Journal of Survey in Fisheries Sciences 4(1) 54-93 2017

A Review of Fish Taxonomy Conventions and Species Identification Techniques

Keat-Chuan Ng C.1; Aun-Chuan Ooi P.1; Wong W.L.1; Khoo G.1*

Received: December 2016 Accepted: March 2017

Abstract Taxonomists, ecologists, geneticists or researchers from other biological fields who wish to adopt fish as a constituent of their studies often become discouraged when they find that ichthyology is a complex subject. In fish-based studies, the failure to recognize fishes as distinct biological units can lead to wrong diagnosis. Hence, this review paper attempts to clarify and discuss the latest schools of thought pertaining to fish taxonomy and the techniques for species identification. It is hoped that the contents and illustrations in this paper will assist researchers in laying a good foundation to inform their studies.

Keywords: Fish, Morphology, Molecular, Taxonomy, Species identification

1-Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900 Kampar, Perak, Malaysia. *Corresponding author's Email: [email protected] 55 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

Introduction interbreed in natural conditions. In the The term “fish” is usually a convenient “evolutionary species” concept, a species description for a group of poikilothermic is a representative of a lineage having its (cold-blooded) aquatic vertebrates under own evolutionary affinity and historical the Chordata phylum that breathe with destiny. As for the “phylogenetic species” gills (Nelson, 2006). Scientifically, the concept, species is viewed as a collective term of “fish” primarily refers monophyletic set of organism with to Agnatha (jawless fishes), common ancestors. In practice, each of Chondrichthyes (sharks and rays), these major concepts is prone to some Sarcopterygii (lobe-finned fishes), and level of subjectivity. Regardless of Actinopterygii (ray-finned fishes). concept, wildlife scientists, especially Actinopterygians, the bony or ray-finned ichthyologists, typically identify and fishes, are without a doubt the majority of name fishes by either by their consistency fishes found in freshwaters. in morphological, and more recently, Actinopterygians have lepidotrichia which molecular characteristics. are characterized by fins of membranous While most researchers are concerned webs held together by bony spines, or with fishes as a food source and their rays. This niche character differentiates work involves enriching the body of Actinopterygians from Sarcopterygians aquaculture knowledge, there are some which possess lepidotrichia that are who are interested in their diversity, fleshy. distribution patterns, ecology and Although in early 20th century, the functional physiology. Recently, there has ichthyologist Regan (1910) defined a fish also been an overwhelming interest in the species as a product of interrelated molecular constitution of fishes (Wong et communities with common morphological al., 2011; Pereira et al., 2013; Rakshit et features (today this is termed as al., 2015 Quraishia et al., 2015) and their “morphospecies”), it should be noted that function as biological indicators to the species classification concept differs monitor waterbody pollution (Fonge et among scientists. While authorities such al., 2011; Khodadoust et al., 2013; as Nelson (2006) and Mayr (1942) accept Authman et al., 2015). Correspondingly, the “biological species” concept, others the interest in fish has expanded like Simpson (1951) promotes the exponentially, and the ichthyology “evolutionary species” concept. Then discipline is often sought to contribute too there is Cracraft (1983) who prefers to many other fields of studies (Padilla and adopt the “phylogenetic” or “cladistic” Williams, 2004; Lauder et al., 2007; Feist species concept. and Longshaw, 2008; Rudkowska et al., The oldest and most widely practised 2010). Generally, species is the basic unit “biological species” concept postulates in these studies and sound taxonomy is a that species are part of a group prerequisite to prevent confusion and composition that breed or can potentially misinterpretation. Journal of Survey in Fisheries Sciences 4(1) 2017 56

However, researchers who wish to rules, and yet set out to conduct fish- adopt fish as a major or minor component based studies and publish papers. Since of their studies will be discouraged when they lack field experiences, many are they discover that ichthyology is not an unaware of distinctive fish characteristics easy subject, more so fish taxonomy. such as phenotypic polymorphisms, Also, it is a common knowledge that there sexual dimorphism and behavioural is already an acute shortage of fish divergence due to the regional speciation taxonomists and finding a fish taxonomist process (Waugh, 2007). Failing to to assist in a study is often difficult. Such recognize such exceptions can lead to is the same case with many other taxa. wrong species diagnosis. Some Since fish diversity can be high, researchers restrict themselves to especially in tropical countries, a laboratories, ornamental fish and taxonomist is typically overwhelmed with aquaculture farms, and their specimens constant scientific name revisions, field may look very different from the wild collection expeditions and managing a type which the scientific name was museum. Moreover, taxonomy cannot be derived from. Ideally, it is advisable to commercialized and it sees very little treat a selective bred variety raised in funding in many countries. Thus, the artificial conditions differently. discipline rarely attracts students or can Otherwise, publication with nomenclature sustain career taxonomists in the errors will be perpetuated through citation universities. Such a problem has caused and cause a chaotic situation. taxonomic errors in published papers and In lieu of concerns highlighted, this the condition is now widely known as the review attempts to provide a concise “taxonomy impediment” (Wheeler et al., introduction to this complex but important 2004; de Carvalho et al., 2007). It is often field. To understand fish as a biological said that the discipline of taxonomy unit, the readers should also have some would be extinct earlier than most background in zoology. Our objective is endangered species. not to polarize techniques for fish On hindsight, the advancement of identification because we are convinced molecular, computerized and statistical that each technique has its merits. Their techniques have led many to believe that shortcomings will, however, be discussed “species” can be easily characterized by to assist researchers in making sound nucleotide sequences, software and judgments and decisions. mathematical calculations, and the This paper reviews and discusses knowledge in taxonomy is no longer taxonomic concerns of freshwater species needed. Ebach and Holdrege (2005) warn that belong to the Actinopterygii class, us that there are a growing number of and we assume that readers have some researchers who have never wet their feet familiarity with ray-finned fish anatomy in the rivers to observe species or build and the common species. Given that a competency in applying nomenclature picture is worth a thousand words, we 57 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification … believe that taxonomy can be easier to clustering species that looked similar master if the reader is provided with because they believed that these species detailed scientific illustrations and colour share a common biological lineage. In the images. This review is by no means mid-18th century, the evolution hypothesis comprehensive but we hope it will set a was a new and strange concept. good foundation for those who wish to Eventually this was proven to be factual make a competent start in species-level in the advent of modern molecular and research. genetic assessment technologies. In general, today, there is a consensus Why are there do many species? among scientists that all species on Earth Teleost species form the largest category are interlinked with a hierarchical and among vertebrate animals and their evolutionary tree with millions of numbers have reached more than 32,500 branches. Each branch itself is a valid marine and freshwater species under representation of the natural history of a 515 families (Nelson, 2006). In the global particular species and its pedigree. But context, there are roughly 11,952 of why did the branches have to extend and freshwater species (Helfman et al., 2009). multiply in the first place? What causes Ricklefs (2004) suggests that competition the divergence? and mutualism among species have an When gene flow among populations is effect on species abundance while Wright interrupted by natural (e.g., geographic et al. (2003) speculate that species barriers created by earthquakes) or diversity is the result of productivity from artificial means (e.g., man-made barriers available “energy” in a particular region. in aquaculture farms and dams), two types If a region lacks energy (e.g., low food of speciation will occur, namely allopatric availability in the desert), species richness speciation and sympatric speciation is typically low. However, in the case of (Butlin et al., 2016) (Fig. 2). Allopatric fish, MacArthur’s (1969) hypothesis speciation occurs when a population is seems to be the most probable as he separated by a barrier and such isolation suggests that species diversity is prevents the two or more sub-populations accelerated if there are more areas to host from mating. Given time, the lack of gene suitable habitats. The hypothesis flow among the sub-populations will corresponds with the reality today as large cause biological incompatibility and freshwater regions seem to demonstrate divergence would be triggered (Mayr, more genera and species, for example the 1959; Turelli et al., 2001; Singh 2012). Neotropical region (705 genera, 4,035 species) compared to the Australian region (94 genera, 261 species) (Leveque et al., 2008) (Fig. 1). Early taxonomists, namely Linnaeus and Darwin, had started cataloguing and Journal of Survey in Fisheries Sciences 4(1) 2017 58

Figure 1: Major freshwater fish Eco regions encompassing 1,054 rivers as classified by the Fish- SPRICH database (Source: Brosse et al., 2012).

Figure 2: Modes of speciation.

In sympatric speciation, biologists branch would still maintain a certain highlight that ecological shift and degree of morphological similarity (Butlin resource competition are the key drivers et al., 2016). (Mayr, 1947; Dieckmann and Doebeli, 1999; Bolnick and Fitzpatrick, 2007; Taxonomy and systematics Mallet et al., 2009). They reasoned that The word taxonomy originated for Greek new species may arise within a population word taxis, meaning arrangement, and from biological reproductive barriers nomos, meaning law. The science of between mutants that are better adapted biological taxonomy is responsible for and parent populations. Nonetheless, discovering, describing, classifying, despite further speciation in both space naming and treating each species as the and time, and regardless of allopatric or basic unit. Species are given names in sympatric speciation, species within a accordance to the protocol set by 59 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

Linnaeus’ binomial nomenclature system studies require considerable identification (Enghoff, 2009). Systematics on the other skills, experiences and familiarity with hand is the science of distinguishing local species. Nonetheless, this may not orderliness and classification of a taxon be as complex as it sounds because each into hierarchical series to emphasize their species is normally distinctive in interrelationships (Mayr, 1942; Guerra- appearance and has a certain “look” (Fig. Gracia et al., 2008). The word 3). systematics stems from Greek word At a higher level and broader systema. Nelson (2006) tells us that a perspective, systematists are experts who systematist seeks the broadest outlook to examine historical discrepancies, resolve family, relative, order or grouping ambiguities, errors and variant names of orderliness. Taxonomy and systematics species, genus and family. For example, are not entirely different schools of there is the problem with regards to thought, but rather overlapping fields whether Eleotridae or Eleotrididae should (Wilson, 1985; Lincoln et al., 1998). be used for the members of sleeper fishes Kapoor (1998) and Wägele (2005) also (Robins, 1991). Thankfully, species highlight that the term “systematics” is classification and naming consistency is often used synonymously with taxonomy. slowly being resolved and currently It must be clarified that this review adopts governed by the International Nelson’s (2006) argument that biological Commission on Zoological Nomenclature classification is based on systematic (ICZN). However, fish taxonomic studies and taxonomy is part of problems cannot be resolved quickly as systematics. desired because ICZN also has to address A proper taxonomy is a first-hand and issues affecting other taxa. For the fish exhaustive undertaking. Whether one taxon, appreciatively, there are dedicated adopts the “biological species” concept ichthyologists who take it upon (Mayr, 1942; Nelson, 2006), themselves to diligently keep track of the “evolutionary species” concept (Simpson, latest development and progressively 1951) or the “phylogenetic species” publish the most updated information. concept (Cracraft, 1983) as explained Every species belongs to a genus earlier, all identification processes start (plural: genera), every genus to a family, which examining morphotypes at the every family to an order, every order to a earliest stage of discovery. Specimens are class, every class to a phylum (plural: physically scrutinized from small phyla) and finally all phyla are placed microscopic configuration of scales to under an overarching kingdom (Fig. 4). large membrane patterns of the caudal fin. Each phylum is regarded as a Each physical variance, no matter how representation of a large grouping of small, on a fish body is useful species that shares a common ancestor in information. Naturally, all fish-based evolution. Journal of Survey in Fisheries Sciences 4(1) 2017 60

Figure 3: Species from each family have a similar morphological profile to provide identification clues (Source: Adapted from Rainboth, 1996).

