Bergmann\u27s Clines in Ectotherms: Illustrating a Life-History Perspective with Sceloporine Lizards

The generality and causes of Bergmann\u27s rule have been debated vigorously in the last few years, but Bergmann\u27s clines are rarely explained in the context of life-history theory. We used both traditional and phylogenetic comparative analyses to explore the causes of latitudinal and thermal clines in the body size of the eastern fence lizard (Sceloporus undulatus). The proximate mechanism for larger body sizes in colder environments is delayed maturation, which results in a greater fecundity but a lower survival to maturity. Life-history theory predicts that a higher survivorship of juveniles in colder environments can favor the evolution of a Bergmann\u27s cline. Consistent with this theory, lizards in colder environments survive better as juveniles and delay maturation until reaching a larger body size than that of lizards in warmer environments. We expect similar relationships among temperature, survivorship, and age/size at maturity exist in other ectotherms that exhibit Bergmann\u27s clines. However, life-history traits of S. undulatus were more strongly related to latitude than they were to temperature, indicating that both abiotic and biotic factors should be considered as causes of Bergmann\u27s clines. Nonetheless, analyses of the costs and benefits of particular body sizes in different thermal environments will enhance our understanding of geographic variation

Kepler-16: A Transiting Circumbinary Planet

We report the detection of a planet whose orbit surrounds a pair of low-mass stars. Data from the Kepler spacecraft reveal transits of the planet across both stars, in addition to the mutual eclipses of the stars, giving precise constraints on the absolute dimensions of all three bodies. The planet is comparable to Saturn in mass and size, and is on a nearly circular 229-day orbit around its two parent stars. The eclipsing stars are 20% and 69% as massive as the sun, and have an eccentric 41-day orbit. The motions of all three bodies are confined to within 0.5 degree of a single plane, suggesting that the planet formed within a circumbinary disk.Comment: Science, in press; for supplemental material see http://www.sciencemag.org/content/suppl/2011/09/14/333.6049.1602.DC1/1210923.Doyle.SOM.pd

1993 Progress Reports

The 1993 Progress Reports which contain Blueberry Tax Supported Weed Management and Pruning Project Reports, and CSRS Supported Weed Management and Pruning Project Reports, pertain to and report on research conducted in 1992. They were prepared for the Maine Wild Blueberry Commission and the University of Maine Wild Blueberry Advisory Committee by researchers at the University of Maine, Orono. Projects in this report include: Progress Reports 1. Effects of Irrigation on Low bush Blueberry Yield and Quality 2. Economics of Investing in Irrigation for Lowbush Blueberries 3. Diammonium Phosphate Study 4. Phosphorus Dose/Response Curve 5. Winter Injury Protection by Potassium 6. Multiple Cropping of Wild Stands 7. Effect of Boron on Lowbush Blueberry Fruit Set and Yield 8.Determination of Pesticide Residue Levels in Freshly Harvested and Processed Lowbush Blueberries 9. Effects of Calcium Salts and Citric Acids on the Quality of Canned Lowbush Blueberries- missing 10. Investigation of PreProcess Changes- missing 11. The Effect of Fertilization and Irrigation on Blueberry Fruit Control - missing 12. Pollination Ecology of Lowbush Blueberry in Maine 13. Control of Secondary Blueberry Pests 14. Control of Blueberry Maggot 15. Biology and Action Thresholds of Secondary Blueberry Pests 16. Cold-Hardiness of Native Lowbush Blueberries 17. Design, Fabrication, and Testing of an Experimental Sterilizer for Blueberry Fields 18. Canned Product Quality - Heat Resistant Molds 19. Sanitation for Disease Control Blueberry Tax Supported Weed Management and Pruning Project Reports 20. Evaluation of Postemergence Applications of Tribenuron Methyl for Bunchberry Control 21. Comparison of Poast and Select for Suppression of Bunchgrass 22. Effect of Time of Fall Pruning on Growth and Productivity of Blueberries. and Evaluation of Infrared Burner to Prune Blueberries 23. Evaluation of Velpar impregnated DAP for weed control 24. Thresholds of Dogbane and Bracken Fern for Mechanical and Chemical Control in Lowbush Blueberry Fields 25. Effect of Time and Rate of Application of Clopyralid for Control of Vetch in Lowbush Blueberries 26. Hexazinone Ground Water Survey 27. Composting Blueberry Processing Waste 28. Hexazinone Movement in a Blueberry Soil in Maine CSRS Supported Weed Management and Pruning Project Reports 29. Evaluation of the Suitability of Remote Sensing to Evaluate Plant Cover in Lowbush Blueberry Fields 30. Obstruction Removal in Lowbush Blueberry Fields 31. Evaluation of Pressurized Rope Wick Wick Master Wiper for Treating Weeds Growing Above Lowbush Blueberries 32. Evaluation of Infrared Burner for Weed Control 33. Blueberry Extension Education Program Base Miscellaneous 34. Comparison of N, NP, and NPK Fertilizers to Correct Nitrogen and Phosphorus Deficienc

