Aquatic stable isotope ecology: theory & practice: 21-26 July 2015
Location: Instituto Antofagasta, Campus Coloso, Universidad de Antofagasta (Google Map here)
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Background: Stable isotope analysis (SIA) is increasingly becoming a standard tool in many branches of ecology, especially those examining aquatic taxa and ecosystems. The technique is used to provide information at a range of levels of biological organisation from the organ, individual organisms, population, and species through to the ecosystem/landscape level, and also to understand global biogeochemical cycles and environmental change. A good understanding of the potential (and limitations) of SIA is useful for biologists aiming to understand the literature and to develop their own research careers.
Course Description: The course is targeted at postgraduate students and early career researchers aiming to understand the theoretical background and the practical application of stable isotope analysis (SIA) in aquatic ecology (both marine and freshwater).
The course will involve the students gaining an understanding of the theoretical background and practical application of stable isotope analysis through the use of literature case studies and analysis of real datasets. Focusing on aquatic ecosystems and featuring hands-on data-analysis throughout, the course covers many different areas of isotope ecology including: i) Fundamentals of stable isotope ratios and their analysis; ii) Biogeochemical cycling; iii) Trophic ecology; iv) and isotopes as measures of ecosystem function and environmental change.
The course is divided into four parts: one involving lectures and discussions; a second involving computer-based practical data-analysis sessions; a third involving the students presenting a critical assessment of key stable isotope papers; and finally a round-table mini-workshop where we examine and discuss isotope data or proposed isotope studies provided by the delegates.
Learning outcomes: To provide an understanding of isotope ecology and the chemical, biochemical and biological foundations of variation in stable isotope ratios. To understand typical and potential applications of SIA in aquatic ecology. To become experienced in analysis of stable isotope data. To develop statistical and presentation skills.
Teaching approach: The course includes a mixture of case-study led lectures, computer-based practicals, discussion and a mini-project where students will present a summary and critically evaluation of a key stable isotope ecology paper (supplied). Practical sessions will involve the student undertaking worked examples of different analytical problems, with real-world datasets.
Evaluation: Students will be assessed on the results of each practical session (100 %).
Lunches: Lunches will be between 12:00 - 13:00
Activites: All activities will be held in the Instituto de Antofagasta, Campus Coloso, Universidad de Antofagasta
Timetable: Download in Word or PDF format
Course materials: (password protected)
Date |
AM Activity |
PM Activity |
Tuesday 21 July |
Travel to Antofagasta |
17:00 Welcome and ice breaker (Instituto de Antofagasta) |
Wednesday 22 July |
9:00 Introduction to course & speakers. Introduction to Journal club –outline of mini-group project 9:30 Introduction to course delegates (short presentation of 5 minutes per person) 10:30 Lecture 1: Theory of stable isotope analysis |
12:00 - 13:00 Lunch 13:00 - 18:00 Data practical 1: Preparation of stable isotope data for analysis Laboratory practical 1: Sample collection and preparation. Coffee break 15:30 - 16:00
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Thursday 23 July |
9:00 Lecture 2: Biogeochemical and geographical drivers of isotopic variation 10:30 Lecture 3: Individual drivers of isotopic variation |
12:00 - 13:00 Lunch 13:00 Data practical 2: Statistical analysis of isotopic variation between individuals and groups 15:30 - 16:00 Coffee break 16:00 - 18:00 Data Practical 3: Going from isotope data to ecological information 1 (estimating trophic position) |
Friday 24 July |
9:00 Lecture 4: Using stable isotopes to understand consumer diet and habitat use I 10:30 Lecture 5: Using stable isotopes to understand consumer diet and habitat use II |
12:00 - 13:00 Lunch 13:00 Data Practical 4: Simple mixing models 15:30 - 16:00 Coffee break 16:00 - 18:00 Data Practical 5: More complex mixing models: SIAR |
Saturday 25 July |
9:00 Lecture 6: Putting it all together – tips (and pitfalls) for writing an isotope ecology paper 10:00 Journal Club: IsoGroup presentations – Groups present their critical reviews of key isotope ecology papers |
12:00 - 13:00 Lunch 13:00 Data Practical 6: More complex mixing models: MixSIAR 15:30 - 16:00 Coffee break 16:00 - 18:00 Data Practical 7: Estimating isotopic niche width with SIBER
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Sunday 26 July |
9:00 Show us your data: interactive workshop on student isotope data |
12:00 - 13:00 Lunch 13:00 Show us your data 2: interactive workshop on student isotope data 15:30 - 16:00 Coffee break 18:00 Course ends! |
Applying for the course: Places on the course are limited so preference will be for applicants currently using (or who will be using) stable isotopes in their research . Please send a current academic CV (in English), a letter of support from your academic supervisor and a one page letter of intention detailing why you want to attend the course and how it will help your research, to Chris@harrodlab.net. Please include information on your area of research and how you wish to use (or how you have used) stable isotope analysis to fulfil your objectives.
In your letter, please let us know if you have any particular dietary requirements for coffee breaks or lunch (e.g. food allergies) or health issues that we should be aware of. Please include contact details and a recent photo that we can use for the course materials.
Technical points: Students should bring a laptop computer capable of data manipulation and analysis i.e. with spreadsheet (e.g. Excel) and R installed. It is assumed that those attending the course will be able to manage data sets and understand the theory behind basic statistical analyses (correlation, regression, t-tests, ANOVA and their non-parametric equivalents) and basic graphical outputs (histograms, box-whisker plots, scatterplots).
We will use RStudio, so this should be installed on each laptop (and students should know how to use it). Students will have to give short presentations, so they should also have suitable presentation software installed. We will use a number of R packages (see table below) that should be installed prior to the course. Please also download PAST.
Name |
URL |
Use |
R |
R – base system for data analysis |
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R Studio |
User interface for R |
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SIAR & SIBER |
https://github.com/AndrewLJackson/siar |
Mixing model |
MixSIAR |
Mixing model |
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ggplot2 |
Graphing package, an add-on to base R |
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Stable Isotope Mixing Polygon Simulation |
Estimating suitability of sources for inclusion in mixing model |
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PAST |
Free (and very easy to use) statistical software for |