Figure 4: Taxonomic ranking and naming convention.

Ray-finned fish which is reviewed in this ranking. According to ICZN regulation, paper belongs to the Actinopterygii class the family-group name must always end under the Chordata phylum in the with the “idae” suffix (e.g., Cyprinidae) Animalia kingdom. Such is the ranking and the subfamily-group name must end and principle of taxonomy practice used with the “inae” suffix (e.g., Cyprininae). to organize all biological units. At time of At a higher level, the order-group name writing, some experts have arrived at should end with the “iformes” suffix (e.g., some agreement and the “Family-group Cypriniformes) and the suborder-group Names of Recent Fishes” published by name must end with the “oidea” suffix Van der Laan et al. (2014) seems to be the (e.g., Cyprinioidea). The family names are most updated for family naming. always capitalized but never italicized. In fish taxonomy, there are established conventions for expressing taxonomic 61 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

How species are named and why its scientific name Trichogaster leeri is a In Latin, species means “a kind, unique name and there is no chance that appearance and quality”. Depending on the name may be mistaken with other locality, people have various vernacular species. Ideally, a scientific name may and common names for a fish species. For even tell something about the species' key example, the common names Pearl characteristics (Fig. 5), its habit, Gourami, Diamond Gourami and Mosaic discoverer and perhaps the location where Gourami all refer to the same species. it was first found. Therefore, the use of common names can be confusing and misleading. However,

Figure 5: The species name Leptobarbus rubripinna is derived from Greek word “leptós” which means thin or slender, and the Latin word “barbus” meaning barbel. Rubripinna originates from the Latin words “ruber” and “pinna” which mean red and fin, respectively.

Another interesting example is the brittani) was named after a prominent fighting fish species, Betta persephone, ichthyologist Maurice Kottelat, and a which is named after Persephone the species that is named Anguilla borneensis daughter of Zeus in Greek mythology. tells us that it was first described from Also known as the princess of darkness specimens found in Borneo island. Those because she is said to rule the underworld, familiar with Latin or Greek, the Persephone was the perfect epithet for B. traditional language used in scientific persephone which typically inhabits the names, would also be able to tell that the black water in peat-swamp habitats of catfish Clarias leiacanthus should have Southeast Asia. Another fighting fish pectoral spines with smooth anterior edge; species the Betta gladiator need no in Greek, “leios” means smooth and further explanation as to why the epithet “akathos” means thorn. The Bihunichthys was given. monopteroides was named after a popular The Kottelatia genus (with only one food in Southeast Asia; “bihun” is a local recognized cyprinid species, Kottelatia name for rice noodle and “ichtys” means Journal of Survey in Fisheries Sciences 4(1) 2017 62 fish in Greek. Sure enough, it is a very hosts an isolated Channa gachua small and thin spineless eel that resembles population …). This is to ensure that the rice noodles. From examples mentioned, a species name is outstanding and can be scientific name can be communicative and easily singled out during reading. When gives species stable and universal handwritten, species name should be designations for easy retrieval. underlined for the same reason. The first The scientific naming that we practice part may be used alone but the second today would not be possible without the part is never used by itself. foundation laid by Carl Linnaeus (1707- A species name must be written in full 1778). Often confused by the many the first time is it expressed in a dialectal names during his specimen manuscript (e.g., Cyprinus hyperdorsalis) collection work in various countries, and thereafter the first part, or genus Linnaeus was convinced that species name, can be abbreviated with initial names must be standardized. In 1735, he capital letter (e.g., C. hyperdorsalis) on published a small pamphlet titled Systema the condition that there is no Naturae (The System of Nature) to misconstruing with other genera (i.e., introduce his new system of giving and bearing in mind “C. can also mean organizing species names. Linnaeus also Channa or Clarias if these genera appear decided that species names should be on the same paper). In cases where an given in Latin or Greek in two parts. Thus abbreviated initial capital letter may cause the binomial nomenclature system was confusion, two letters may be used (e.g., conceived. Although the Systema Ch. for Channa or Cl. for Clarias). There Naturae was meant for naming plants, it is no absolute rule and the objective is to soon gained popularity due to its avoid misinterpretation. practicality and it was quickly adopted by Additionally, “sp.” (Singular) or “spp.” taxonomists of various taxa. (Plural) may be used to represent The rule of binomial nomenclature “species” to indicate partially identified dictates that the first part of species name species with the genus known. For comprises of its genus (noun) and it is example, when a specimen is recorded as always capitalized (e.g., Cyprinus). The Cyprinus sp. it denotes that a specimen of second part is used to describe the the Cyprinus genus cannot be identified to species’ attribute or epithet (adjective) species level, possibly due to it being a and it is never capitalized (e.g., Cyprinus small juvenile which makes positive hyperdorsalis; “hyper” meaning “over” in identification difficult. For species with Greek and “dorsalis” meaning the back problematic identification, it may also be part of the body in Latin). The first and recorded with the term “cf.” added second part is always italicized. However, between the scientific names. It is simply if the neighbouring texts are italicized, a short term for “confer” or “compare then the first and second name would be with”. For example, when a species is non-italicized (e.g., in mesohabitat that referred as Rasbora cf. elegans, it implies 63 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification … the species it most likely belongs to but when submitting a manuscript for peer the designation is still marred by review, it would be wise to countercheck unresolved taxonomic issues or more the journal's submission instructions on work is needed to be completely sure. how to quote the target species. Alternatively, the term “aff.” is sometimes added between the scientific name when a Species identification at the specimen cannot be matched to any morphological level species known to science, or it is a new Since humans learnt how to hunt fish, species that is yet to be named. The term species were identified based on some is a short form of “affinis” in Latin which simple anatomical features. Observation means “akin to”. The insertion of “aff.” is of specimen anatomy and differentiating to associate the possibility of a new fish species based on their morphological species with the closest species (e.g., features is the most practical, rapid and Rasbora aff. elegans). low cost method. Besides experienced It would be advisable to describe the local fisherman and fish mongers, people genus, species, author and year in full who live by the river or wetland would when a species name is expressed as part learn to identify fishes at a young age. of a manuscript title, or the first time it is This is due to knowledge and memory written in the manuscript. The author(s)’ acquired from long-term observation or name(s) who first coined the binomial through oral tradition maintained by name and year of publication should be elders. Such traditional knowledge has included (e.g., Cyprinus hyperdorsalis been interweaved into modern Nguyen, 1991) because it is a good ichthyology by many researchers practice to ensure the manuscript author is (Calamia, 1999; Drew, 2005; Stacey et explicitly referring to a species described al., 2008; MacLean et al., 2009; Ferreira by a particular taxonomist in a particular et al., 2014), and the term for it is year. The author’s name is typically “traditional ecological knowledge” (TEK) enclosed in parentheses when the genus is (Berkes et al., 2000). For those keen in no longer the original one used. taxonomy, however, there is a need to Alternatively, the author’s name is adopt a more precise and sound approach. enclosed within parenthesis when a Fish identification is the most species has been transferred from the important component in any fish-based original genus in which it was first study and acquiring reasonable described; e.g. Cyprinus melanes (Mai, competency always begins with the study 1978). This puts the author and the reader of fish anatomy. Fundamentally, fish in a safer position because literature that species have to “go with the flow”. It is adopts fish as a subject can be flawed by apparent that the anatomy of fish is synonyms and obsolete species’ names. It shaped by the physical properties of should be noted that the author citation is water, the essential liquefied medium in treated differently in various taxa. Also, which the fish adopts as habitat. Water is Journal of Survey in Fisheries Sciences 4(1) 2017 64 dense but holds relatively small amounts and it forms the main body that lies of oxygen which affects fish respiratory between the head and caudal (Fig. 6). In function. Water also absorbs light in most species, the trunk is narrowed down higher intensity than air which affects fish at an area called the caudal peduncle visual capacity. Water can flow fast or not where it is connected to the caudal fin, at all, and this affects how fishes which is a prominent feature on the body manoeuvre in water. Such a complex and of a fish. fluid environment calls for special Body flexure attained by contractions adaptations to live in and fishes have of the myomeres and thrust from fins is evolved precisely to fit in. responsible for fish propulsion. Fin shapes In general, most biological adaptations and sizes vary tremendously and they are in fish occur in the body, mouth, fins, skin used for stabilizing, reversing, stopping, coloration and reproductive traits. The descending, ascending and manoeuvring. body of a bony ray-finned fish comprises In morphometric (Figs. 7 and 8) and 3 sections; the head, trunk and caudal or meristic identification of fishes, the tail. The head is a region from the mouth positions of fins, numbers and types of tip to the posterior edge of the gill cover. ray or spine composition are useful (Figs. The trunk contains the abdominal cavity 9, 10 and 11).

Figure 6: An example of key morphological features of a species from the Cyprinidae family (Source: Adapted from Rainboth, 1996).

Figure 7: Common morphometric data collected for fish identification (Source: Adapted from Rainboth, 1996). 65 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

Figure 8: Common measurements between key points to construct patterns that quantify morphometric variance between species (Source: Adapted from Strauss and Bookstein, 1982).

Figure 9: A close-up view of fin rays which epitomises fish under the Actinopterygii class.

Journal of Survey in Fisheries Sciences 4(1) 2017 66

Figure 10: An example of fin positions and ray structures of a fish with a contiguous dorsal fin.

