FISH ON LINE

A draft guide to learning and teaching ichthyology

using the FishBase information system[1]

 by

Daniel Pauly[2]

Rainer Froese[3]

and

Maria Lourdes Palomares^c

Abstract:

This guide provides a structure and case study material for a computer-based course in ichthyology for upper undergraduate and graduates 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 CD-ROM (for the Windows operating system) and on the Internet (www.fishbase.org/search.cfm).

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; Morphology and biodiversity; Reproduction; Physiology; and Fishes as part of 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.

It is anticipated that this guide will improve as our experience with FishBase as a teaching tool improves. Thus, a final chapter describes how users (both students and teachers) may contribute to the frequent updates that are anticipated for this guide, and to completing the coverage by FishBase of the biology of fishes.

1.     CONTENTS

2.      Introduction

2.1.   What is ichthyology?

2.2.   What is FishBase?

2.3.   Why use one to teach the other?

3.      Evolution and Classification

3.1.   Phylogeny and classification

3.2.   Darwin and natural selection

3.3.   The species concept

3.3.1.      What’s in a name?

3.3.2.      Subspecies vs. populations

3.3.3.      Within-species diversity

3.3.4.      Common names

3.3.5.      Exercise 1

4.      Morphology and Biodiversity

4.1.   Diversity of Indo-Pacific shore fishes

4.2.   Diversity of shapes and sizes

4.2.1.      Exercise 2

4.3.   Diversity of brain sizes

4.3.1.      Exercise 3

4.4.   Diversity of growth and mortality

4.4.1.      Exercise 4

4.5.   Diversity of habitats: inferences from occurrence records

4.5.1.      Exercise 5

4.6.   Diversity of colors and sexual selection

4.6.1.      Exercise 6

4.7.   Diversity of food and feeding habits

4.7.1.      Table 1

4.7.2.      Exercise 7

5.      Reproduction

5.1.   The reproductive load concept

5.2.   Small eggs and no worries

5.2.1.      Exercise 8

5.3.   Large eggs and parental investment

5.3.1.      Exercise 9

5.4.   Variation on the basic themes

5.4.1.      Exercise 10

6.      Physiology

6.1.   Metabolism, gills and size

6.1.1.      Table 2

6.1.2.      Exercise 11

6.2.   Food consumption

6.2.1.      Exercise 12

6.3.   Estimating food consumption from empirical models

6.3.1.      Exercise 13

7.      Fish as Part of Exploited Ecosystems

7.1.   Food webs and trophic levels

7.2.   Trophic levels and sizes of fish

7.3.   Formal description of food webs

7.3.1.      Exercise 14

8.      Contributing to FishBase

9.      Acknowledgements

10.  References

11.  Appendices

11.1.                    Appendix A: Ichthyology resources on the net

11.2.                    Appendix B: fish-related web resources for UBC students

2.     Introduction

2.1.                      What is ichthyology?

Ichthyology, commonly defined as “the study of fish” or “that branch of zoology dealing with fish” has a long documented history, dating thousands of years back to the ancient Egyptians, Indians, Chinese, Greeks and Romans (Cuvier 1828).

This long, sustained interest in fish is due to their double role as highly speciose denizens of a fascinating, yet alien world, and as human food. It has generated, over the centuries, highly heterogeneous information—mainly taxonomic, but also referring to zoogeography, behavior, food, predators, environmental tolerances, etc.

This huge amount of information, embodied in a widely scattered literature, has gradually forced ichthyologists to specialize, and thus accounts on fish are now either global, but highly specialized (e.g. Eschmeyer’s Catalog of fishes (1998) or Pietsch and Grobecker’s Frogfishes of the world (1987) to name two outstanding representatives), or local and deep (e.g. Fryer and Iles’ Cichlid Fishes of the Great Lakes of Africa (1972) or Groot and Margolis’ Pacific Salmon Life Histories (1991).

Thus, with a few exceptions such as the massive Diversity of fishes (Helfman et al. 1997), texts are lacking which bring together, on a global basis, all aspects of ichthyology, such that they can be used for a specialized course, and/or independent learning.

