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Review on Fish Identification Tools and Their Importance in Biodiversity and

Fisheries Assessments

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 International Journal of Sciences:
Basic and Applied Research
(IJSBAR)
ISSN 2307-4531
(Print & Online)

http://gssrr.org/index.php?journal=JournalOfBasicAndApplied
---------------------------------------------------------------------------------------------------------------------------

Review on Fish Identification Tools and Their Importance

in Biodiversity and Fisheries Assessments

Adil Sidahmed Omer*

Department of Environment &Natural Recourses, Faculty of Applied Sciences, Red Sea University, Sudan
Email: [email protected]

Abstract

The present review provides an appraisal of existing, state-of-the-art fish identification (ID) tools and
shows their potential for providing the right solution in different real-life situations. The ID tools
reviewed are: Use of scientific experts (taxonomists) and folk local experts, taxonomic reference
collections, image recognition systems, field guides based on dichotomous keys; interactive electronic
keys (e.g. IPOFIS), morphometrics (e.g. IPez), scale and otolith morphology, genetic methods (Single
nucleotide polymorphisms [SNPs] and Barcode [BOL]) and Hydroacoustics. It is expected that it will
help fisheries biologists, environmental administrators and other end users to select the best available
species identification tools for t h e i r o w n purposes.

Keywords: identification; tools; fisheries; experts; species.

1. Introduction

Fishes show an astonishing diversity of shapes, sizes, and colours. The delimitation and recognition of fish
species is not only of interest for taxonomy and systematics, but it is also a requirement in studies of natural
history and ecology, fishery management, tracking the dispersal patterns of eggs and larvae, estimations of
recruitment and spawn areas, and authentication of food products [1]. Fish identification is traditionally based
on Morphological features. However, due to high diversity and m o r p h o l o g i c a l plasticity, in many cases,
fish and their diverse developmental stages are difficult to identify by using morphological characteristics
alone.

------------------------------------------------------------------------
* Corresponding author.

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Although the need for taxonomic expertise has never been as pronounced as it is today, this has not
translated into training more taxonomists and providing more funding for necessary developments in
taxonomy [4,6]. Instead, more and more individuals without a taxonomic background, such as fishery
inspectors and observers, customs officers, data collectors, traders and others, have been tasked with
the complex and often difficult assignment of identifying aquatic species. These less- experienced users
are often faced with confusing and inadequate i n f o r m a t i o n on the species they encounter and how to
identify them reliably. Products such as the species catalogues and field guides produced by the FAO
Fish Finder Programme can help in countries and regions for which they exist, and web resources, such
as Fish Base [8,10] the Catalog of Fishes [9] offer guidance to resolve issues regarding the correct scientific
name for a species. Nonetheless, greater efforts are needed to ensure a correct identification of aquatic
resources under management and conservation regimes. In recent decades, many new and promising
t e c h n i q u e s for the identification of fishes have emerged, in particular based on genetics, interactive
computer soft- ware, image recognition, hydroacoustics and morphometrics. However, with few
exceptions, such advances in academic research have not yet been translated into user-friendly applications
for non-specialists and still require further investments to mature into globally applicable tools [16]. Public
consciousness about the need to conserve biodiversity has recently been growing. In all parts of the
world, policy-makers, funding agencies and scientists have made it a priority to advance policies and
knowledge for this purpose. This interest was prompted by the realization that taxonomic resources
around the world are declining at a rapid pace and that this is having a negative impact on human
well-being and survival. It has become clear that taxonomic information is not a luxury – it is a real need
in a world with a still-growing human population generating enormous pressure on natural resources.
More and more organisms are shipped around the world and marketed continents away from their
origins, thus generating an increased need for global fish identification tools to provide reliable
information to consumers, customs officers and fishery inspectors. However, worldwide, there exist
more than 32 500 species of fin fishes and the amount of information required to separate them all is
extremely difficult to process; therefore, fish identification is usually conducted at local or regional
scales [3,15]. The increasing globalization of fishery products thus introduces new challenges to the
identification of aquatic organisms. In addition, new emerging applications require accurate species
identification (e.g. marine hydrokinetic energy and ocean observatories). The collection of species- and
population-specific information for the purpose of sustainable fishery management has a long tradition.
For many decades, FAO has been collecting global statistical catch data and analyzing the results in two
of its flagship publications: (i) The State of World Fisheries and Aquaculture and the Review of the state
of world marine fishery resources. While progress has been made in the reporting of fishery data, much
improvement is still needed for a more reliable and comprehensive assessment of the stock status of many
commercially exploited aquatic species. Not only the taxonomic resolution of catch data could be better
for many areas and species, but there is a real concern about the proportion of possible
misidentifications in the catch statistics received by FAO, with severe implications for the ability to

