC
- Abstract
Stenotrophomonas maltophilia is a Gram-negative aerobic bacterium and emerging nosocomial pathogen. Here, we present a draft genome sequence for an S. maltophilia strain assembled from a metagenomic DNA extract isolated from a laboratory stock of the nematode worm Caenorhabditis remanei ., (Copyright © 2017 Fierst et al.)
- Published
- 2017
- Full Text
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35. Geographic Variation of Plant Circadian Clock Function in Natural and Agricultural Settings.
- Author
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Greenham K, Lou P, Puzey JR, Kumar G, Arnevik C, Farid H, Willis JH, and McClung CR
- Subjects
- Adaptation, Physiological physiology, Canada, Ecosystem, Geography, Species Specificity, Temperature, United States, Circadian Clocks physiology, Circadian Rhythm physiology, Mimulus physiology, Plant Leaves physiology, Glycine max physiology
- Abstract
The increasing demand for improved agricultural production will require more efficient breeding for traits that maintain yield under heterogeneous environments. The internal circadian oscillator is essential for perceiving and coordinating environmental cues such as day length, temperature, and abiotic stress responses within physiological processes. To investigate the contribution of the circadian clock to local adaptability, we have analyzed circadian period by leaf movement in natural populations of Mimulus guttatus and domesticated cultivars of Glycine max. We detected consistent variation in circadian period along a latitudinal gradient in annual populations of the wild plant and the selectively bred crop, and this provides novel evidence of natural and artificial selection for circadian performance. These findings provide new support that the circadian clock acts as a central regulator of plant adaptability and further highlight the potential of applying circadian clock gene variation to marker-assisted breeding programs in crops.
- Published
- 2017
- Full Text
- View/download PDF
36. Localization of RR-1 and RR-2 cuticular proteins within the cuticle of Anopheles gambiae.
- Author
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Vannini L and Willis JH
- Subjects
- Animals, Antibodies chemistry, Cell Membrane metabolism, Chitin chemistry, Chitin metabolism, Gene Expression Regulation, Developmental, Immunohistochemistry, Microscopy, Electron, Microscopy, Electron, Transmission, Peptides chemistry, Protein Binding, Anopheles metabolism, Gene Expression Regulation, Insect Proteins metabolism
- Abstract
The largest arthropod cuticular protein family, CPR, has the Rebers and Riddiford (R&R) Consensus that in an extended form confers chitin-binding properties. Two forms of the Consensus, RR-1 and RR-2, have been recognized and initial data suggested that the RR-1 and RR-2 proteins were present in different regions within the cuticle itself. Thus, RR-2 proteins would contribute to exocuticle that becomes sclerotized, while RR-1s would be found in endocuticle that remains soft. An alternative, and more common, suggestion is that RR-1 proteins are used for soft, flexible cuticles such as intersegmental membranes, while RR-2s are associated with hard cuticle such as sclerites and head capsules. We used TEM immunogold detection to localize the position of several RR-1 and RR-2 proteins in the cuticle of Anopheles gambiae. RR-1s were localized in the procuticle of the soft intersegmental membrane except for one protein found in the endocuticle of hard cuticle. RR-2s were consistently found in hard cuticle and not in flexible cuticle. All RR-2 antibodies localized to the exocuticle and four out of six were also found in the endocuticle. Hence the location of RR-1s and RR-2s depends more on properties of individual proteins than on either hypothesis., (Copyright © 2016 Elsevier Ltd. All rights reserved.)