Figure 11: A specimen from the Gastromyzon genus with specialized suctorial pectoral fins and fused pelvic fins for adhering to substratum rocks in riffles.

There are two fundamental types of fin “ribbon-fins” (Curet et al., 2011), and rays, namely the true spinous rays and what makes them so special is that the soft rays that form the framework for fins. entire stretch of the anal fin is actuated by Spinous rays are stiff and typically muscles along the body length. In eels, a unbranched, and they are located in a ribbon-fin may be present but the caudal single fin’s anterior part while soft rays fin is almost absent and they rely mostly consist of longitudinal supports and are on snake-like rectilinear locomotion for typically branched. Even so, there are swimming. exceptions. Some species like the Most bony fishes have homocercal Silurichthys indragiriensis and Wallago caudal fins that can be forked, rounded, attu propel themselves forward or truncated, and other symmetrical and non- backward by wavelike flexure of long symmetrical forms (Fig. 12). Generally, anal fins. Ichthyologists call these fins fishes with tapered body and fins are 67 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification … proficient in high-speed propulsion in fast As expected, scale counts are crucial for flowing waters while fish with rounded fish identification (Fig. 14). Some genera body and fins are associated with low- such as Clarias, Mystus and Ompok are speed movement in slow waters. without scales, but they are no less Mouth form and position also vary vulnerable. The skin of scaled and scale- greatly among fishes (Fig. 13). In most less fishes also secretes mucus to function fishes, the mouth is located terminally at as a sealant or protection against anterior tip of the head (e.g., Pristolepis infection, and to reduce hydraulic friction spp. and Oreochromis spp.), but in some while swimming. others it may be inferior (beneath the Evidently, some of the most interesting snout, e.g., Pangio spp.) or superior features of fishes are their pigmentation (upturned, e.g., Belodontichthys dinema) patterns (Fig. 15) which can be used as depending on their feeding habits. critical references for taxonomic Generally, terminal mouths belong to identification purposes. Body colouration species that prefer to bite or seize their is indeed an interesting subject in the prey while those with inferior mouths are context of fish as a biological indicator. bottom feeders. Insectivorous fishes such Like all animals, fishes cannot synthesize as the archer fish (Toxotes spp.) typically pigments. They have to ingest colourant have superior mouths and they feed on pigment like carotenoids from the food insects that fall on the water surface. they consume within their habitats, and Some freshwater species like the river these can include fruits, insects and pipefish of the genus Doryichthys have a phytoplankton (Grether, 2000). This can tubular mouth to suck food from crevices. reflect their foraging tendencies, habitat Most fishes have protective scales health and especially the presence of which vary greatly in size, structure, insect diversity as a rich source of squamation (scale coverage), pigments. Many studies have shown that arrangement, sequence and colouration. fish mating behaviour is affected by Scientifically, scales of teleost fishes can pigment availability from feeding habitats be classified into the placoid, cosmoid, and this, in turn, affects mate choice and elasmoid and ganoid categories (Sudo et population abundance (Endler, 1980; al., 2002). Teleost scales possess Basolo, 1990; Houde, 1997; Blount et al., outstanding hydrodynamic properties and 2003). provide a resistant layer to protect fishes from injury (Bruet et al., 2008). Scaled skin is also known to play a critical role in supporting fish locomotion by synchronizing wave propagation (Long et al., 1996), and by accumulating potential energy like tendons (Hebrank and Hebrank, 1986) for swimming efficiency. Journal of Survey in Fisheries Sciences 4(1) 2017 68

Figure 12: Common caudal fin shapes (Source: Adapted from Rainboth, 1996).

Figure 13: Common mouth types.

Figure 14: Common meristic data collected by taxonomists (Source: Adapted from Rainboth, 1996 and Ambak, 2012).

69 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

Figure 15: Common terms used to describe body markings and patterns on a representative teleost.

Journal of Survey in Fisheries Sciences 4(1) 2017 70

The fundamental colour constituent in or fully (Slavík et al., 2016). Individuals fishes is the dermal chromatophore unit affected by albinism are typically pale, (pigment cell) which consists of the: 1) light pink, white or yellow (Lechner and melanophore which contains melanin Ladich, 2010). Their eyes are generally (browns, blacks, and greys), 2) pink because blood is seen through the xanthophore and erythrophore which colourless retina (Van Grouw, 2006). harbour carotenoids (yellows, orange and Conversely, leucism is a condition red), and 3) iridophore, or sometimes characterized by the reduction or absence termed as iridocyte, which naturally of most, if not all, of the pigment cell reflects external light source and provides types. Leucoptic individuals are generally fishes their iridescence (Hawkes, 1974; pale, white or yellow but they exhibit Fujii et al., 1989; Metz et al., 2006). normal retinal pigmentation (Quigley and Chromatophores can naturally contract or Wallace, 2013). Melanism is the exact expand to induce or change colours to opposite of albinism where excessive blend into the aquatic environment for development of dark-coloured pigment camouflaging purposes. In some cases, a melanin occurs and the affected individual combination of chromatophore units can is typically dark brown or black (Regan, produce interesting colours. For example, 1961). It is a form of polymorphism that in the Siamese fighting fish (Betta is widespread in fishes, and it may be splendens), a wide variety of bodily genetically determined and/or influenced colours can be exhibited by the by the environment (Price et al., 2006). permutation of iridophores, For example, melanin polymorphism has melanophores, erythrophores and been report in Gambusia holbrooki, xanthophores (Khoo et al., 2012; Khoo et Siphateles bicolor mohavensis and al., 2014). Amphilophus labiatus (Horth, 2002; It must be cautioned that identifying Henkanaththegedara and Stockwell, 2011; species by their body colouration and Sowersby et al., 2014). When an patterns alone is not entirely robust. In individual exhibits abnormal deep yellow, certain cases, individuals in a natural orange or reddish pigmentation on the population may be affected by genetically body, this is attributed to excessive inherited conditions that cause them to development of the xanthophores and exhibit albinism, leucistic, melanistic and erythrophores (Khoo et al., 2012). xanthic abnormalities. Albino individuals Xanthic variety of the Cyprinus carpio such as Silurus glanis, Astyanax and Carasszus auratus with red, orange mexicanus, Hydrolagus colliei and and yellow pigmentation were first Genidens planifrons have been reported reported and domesticated in China and (Dingerkus et al., 1991; Jeffery, 2006; Japan as ornamental species (Kajishima, Reum et al., 2008; Leal et al, 2013) and 1977; Balon, 1995). Wild individuals these individuals are unable to synthesize from species such as Cyprinodon tyrosine and melatonin hormones partially bifasciatus have also been found to be 71 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification … xanthic (Carson 2011). On the other hand, those of terrestrial vertebrates. In fact, an axanthic individual that lacks they are endowed with more sensitive and xanthophores may be black, white, and/or complex sensory organs to detect blue (Lewand et al., 2013). For example, vibration and sound. Fishes possess the Parichy (2006) reported that axanthic cephalic-lateralis system (Nelson, 1972) individuals have been found in species that comprises a series of neuromast from the Danio genus. sensory cells that run across the outer Being fully aquatic, fishes have vastly layer of the head and body (Fig. 16). different sensory systems compared to

Figure 16: An illustration of the fish cephalic-lateralis system consisting of neuromast sensors that run across canals on the head and body (Source: Adapted from Nelson, 1972 and Iwata and Jeon, 1995).