manage aquatic organisms sustainably [12]. With its Fish Finder Programme, FAO has contributed to
improving fish identification everywhere and produced more than 200 species identification guides including
taxonomic descriptions for more than 8 000 species and an archive of more than 40 000 scientific illustrations

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[2,5]. Although the program struggles owing to funding constraints and competing priorities at FAO, it
continues generating products to assist with fish identification in many parts of the world.

2. Fish Taxonomy in Biodiversity and Fishery Assessment and Management

A stable naming and indexing system is essential to global communication about organisms, and
such a system is maintained by the International Code of Zoological Nomenclature. The science of
taxonomy, among other things, provides the methods and the manuals for the identification of organisms.
Although largely based on observations of characters that local fishers may also use, taxonomic
research offers the tools for a regionally and globally valid identification. Some examples of fundamental
taxonomic tools for the use in fisheries include Fish Base [11], the book Fishes of the North-eastern Atlantic
and the Mediterranean and a series of catalogues and regional checklists provided by FAO. Although
surveying, mapping, taxonomic characterization, and naming of the global marine and freshwater
fish fauna are fundamental to a healthy fishery, the importance of taxonomic work is not fully
recognized in the fisheries sector, particularly not in the boreal regions where “everything is known”.
However, a lack of pertinent taxonomic information or lack of user experience can actually or potentially
lead to undesired consequences for fishery management, and fish taxonomists are urgently needed to
provide reliable name standards and identification tools for fishery purposes. In many regions of the
world, f i s h stocks are being exploited without much taxonomic assistance. However, it is impossible to
develop conservation plans and long-term management without knowing what species are involved, and
preferably also whether subpopulations exist, and how to identify them. Important faunal guides have been
published by South Africa, Japan and Australia, but in these regions new species continue to be
discovered, both from fresh material and from old museum specimens [2,3,7].

Taxonomic resources may also play a role in prospecting for new resources as is done particularly in
aquaculture. Involving taxonomists in aquaculture is always recommended in order to prevent expensive
errors based on the erroneous identification of species, e.g. to avoid a “new” species being imported to
locations where it (or a very similar form) already exists but is known under an incorrect name.

3. Species IdentificationTools

Species Identification Tools included in this review

This review covers most methods that are currently used for the identification of aquatic species.
They include traditional, long-trusted and tested tools, such as the use of trained taxonomists,
reference collections or field guides based on dichotomous keys, as well as more recently developed
tools, some of which are still in the experimental stage, e.g. image recognition systems (IRSs),
interactive electronic keys, computer-based morphometric identification (IPez) and genetic methods. In
addition, the use of local (folk) expertise, scales, otoliths and hydroacoustics are reviewed.