- Published
- 2017
- Full Text
- View/download PDF
37. Population structure and local selection yield high genomic variation in Mimulus guttatus.
- Author
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Puzey JR, Willis JH, and Kelly JK
- Subjects
- Gene Flow, Gene Frequency, Genome, Plant, Genotype, Haplotypes, North America, Genetics, Population, Mimulus genetics, Selection, Genetic
- Abstract
Across western North America, Mimulus guttatus exists as many local populations adapted to site-specific environmental challenges. Gene flow between locally adapted populations will affect genetic diversity both within demes and across the larger metapopulation. Here, we analyse 34 whole-genome sequences from the intensively studied Iron Mountain population (IM) in conjunction with sequences from 22 Mimulus individuals sampled from across western North America. Three striking features of these data address hypotheses about migration and selection in a locally adapted population. First, we find very high levels of intrapopulation polymorphism (synonymous π = 0.033). Variation outside of genes is likely even higher but difficult to estimate because excessive divergence reduces the efficiency of read mapping. Second, IM exhibits a significantly positive genomewide average for Tajima's D. This indicates allele frequencies are typically more intermediate than expected from neutrality, opposite the pattern observed in many other species. Third, IM exhibits a distinctive haplotype structure with a genomewide excess of positive associations between rarer alleles at linked loci. This suggests an important effect of gene flow from other Mimulus populations, although a residual effect of population founding might also contribute. The combination of multiple analyses, including a novel tree-based analytic method, illustrates how the balance of local selection, limited dispersal and metapopulation dynamics manifests across the genome. The overall genomic pattern of sequence diversity suggests successful gene flow of divergent immigrant genotypes into IM. However, many loci show patterns indicative of local adaptation, particularly at SNPs associated with chromosomal inversions., (© 2016 John Wiley & Sons Ltd.)
- Published
- 2017
- Full Text
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38. The genetic architecture of local adaptation and reproductive isolation in sympatry within the Mimulus guttatus species complex.
- Author
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Ferris KG, Barnett LL, Blackman BK, and Willis JH
- Subjects
- Biological Evolution, Gene Flow, Genetic Pleiotropy, Mimulus physiology, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Adaptation, Biological genetics, Flowers physiology, Mimulus genetics, Reproductive Isolation, Sympatry
- Abstract
The genetic architecture of local adaptation has been of central interest to evolutionary biologists since the modern synthesis. In addition to classic theory on the effect size of adaptive mutations by Fisher, Kimura and Orr, recent theory addresses the genetic architecture of local adaptation in the face of ongoing gene flow. This theory predicts that with substantial gene flow between populations local adaptation should proceed primarily through mutations of large effect or tightly linked clusters of smaller effect loci. In this study, we investigate the genetic architecture of divergence in flowering time, mating system-related traits, and leaf shape between Mimulus laciniatus and a sympatric population of its close relative M. guttatus. These three traits are probably involved in M. laciniatus' adaptation to a dry, exposed granite outcrop environment. Flowering time and mating system differences are also reproductive isolating barriers making them 'magic traits'. Phenotypic hybrids in this population provide evidence of recent gene flow. Using next-generation sequencing, we generate dense SNP markers across the genome and map quantitative trait loci (QTLs) involved in flowering time, flower size and leaf shape. We find that interspecific divergence in all three traits is due to few QTL of large effect including a highly pleiotropic QTL on chromosome 8. This QTL region contains the pleiotropic candidate gene TCP4 and is involved in ecologically important phenotypes in other Mimulus species. Our results are consistent with theory, indicating that local adaptation and reproductive isolation with gene flow should be due to few loci with large and pleiotropic effects., (© 2016 John Wiley & Sons Ltd.)
- Published
- 2017
- Full Text
- View/download PDF
39. Immunolocalization of cuticular proteins in Johnston's organ and the corneal lens of Anopheles gambiae.
- Author
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Vannini L and Willis JH
- Subjects
- Animals, Arthropod Proteins metabolism, Blotting, Western, Immunohistochemistry, Microscopy, Electron, Transmission methods, Anopheles metabolism, Arthropod Proteins analysis, Compound Eye, Arthropod ultrastructure
- Abstract
Previous work with EM immunolocalization examined the intracuticular placement of several antibodies directed against cuticular proteins (CPs) in various structures of Anopheles gambiae. Those structures had long stretches of fairly uniform cuticle. We have now used 19 antibodies directed against members of five CP families on two adult structures with considerable complexity, Johnston's organ and the corneal lens of the compound eye. We also localized chitin with colloidal-gold labeled wheat germ agglutinin. Twelve of these antibodies recognized structures in Johnston's organ. Only 6 were detected in the outer pedicel wall, but the internal structures were more complex with distinct distributions of members of the five CP families in six different structures. The corneal lens had four distinct regions of laminar cuticle. Thirteen of the 15 members of the CPR family were detected, none from the other CP families. Specific antibodies were localized to different regions and in different laminae within a region. The specificity of deployment of cuticular proteins revealed in this study is helping to explain why An. gambiae allocates about 2% of its protein coding genes to structural CPs., (Copyright © 2016 Elsevier Ltd. All rights reserved.)