The neuromast contains fine hair cells schooling synchronization (Partridge and oriented in a manner to detect the Pitcher, 1979). The patterns and direction of vibration. Vibration signals configuration of cephalic-lateralis system are then transmitted through special on fish bodies are sometimes used for fish canals and pits containing endolymphic identification such as those from the fluid to amplify the signals and thereafter Kryptoglanis, Pseudorasbora and pass on to the brain. The location of the Caecieleotri genus (Moncey, 2012; lateralis system in fish can reflect their Kawase and Hosoya, 2015; Walsh and feeding habits. Bottom feeders tend to Chakrabarty, 2015). have the lateralis system on top of the In the case of cryptic species when the body to detect vibration from predators species are too difficult to be that are lurking above. Those which feed differentiated because they show small on the water surface normally have the external anatomical and morphological system along the ventral margin of the deviations between species in the same body to track the presence of predators genus, ichthyologists have relied on the below. Studies have also shown that the internal organs to characterise them lateralis system is responsible for obstacle (McCune, 1981). Where necessary, gill avoidance, triggering startle response and rakers from the first gill arch on the left Journal of Survey in Fisheries Sciences 4(1) 2017 72 side of the body are also counted for archive and share Fourier spectrum (FFT), meristic characterization such as species wavelet analysis (WT) and curvature scale from the Coregonus, Garra and Labeo space analysis (CSS) data of otoliths genus (Amundsen et al., 2004; Ayoade et (Lombarte et al., 2006). At time of this al., 2004; Krupp and Budd, 2009). writing, the AFORO archive contains Correspondingly, in some species, the 4,672 high resolution images of 1,441 pharyngeal teeth found on the fifth gill species from 221 families for reference. arch are counted from left to right to assist in meristic identification of species such Species Identification at the Molecular as those from the Moxostoma, Cycleptus, Level Danio and Epalzeorhynchos genus Morphological characterization is not (Eastman 1977; Pasco-Viel et al., 2010). entirely robust. As mentioned earlier, the All teleost fishes have an inner ear as concept of “species” is still subjected to an auditory system. Instead of bony debate and not all taxonomists assign ossicles, fishes have three pairs of meaningful categories to organisms by calcareous “ear stones”, or scientifically morphotype. In many cases when termed as otoliths (Greek for “ear certainty cannot be attained, researchers stones”). The lapillus (“little stone” in use terms like “subspecies”, “strain” or Latin) functions in maintaining body “variant”. These are highly subjective and balance and orientation, and the other confusing. In fish especially, two, namely asteriscus (“little star” in morphological plasticity between Latin) and sagittal (“arrow” in Latin), individuals of the same species is peruse acoustic reception. Otoliths are inherent. For example, body colour tones enclosed in a membranous sac together and polymorphism exhibited by with sensory hair cells or ciliary bundles. individuals of the same species may vary Detection of mechanical signals will considerably depending on the diet occur when there are dynamic interactions regime, habitat and season such as species between otoliths and cilia (Assis, 2003; from the Betta, Poecilia and Danio genus Campana, 2005). Since Koken (1884) (Khoo et al., 1997; Price et al., 2008). reported that fish species can be And this is where molecular analysis has characterised by having otoliths of become a viable alternative. different shapes and sizes, otolith Each organism is characterized by a morphometry is fast becoming a trend to unique set of biological attributes that identify fishes and some species such as enhance its fitness to survive in a niche Netuma bilineata, Nuchequula nuchalis, environment. Correspondingly, to adjust Coilia dussumieri and Garra rufa (Chen to any changes in the environment, an et al., 2011; Thuy et al., 2015; Salimi et organism is naturally subjected to genetic al., 2016; Yedier et al., 2016). In 2006, drift, mutation or variation the AFORO online database was launched (polymorphism) as a mechanism to adapt. (http://www.cmima.csic.es/aforo/) to Such natural phenomenon provides 73 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification … markers at molecular level to detect order or sequence in each gene is unique individual or species uniqueness (Sanger to every species. Since Razin and Rottem et al., 1977). All molecular methods (1967) have successfully employed depend on DNA marker or protein protein analysis for characterising sequence analysis and comparison to microorganism species, modern advances determine molecular divergence over have adapted the concept of analysing A- evolutionary time based on the null G-C-T bases in various DNA genetic hypothesis of molecular evolution, or markers. In fish identification, the better known as the “neutral theory” common DNA analyses applied are length (Kimura, 1968). Essentially, all methods polymorphism (RFLP), amplified assume that individuals from the same fragment length polymorphism (AFLP), species have specific DNA (or protein) random amplified polymorphic DNA sequences that vary, to a certain extent, (RAPD), microsatellites or simple from individuals that belong to other sequence repeat (SSR), single nucleotide species. Nonetheless, the variance, or polymorphism (SNP) and expressed “signature” of speciation (Sbordoni, sequence tag (EST) markers (O’Reilly 2010), is dependent on time and space and and Wright, 1995; Khoo et al., 2003; subjected to biological productivity of Sampaio et al., 2003; Teletchea, 2009; individuals, dispersal pattern and natural Chauhan and Rajiv, 2010; Khoo et al., genetic drift. Therefore, genetic 2011; Kress et al., 2015). variability also occurs among individuals Fish genome typically contains of the same species. This means roughly a billion nucleotide pairs (Stepien establishing a credible locus, or the and Kocher, 1997), and analysing all of position of a gene (Khoo et al., 2011) them would be too daunting and the from a phenotype is a prerequisite as results would cause an information master reference for comparison purposes. overload. Since Herbert et al. (2003) DNA markers can be classified in two discovered a technique to amplify the different types, namely type I which are mitochondrial cytochrome c oxidase markers associated with genes with subunit 1 (COI) gene. There is now a known function and type II which are consensus to analyse a 648-base pair (bp) markers are with anonymous genomic region of COI to rapidly identify a fish segments (Chauhan and Rajiv, 2010). For species (Cawthorn et al., 2012). Such an example, allozyme markers are classified approach is now known as DNA as type I protein markers and barcoding and it has gained widespread microsatellites and other neutral markers acceptance as a fast, cost effective and are considered type II (Hinsinger et al., standardised technique. So far, the Fish 2015). The DNA in all organisms is a Barcode of Life Initiative has barcoded composition of four chemical bases – 7,882 fish species, which is only adenine (A), guanine (G), cystosine (C), approximately 25% of the estimated and thymine (T) (Avise, 1994). Their Journal of Survey in Fisheries Sciences 4(1) 2017 74

31,220 species present globally (Jinbo et metabarcoding" to refer to their ability to al., 2011). automatically identify multiple species It should be stressed that identified from a single bulk sample (Taberlet et al., species through DNA barcode is only as 2012). Because NGS technologies can good as the voucher specimen's DNA extract massive numbers of reads, the barcode made available and archived in results increase the chances of finding and platform such as GenBank. Hence, if a annotating matches (Hemmer-Hansen et DNA barcode is inaccurate or al., 2014). So far, technological platforms compromised due to issues such as that are able to produce and analyse carryover DNA contamination, gigabases of DNA sequence include incomplete genotyping of loci throughout Illumina, Roche, AB SOLiD, 454 GS the genome, low/wrong quality DNA FLX, Ion Torrent, HeliScope, Starlight material, human errors, biases and some and PacBio (Rothberg and Leamon, 2008; other critical risks (Bridge et al., 2003; Pandey et al., 2008; Davey and Blaxter, Forster, 2003; Moritz and Cicero, 2011; Hemmer-Hansen et al., 2014). They 2004; Smith and Burgoyne, 2004; Ebach differ from each other based on amount of and Holdrege, 2005; Meyer and Paulay, sequence information generation, 2005; Will et al., 2005), the identification chemistry protocol for sequencing and the process would be erroneous. Ross et al. length of sequence read (Mehinto et al., (2008) proposed that reference sequences 2012). of at least five or more voucher specimens from various geographical sites should be Reference Type and Traceability acquired. Unfortunately, this also means The hallmark of the taxonomy discipline that DNA analysis is not a one minute is its persistency in collecting, preserving procedure. To conduct it properly, the and managing specimens as essential process of acquiring exemplar genotypes physical references for species-level is tedious and costly because some research. Although ecologists, species are found in large regions and conservationists, aquaculturists or various countries. researchers who adopt fish as a part of In the recent years, DNA sequencing their studies need not master the specifics techniques have made substantial progress in specimen management, it is useful to and they are able to analyse 30 to 1,500 briefly understand the ICZN zoological nucleotides (nt) for hundreds of thousands code and terms as a precaution against to millions of DNA molecules in a single negligence when tracing the correct process within a complex or degraded binomial nomenclature and description of DNA source (Davey and Blaxter, 2011; fish. Mehinto et al., 2012). These are classified Fundamentally, in taxonomy, as next-generation sequencing (NGS) a “type” is a specimen of a distinct technologies (Tillmar et al., 2013) and species which is used as master reference sometimes termed as "DNA (Krell and Wheeler, 2014). Each species 75 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification … or subspecies that is scientifically named around the world for the type series (a by the original author (discoverer) is range of specimens showing variation in traceable to a name-bearing specimen the species). These comparable specimens which was first found and kept in a are termed as “paratypes” and they have particular museum. A new species cannot no name-bearing role. be described and registered formally In situations when the researcher fails without depositing a single physical to establish a holotype, the existing two or whole fish known as a “holotype” in the more specimens collected and deposited museum (Clemann et al., 2014; Kumar in the museums can be used to describe and Hassan, 2015). As sexual dimorphism and name a species. These deposited occurs in many fish species, it is good specimens are known as “syntypes” practice to deposit an opposite sex although such practice is now rarely used specimen of the holotype and it is in contemporary taxonomy. A master assigned as an “allotype” (Jorge et al., reference specimen selected from 2014). Also, polymorphisms may occur in syntypes is termed as “lectotype” and certain fishes and a holotype is not when a lectotype is finally established, all expected to be a typical representative other syntypes shall be, by default, (Hulsey, 2005), although in an ideal case reassigned as “paralectotypes”. it should be. To mitigate this, Correspondingly, any duplicate specimen morphotypes that show morphological of the lectotype is called an variants of a species can be established, “isolectotype”. Finally, specimens that and molecular analysis is usually carried have been erroneously described, named out to determine whether the variations or labelled are annotated as “non-types”. are due to polymorphism or if it is a new All terminologies pertaining to types species (Simonov, 2008). mentioned in this section are elaborated in A researcher may also designate a detail by ICZN at the website duplicate specimen of the holotype and http://www.iczn.org/iczn/index.jsp. such a specimen is termed as an The responsibility rests on the “isotype”. When a better specimen is taxonomist to maintain the specimens and eventually deposited, the holotype is not make them accessible for current and superseded. According to the ICZN code, future studies (Krell and Wheeler, 2014; such a specimen which provides better Rocha et al., 2014). To consolidate a large clarity is known as an “epitype” and it quantity of voucher specimen database in may be deposited when the holotype is a museum, the taxonomist is also evidently imprecise. In the case when a expected to occasionally publish holotype is lost or damaged, a “neotype” monographs that contain summarised specimen may also be deposited as information of all species in a group to replacement. While there can only be one update the scientific community (Grinnell, holotype, taxonomists can continue to 1910; Pyke et al., 2010; Kottelat, 2013). deposit specimens in any museums Journal of Survey in Fisheries Sciences 4(1) 2017 76

In the advent of technological In principle, a scientific finding must be advancement, non-destructive methods reproducible. When an author declares such as high-resolution photography, and publishes the description of a new computerised tomography (CT) scan and species, a specimen (i.e., haplotype) must radiography methods that can record the be deposited permanently in the museum physical characteristics of specimens, the so that the author's claim can be critically work of a taxonomist has expanded over appraised and reappraised by others the years. There are already attempts to (Rocha et al., 2014). The specimen can be digitalize specimens using these refuted or disputed by other ichthyologists technologies. For example, Berquist et al. to allow for revisions. Similarly, when a (2012) have progressively scanned researcher conducts a fish inventory specimens with the magnetic resonance investigation that results in a scientific or imaging (MRI) technology and created an journal report, it is a good practice online digital archive called Digital Fish (although not compulsory) to collect Library (DFL, voucher specimens for future verification http://www.digitalfishlibrary.org) to share and to promote transparency. This high-resolution and high-contrast visual approach also provides physical records data. The Biovisualization Center at the that allow researchers to scrutinize the University of Washington has also just inter- and intraspecific variation of initiated a program that applies the CT species collected at different periods of scanning technology and the captured 3D time and localities. morphology data of fish specimens is Specimens are typically acquired by shared through the Open Science various capturing methods as discussed Framework website widely elsewhere by literature such as by (https://osf.io/ecmz4/wiki/Fishes/). Such handnets, traps, seine nets, electrofishing innovations have the potential to replace and even by buying directly from pale and degraded voucher specimens that fishermen or the local fresh markets. Once have been preserved for a long period of obtained, they must be immediately time in alcohol. Morphological and labelled with 1) serial number, 2) species meristic database compilation can be name, 3) name of collector, 4) location, 5) instantly peer-reviewed and shared online date of collection, 6) GPS coordinates, with any amateurs or experts located and 7) some description of the specimens’ anywhere around the world. This is an colour and body markings in fresh should opportunity for scientists to engage more be recorded (Fischer, 2013; Motomura with the society and garner support from and Ishikawa, 2013). This may be the public and policymakers for fish supported by high resolution photographs conservation. of the whole fish and specific parts with distinctive characters (Figs. 17, 18 and Specimen Collection and Preservation 19). 77 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

Figure 17: Fresh specimen is photographed facing left together with a ruler to indicate scale.