A few methods are not assessed in detail as they are either too generic, e.g. identification of fishes by
browsing images (using the web), or because they are of limited application, e.g. the use of bones, animal

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sounds or electric signals (Table 1)

Table 1: Species Identification Tools

CATEGORY METHODS REVIEW METHODS NOT

REVIEWED

WHOLE ORGANISMS

t Scientific expert (taxonomist) onsite

Expert authority t Folk local experts

t Local reference collections Image browsing

Images/specimen only t Image recognition systems (addressed under web
tools)

t Field guides based on dichotomous

keys: printed or electronic
products; may use text or images for
Identification keys, characters and taxa
text- and/or image- t Interactive electronic keys, e.g.
based IPOFIS
t Polythetic keys; morphometrics, e.g.
Ipez

BODY PARTS
t Scales Bones (addressed under
Anatomy t Otoliths web tools)

t With SNPs
Genetics t With BOL

EXTRINSIC AND OTHER ATTRIBUTES

Sounds produced by
Acoustics t Hydroacoustics organisms

Electrics Electric signalsNote

Source: Fischer, J. ed. 2013

3.1 On-site Taxonomist

Trained taxonomists, preferably with a PhD in systematic biology and postdoctoral experience, are
familiar with a large number of species and have specialist competence in a special group (e.g. a family or a
fauna). They know about nomenclatural rules and morphometric methods for species identification and have a
high awareness of the level of accuracy of their identifications. Moreover, they usually identify species

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relatively quickly. There may be conceptual differences between individual taxonomists that could lead to
limited repeatability of certain identifications, but the accuracy should still be high. Taxonomists are most
helpful with fresh or preserved whole specimens. However, there is a severe lack of taxonomists in many
regions limiting the access to this ID tool.

3.2 ID-tool: Local (folk) expert

Folk taxonomies a r e systems of categorization created by non-scientists in order to organize, name, and
understand the natural world. Folk taxonomies frequently diverge on some points from the phylogeny
established by the scientific study of taxonomy but they also tend to align with scientific classifications on
other points. Sometimes, folk taxonomies lump together many biological species under a single name, or
place species from several different biological orders in the same group.

Sometimes there is one-to-one correspondence, and sometimes folk taxonomies differentiate where
scientific taxonomies do not. Differentiation between types in folk taxonomies is determined by a wide
variety of attributes, some of which may not be immediately obvious to outsiders; morphology and
behavior are important but so are the cultural significance and practical utility of the species constituting
each group.

3.3 Local reference collection

Reference collections consist of preserved specimens of whole fish, otoliths, disarticulated bones, scales,
pharyngeal bones, or similar body parts used in identification work. Local reference collections are
mainly found in research institutions (and fisheries agencies) and are dedicated to a restricted
g e o g r a p h i ca l area (or a special purpose research).

Local reference collections may be a sufficient tool for identification work in a restricted area and
reduce the need for expert consultancy, keys, field guides and other methods. They are especially useful
for smaller institutions in field-like situations and can be used also for continuous training of new staff.

3.4 Image recognition system

In this method, the user provides a photograph (image) of the fish as input and a software (IRS) identifies
the fish to a taxonomic level. The identification process is based on the automatic characterization of
image visual properties (e.g. color, texture a n d shape) using computer vision techniques, i.e. image
retrieval and/or classification approaches that exploit feature vectors and similarity functions. Image
processing methods are used to encode visual properties into feature vectors, and similarity functions are
used to compute the similarity of two images by taking into account their feature vectors.

3.5 Field guides based on dichotomous keys

Diagnostic taxonomic keys are a common traditional means to identify organisms, and they form an

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important part of most field guides. A taxonomic key is an ordered sequence of alternative choices, as
provided by diagnostic (morphological) characters of organisms, that leads to a reliable identification
of an organism or class of organisms. Diagnostic characters used in a key are defined and may be
illustrated for clarity. The formal or taxonomic scope of a key is usually restricted to printed material or
presented in digital format.

3.6 Integrated Photo-based Online Fish-Identification System (IPOFIS) exemplifying Interactive

Electronic Keys (IEKs)

An IPOFIS is a photo-based online fish identification system that integrates three methods: visual
inspection, dichotomous keys, and a multi attribute query procedure. Each fish species is represented
by multiple color photographs of different individuals and close-ups of important identification features.
The system efficiently organizes and presents these photographs and associated morphometric
information in an interactive format that facilitates fast and accurate identification. An IPOFIS i s
designed to be applied by users with no scientific training. Costs are relatively low and are
generally limited to online access on a computer. The time required for fish identification generally
ranges from 3 to 30 minutes, depending on how distinctive the specimen is.