- Published
- 2016
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40. Distribution of cuticular proteins in different structures of adult Anopheles gambiae.
- Author
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Zhou Y, Badgett MJ, Bowen JH, Vannini L, Orlando R, and Willis JH
- Subjects
- Animals, Anopheles growth & development, Anopheles metabolism, Chromatography, Liquid, Insect Proteins metabolism, Larva genetics, Larva metabolism, Male, Organ Specificity, Sequence Analysis, DNA, Tandem Mass Spectrometry, Anopheles genetics, Insect Proteins genetics, Proteome
- Abstract
Anopheles gambiae devotes over 2% (295) of its protein coding genes to structural cuticular proteins (CPs) that have been classified into 13 different families plus ten low complexity proteins not assigned to families. Small groups of genes code for identical proteins reducing the total number of unique cuticular proteins to 282. Is the large number because different structures utilize different CPs, or are all of the genes widely expressed? We used LC-MS/MS to learn how many products of these genes were found in five adult structures: Johnston's organs, the remainder of the male antennae, eye lenses, legs, and wings. Data were analyzed against both the entire proteome and a smaller database of just CPs. We recovered unique peptides for 97 CPs and shared peptides for another 35. Members of 11 of the 13 families were recovered as well as some unclassified. Only 11 CPs were present exclusively in only one structure while 43 CPs were recovered from all five structures. A quantitative analysis, using normalized spectral counts, revealed that only a few CPs were abundant in each structure. When the MS/MS data were run against the entire proteome, the majority of the top hits were to CPs, but peptides were recovered from an additional 467 proteins. CP peptides were frequently recovered from chitin-binding domains, confirming that protein-chitin interactions are not mediated by covalent bonds. Comparison with three other MS/MS analyses of cuticles or cuticle-rich structures augmented the current analysis. Our findings provide new insights into the composition of different mosquito structures and reveal the complexity of selection and utilization of genes coding for structural cuticular proteins., (Copyright © 2016 Elsevier Ltd. All rights reserved.)
- Published
- 2016
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41. Disruption of endosperm development is a major cause of hybrid seed inviability between Mimulus guttatus and Mimulus nudatus.
- Author
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Oneal E, Willis JH, and Franks RG
- Subjects
- Crosses, Genetic, Fruit growth & development, Germination, Phenotype, Pollen Tube growth & development, Self-Fertilization, Staining and Labeling, Sympatry, Endosperm embryology, Hybridization, Genetic, Mimulus embryology, Mimulus genetics
- Abstract
Divergence of developmental mechanisms within populations could lead to hybrid developmental failure, and might be a factor driving speciation in angiosperms. We investigate patterns of endosperm and embryo development in Mimulus guttatus and the closely related, serpentine endemic Mimulus nudatus, and compare them to those of reciprocal hybrid seed. We address whether disruption in hybrid seed development is the primary source of reproductive isolation between these sympatric taxa. M. guttatus and M. nudatus differ in the pattern and timing of endosperm and embryo development. Some hybrid seeds exhibit early disruption of endosperm development and are completely inviable, while others develop relatively normally at first, but later exhibit impaired endosperm proliferation and low germination success. These developmental patterns are reflected in mature hybrid seeds, which are either small and flat (indicating little to no endosperm) or shriveled (indicating reduced endosperm volume). Hybrid seed inviability forms a potent reproductive barrier between M. guttatus and M. nudatus. We shed light on the extent of developmental variation between closely related species within the M. guttatus species complex, an important ecological model system, and provide a partial mechanism for the hybrid barrier between M. guttatus and M. nudatus., (© 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.)
- Published
- 2016
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42. A Segregating Inversion Generates Fitness Variation in Yellow Monkeyflower (Mimulus guttatus).