Figure 18: A live specimen is best photographed with high-resolution photography to record subtle details and colouration.

Figure 19: Noticeable variations of the same species should be photographed for species-level studies. For example, in the case of Tor tambra (above), individuals in the same population may display differing forms of mental lobe and barbels (Roberts, 1999).

Journal of Survey in Fisheries Sciences 4(1) 2017 78

Specimens should be cleaned and can (2006) suggest that in the absence of either be frozen or immediately fixed in refrigeration during field work, specimens formalin or alcohol before being fixed in 10% buffered formalin or 95% transferred to depositories. alcohol should be analyzed with DNA In fish taxonomy, the left side of the processes within one week to produce the fish body is examined. Therefore if best results. muscle tissue is required for molecular In the museums and depositories, analysis, it should be dissected from the taxonomists are cautious when fixing and right side of the body. In small fishes storing specimens (Fig. 20) since any flaw where muscle tissues are difficult to in the process will devalue their academic excise, the right pelvic fin may be significance. Specimens are usually fixed collected as an alternative (Shiozawa et in 10% formalin solution and large sized al., 1992). Typically, 1.0 cm3 tissue from specimens are incised on the right side to the fresh muscle contains enough genomic enable better absorption of formalin material for molecular study and it should (Schander and Halanych, 2003; Garrigos be stored in 95% alcohol and then et al., 2013). For the same purpose, refrigerated at -20°C (Motomura and formalin may also be injected into the Ishikawa, 2013). Preferably, it should be abdomen by using a syringe (Motomura free from fat and blood which may and Ishikawa, 2013). hamper the DNA purification process (Wong et al., 2012). Chakraborty et al.

Figure 20: Fixed specimens are usually stored in glass jars with heads pointing downwards. Note that specimens become pale and lose their colouration quality, which is why photography of live specimens is crucial as part of the data collection process.

79 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

Taxonomic Key 9. Field notes – description of sympatric After fixing, labelling and cataloguing a and syntonic species found in the same specimen, a competent taxonomist would habitat when the specimen is collected. carry out the standard morphometrics, 10. Remarks or comments – description of meristics and sometimes molecular precautions as a measure against analyses as mentioned earlier. As a misidentification and any other useful minimum, the taxonomist would information for effective identification. subsequently generate a report with the If a potential new species is following information (Fischer, 2013) for encountered, the specimen and full- each species; colour photographs are to be sent to an 1. Species name, author and year. authority of the genus for further 2. Material examined – description of type investigation. This shall be recorded in material and voucher specimen this section. examined. A competent taxonomist would update 3. Diagnosis – description of the the field “taxonomic key” for the specimen’s key markers or corresponding genus once a new species morphological features that has been identified. It is a conventional differentiates it from nearest congeners tool meant for quick and practical from the same watershed and other identification based on the major watersheds. Diagrams may be included morphological characters (Fig. 21) of a for clarity. species (Fischer, 2013). A typical 4. Description – description of major taxonomic key is organized in a series morphological and meristic data. diagnostic characteristic of a species that 5. Pigmentation in life – description of lead the user to the correct name of a colour, marking and patterns on the given specimen. A taxonomic key is body and fins of a fresh specimen. called a dichotomous key (in Latin 6. Colour in formalin or alcohol – “dichotomous” means in two parts) description of colour, markings and because only two marker options are patterns on the body and fins of the offered in each step (Fig. 22). The fixed specimen. markers provided may be quantitative 7. Distribution – description of location (e.g., scale count) or qualitative (e.g., where the specimen and the species body colour). Once created, the key can can be typically found according to be continuously improved by taxonomists published literature. based on feedback from users. 8. Etymology – description of the Greek/Latin word or rationale behind the scientific name (binomial nomenclature) assigned to the species. Journal of Survey in Fisheries Sciences 4(1) 2017 80

Figure 21: The key characteristics of a genus are typically described at the start of the taxonomic key. For example, the Glyptothorax genus’s key characteristic is the presence of a unique thoracic adhesive apparatus (arrow) that can only be observed in the ventral view.

Figure 22: An example of a dichotomous key produced by Silfvergrip (2009, p.25) for the identification of freshwater eels from the Anguillidae family.

81 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

Integrative taxonomy family due to species and subspecies from There are species within the same genus the family have sympatric distribution and that possess small variations that are not the morphological characters among them easy to discriminate. This is compounded are hard to distinguish (Castle and by the unstable and convoluted taxonomic Williamson, 1974; Aoyama et al., 2000; history of some species which can Arai and Wong 2016). For example, experience numerous revisions of species Sugeha and Suharti (2009) found names because taxonomists may not share difficulty in distinguishing Anguilla the same assumptions and approaches. bicolor bicolor and Anguilla bicolor Correspondingly, it is fair to expect that pacifica based on morphological the science of taxonomy and systematics attributes alone. However, they were able is constantly in flux and revisions may be to make a distinction between the species frequent. by their adult sizes. Generally, A. bicolor A classic example is the case of bicolor is longer and heavier than A. Neolissochilus spp. and Tor spp. found in bicolor pacifica. They also found that A. Southeast Asia. These genera are typically bicolor bicolor tend to occur in Sumatra prone to trophic polymorphism and and Java region and A. bicolor pacifica is display conspicuous oral morphology found in Sulawasi and New Guinea region variation (Roberts and Khaironizam, of Indonesia. As such, they have proposed 2008) that have confused even the most that the two subspecies can be experienced ichthyologists. For example, distinguished by the geographic approach. in early 20th Century, members of the Subsequently, Teng et al. (2009) resolved Neolissochilus genus were placed in the the issue by conducting a phylogenic Barbus genus (Boulenger, 1893; Duncker, study and validated the notion that 1904). Later they were reassigned Anguilla species and subspecies can respectively to Labeobarbus, cluster regionally (Fig. 23). Crossochilus, Puntius and Acrossocheilus The case of Anguilla genus is a classic (Weber and de Beaufort 1916; Ahl 1933; example how the combination of Fowler 1934; Herre and Myers 1937; morphological and molecular approaches, Smith 1945) before being finalized as generally termed as integrative taxonomy Neolissochilus, a new genus created by (Goulding and Dayrat, 2016), are crucial Rainboth (1996). in gaining and expanding the In cases when the taxonomy of a understanding of taxonomy and diversity particular genus has stabilized, in fish. This demonstrates that the misidentification can still be common broadest range of methods should be because small variations can be difficult utilized to answer and solve taxonomic to be distinguished. For example, in the concerns. past decades, there were numerous reports that highlighted misidentification of the freshwater eels from the Anguillidae Journal of Survey in Fisheries Sciences 4(1) 2017 82

Figure 23: The morphological phylogenetic tree of the genus Anguilla showing correlation species occurrence in various regions (Source: Teng et al., 2009).

Acknowledgements between two species of freshwater eels, We wish to extend our deepest gratitude Anguilla celebesensis and A. interioris. to all past and present taxonomists around Ichthyological Research, 47, 157-161. the world whose life time work and Arai, T. and Wong L.L., 2016. publications have provided substance for Validation of the occurrence of the this manuscript. tropical eels, Anguilla bengalensis bengalensis and A. bicolor bicolor at References Langkawi Island in Peninsular Ahl, E., 1933. Ueber eine kleine Malaysia, Malaysia. Tropical Fischsammlung aus dem Toba-See in Ecology, 57(1), 23-31. Sumatra. Sitzungsberichte der Assis, C.A., 2003. The lagenar otoliths of Gesellschaft Naturforschender teleosts: Their morphology and its Freunde, 514–516. application in species identification, Amundsen, P., Bøhn, T. and Våga, phylogeny and systematics. Journal of G.H., 2004. Gill raker morphology and Fish Biology, 62(6), 1268–1295. feeding ecology of two sympatric Authman, M.M.N., Zaki, M.S., Khallaf, morphs of European whitefish E.A. and Abbas, H.H., 2015. Use of (Coregonus lavaretus). Annales fish as bio-indicator of the effects of Zoolologici Fennici, 41, 291–300. heavy metals pollution. Journal of Aoyama, J., Watanabe, S., Ishikawa, S., Aquatic Research and Development, 6, Nishida, M. and Tsukamoto, K., 328. 2000. Are morphological characters distinctive enough to discriminate 83 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

Avise, J.C., 1994. Molecular markers, Review of Ecology, Evolution, and natural history, and evolution. New Systematics, 38, 459–487. York: Chapman and Hall. Boulenger, G.A., 1893. List of the fishes Ayoade, A.A., Sowunmi, A.A. and collected by Mr E.W. Oates in Nwachukw, H.I., 2004. Gill southern Shan State and presented by asymmetry in Labeo ogunensis from him to the British Museum. The Annals Ogun River, Southwest Nigeria. and Magazine of Natural History, Revista de Biologia Tropical, 5(1), 12(6), 198–203. 171-175. Bridge, P.D., Roberts, P.J., Spooner, Balon, E.K., 1995. Origin and B.M. and Panchal, G., 2003. On the domestication of the wild carp, unreliability of published DNA Cyprinus carpio: From sequences. New Phytologist, 160, 43– Romangourmets to the swimming 48. flowers. Aquaculture, 129, 3-48. Britton, J.R. and Davies, G.D., 2006. Basolo, A.L., 1990. Female preference First record of the white catfish predates the evolution of the sword in Ameiurus catus in Great Britain. swordtail fish. Science, 250, 808–810. Journal of Fish Biology, 69, 1236– Berkes, F., Coldings, J. and Folke, C., 1238. 2000. Rediscovery of Traditional Bruet, B., Song, J., Boyce, M. and Ecological Knowledge as Adaptive Ortiz, C., 2008. Materials design Management. Ecological Applications, principles of ancient fish armour. 10, 1251-1262. Nature Materials, 7, 748-756. Berquist, R.M., Gledhill, K.M., Butlin, R.K., Galindo, J. and Grahame, Peterson, M.W., Doan, A.H., Baxter, J.W., 2016. Sympatric, parapatric or G.T., Yopak, K.E., Kang, N., allopatric: the most important way to Walker, H.J., Hastings, P.A. and classify speciation? Philosophical Frank, L.R., 2012. The Digital Fish Transactions of the Royal Society B, Library: Using MRI to Digitize, 363, 2997–3007. Database, and Document the Calamia, M.A., 1999. A methodology for Morphological Diversity of Fish. PLoS incorporating traditional ecological ONE, 7(4), e34499. knowledgewith geographic information Blount, J.D., Metcalfe, N.B., Birkhead, systems for marine resource T.R. and Surai, P.F., 2003. management in the Pacific. Carotenoid modulation of immune http://www.spc.int/Coastfish/publicatio function and sexual attractiveness in ns/bulletins/traditional- zebra finches. Science, 300, 125–127. management/212-traditional- Bolnick, D.I. and Fitzpatrick, B.M., information-bulletin-10.html 2007. Sympatric Speciation: Models Campana, S.E., 2005. Otolith science and Empirical Evidence. Annual entering the 21st century. Marine and Freshwater Research, 56, 485–495. Journal of Survey in Fisheries Sciences 4(1) 2017 84

