FISH ON LINE
A guide to learning and teaching ichthyology
using the FishBase Information System
by
Daniel Pauly
Fisheries Centre, University of British Columbia, 2202 Main Mall, Vancouver, B.C., Canada, V6T 1Z4; e-mail: d.pauly@fisheries.ubc.ca
Rainer Froese
GEOMAR Helmholtz-Centre for Ocean Research, Düsternbrooker Weg 20, 24105 Kiel, Germany; e-mail: rfroese@geomar.de
Maria Lourdes Palomares
Fisheries Centre, University of British Columbia, 2202 Main Mall, Vancouver, B.C., Canada, V6T 1Z4; e-mail: m.palomares@fisheries.ubc.ca
Konstantinos I. Stergiou
Department of Zoology, School of Biology, Aristotle University of Thessaloniki,
UP Box 134, Thessaloniki, 541 24, Greece, email: kstergio@bio.auth.gr;
also at Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, Aghios Kosmas, 16604 Athens, Greece
Charis Apostolidis 2
Department of Zoology, School of Biology, Aristotle University of Thessaloniki,
UP Box 134, Thessaloniki, 541 24, Greece;
also at Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, Aghios Kosmas, 16604 Athens, Greece
1 Version 3, August 2014
2 Partially contributed to Chapter 7
Abstract
This guide provides a structure and case study material for a computer-based course in ichthyology for upper undergraduate and graduate students in biology or environmental science.
The key resource made accessible through this guide is FishBase, a large database on the biology of fish, available on the Internet (www. fishbase.org).
Following brief introductions to ichthyology and to FishBase, and to the use of the latter to teach the former, the key aspects of ichthyology are presented in five chapters covering Evolution and Classification; Biodiversity and Morphology; Reproduction; Physiology; and Fish as Part of Exploited Ecosystems.
For each of these chapters, one or several 'Exercises' are presented describing how the relevant topics are covered in FishBase and describing how to access that information. 'Tasks for the Student' are provided, along with Internet links to relevant sources other than FishBase. For completing the exercises, students are adviced to also consult the theoretical background provided in the FishBase book (i.e., FishBase 2000: Concepts, design and data sources), which is also available online (/manual/English/contents.htm).
This is the second version of the guide, which expands that by Pauly et al. (2000). It is anticipated that this guide will continue to be updated as our experience with FishBase as a teaching tool improves. To this end, a final chapter describes how users (both students and teachers) may contribute to the updates that are anticipated for this guide, and to completing the coverage by FishBase of fishes at all levels of biological organization (i.e., individual, population, communitity, ecosystem).
1. Introduction
1.1. What is ichthyology?
1.2. What is FishBase?
1.3. Why use one to teach the other?
2. Evolution and Classification
2.1. Phylogeny and classification
2.2. Darwin and natural selection
2.3. The species concept
2.3.1. What's in a name?
2.3.1.1. Exercise
2.3.2. Subspecies vs. populations
2.3.3. Within-species diversity
2.3.4. Common names
2.3.4.1. Exercise
3. Biodiversity and Morphology
3.1. Diversity of Indo-Pacific shore fishes
3.1.1. Exercise
3.2. The species-area relationship and latitudinal variations in diversity
3.2.1. Exercise
3.3. Diversity of shapes
3.3.1. Exercise
3.4. Diversity of scales
3.4.1. Exercise
3.5. Diversity of colors and sexual selection
3.5.1. Exercise
3.6. Diversity of sizes
3.6.1. Exercise
3.7. The length-weight relationship (L-W)
3.7.1. Exercise
3.8. Diversity of growth
3.8.1. Exercise
3.9. Diversity of ages, longevity, senence and mortality
3.9.1. Exercise
3.10. Diversity of habitats: inferences from occurrence records
3.10.1. Exercise
3.11. Diversity of food and feeding habits
3.11.1. Exercise
4. Reproduction
4.1. The reproductive load concept
4.1.1. Exercise
4.2. Small eggs and no worries
4.2.1. Exercise
4.3. Large eggs and parental investment
4.3.1. Exercise
4.4. Variations on the basic theme
4.4.1. Exercise
5. Physiology
5.1. Metabolism, gills and size
5.1.1. Exercise
5.2.1. Exercise
5.3.1. Exercise
5.4. Fish sounds
5.4.1. Exercise
5.5. Food consumption
5.5.1. Exercise
5.6. Estimating food consumption from empirical models
5.6.1. Exercise
6. Fish as Part of Exploited Ecosystems
6.1. Food webs and trophic levels
6.1.1. Exercise
6.2. Trophic levels and sizes of fish
6.2.1. Exercise
6.3. Trophic signatures
6.3.1. Exercise
6.4. Formal description of food webs
6.4.1. Exercise
6.5. Fisheries Management: Keep it simple
6.5.1. Lm and minimum landing sizes
6.5.1.1. Exercise
6.5.2. Three simple management indicators
6.5.2.1. Exercise
6.6. Effects of fishing on ecosystems
6.6.1. Exercise
6.7. Effects of aquaculture on ecosystems
6.7.1. Exercise
6.8. FishBase, archaeology and sifting baselines
6.8.1. Exercise
7.1. Traditional vs. Bayesian statistics
7.1.1. A few more words on priors
7.1.2. Tools used in Bayesian data analysis
7.2. Examples of Bayesian applications to fisheries
7.2.1. Length at maturity - Using prior knowledge
7.2.2. Fitting the von Bertalanffy growth model using prior knowledge
7.2.2.1 R code for fitting von Bertalanffy equation
7.3 FishBase and Bayesian inference
7.3.1. Estimating the maximum sustainable yield (MSY) from catch and resilience: the Catch-MSY Tool
7.3.2. Bayesian analysis of length-weight relations (LWR)
7.3.2.1 Exercises
8.1. Exercise
10. Appendix
10.1. Classification-related topics covered in FishBase
10.2. Biodiversity-related topics covered in FishBase
10.3. Brain size-related topics covered in FishBase
10.4. Size, growth and mortality-related topics covered in FishBase
10.5. Distribution and occurrence-related topics covered in FishBase
10.6. Morphology-related topics covered in FishBase
10.7. Food and feeding habits-related topics covered in FishBase
10.8. Reproduction-related topics covered in FishBase
10.9. Reproductive strategies (sex change)-related topics covered in FishBase
10.10. Metabolism-related topics covered in FishBase
10.11. Ration-related topics covered in FishBase
10.12. Food consumption-related topics covered in FishBase
10.13. Food web-related topics covered in FishBase
11. References
Version 3, August 2014