- Author
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Lee YW, Fishman L, Kelly JK, and Willis JH
- Subjects
- Chromosome Mapping, Gene Frequency, Genetic Linkage, Genetics, Population, Genotype, Heterozygote, Inbreeding Depression, Phenotype, Polymorphism, Genetic, Quantitative Trait Loci, Recombination, Genetic, Translocation, Genetic, Chromosome Inversion, Genetic Fitness, Mimulus genetics
- Abstract
Polymorphic chromosomal rearrangements can bind hundreds of genes into single genetic loci with diverse effects. Rearrangements are often associated with local adaptation and speciation and may also be an important component of genetic variation within populations. We genetically and phenotypically characterize a segregating inversion (inv6) in the Iron Mountain (IM) population of Mimulus guttatus (yellow monkeyflower). We initially mapped inv6 as a region of recombination suppression in three F2 populations resulting from crosses among IM plants. In each case, the F1 parent was heterozygous for a derived haplotype, homogenous across markers spanning over 5 Mb of chromsome 6. In the three F2 populations, inv6 reduced male and female fitness components. In addition,i nv6 carriers suffered an ∼30% loss of pollen viability in the field. Despite these costs, inv6 exists at moderate frequency (∼8%) in the natural population, suggesting counterbalancing fitness benefits that maintain the polymorphism. Across 4 years of monitoring in the field, inv6 had an overall significant positive effect on seed production (lifetime female fitness) of carriers. This benefit was particularly strong in harsh years and may be mediated (in part) by strong positive effects on flower production. These data suggest that opposing fitness effects maintain an intermediate frequency, and as a consequence, inv6 generates inbreeding depression and high genetic variance. We discuss these findings in relation to the theory of inbreeding depression and the maintenance of fitness variation., (Copyright © 2016 by the Genetics Society of America.)
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- 2016
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43. The CPCFC cuticular protein family: Anatomical and cuticular locations in Anopheles gambiae and distribution throughout Pancrustacea.
- Author
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Vannini L, Bowen JH, Reed TW, and Willis JH
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- Animals, Anopheles anatomy & histology, Anopheles genetics, Anopheles metabolism, Arthropod Proteins chemistry, Arthropod Proteins genetics, Crustacea chemistry, Crustacea genetics, Epidermis chemistry, Insecta chemistry, Insecta genetics, Larva metabolism, Molting, Nymph metabolism, Phylogeny, Protein Structure, Tertiary, RNA, Messenger metabolism, Anopheles chemistry, Arthropod Proteins metabolism, Crustacea metabolism, Epidermis metabolism, Insecta metabolism
- Abstract
Arthropod cuticles have, in addition to chitin, many structural proteins belonging to diverse families. Information is sparse about how these different cuticular proteins contribute to the cuticle. Most cuticular proteins lack cysteine with the exception of two families (CPAP1 and CPAP3), recently described, and the one other that we now report on that has a motif of 16 amino acids first identified in a protein, Bc-NCP1, from the cuticle of nymphs of the cockroach, Blaberus craniifer (Jensen et al., 1997). This motif turns out to be present as two or three copies in one or two proteins in species from many orders of Hexapoda. We have named the family of cuticular proteins with this motif CPCFC, based on its unique feature of having two cysteines interrupted by five amino acids (C-X(5)-C). Analysis of the single member of the family in Anopheles gambiae (AgamCPCFC1) revealed that its mRNA is most abundant immediately following ecdysis in larvae, pupae and adults. The mRNA is localized primarily in epidermis that secretes hard cuticle, sclerites, setae, head capsules, appendages and spermatheca. EM immunolocalization revealed the presence of the protein, generally in endocuticle of legs and antennae. A phylogenetic analysis found proteins bearing this motif in 14 orders of Hexapoda, but not in some species for which there are complete genomic data. Proteins were much longer in Coleoptera and Diptera than in other orders. In contrast to the 1 and occasionally 2 copies in other species, a dragonfly, Ladona fulva, has at least 14 genes coding for family members. CPCFC proteins were present in four classes of Crustacea with 5 repeats in one species, and motifs that ended C-X(7)-C in Malacostraca. They were not detected, except as obvious contaminants, in any other arthropod subphyla or in any other phylum. The conservation of CPCFC proteins throughout the Pancrustacea and the small number of copies in individual species indicate that, when present, these proteins are serving important functions worthy of further study., (Copyright © 2015 Elsevier Ltd. All rights reserved.)
- Published
- 2015
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44. Correction: Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes.
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Fierst JL, Willis JH, Thomas CG, Wang W, Reynolds RM, Ahearne TE, Cutter AD, and Phillips PC
- Published
- 2015
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45. Leaf shape evolution has a similar genetic architecture in three edaphic specialists within the Mimulus guttatus species complex.