Carson, E.W., 2011. Low but Stable vertebrate voucher specimens, with Frequency of Xanthic Phenotypes in a guidelines for ethical collection. Population of the Twoline Pupfish, Memoirs of Museum Victoria, 72, 141- Cyprinodon bifasciatus. The American 151. Midland Naturalist, 166(2), 462-466. Cracraft, J., 1983. Speciation and its Castle, P.H.J. and Williamson, G.R., ontology: The empirical consequences 1974. On the validity of the freshwater of alternative species concepts for eel species Anguilla ancestralis from understanding patterns and processes Celebes. Copeia, 2, 569-570. of differentiation. Speciation and its Cawthorn, D.M., Steinman, H.A. and Consequences, 28–59. Witthuhn, R.C., 2012. DNA Curet, O.M., Patankar, N.A., Lauder, barcoding reveals a high incidence of G.V. and MacIver, M.A., 2011. fish species misrepresentation and Mechanical properties of a bio-inspired substitution on the South African robotic knifefish with an undulatory market. Food Research International, propulsor. Bioinspiration and 46, 30–40. Biomimetics, 6(2), 1-9. Chakraborty, A., Sakai, M. and Davey, J.W. and Blaxter, M.L., 2011. Iwatsuki, Y., 2006. Museum fish RADSeq: Next-generation population specimens and molecular taxonomy: A genetics. Briefings in Functional comparative study on DNA extraction Genomics, 9(5), 416-423. protocols and preservation de Carvalho, M.R., Bockmann, techniques. Journal of Applied F.A., Amorim, D.S., de Vivo, M., de Ichthyology, 22(2), 160-166. Toledo-Piza, M., Menezes, N.A., de Chauhan, T. and Rajiv, K., 2010. Figueiredo, J.L., Castro, R.M., Gill, Molecular markers and their A.C., McEachran, J.D., Compagno, applications in fisheries and L.J., Schelly, R.C., Britz, aquaculture. Advances in Bioscience R., Lundberg, J.G., Vari, R.P. and Biotechnology, 1, 281-291. and Nelson G., 2007. Revisiting the Chen, W., Al-Husaini, M., Beech, M., taxonomic impediment. Science, 307, Al-Enezi, K., Rajab, S. and Husain, 353. H., 2011. Discriminant analysis as a Dieckmann, U. and Doebeli, M., 1999. tool to identify catfish (Ariidae) On the origin of species by sympatric species of the excavated archaeological speciation. Nature, 400, 354-357. otoliths. Environmental Biology of Dingerkus, G., Seret, B. and Guilbert, Fishes, 90, 287–299. E., 1991. The first albino Wels, Silurus Clemann, N., Rowe, K.M.C., Rowe, glanis Linnaeus, 1758, from France, K.C., Raadik, T., Gomon, M., with a review of albinism in catfishes Menkhorst, P., Sumner, J., Bray, D., (Teleostei: Siluriformes). Cybium, 15, Norman, M. and Melville, J., 2014. 185–188. Value and impacts of collecting 85 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

Drew, J.A., 2005. Use of Traditional Fischer, J., 2013. Fish identification tools Ecological Knowledge in Marine for biodiversity and fisheries Conservation. Conservation Biology, assessments: Review and guidance for 19, 1286-1293. decision-makers. FAO Fisheries and Duncker, G., 1904. Die fische de Aquaculture Technical Paper No. 585. Malayichen Halbinsel. Mitteilungen Rome: FAO. aus dem Naturhistorischen Museum in Fonge, B.A., Tening, A.S., Egbe, A.E., Hamburg, 21, 133–207. Awo, E.M., Focho, D.A., Oben, P.M., Eastman, J.T., 1977. The Pharyngeal Asongwe, G.A. and Zoneziwoh, Bones and Teeth of Catostomid Fishes. R.M., 2011. Fish (Arius heudelotii American Midland Naturalist, 97(1), Valenciennes, 1840) as bioindicator of 68-88. heavy metals in Douala Estuary of Ebach, M.C. and Holdrege, C., 2005. Cameroon. African Journal of DNA barcoding is no substitute for Biotechnology, 10(73), 16581-16588. taxonomy. Nature, 434. Forster, P., 2003. To err is human. Endler, J.A., 1980. Natural selection on Annals of Human Genetics, 67, 2-4. color patterns in Poecilia reticulata. Fowler, H.W., 1934. Zoological results Evolution, 34, 76–91. of the third de Schauensee Siamese Enghoff, H., 2009. What is taxonomy? – Expedition, Part I – Fishes. An overview with myriapodological Proceedings of the Academy of Natural examples. Soil Organism, 81(3), 441– History of Philadelphia, 86, 67-163. 451. Fujii, R., Kasuwaka, H., Miyaji, K. and Feeley, K.J. and Silman, M.R., 2011. Oshima, N., 1989. Mechanism of skin Keep collecting: accurate species coloration and its changes in the blue- distribution modelling requires more green damselfish. Zoological Science, collections than previously thought. 6, 477-486. Diversity and Distributions, 2011, 1-9. Garrigos, Y.E., Hugueny, B., Koerner, Feist, S.W. and Longshaw, M., 2008. K., Ibañez, C., Bonillo, C., Pruvost, Histopathology of fish parasite P., Causse, R., Cruaud, C. and infections– Importance for populations. Gaubert, P., 2013. Non-invasive Journal of Fish Biology, 73, 2143– ancient DNA protocol for for fluid- 2160. preserved specimens and phylogenetic Ferreira, H.M., Reuss-Strenzel, G.M., systematics of the genus Orestias Alves, J.A. and Schiavett, A., 2014. (Teleostei: Cyprinodontidae). Zootaxa, Local ecological knowledge of the 3640 (3), 373-394. artisanal fishers on Epinephelus itajara Godfray, H.C.J., 2002. Challenges for (Lichtenstein, 1822) (Teleostei: taxonomy. Nature, 417, 17-19. Epinephelidae) on Ilhéus coast – Bahia Goulding, T.C. and Dayrat, B., 2016. State, Brazil. Journal of Ethnobiology Integrative taxonomy: Ten years of and Ethnomedicine, 10(51), 1-15. practice and looking into the future. Journal of Survey in Fisheries Sciences 4(1) 2017 86

Archives of Zoological Museum of Henkanaththegedara, S.M. and Lomonosov Moscow State University, Stockwell, C.A., 2011. Melanism In 54, 116-133. Endangered Mohave Tui Chub Grether, G.F., 2000. Carotenoid Siphateles Bicolor Mohavensis Snyder limitation and mate preference 1918 (Cypriniformes: Cyprinidae). evolution: a test of the indicator Western North American Naturalist, hypothesis in guppies (Poecilia 71(1), 127-130. reticulata). Evolution, 54, 1712-1724. Herre, A.W. and Myers. G.S., 1937. A Grinnell, J., 1910. The methods and uses contribution to the ichthyology of the of a research museum. Popular Science Malay Peninsula. Bulletin of the Monthly, 77, 163-169. Raffles Museum, 13, 5-75. Guerra-Gracia, J.M., Espinosa, F. and Hinsinger, D.D., Debruyne, R., Garcia-Gomez, J.C., 2008. Trends in Thomas, M., Denys, G.P.J., Taxonomy today: an overview about Mennesson, M., Utge, J. and Dettai, the main topics in Taxonomy. A., 2015. Fishing for barcodes in the Zoologica Baetica, 19, 15-49. Torrent: from COI to complete Hawkes, J.W., 1974. Structure of fish mitogenomes on NGS platforms. DNA skin. Cell and Tissue Research, 149, Barcodes, 3, 170–186. 147-172. Horth, L., 2002. Melanic body colour Hebert, P.D.N., Ratnasingham, S. and and aggressive mating behaviour are de Waard, J.R., 2003. Barcoding correlated traits in male mosquitofish animal life: Cytochrome c oxidase (Gambusia holbrooki). Proceedings of subunit 1 divergences among closely the Royal Society of London Series B, related species. Proceedings of the 270, 1033-1040. Royal Society B, 270, 96-99. Houde, A.E., 1997. Sex, color, and mate Hebrank, M.R. and Hebrank, J.H., choice in guppies. Princeton: Princeton 1986. The mechanics of fish skin – University Press. lack of an external tendon role in 2 Hulsey, C.D., Hendrickson, D.A. and teleosts. Biological Bulletin, 171(1), García de León, F.J., 2005. Trophic 236-247. morphology, feeding performance and Helfman, G.S., Collette, B.B., Facey, prey use in the polymorphic fish D.E. and Bowen, B.W., 2009. The Herichthys minckleyi. Evolutionary diversity of fishes: Biology, evolution Ecology Research, 7, 1–22. and ecology. Oxford: Wiley-Blackwell Iwata, A. and Jeon, S.R., 1995. Publishing. Descriptions of Cephalic Canals of Hemmer-Hansen, J., Therkildsen, N.O. Lophiogobius ocellicauda. Japanese and Pujolar, J.M., 2014. Population Journal of Ichthyology, 42, 329-333. Genomics of Marine Fishes: Next- Jeffery, W.R., 2006. Regressive Generation Prospects and Challenges. evolution of pigmentation in the Biological Bulletin, 227, 117-132. 87 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