3.7 IPez (morphometric software)

IPez is an automated, computer- software-based species identification system for marine and
freshwater fish species. It uses a large number of morphometric measurements and it is based on
machine learning techniques.

One day of training is needed in order to learn how to use the system. The user needs a computer,
and the time required for fish identification will usually be lower than five minutes and depends on the
user’s expertise. The software can generate results with100 percent accuracy provided it has been fed
with baseline measures of at least 15 to 20 individuals of different sizes per species.

3.8 Scales

Fish scales have been extensively used in fish species identification since the early1900s. Not only is their
count important in key classification; also descriptions of their shape and particular features have been
used in keys to recognize families or distinguish between close species. Moreover, alternative methods of
shape analysis, based on landmark data, have found wide applicability in biology because of the natural
links between homologies and measurements, the statistical properties of the resulting shape spaces and
good statistical power. Fish-scale shape is especially useful for discrimination among genera, species and
also sympatric populations.

3.9 Otoliths

The use of otoliths for species and stock identification is well established. While this method is more

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laborious than the use of fish scales and also requires more knowledge and training, its superior
accuracy (exceeding 80 percent for congeneric species) can justify the additional effort. The main limitation
of this ID tool consists in its destructiveness (the extraction of otoliths kills the fish) and in the fragility
of the otoliths (they easily break during extraction and manipulation). In addition, the morphometric
analysis is difficult because of the concave form of otoliths and overall variability of shape.

3.10 Genetic identification through single nucleotide polymorphisms (SNPs)

Single nucleotide polymorphisms (SNPs) are single mutational differences among individuals at specific
loci in the genome that are typically distributed throughout the genome of individuals and are highly
abundant. At the population level for example, the frequencies of the various mutational differences can
yield population- specific genetic signatures. Importantly, the SNPs to be applied can be readily tailored
to accommodate a wide range of differing levels of genetic differentiation, also at spatial scales relevant
for fishery policy and management. To enable the use of SNPs for fish population identification, a
genetic baseline has to be created. Specimens of a given species are collected across a geographical range
and SNPs identified that reveal population-specific genetic signatures. A major asset of DNA-based
analytical procedures is that they can be applied throughout the food supply chain, from whole
specimens to trace samples (e.g. scales and fins), through to highly processed fish products. In addition,
DNA analysis is readily used not only on contemporary fish samples but also on archived historical
material (e.g. bones and/or scales from museums, and archived otoliths from fishery agencies).

3.11 Genetic Identification Using Barcoding

Barcoding is defined as the use of a standardized short region of DNA to verify species identity, which
typically for fish is the CO1 region of mitochondrial DNA, with the generation of publicly accessible and
highly comparable data. All publicly accessible data are available from one website (Barcode of Life
Database), and information on specimen vouchers, photographs and other biological information is
available from the same site (fish barcode of life( on line)). Currently, the practice relies on high
throughput DNA sequencing, which is typically undertaken by commercial sequencing centers.
Effort is currently being put into the development of hand-held barcoding devices for use in the field.

3.12 Acoustic Fish Identification

Active acoustic technologies use sound to sample distributions, densities, individual lengths and,
potentially, species through the entire wa t e r c o l u m n . A pulse of sound is sent into the water, and
then reflected echoes are used to derive the location and size of individual and aggregations of fish
and zooplankton. Two current technologies used include echo sounders with single or multiple
discrete frequencies, and broadband sonars that transmit a continuous frequency band. Analytic
techniques compare echo amplitudes from single animals or aggregations as a function of frequency. In
addition to identification algorithms, trawl samples are regularly used to verify the identity of acoustic
targets.

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4. Conclusion

Each of the presented species ID methods has its particular strengths and weaknesses, and its best uses
depend on the requirements and available resources for the fish identification. The selection of the best
species ID tools should start at the planning level of an activity and consider budgetary and staffing
implications.

Acknowledgment

The author would like to thank everyone contributed in a way or another while conducting this piece of work.

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