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Ferris KG, Rushton T, Greenlee AB, Toll K, Blackman BK, and Willis JH
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- Chromosome Mapping, Crosses, Genetic, Genes, Plant, Genetic Association Studies, Phenotype, Quantitative Trait Loci genetics, Species Specificity, Biological Evolution, Mimulus anatomy & histology, Mimulus genetics, Plant Leaves anatomy & histology, Plant Leaves genetics
- Abstract
Background and Aims: The genetic basis of leaf shape has long interested botanists because leaf shape varies extensively across the plant kingdom and this variation is probably adaptive. However, knowledge of the genetic architecture of leaf shape variation in natural populations remains limited. This study examined the genetic architecture of leaf shape diversification among three edaphic specialists in the Mimulus guttatus species complex. Lobed and narrow leaves have evolved from the entire, round leaves of M. guttatus in M. laciniatus, M. nudatus and a polymorphic serpentine M. guttatus population (M2L)., Methods: Bulk segregant analysis and next-generation sequencing were used to map quantitative trait loci (QTLs) that underlie leaf shape in an M. laciniatus × M. guttatus F2 population. To determine whether the same QTLs contribute to leaf shape variation in M. nudatus and M2L, F2s from M. guttatus × M. nudatus and lobed M2L × unlobed M. guttatus crosses were genotyped at QTLs from the bulk segregant analysis., Key Results: Narrow and lobed leaf shapes in M. laciniatus, M. nudatus and M. guttatus are controlled by overlapping genetic regions. Several promising leaf shape candidate genes were found under each QTL., Conclusions: The evolution of divergent leaf shape has taken place multiple times in the M. guttatus species complex and is associated with the occupation of dry, rocky environments. The genetic architecture of elongated and lobed leaves is similar across three species in this group. This may indicate that parallel genetic evolution from standing variation or new mutations is responsible for the putatively adaptive leaf shape variation in Mimulus., (© The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)
- Published
- 2015
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46. Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes.
- Author
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Fierst JL, Willis JH, Thomas CG, Wang W, Reynolds RM, Ahearne TE, Cutter AD, and Phillips PC
- Subjects
- Animals, Caenorhabditis physiology, Caenorhabditis elegans genetics, DNA Transposable Elements, Female, Helminth Proteins genetics, Male, Self-Fertilization, X Chromosome, Biological Evolution, Caenorhabditis genetics, Genome Size, Genome, Helminth, Reproduction genetics
- Abstract
The self-fertile nematode worms Caenorhabditis elegans, C. briggsae, and C. tropicalis evolved independently from outcrossing male-female ancestors and have genomes 20-40% smaller than closely related outcrossing relatives. This pattern of smaller genomes for selfing species and larger genomes for closely related outcrossing species is also seen in plants. We use comparative genomics, including the first high quality genome assembly for an outcrossing member of the genus (C. remanei) to test several hypotheses for the evolution of genome reduction under a change in mating system. Unlike plants, it does not appear that reductions in the number of repetitive elements, such as transposable elements, are an important contributor to the change in genome size. Instead, all functional genomic categories are lost in approximately equal proportions. Theory predicts that self-fertilization should equalize the effective population size, as well as the resulting effects of genetic drift, between the X chromosome and autosomes. Contrary to this, we find that the self-fertile C. briggsae and C. elegans have larger intergenic spaces and larger protein-coding genes on the X chromosome when compared to autosomes, while C. remanei actually has smaller introns on the X chromosome than either self-reproducing species. Rather than being driven by mutational biases and/or genetic drift caused by a reduction in effective population size under self reproduction, changes in genome size in this group of nematodes appear to be caused by genome-wide patterns of gene loss, most likely generated by genomic adaptation to self reproduction per se.
- Published
- 2015
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47. Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.