cavefish Astyanax. Israel Journal Assignment of RAPD Markers to of Ecology & Evolution, 52, 405-422. Multipoint Linkage Groups. Marine Jinbo, U., Kato, T. and Ito, M., 2011. Biotechnology, 5, 279-293. Current progress in DNA barcoding Khoo, G., Lim, T.M. and Phang, and future implications for V.P.E., 2011. A Review of PCR-Based entomology. Entomological Science, DNA Fingerprinting Using Arbitrary 14(2), 107-124. Primers in Tropical Ornamental Fishes Jorge, F., Perera, A., Rocas, V., of South East Asia. Journal of Carretero, M.A., Harris, D.J. and Advanced Medical Research, 1, 71-93. Poulin, R., 2014. Evolution of Khoo, G., Lim, T.M. and Phang, alternative male morphotypes in V.P.E., 2012. Ultrastructure of oxyurid nematodes: A case of erythrophores and xanthophores of the convergence? Journal of Evolutionary Siamese Fighting Fish, Betta Biology, 27, 1631-1643. splendens. The Israeli Journal of Kajishima, T., 1977. Genetic And Aquaculture, 64, 1-7. Developmental Analysis Of Some New Khoo, G., Lim, T.M. and Phang, Color Mutants In The Goldfish, V.P.E., 2014. Cellular basis of metallic Carassius Auratus. Genetics, 86, 161- iridescence in the Siamese fighting 174. fish, Betta splendens. The Israeli Kapoor, V.C., 1998. Principles and Journal of Aquaculture, 66, 1-10. practices of animal taxonomy. Science Khoo, G., Loh, E.Y.F, Lim, T.M. and Publishers. Phang, V.P.E., 1997. Genetic Kawase, S. and Hosoya, K., 2015. variation in different varieties of Pseudorasbora pugnax, a new species Siamese fighting fish using isoelectric of minnow from Japan, and focusing of sarcoplasmic proteins. redescription of P. pumila (Teleostei: Aquaculture International, 5, 537-549. Cyprinidae). Ichthyology Exploration Kimura, M., 1968. Evolutionary rate at of Freshwaters, 25(4), 289-298. the molecular level. Nature, 624-626. Khodadoust, D., Ismail, A., Zulkifli, Koken, E., 1884. Über Fisch-Otolithen, S.Z. and Tayefeh, F.H., 2013. Short insbesondere u ber diejenigen der Time Effect of Cadmium on Juveniles norddeutschen Oligocän- and Adults of Java Medaka (Oryzias Ablagerungen. Zeitschrift der javanicus) Fish as a Bioindicator for deutschen Geologischen Gesellschaft, Ecotoxicological. Life Science Journal, 36, 500-565. 10(1), 1857-1861. Kottelat, M., 2013. The Fishes of the Khoo, G., Lim, M.H., Suresh, H., Gan, Inland Waters of Southeast Asia: A D.K.Y., Lim, K.F., Chen, F., Chan, Catalogue and Core Bibliography of W.K., Lim, T.M. and Phang, V.P.E., the Fishes Known to Occur in 2003. Genetic Linkage Maps of the Freshwaters, Mangroves and Estuaries. Guppy (Poecilia reticulata): Journal of Survey in Fisheries Sciences 4(1) 2017 88

The Raffles Bulletin of Zoology, 27, 1- 2008. Global diversity of fish (Pisces) 663. in freshwater. Hydrobiologia, 595, Krell, F.T. and Wheeler, Q.D., 2014. 545-567. Specimen collection: Plan for the Lewand, K.O., Hyde, J.R., Buonaccorsi, future. Science, 344, 815-816. V.P. and Lea, R.N., 2013. Orange Kress, J.W., Garcia-Robledo C., coloration in a black-and-yellow Uriarte M., and Erickson, D.L., rockfish (Sebastes chrysomelas) from 2015. DNA barcodes for ecology, central California. California Fish and evolution, and conservation. Trends in Game, 99(4), 237-239. Ecology and Evolution, 30, 25-35. Lincoln, R., Boxshall, G. and Clark, Krupp, F. and Budd, K., 2009. A new P.A., 1998. A dictionary of Ecology, species of the genus Garra (Teleostei: Evolution and Systematics. Cyprinidae) from Oman. International Cambridge: Cambridge University Journal of Ichthyology, 15(2), 117- Press. 120. Lombarte, A., Chic, Ò., Parisi- Kumar. V. and Hassan, M.A., 2015. Baradad, V., Olivella, R., Piera, J. Methods and Procedures of Sampling, and García-Ladona, E., 2006. A web- Preservation and Identification for Fish based environment from shape analysis Taxonomy Studies. World Journal of of fish otoliths. The AFORO database. Fish and Marine Sciences, 7(2), 105- Scientia Marina, 70, 147-152. 108. Long, J.H., Hale, M.E., McHenry, M.J. Lauder, G.V., Anderson, E.J., and Westneat, M.W., 1996. Functions Tangorra, J. and Madden, P.G.A., of fish skin: flexural stiffness and 2007. Fish biorobotics: kinematics and steady swimming of Longnose gar hydrodynamics of self-propulsion. The Lepisosteus osseus. Journal of Journal of Experimental Biology, 210, Experimental Biology, 199(10), 2139- 2767-2780. 2151. Leal, M.E., Schulz, U.H., Albornoz, MacArthur, R.H., 1969. Patterns of P.L., Machado, R., Ott, P.H., 2013. communities in the tropics. Biological First record of partial albinism in two Journal of the Linnean Society, 1, 19- catfish species of genidens 30. (Siluriformes: Ariidae) in an MacLean, M., Breeze, H. and Doherty, estuary of Southern Brazil. P., 2009. Using Fish Harvesters’ Local Brazilian Archives of Biology and Ecological Knowledge (LEK) in Technology, 56, 237- 240. Support of Identifying Ecologically Lechner, W. and Ladich, F., 2010. How and Biologically Significant Areas do albino fish hear? Journal of (EBSAs) on the Offshore Eastern Zoology, 283, 186-192. Scotian Shelf. Oceans and Habitat Leveque, C., Oberdorff, T., Paugy, D., Report 2009. Nova Scotia: Fisheries Stiassny, M.L.J. and Tedesco, P.A., and Oceans Canada. 89 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

Mallet, J., Meyer, A., Nosil, P. and Motomura, H. and Ishikawa, S., 2013. Feder, J.L., 2009. Space, sympatry Fish collection building and procedures and speciation. Journal of manual. The Kagoshima University Evolutionary Biology, 22, 2332-2341. Museum, Kagoshima and the Research Mayr, E., 1942. Principles of Systematic Institute for Humanity andature, Zoology. New York: McGraw-Hill. Kyoto. Mayr, E., 1947. Ecological factors in http://www.museum.kagoshima- speciation. Evolution, 1, 263-288. u.ac.jp/staff/motomura/CollectionMan Mayr, E., 1959. Isolation as an ual_lowres.pdf evolutionary factor. Proceedings of the Nelson, G.J., 1972. Cepahlic sensory American Philosophical Society, 103, canals, pitlines, and the classification 221-230. of esocoid fishes, with notes on McCune, A.R., 1981. Quantitative galaxiids and other teleosts. American description of body form in fishes: Museum Novitates, 2492, 1- 49. Implication for species level taxonomy Nelson, J.S., 2006. Fishes of the World, and ecological influences. Copeia, 4, 4th Edition. New Jersey: John Wiley 897-901. and Sons Inc. Mehinto, A.C., Martyniuk, C.J., Spade, O’Reilly, P. and Wright, J.M., 1995. D.J. and Denslow, N.C., 2012. The evolving technology of DNA Applications of next-generation fingerprinting and its application to sequencing in fish ecotoxicogenomics. fisheries and aquaculture. Journal Frontiers in Genetics, 3, 1-10. of Fish Biology, 47, 29–55. Metz, J.R., Peters, J.M.J and Flik, G., Padilla, D.K. and Williams, S.L., 2004. 2006. Molecular biology and Beyond ballast water: aquarium and physiology of the melanocortin system ornamental trades as sources of in fish: A review. General and invasive species in aquatic ecosystems. Comparative Endocrinology, 148, 150- Frontiers in Ecology and the 162. Environment, 2(3), 131-138. Meyer, C.P. and Paulay, G., 2005. DNA Pandey, V., Nutter, R.C. and Prediger, Barcoding: Error Rates Based on E., 2008. Applied biosystems SOLID Comprehensive Sampling. PLoS system: ligation-based sequencing, In: Biology, 3(12). Next Generation Genome Sequencing: Moncey, V., 2012. Occurrence, Towards Personalized Medicine. distribution and troglomorphisms of Weinheim: Wiley-VCH. subterranean fishes of peninsular India. Parichy, D.M., 2006. Evolution of Danio Current Science, 102(7), 1028-1034. pigment pattern development. Moritz, C. and Cicero, C., 2004. DNA Heredity, 1–11 barcoding: promise and pitfalls. PLoS Partridge, B.L. and Pitcher, T.J., 1979. Biology, 2. The Sensory Basis of Fish Schools: Relative Roles of Lateral Line and Journal of Survey in Fisheries Sciences 4(1) 2017 90

Vision. Journal of Rakshit, A., Paul, A., Bhattacharjee, S., Comparative Physiology, 135, 315- Banik, T., Saran, R., Mandal, B., 325. Poddar, D. and Gangopadhyay, K., Pasco-Viel, E., Charles, C., Chevret, P., 2015. Cytogenetic and molecular Semon, M., Tafforeau, P., Viriot, L. profiling of spotted snake head fish and Laudet, V., 2010. Evolutionary Channa punctatus (Bloch, 1793) from Trends of the Pharyngeal Dentition in three districts (Nadia, Hooghly and Cypriniformes (Actinopterygii: north 24 Parganas) of west Ostariophysi). PLoS ONE, 5(6). Bengal, India. International Journal of Pereira, L.H.G., Hanner, R., Foresti, F. Fisheries and Aquatic Studies, and Oliveira, C., 2013. Can DNA 3(1), 312-319. barcoding accurately discriminate Razin, S. and Rottem, S., 1967. megadiverse Neotropical freshwater Identification of Mycoplasma and fish fauna? BMC Genetics, 14(20), 1- other microorganisms by 14. polyacrylamide-gel electrophoresis of Price, A.C., Cameron, J., Weadick, cell proteins. Journal of Bacteriology, Shim, J. and Rodd, F.H., 2006. 94, 1807-1810. Pigments, Patterns, and Fish Behavior. Regan, C.T., 1910. The Asiatic fishes of Zebrafish, 5(4), 297-307. the family Anabantidae. Proceedings Pyke, G.H. and Ehrlich, P.R., 2010. of the Zoological Society of London, Biological collections and ecological / 767-787. environmental research: A review, Regan, J.D. 1961. Melanism in the some observations and a look to the poecillid fish, Gambusia affinis (Baird future. Biological Reviews, 85(2), 247- and Girard). American Midland 266. Naturalist, 65, 139–143. Quigley, D.T.G. and Wallace, E., 2013. Reum, J.C., Paulsen, C.E., Pietsch, Note first record of leucism in hake T.W. and Parker-Stetter, A.L., 2008. Merluccius merluccius (L.). Bulletin of First Record of An Albino the European Association of Fish Chimaeriform Fish, Hydrolagus Pathologists, 33(3), 97-98. Colliei. Northwestern Naturalist, 89, Quraishia, S.F., Panneerchelvam, S., 60– 62. Zainuddin, Z. and Rashid, N.H.A., Ricklefs, R.E., 2004. A comprehensive 2015. Molecular Characterization of framework for global patterns in Malaysian Marine Fish Species using biodiversity. Ecology Letters, 7, 1-15. Partial Sequence of Mitochondrial Roberts, T.R. and Khaironizam, M.Z., DNA 12S and 16S rRNA Markers. 2008. Trophic Polymorphism in the Sains Malaysiana, 44(8), 1119- Malaysia Fish Neolissochilus Soroides 1123. and other Old World Barbs (Teleostei, Rainboth, J., 1996. Fishes of Cambodian Cyprinidae). Natural History Bulletin Mekong. Rome: FAO. of the Siam Society, 56(1), 25-53. 91 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