2.2.                      What is FishBase?

FishBase is an information system available in the form of CD-ROMS and on-line, at www.fishbase.org/search.cfm, covering all fishes of the world in a fashion that is both global and deep. FishBase 99, whose accompanying book is available both in English and French, covers over 23,000 species of fish, i.e. most of the 25,000 extant species, and addresses the needs of a vast array of potential users, ranging from fisheries managers to biology teachers. The features of FishBase that enable it to meet such a wide range of needs reside in its architecture, which makes extensive use of modern relational database techniques.

Other features of FishBase are:

·        all information on a given species in the database is accessible through a unique scientific or common name;

·        the wide use of multiple choice field structures standardized qualitative information;

·        numeric fields record quantitative information that has been previously standardized;

·        numerous cross-relationships between data tables enable previously unknown relationships to be discovered; and

·        complementary databases provided by colleagues and linked to FishBase proper, contribute to making the combined package the most comprehensive data source of its kind.

2.3.                      Why use one to teach the other?

For teachers of aquatic biology, or of specialized ichthyology courses, the uses of FishBase will range from practical solutions to theoretical issues:

·        FishBase is directly useable as data source (i.e., as an electronic encyclopedia on fish), thus complementing classical sources of information on fish, e.g., the Zoological Record or Aquatic Science and Fisheries Abstracts, and helping overcome the lack of scientific literature, especially in developing countries;

·        the many pictures in FishBase can be used, just as those in taxonomic books, to provide students with a visual impression of the morphological and color diversity of fish, and/or of specific features of various groups;

·        students will be able to assess the state of knowledge on various groups of fish, and thus obtain some guidance in identifying worthwhile projects; and

·        the synoptical view that FishBase produces by assembling and structuring all available information on one species will help students to obtain material for study (see above) and, perhaps more importantly, to develop a sense of how scattered bits of knowledge can be used to ‘reconstruct’ species, and to show how these fit into their environments, thus encouraging a ‘holistic view’, as now required for most of what we do in the biological sciences.

Thus, a series of lectures on ichthyology may be conceived, based on the following elements:

·        show FishBase pictures through an introductory lecture, to highlight the diversity and colorfulness of fish and similarity of external morphology in related groups (this hopefully would serve to generate interest in the course as a whole, and introduce fish classification);

·        compare the early classification schemes in Cuvier (1828) with a recent one, e.g., that in the Catalog of fishes (Eschmeyer 1998), ‘hosted’ by FishBase and largely identical with the widely used classification in Nelson (1994);

·        introduce the species concept and its requirements (a formal description with figures, a binomen, a holotype, a type locality, etc.) and implications (synonymies, sister species, etc.), using FishBase as source of examples, and its Glossary for definition of terms;

·        define the characteristics (meristics, morphometrics) through which fish species are usually defined and hence identified, and compare identification through keys with computer-based identification using the appropriate FishBase routine (see ‘Quick Identification’);

·        show how museum and other occurrence records, as included in FishBase, can be used to define distribution ranges and habitats, which can then be used for ecological inferences;

·        show how the latitudinal ranges of fish species can be used to test various hypotheses, e.g., on the relationship between fish biodiversity and shelf area (for marine species) or land area (for freshwater species);

·        define and illustrate various life history strategies, and analyze their frequency distribution throughout the world. Show, e.g., that salmon-type anadromy is extremely rare in subtropical or tropical species (it is well documented only in hilsa, Tenualosa ilisha, ranging from Iraq to Myanmar). Show how students can identify the relative frequencies of different strategies and draw inferences from these;

·        let each student select a species, print out the relevant FishBase synopsis and complement it based on a literature review (and send the result to the FishBase Team); and

·        show or let students derive quantitative relationships between different expressions of fish physiology (e.g., respiration, growth) and temperature (and hence latitude) and identify modifying factors (salinity, gill size, food type, etc.).

In the context of higher education, FishBase may also serve as background for Bachelor’s or Master’s theses wherein an area of ichthyology not presently or suitably covered by the tables in the latest version of FishBase would be ‘broken up’ into choice, numeric and text fields, entered and then analyzed on a comparative basis[4].