- Author
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Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arcà B, Arensburger P, Artemov G, Assour LA, Basseri H, Berlin A, Birren BW, Blandin SA, Brockman AI, Burkot TR, Burt A, Chan CS, Chauve C, Chiu JC, Christensen M, Costantini C, Davidson VL, Deligianni E, Dottorini T, Dritsou V, Gabriel SB, Guelbeogo WM, Hall AB, Han MV, Hlaing T, Hughes DS, Jenkins AM, Jiang X, Jungreis I, Kakani EG, Kamali M, Kemppainen P, Kennedy RC, Kirmitzoglou IK, Koekemoer LL, Laban N, Langridge N, Lawniczak MK, Lirakis M, Lobo NF, Lowy E, MacCallum RM, Mao C, Maslen G, Mbogo C, McCarthy J, Michel K, Mitchell SN, Moore W, Murphy KA, Naumenko AN, Nolan T, Novoa EM, O'Loughlin S, Oringanje C, Oshaghi MA, Pakpour N, Papathanos PA, Peery AN, Povelones M, Prakash A, Price DP, Rajaraman A, Reimer LJ, Rinker DC, Rokas A, Russell TL, Sagnon N, Sharakhova MV, Shea T, Simão FA, Simard F, Slotman MA, Somboon P, Stegniy V, Struchiner CJ, Thomas GW, Tojo M, Topalis P, Tubio JM, Unger MF, Vontas J, Walton C, Wilding CS, Willis JH, Wu YC, Yan G, Zdobnov EM, Zhou X, Catteruccia F, Christophides GK, Collins FH, Cornman RS, Crisanti A, Donnelly MJ, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Hansen IA, Howell PI, Kafatos FC, Kellis M, Lawson D, Louis C, Luckhart S, Muskavitch MA, Ribeiro JM, Riehle MA, Sharakhov IV, Tu Z, Zwiebel LJ, and Besansky NJ
- Subjects
- Animals, Anopheles classification, Base Sequence, Chromosomes, Insect genetics, Drosophila genetics, Humans, Insect Vectors classification, Molecular Sequence Data, Phylogeny, Sequence Alignment, Anopheles genetics, Evolution, Molecular, Genome, Insect, Insect Vectors genetics, Malaria transmission
- Abstract
Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts., (Copyright © 2015, American Association for the Advancement of Science.)
- Published
- 2015
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48. The extent and genetic basis of phenotypic divergence in life history traits in Mimulus guttatus.
- Author
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Friedman J, Twyford AD, Willis JH, and Blackman BK
- Subjects
- DNA, Plant genetics, Flowers anatomy & histology, Flowers physiology, Genetics, Population, High-Throughput Nucleotide Sequencing, North America, Sequence Analysis, DNA, Genetic Pleiotropy, Mimulus genetics, Phenotype, Quantitative Trait Loci, Selection, Genetic
- Abstract
Differential natural selection acting on populations in contrasting environments often results in adaptive divergence in multivariate phenotypes. Multivariate trait divergence across populations could be caused by selection on pleiotropic alleles or through many independent loci with trait-specific effects. Here, we assess patterns of association between a suite of traits contributing to life history divergence in the common monkey flower, Mimulus guttatus, and examine the genetic architecture underlying these correlations. A common garden survey of 74 populations representing annual and perennial strategies from across the native range revealed strong correlations between vegetative and reproductive traits. To determine whether these multitrait patterns arise from pleiotropic or independent loci, we mapped QTLs using an approach combining high-throughput sequencing with bulk segregant analysis on a cross between populations with divergent life histories. We find extensive pleiotropy for QTLs related to flowering time and stolon production, a key feature of the perennial strategy. Candidate genes related to axillary meristem development colocalize with the QTLs in a manner consistent with either pleiotropic or independent QTL effects. Further, these results are analogous to previous work showing pleiotropy-mediated genetic correlations within a single population of M. guttatus experiencing heterogeneous selection. Our findings of strong multivariate trait associations and pleiotropic QTLs suggest that patterns of genetic variation may determine the trajectory of adaptive divergence., (© 2014 John Wiley & Sons Ltd.)
- Published
- 2015
- Full Text
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49. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.