Roberts, T.R., 1999. Fishes of the Candida albicans strains. Journal of Cyprinid Genus Tor in The Nam Clinical Microbiology, 41, 552-557. Theun Watershed (Mekong Basin) Of Sanger, F., Nicklen, S. and Coulson Laos, With Description Of A New A.R., 1977. DNA sequencing with Species. Raffles Bulletin of Zoology, chain-terminating inhibitors. 47(1), 225-236. Proceedings of the National Academy Robins, C.R., Bailey, R.M., Bond, C.E., of Sciences, 74(12), 5463-5467. Brooker, J.R., Lachner, E.A., Lea, Sbordoni, V., 2010. Strength and R.N. and Scott, W.B., 1991. Common Limitations of DNA Barcode under the and scientific names of fishes from the Multidimensional Species Perspective. United States and Canada, 5th edition. Tools for Identifying Biodiversity: American Fisheries Society Special Progress and Problems, 275-280. Publication No. 20. Schander, C. and Halanych, K., 2003. Rocha, L.A. et al. (120 co-authors), DNA, PCR and formalinized animal 2014. Specimen collection: An tissue - A short review and protocols. essential tool. Science, 344, 814-815. Organisms Diversity & Ross, H.A., Murugan, S. and Li, Evolution, 3(3), 195-205. W.L.S., 2008. Testing the Reliability Shiozawa, D.K., Kudo, J., Evans, R.P., of Genetic Methods of Species Woodward, S.R. and Williams, R.N., Identification via Simulation. 1992. DNA extraction from preserved Systematic Biology, 57(2), 216–230. trout tissues. Great Basin Naturalist, Rothberg, J. and Leamon, J., 2008. The 5(1), 29-34. development and impact of 454 Silfvergrip, A.M.C., 2009. CITES sequencing. Nature Identification Guide to the Freshwater Biotechnology, 26(10), 1117-1124. eels (Anguillidae). Swedish Museum Rudkowska, I., Marcotte, B., Pilon, G., of Natural History, Swedish Lavigne, C., Marette, A. and Vohl, Environmental Protection Agency. M.C., 2010. Physiological Genomics, Simonov, V.M., 2008. An approach for 40(3), 189-194. genetic fish groups identification using Salimi, N., Loh, K.H., Dhillon, S.K. and adaptability and characteristics of Chong, V.C.. 2016. Fully-automated morphotype. Bulgarian Journal of identification of fish species based on Agricultural Science, 14(2), 145-149. otolith contour: using short-time Simpson, G.G., 1951. The species Fourier transform and discriminant concept. Evolution, 5, 285-298. analysis (STFT-DA). Peer J, 1-15. Singh, B.N, 2012. Concepts of species Sampaio, P., Gusmao, L., Alves, C., and modes of speciation. Current Pina-Vaz, C., Amorim, A. and Pais, Science, 103(7), 784-790. C., 2003. Highly polymorphic Slavík, O., Horký, P. and microsatellite for identification of Wackermannová, M., 2016. How does agonistic behaviour differ in Journal of Survey in Fisheries Sciences 4(1) 2017 92

albino and pigmented fish? Peer J, 4, Mechanical Systems Machine Elements e1937. and Manufacturing, 45(4), 1100- Smith, H.M., 1945. The freshwater fishes 1105. of Siam or Thailand. Bulletin of the Sugeha, H. and Suharti, S., 2009. United States Natural Museum, 188, 1- Discrimination and Distribution of 622. Two Tropical Short-Finned Eels Smith, L.M. and Burgoyne, L.A., 2004. (Anguilla bicolor bicolor and Anguilla Collecting, archiving and processing bicolor pacifica) in the DNA from wildlife samples using IndonesianWaters. Publications of the FTA(R) databasing paper. BMC Seto Marine Biological Laboratory, 9, Ecology, 2004, 4(4), 1-11. 1-14. Sowersby, W., Lehtonen, T.K. and Taberlet P., Coissac E., Pompanon F., Wong, B.B.M., 2014. Background Brochmann C., Willerslev E., 2012. matching ability and the maintenance Towards next-generation biodiversity of a colour polymorphism in the red assessment using DNA metabarcoding. devil cichlid. Journal of Evolutionary Molecular Ecology, 21, 2045-2050. Biology, 1-8. Teletchea, F., 2009. Molecular Stacey, N., Karam, J., Dwyer, D., identification methods of fish species: Speed, C. and Meekan, M., 2008. Reassessment and possible Assessing Traditional Ecological applications. Reviews in Fish Knowledge of Whale Sharks Biology and Fisheries, 19, 265–293. (Rhincodon typus) in eastern Teng, H.Y., Lin, Y.S. and Tzeng, C.S., Indonesia: A pilot study with fishing 2009. A new anguilla species and a communities in Nusa Tenggara Timur. reanalysis of the phylogeny of Canberra: Charles Darwin University. freshwater eels. Zoological Studies, Stepien, C. and Kocher, T.D., 1997. 48(6), 808-822. Molecular systematics of fish: Chapter Termvidchakorn, A. and Hortle, K.G., 1, Molecules and morphology in 2013. A guide to larvae and juveniles studies of fish evolution. Academic of some common fish species from the Press. Mekong River Basin. MRC Technical https://www.utoledo.edu/nsm/lec/pdfs/ Paper No. 38. Phnom Penh: Mekong moschp1.pdf River Commission. Strauss, R.E. and Bookstein, F.L., 1982. Thuy, T.T., Hau, T.D., Nguyen, T.T.D. The Truss: Body Form Reconstructions and Thanh, T.T., 2015. Diversity of In Morphometrics. Systematic Zoology, otolith morphology in Nuchequula 31(2), 113-135. nuchalis (Temminck and Schlegel, Sudo, S., Tsuyuki, K., Ito, Y. and 1845) larvae and juvenilles collected Ikohagi, T., 2002. A study on the in the Tien Yen Estuary, Northern surface shape of fish scales. JSME Vietnam. Tropical Natural International Journal Series C – History, 15(1), 69-79. 93 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

Tillmar, A.O., Dell'Amico, B., barcoding and the need for integrative Welander J, and Holmlund, G., taxonomy. Systematic Biology, 54(5), 2013. A universal method for species 844-851. identification of mammals utilizing Wilson, E.O., 1985. Time to revive next generation sequencing for the systematics. Science, 230. analysis of DNA mixtures. PLoS ONE, Wong, L.L., Peatman, E., Lu, J., 8(12), e83761. Kucuktas, H., He, S., Zhou, C.J., Turelli, M., Barton, N.H. and Coyne, J. Nanakorn, U. and Liu, Z.J., 2011. A., 2001. Theory and speciation. DNA barcoding of catfish: Species Trends in Ecology and Evolution, authentication and phylogenetic 16(7), 330-343. assessment. PLoS ONE, 6(3), e17812. Van der Laan, R., Eschmeyer, W.N. Wong, P.B.Y, Wiley, E.O., Johnson, and Fricke, R., 2014. Family-group W.E., Ryder, O.A., Brien, S.J.O, names of Recent fishes. Zootaxa, Haussler, D., Koepfli, K.P., Houck, 3882(2), 1-230. M.L., Perelman, P., Mastromonaco, Van Grouw, H., 2006. Not every white G., Bentley, A.C., Venkatesh, B., bird is an albino: Sense and nonsense Zhang, Y.P., Murphy, R.W. and about colour aberrations in birds. G10KCOS, 2012. Tissue sampling Dutch Birding, 28, 79–89. methods methods and standards for Wägele, J.W., 2005. Foundations of vertebrate genomics. GigaScience, 1, phylogenetic systematics. Verlag Dr. 8. Friedrich Pfeil. München: Germany. Wright, S., Gray, R.D. and Gardner, Walsh, S.J. and Chakrabarty, P., 2015. R.C., 2003. Energy and the rate of A new genus and species of blind evolution: inferences from plant rDNA sleeper (Teleostei: Eleotridae) from substitution rates in the western Oaxaca, Mexico: First Obligate Cave Pacific. Evolution, 57, 2893-2898. Gobiiform in the Western Hemisphere. Yedier, S., Kontaş, S., Bostanc, D. and Copeia, 104(2), 506-517. Polat, N., 2016. Otolith and scale Waugh, J., 2007. DNA barcoding in morphologies of doctor fish (Garra animal species: Progress, potential and rufa) inhabiting Kangal Balıklı Çermik pitfalls. BioEssays, 29, 188-197. thermal spring (Sivas, Turkey). Iranian Weber, M. and de Beaufort, L.F., 1916. Journal of Fisheries Sciences, 15(4), The fishes of the Indo-Australian 1593-1608. Archipelago. Leiden: E.J. Brill. Wheeler, Q.D., Raven, P.H. and Wilson, E.O. 2004. Taxonomy: Impediment or expedient? Science, 303 (5656), 285. Will, K.W., Mishler, B.D. and Wheeler, Q.D., 2005. The perils of DNA