3.     Evolution and Classification

3.1.                      Phylogeny and Classification

There are different ways in which objects can be classified and the human mind is very good at generating criteria for classification. This is why the following list, assembled by the Argentinean author Jorge Luis Borges, and purportedly extracted from an ancient Chinese encyclopedia (Lakoff 1987), strikes us as funny:

“…it is written that animals are divided into:

·        those that belong to the Emperor;

·        embalmed ones;

·        those that are trained;

·        suckling pigs;

·        mermaids;

·        fabulous ones;

·        stray dogs;

·        those that are included in this classification;

·        those that tremble as if they were mad;

·        innumerable ones;

·        those drawn with a very fine camel’s hair brush;

·        others;

·        those that have just broken a flower vase;

·        those that resemble flies from a distance.”

The two major criteria that are used to classify things (neither met by Borges’ list), are utility or affinity:

·        Utility generates classifications whose objects are easy to find. An example of such a classification would be a dictionary, whose entries are arranged alphabetically;

·        Affinity, on the other hand generates classification wherein adjacent objects s are straightforward to compare (because adjacent entries share important features).

In the European middle ages, animal books (‘Bestiarum’) were usually ordered alphabetically. However, such ordering eventually struck people as odd, especially as people realized, in the course of long debates on ‘universals’ (on whether names are ‘natural’ attributes of things, or not), that names are arbitrary labels.

Thus, authors gradually began seeking for natural classifications, wherein organisms are ordered by affinities, these affinities being initially conceived as reflective of the general rules which god used when creating these organisms.

The work of Linnaeus, whose Systema Naturae, the tenth edition of which in 1758 still marks the beginning of zoological nomenclature, is an example of such attempts to identify the underlying affinities among plants and animals. The resulting ‘natural’ classifications have started to make sense, however, only since Darwin, in The Origin of Species (1859), provided a rationale for affinities, that is, shared ancestry. Darwin not only provided a basis for the affinities between organisms, however. He also provided a mechanism by which new species and higher taxa emerged out of common ancestors. This mechanism he called natural selection.

3.2.                      Darwin and Natural selection

Natural selection is the core of Charles Darwin’s work and is best defined in his own terms: “many of every species are destroyed either in egg or [young or mature (the former state the more common)]. In the course of thousand generations infinitesimally small differences must inevitably tell; when unusually cold winter, or hot or dry summer comes, then out of the whole body of individuals of any species, if there be the smallest differences in their structure, habits, instincts [senses], health, etc., <it> will on an average tell; as conditions change a rather larger proportion will be preserved: so if the chief check to increase falls on seeds or eggs, so will, in the course of 1,000 generations, or ten thousand, those seeds (like one with down to fly) which fly furthest and get scattered most ultimately rear most plants, and such small differences tend to be hereditary like shades of expression in human countenance. (Darwin 1842)

Natural selection, thus, consists of three elements:

·        organisms usually produce far more progeny than their habitat can accommodate;

·        each member of the progeny differs in some inheritable attributes or properties;

·        there is a tendency for those progeny with attributes or properties that are more suitable for the habitat in question to suffer a lower rate of mortality and to reproduce better than their siblings.

These three features jointly cause animals and plants to try to track fluctuation of the environment. In this process, and in conjunction with other mechanisms such as the ‘founder effect’ and the effect of neutral selection, isolated populations can become so different from a mother species that they will not be able to mate if the barrier that once separated them disappears.

3.3.                      The species concept

Species are “groups of actually (or potentially) interbreeding natural populations which are reproductively isolated from other such groups” (Mayr 1942, p. 120).

3.3.1.      What’s in a name?

Since species are the basic rank of biological nomenclature, naming species is very important and we now follow for this a model proposed by Linnaeus, (see above), wherein the species is defined by a so-called binomen consisting of a unique genus name, always starting with a capital letter, and a species epithet , which is never capitalized; both are written in italics font. With regard to the capitalization rule, simply recall that the binomen is the short version of an earlier mode of description wherein a whole paragraph was used to describe, and thereby define, a species. The binomen, thus, was the start of a sentence.

An important addition to a species name is the name of the author who first described that species and the date of that description; as in, for example, the Linnaean species Salmo trutta Linnaeus, 1758. At times you will encounter a species, e.g. Oncorhynchus mykiss, with an author’s name and date in brackets, e.g. (Walbaum, 1792). In this case, it means that the species whose epithet is mykiss was originally described as a memeber of another genus, in this case Salmo, and due to better understanding of its relationships with other trouts, was subsequently moved into the genus Oncorhynchus which it is now a member.

Another rule important to animal species names are that the genus part of the name must be unique to the animal kingdom. From the year 2000 on, it must also be unique among all organisms. Thus, when a generic name is coined, the author must verify that this name has never been used by any other zoologist, and, from 2000 on, by any botanist, bacteriologist, etc. The apparently daunting task is not impossible, however, as global catalogues of organism names are now being created; the most important of these is the Species 2000 catalogue (see www.sp2000.org).

3.3.2.      Subspecies vs. populations

Given the mechanism of natural selection, every fish population can be conceived as being a potential new species. All one needs to imagine is that populations become isolated from others long enough for their members to lose the ability to mate with those of other populations. However, as long as some members of each population continue to mate with members of other populations of the same species, a mating barrier will not emerge (only a small gene flow is required to prevent the emergence of a mating barrier). Thus populations, though it might be easy to define them in terms of attributes such as number of scales or spines or body proportions, should not be given full taxonomic status because (contrary to species) they usually do not maintain themselves over a long period. Not having taxonomic status also means they should not have formal names, such as the trinomen that are still frequently used today, e.g. Oreochromis niloticus niloticus. The third part of the trinomen refers to a subspecies, which is, in fact, a population, or, to use a term much used in earlier times, a ‘race’.

3.3.3.      Within-species diversity

Species differ as to the extent of their diversity. Some species consist of a single population of a few individuals — these are often endangered species. Others have wide ranges and a rich structure of populations – the situation which tempted authors to define subspecies as populations at opposite ends of a geographical range often differ in several characters. However, its is usually not objectively defined within-species diversity which has motivated authors to define subspecies, but national or local research traditions, and the resources available for taxonomy. Thus, Berg (1965) established numerous subspecies and even lower taxa for the fishes of adjacent lakes and rivers of the former Soviet Union, while subspecies are rarely proposed by taxonomists working on the many coral reef species of the Indo-Pacific, although their distribution spans thousands of kilometers, and detailed studies may justify this (at least if one believes in subspecies).

3.3.4.      Common names

The common names of fish are what most people know about most fish. Thus, capturing the common names of fish in various languages captures most of what people who speak these languages know about fish. For this reason, FishBase includes over 90,000 names of fish in over 100 languages, ranging from widespread languages such as English or Spanish, to languages spoken by few speakers, such as Haida in Haida Gwaii, British Columbia. Anthropologists, notably Berlin (1965), have established that essentially all ethnic groups in the world spontaneously differentiate a similar number (about 500) of ‘kinds’ of organisms, the kinds roughly corresponding to genera, with important species being named, as well as some of their life history stages.

The sounds in fish names also generate interesting patterns. Thus, small fishes (i.e., fishes with small values of Lmax) tend to have names containing high pitch sound such as ‘i’ or ‘ee’, while large fish tend to have names with lower pitch sounds, such as ‘a’, or ‘aa’ (Berlin 1992; Palomares et al. 1999).

3.3.5.      Exercise 1

4.     Morphology and Biodiversity

The diversity of fish is larger than for any other vertebrate group. Not only are there more species of fish (25,000) than of all other vertebrates together, but also the range of body shapes and sizes of fish is larger than for mammals, birds or reptiles. Consequently, the range of habitat occupied is larger as well.

4.1.                     Diversity of Indo-Pacific shore fishes

The triangle formed by Indonesia, the Philippines and New Guinea, collectively referred to as the ‘East Indies’, form the center of marine fish biodiversity in the Indo-Pacific, with about 2,800 species naturally occurring there. These numbers drop with distance from this center to about 500 species in Hawaii and 120 species in the Easter Islands. The number of endemic species, i.e., fishes that do not occur outside a given area, increases with distance from the center, supporting one hypothesis that species evolved in the outer region and accumulated in the center. Another hypothesis holds that species evolved in the rich and stable habitats of the East Indies and were carried to the periphery by currents. Randall gives 5 explanations for fish biodiversity in the Indo-Pacific:

·        Sea surface temperatures in the East Indies were more stable during the glacial periods and thus extinction rates were lower than in the periphery;

·        Shelf area in the East Indies is much longer than that of the periphery, again making extinctions less likely;

·        Dispersal of shore fishes to remote islands occurs during the planktonic larval phase which lasts from several days to several weeks. However, the larval phase of many species is not long enough for long stretches of open ocean water, thus restricting their distribution;

·        Existing current patterns support dispersal of fish larvae from the area as well as convergence of larvae of species that have evolved in the periphery towards the East Indies;

·        During the last 700,000 years, there have been at least 3 ice age events that reduced the water level in the East Indies and separated populations long enough to become different species.

4.1.1.      Exercise 2

4.2.                     Diversity of shapes and sizes

The shapes of fish are also extremely diverse, and include – besides the torpedo shape perceived as ‘typical’ for fishes and termed ‘fusiform’– shapes ranging from the serpentine (in the Anguilliformes and other orders) to the avian (in ‘flying fishes’), with Latimera chalumnae sporting limbs resembling, but not being used as, those of land-based tetrapods.

Shape and other morphological features are the key characteristics used to date for classifying fishes, and hence understanding their classification requires a basic overview of the basic shapes of fishes, as can be obtained from the outline drawings included, for each of the existing 500 fish families.

Size is the most important attribute of individual organisms; it determines what can be their food, and the extent to which they can be the prey of other organisms. Size also determines how much food an animal requires to eat, how fast it can swim, and to a large extent, where it can live.

The maximum size of fish can range from one centimeter in Philippine gobies, e.g., Pandaka pygmea to 13-15 meters in the Whale shark, Rhincodon typus. This diversity of size allowed widely different environments to be colonized, ranging from temporary puddles to the central gyres of the open ocean. However, colonizing these environments required other adaptations, involving growth and mortality rates, and their various correlates, discussed below.

4.3.                     Diversity of brain sizes

The brain size per body weight of adult animals is related to the sensory and behavioral capabilities of the respective species. For example, fishes with well-developed electrosensing capabilities are known to have large brains. The brain is the organ with the highest energy and oxygen demand, and thus, fishes as well as other animals have evolved brain sizes that are neither too small nor too large respective to the niches they occupy in nature.

4.3.1.      Exercise 3

4.4.                      Diversity of growth and mortality

In spite of this wide diversity of fish sizes, clear patterns do emerge: tropical fish tend to be smaller and faster-growing than their cold-water counterparts and their natural mortality tends to be higher. This is due to high temperature elevating the metabolic rates of tropical fish relative to their cold-water counterparts.

Correspondingly, the natural mortalities experienced by fish, which are a function of their sizes, range from values which exterminate an entire cohort in a few months, e.g., the round herring, to 50 and more years in the lake sturgeon and 150 years in the orange roughy. These enormous differences in life span allow fish to respond differently to habitat variations. Small, short-lived fish track such variations, for example, when growing up in temporary puddles and laying desiccation-proof eggs before they dry up, thus being able to live through dry periods or produce a successful cohort every 1-3 years or so (as may happen in such long-lived fish as cod).

4.4.1.      Exercise 4

4.5.                      Diversity of habitats: inferences from occurrence records

Fish inhabit more diverse habitats than any other group of vertebrates, ranging from Himalayan or Andean brooks at 4000 meters to abyssal depth at 10 kilometers, spanning an extremely high range of pressures. The range of temperatures that can be tolerated is also very large, from minus 2^oC as tolerated by the Antarctic fish, Pagothenia borchgrevinki (which sport anti-freeze substances in their blood; see Eastman and Devries 1985); to up to 40^o C for Oreochromis alcalicus, which lives at the edge of a hot spring in Lake Nakuru in Kenya. (This does not consider the temperature tolerance of deep-sea vent fishes, which have not yet been studied in detail).

Because fish occur only in habitats which they can tolerate, and tend to be abundant in those habitats to which they are best adapted, occurrence records kept by museums can be used to reconstruct the habitat preferences of fishes whose ecology is otherwise unknown. Such records have been named bioquads because they refer to biodiversity and consist of four key elements: (a) the name of the organism; (b) the place where it was caught; (c) the source or person who sampled or identified it; and (d) the date. FishBase makes wide use of bioquads for documenting the distribution of fish and this can be emulated by ichthyology students who may assemble bioquads from FishBase and other sources, notably the Internet. (see Appendix A for sources of bioquads).

4.5.1.      Exercise 5