- Author
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Chipman AD, Ferrier DE, Brena C, Qu J, Hughes DS, Schröder R, Torres-Oliva M, Znassi N, Jiang H, Almeida FC, Alonso CR, Apostolou Z, Aqrawi P, Arthur W, Barna JC, Blankenburg KP, Brites D, Capella-Gutiérrez S, Coyle M, Dearden PK, Du Pasquier L, Duncan EJ, Ebert D, Eibner C, Erikson G, Evans PD, Extavour CG, Francisco L, Gabaldón T, Gillis WJ, Goodwin-Horn EA, Green JE, Griffiths-Jones S, Grimmelikhuijzen CJ, Gubbala S, Guigó R, Han Y, Hauser F, Havlak P, Hayden L, Helbing S, Holder M, Hui JH, Hunn JP, Hunnekuhl VS, Jackson L, Javaid M, Jhangiani SN, Jiggins FM, Jones TE, Kaiser TS, Kalra D, Kenny NJ, Korchina V, Kovar CL, Kraus FB, Lapraz F, Lee SL, Lv J, Mandapat C, Manning G, Mariotti M, Mata R, Mathew T, Neumann T, Newsham I, Ngo DN, Ninova M, Okwuonu G, Ongeri F, Palmer WJ, Patil S, Patraquim P, Pham C, Pu LL, Putman NH, Rabouille C, Ramos OM, Rhodes AC, Robertson HE, Robertson HM, Ronshaugen M, Rozas J, Saada N, Sánchez-Gracia A, Scherer SE, Schurko AM, Siggens KW, Simmons D, Stief A, Stolle E, Telford MJ, Tessmar-Raible K, Thornton R, van der Zee M, von Haeseler A, Williams JM, Willis JH, Wu Y, Zou X, Lawson D, Muzny DM, Worley KC, Gibbs RA, Akam M, and Richards S
- Subjects
- Animals, Circadian Rhythm Signaling Peptides and Proteins genetics, DNA Methylation, Evolution, Molecular, Female, Genome, Mitochondrial, Hormones genetics, Male, Multigene Family, Phylogeny, Polymorphism, Genetic, Protein Kinases genetics, RNA, Untranslated genetics, Receptors, Odorant genetics, Selenoproteins genetics, Sex Chromosomes, Transcription Factors genetics, Arthropods genetics, Genome, Synteny
- Abstract
Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2014
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50. CutProtFam-Pred: detection and classification of putative structural cuticular proteins from sequence alone, based on profile hidden Markov models.
- Author
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Ioannidou ZS, Theodoropoulou MC, Papandreou NC, Willis JH, and Hamodrakas SJ
- Subjects
- Amino Acid Sequence, Animals, Arthropod Proteins genetics, Arthropod Proteins metabolism, Chitin genetics, Chitin metabolism, Computational Biology methods, Markov Chains, Molecular Sequence Data, Multigene Family, Phylogeny, Proteome, Sequence Alignment, Sequence Analysis, Protein, Arthropod Proteins chemistry, Arthropods chemistry, Arthropods genetics, Arthropods metabolism, Chitin chemistry
- Abstract
The arthropod cuticle is a composite, bipartite system, made of chitin filaments embedded in a proteinaceous matrix. The physical properties of cuticle are determined by the structure and the interactions of its two major components, cuticular proteins (CPs) and chitin. The proteinaceous matrix consists mainly of structural cuticular proteins. The majority of the structural proteins that have been described to date belong to the CPR family, and they are identified by the conserved R&R region (Rebers and Riddiford Consensus). Two major subfamilies of the CPR family RR-1 and RR-2, have also been identified from conservation at sequence level and some correlation with the cuticle type. Recently, several novel families, also containing characteristic conserved regions, have been described. The package HMMER v3.0 (http://hmmer.janelia.org/) was used to build characteristic profile Hidden Markov Models based on the characteristic regions for 8 of these families, (CPF, CPAP3, CPAP1, CPCFC, CPLCA, CPLCG, CPLCW, Tweedle). In brief, these families can be described as having: CPF (a conserved region with 44 amino acids); CPAP1 and CPAP-3 (analogous to peritrophins, with 1 and 3 chitin-binding domains, respectively); CPCFC (2 or 3 C-x(5)-C repeats); and four of five low complexity (LC) families, each with characteristic domains. Using these models, as well as the models previously created for the two major subfamilies of the CPR family, RR-1 and RR-2 (Karouzou et al., 2007), we developed CutProtFam-Pred, an on-line tool (http://bioinformatics.biol.uoa.gr/CutProtFam-Pred) that allows one to query sequences from proteomes or translated transcriptomes, for the accurate detection and classification of putative structural cuticular proteins. The tool has been applied successfully to diverse arthropod proteomes including a crustacean (Daphnia pulex) and a chelicerate (Tetranychus urticae), but at this taxonomic distance only CPRs and CPAPs were recovered., (Copyright © 2014 Elsevier Ltd. All rights reserved.)
- Published
- 2014
- Full Text
- View/download PDF
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