1993-94 Progress Report

The 1993 edition of the Progress Reports was prepared for the Maine Wild Blueberry Commission and the University of Maine Wild Blueberry Advisory Committee by researchers at the University of Maine, Orono. Projects in this report include: 1. Effects of irrigation on lowbush blueberry yield and quality 2. The Economics of investigating irrigation for lowbush blueberries 3. Phosphorus dose/response curve 4. Winter injury protection by potassium 5. Multiple cropping of wild stands 6. Effect of Boron and Calcium on lowbush blueberry fruit set and yield 7. Comparison of N, NP, and NPK fertilizers to correct nitrogen and phosphorus deficiency 8. Determination of pesticide residue levels in freshly harvested and processed lowbush blueberries 9. Effects of calcium salts and citric acid on the quality of canned lowbush blueberries 10. Investigation of preprocess changes (chemical, microbiological, and/or physical) that can lead to the development of a simple and inexpensive method to measure preprocess berry spoilage 11. The effect of fertilization and irrigation in blueberry fruit quality 12. Pollination Ecology of lowbush blueberry in Maine 13. Current importance of insects in lowbush blueberry fields 14. Application of heat as a method of controlling secondary pest insects on lowbush blueberry: a feasibility study 15. Control of blueberry maggot 16. Control of secondary blueberry pest insects 17. Biology and action thresholds of secondary blueberry pest insects 18. Cold-hardiness of native lowbush blueberry 19. Design, fabrication, and testing of an experimental sterilizer for blueberry fields 20. Canned Product Quality--Heat-resistant molds 21. Sanitation for disease control 22. Evaluation of Velpar® impregnated DAP and Pronone® for weed control 23. Evaluation of postemergence applications of tribenuron methyl for bunchberry control 24. Evaluation of postemergence applications of a tank mix of tribenuron methyl and hexazinone for bunchberry control 25. Thresholds of dogbane and bracken fem by mechanical and chemical control in lowbush blueberry fields 26. Effect of time of application of clopyralid for control of vetch and effect on flowering in lowbush blueberries 27. Effect of time of fall pruning on growth and productivity of blueberries and evaluation of infrared burner to prune blueberries 28. Evaluation of infrared burner for selective seedling weed control 29. Evaluation of pressurized rope wick Wick Master wiper for treating weeds growing above lowbush blueberries 30. Blueberry Extension Education Program Base 31. Blueberry ICM program for Hancock County 32. Composting blueberry processing waste 33. Hexazinone ground water survey 34. Investigations of Lowbush Blueberry Fruit bud Cold-hardiness 35. Design, Fabrication, and Testing of an Experimental Sterilizer for Blueberry Field

Population Response to Habitat Fragmentation in a Stream-Dwelling Brook Trout Population

Fragmentation can strongly influence population persistence and expression of life-history strategies in spatially-structured populations. In this study, we directly estimated size-specific dispersal, growth, and survival of stream-dwelling brook trout in a stream network with connected and naturally-isolated tributaries. We used multiple-generation, individual-based data to develop and parameterize a size-class and location-based population projection model, allowing us to test effects of fragmentation on population dynamics at local (i.e., subpopulation) and system-wide (i.e., metapopulation) scales, and to identify demographic rates which influence the persistence of isolated and fragmented populations. In the naturally-isolated tributary, persistence was associated with higher early juvenile survival (∼45% greater), shorter generation time (one-half) and strong selection against large body size compared to the open system, resulting in a stage-distribution skewed towards younger, smaller fish. Simulating barriers to upstream migration into two currently-connected tributary populations caused rapid (2–6 generations) local extinction. These local extinctions in turn increased the likelihood of system-wide extinction, as tributaries could no longer function as population sources. Extinction could be prevented in the open system if sufficient immigrants from downstream areas were available, but the influx of individuals necessary to counteract fragmentation effects was high (7–46% of the total population annually). In the absence of sufficient immigration, a demographic change (higher early survival characteristic of the isolated tributary) was also sufficient to rescue the population from fragmentation, suggesting that the observed differences in size distributions between the naturally-isolated and open system may reflect an evolutionary response to isolation. Combined with strong genetic divergence between the isolated tributary and open system, these results suggest that local adaptation can ‘rescue’ isolated populations, particularly in one-dimensional stream networks where both natural and anthropogenically-mediated isolation is common. However, whether rescue will occur before extinction depends critically on the race between adaptation and reduced survival in response to fragmentation

Ensembl 2011

The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish reflecting the popularity and importance of these species in biomedical research. As of Ensembl release 59 (August 2010), 56 species are supported of which 5 have been added in the past year. Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types

Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data

Abstract: Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machine learning (ML) approaches incited us to apply them to classify healthy and diseased people according to their genomic information. The Immunochip dataset containing 18,227 CD patients and 34,050 healthy controls enrolled and genotyped by the international Inflammatory Bowel Disease genetic consortium (IIBDGC) has been re-analyzed using a set of ML methods: penalized logistic regression (LR), gradient boosted trees (GBT) and artificial neural networks (NN). The main score used to compare the methods was the Area Under the ROC Curve (AUC) statistics. The impact of quality control (QC), imputing and coding methods on LR results showed that QC methods and imputation of missing genotypes may artificially increase the scores. At the opposite, neither the patient/control ratio nor marker preselection or coding strategies significantly affected the results. LR methods, including Lasso, Ridge and ElasticNet provided similar results with a maximum AUC of 0.80. GBT methods like XGBoost, LightGBM and CatBoost, together with dense NN with one or more hidden layers, provided similar AUC values, suggesting limited epistatic effects in the genetic architecture of the trait. ML methods detected near all the genetic variants previously identified by GWAS among the best predictors plus additional predictors with lower effects. The robustness and complementarity of the different methods are also studied. Compared to LR, non-linear models such as GBT or NN may provide robust complementary approaches to identify and classify genetic markers

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead