Analysing Environmental Adaptation Using Landscape Genomics in R (EDAP01)
https://www.prstatistics.com/course/adaptive-landscape-genomics-in-r-edap01/ This course will be delivered by Matt Fitzpatrack and Dr Aki Laruson form the 15th - 19th July in Glasgow City Centre. Course Overview: Local adaptation to climate and other environmental drivers increasingly is being studied at the molecular level using high-throughput sequencing methods, with applications spanning both model and non-model organisms. At the same time, statistical tools for modeling and mapping patterns of biodiversity have seen increasing application, including to the challenge of understanding the drivers of spatial variation in adaptive genomic variation and mapping these patterns under current and future climate. This 5-day course will provide the skill set necessary to analyze sequence data for signatures of natural selection and to apply spatial modeling techniques to these patterns to quantify and map population-level genetic variation using two spatial modelling algorithms – Generalized Dissimilarity Modelling (GDM) and Gradient Forest (GF). The course will include introductory lectures, instruction on using the Linux command line for manipulation of genomic data, guided computer coding in R, and exercises for the participants, with an emphasis on visualization and reproducible workflows. Portions of each day will be allotted for students to work through their own datasets with the instructors. Course Programme Sunday 14th Meet at the accommodation at approx. 17:00 onwards Monday 15th – Classes from 09:00 to 17:00 Day 1 – Background and introduction 1) Introduction to approach 2) Data types (spatial, environmental, and genomic) 3) Considerations (quality control, SNP calling, filtering) Tuesday 16th – Classes from 09:00 to 17:00 Day 2 – Natural Selection I 4) Introduction to the genomics of natural selection 5) Review of population genomic approaches to inferring selection 6) Implementing FST- and differentiation-outlier tests and interpreting results Wednesday 17th – Classes from 09:00 to 17:00 Day 3 – Natural selection II 7) Principles of inferring selection from environmental association analyses 8) Review of landscape genomics approaches to inferring selection 9) Preparing SNP data from VCF and environmental data from rasters 10) Implementing multiple association methods (e.g., LFMM, RDA, etc.) and interpreting results Thursday 18th – Classes from 09:00 to 17:00 Day 4 – Spatial Modeling I 11) Introduction to GDM and GF 12) Review of genetic and environmental data preparation 13) Interpreting model results 14) Model fitting / testing / validation / variable selection Friday 19th – Classes from 09:00 to 16:30 Day 5 – Spatial Modeling II 15) Predictions & Applications of GDM / GF 16) Transforming environmental grids 17) Visualizing spatial variation in genetic composition 18) Calculating genetic differences between locations / times 19) Projecting patterns under climate change Email oliverhoo...@prstatistics.com Check out our sister sites, www.PRstatistics.com (Ecology and Life Sciences) www.PRstatistics.com/consultancy (Statistical and bioinformatics consultancy in all fields) www.PRinformatics.com (Bioinformatics and data science) www.PSstatistics.com (Behaviour and cognition) 1. June 10th – 14th 2019 STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR (SIMM04) Glasgow, Scotland, Dr. Andrew Parnell, Dr. Andrew Jackson www.prstatistics.com/course/stable-isotope-mixing-models-using-r-simm04/ 2. June 10th – 14th 2019 INTRODUCTION TO PYTHON FOR BIOLOGISTS (IPYB06) Glasgow, Scotland, Dr. Martin Jones http://www.prinformatics.com/course/introduction-to-python-for-biologists-ipyb06/ 3. June 17th – 21st 2019 ADVANCED PYTHON FOR BIOLOGISTS (APYB03) Glasgow, Scotland, Dr. Martin Jones www.prinformatics.com/course/advanced-python-biologists-apyb03/ 4. June 24th – 28th 2019 MICROBIOME DATA ANALYSIS USING QIIME2 (MBQM01) Glasgow, Scotland, Dr. Yoshiki Vazquez Baeza, Dr. Antonio Gonzalez Pena https://www.prinformatics.com/course/microbiome-data-analysis-using-qiime2-mbqm01/ 5. July 1st – 5th 2019 BIOACOUSTICS FOR ECOLOGISTS: HARDWARE, SURVEY DESIGN AND DATA ANALYSIS (BIAC01) Glasgow, Scotland, Dr. Paul Howden-Leach https://www.prstatistics.com/course/bioacoustics-for-ecologists-hardware-survey-design-and-data-analysis-biac01/ 6. July 8th – 12th 2019 INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING USING R (IBHM03) Glasgow, Scotland, Dr. Andrew Parnell https://www.psstatistics.com/course/introduction-to-bayesian-hierarchical-modelling-using-r-ibhm03/ 7. July 15th – 19th 2019 ANALYSING ENVIRONMENTAL ADAPTATION USING LANDSCAPE GENETICS (EDAP01) Glasgow, Dr. Matt Fitzpatrick https://www.prstatistics.com/course/analysing-environmental-adaptation-using-landscape-genetics-edap01 8. July 29th – August 2nd 2019 INTRODUCTION TO SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R (ISPE01) Glasgow, Scotland, Dr. Jakub Nowosad https://www.prstatistics.com/course/introduction-to-spatial-analysis-of-ecological-data-using-r-ispe01/ 9. September 2nd – 6th 2019 APPLIED METHODS FOR ANALYSING CAPTURE-RECAPTURE (MARK-RECAPTURE) DATA USING SPATIALLY EXPLICIT AND NON-SPATIAL TECHNIQUES (MARK01) Glasgow, Scotland, Dr. Joanne Potts, Dr. David Borchers https://www.prstatistics.com/course/applied-methods-for-analysing-capture-recapture-mark-recapture-data-using-spatially-explicit-and-non-spatial-techniques-mark01/ 10. September 9th – 13th 2019 DATA SCIENCE/ANALYTICS USING PYTHON (DSAP01) Glasgow, Scotland, Dr. Mark Andrews https://www.psstatistics.com/course/data-science-analytics-using-python-dsap01/ 11. September 16th – 20th 2019 R PACKAGE DESIGN AND DEVELOPMENT AND REPRODUCIBLE DATA SCIENCE FOR BIOLOGISTS (RPKG01) Glasgow, Scotland, Dr. Cory Merow, Dr. Andy Rominger https://www.prstatistics.com/course/r-package-design-and-development-and-reproducible-data-science-for-biologists-rpkg01/ 12. September 16th – 20th 2019 STRUCTURAL EQUATION MODELLING AND PATH ANALYSIS (SMPA01) Glasgow, Scotland, Dr. Mark Andrews https://www.psstatistics.com/course/structural-equation-modelling-and-path-analysis-smpa01/ 13. September 23rd – 27th 2019 GENERALISED LINEAR (GLM), NONLINEAR (NLGLM) AND GENERAL ADDITIVE MODELS (GAM’S) (GNAM01) Glasgow, Scotland, Dr. Mark Andrews https://www.psstatistics.com/course/generalised-linear-glm-nonlinear-nlglm-and-general-additive-models-gam-gnam01/ 14. September 30th – October 4th 2019 GEOMETRIC MORPHOMETRICS USING R (GMMR02) Glasgow, Scotland, Prof. Dean Adams, Prof. Michael Collyer, Dr. Antigoni Kaliontzopoulou http://www.prstatistics.com/course/geometric-morphometrics-using-r-gmmr02/ 15. October 7th – 11th 2019 CONSERVATION PLANNING USING PRIORITIZR : FROM THEORY TO PRACTICE (PRTZ01) Athens, GREECE, Dr Richard Schuster and Nina Morell https://www.prstatistics.com/course/conservation-planning-using-prioritizr-from-theory-to-practice-prtz01/ 16. October 14th – 18th 2019 INTRODUCTION TO BEHAVIOURAL DATA ANALYSIS USINR R (IBDA01) Glasgow, Scotland, Dr Will Hoppitt https://www.psstatistics.com/course/introduction-to-behavioural-data-analysis-using-r-ibda01/ 17. November 4th – 8th 2019 Glasgow, Scotland, Dr. Mark Andrews INTRODUCTION TO BAYESIAN DATA ANALYSIS FOR SOCIAL AND BEHAVIOURAL SCIENCES USING R AND STAN (BDRS02) https://www.psstatistics.com/course/introduction-to-bayesian-data-analysis-for-social-and-behavioural-sciences-using-r-and-stan-bdrs02/ 18. November 4th – 8th 2019 BEHAVIOURAL DATA ANALYSIS USING MAXIMUM LIKELIHOOD (BDML01) Glasgow, Scotland, Dr Will Hoppitt https://www.psstatistics.com/course/behavioural-data-analysis-using-maximum-likelihood-bdml02/ 19. November 11th – 15th 2019 APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS (ABME05) Glasgow, Scotland, Dr Matt Denwood, Emma Howard https://www.prstatistics.com/course/applied-bayesian-modelling-for-ecologists-and-epidemiologists-abme05/ 20. November 18th – 22nd 2019 INTRODUCTION TO STRUCTURED POPULATION MODELS AND DEMOGRAPHIC DISTRIBUTION MODELS (IIPM01) Athens, GREECE, Dr Cory Merow https://www.prstatistics.com/course/introduction-to-structured-population-models-and-demographic-distribution-models-iipm01/ 21. November 25th – 29th 2019 ADVANCED RANGE, NICHE, AND DISTRIBUTION MODELING (ASDM01) Athens, GREECE, Dr Cory Merow https://www.prstatistics.com/course/advanced-range-niche-and-distributio -- Oliver Hooker PhD. PR statistics 2019 publications; A way forward with eco evo devo: an extended theory of resource polymorphism with postglacial fishes as model systems. Biological Reviews (2019). prstatistics.com facebook.com/prstatistics/ twitter.com/PRstatistics groups.google.com/d/forum/pr-statistics-post-course-forum prstatistics.com/organiser/oliver-hooker/ 6 Hope Park Crescent Edinburgh EH8 9NA +44 (0) 7966500340 [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
