Taxonomy Of Fishes Research Articles (Page 3)

Osteological features are important to study the taxonomy and phylogenetic relationship of fishes. Since there is no information is available about osteological features of Squalius orientalis , therefore this study was aimed to provide a detailed description of the osteological features of this species from the Urmia lake basin of Iran and comparing it with population of S. orientalis from the Caspian Sea basin. For this purpose, the specimens were collected from Zarineh River of the Urmia lake basin and cleared and stained with alizarin red S and alcian blue for osteological examinations. Finally, a detailed osteological features of this species was provided and compared with those of the Caspian Sea basin. Based on the results, having a longer pre-vomer, dorsally oriented parasphenoid alar, longer ventral blade-shaped process of the orbitosphenoid, concaved masticatory plate, pointed ascending process of the palatine, concaved posterior margin of the opercle, and a small posterior process of the cleithrum can differentiate S. orientalis of the Urmia Lake basin from those of the Caspian Sea basin. In addition, the observed osteological difference suggest that both studied populations belong to same taxon.

Accessing the taxonomy of fish is a basic condition for the conservation of species, and the understanding of their evolutionary relationships. Many Neotropical species of fishes of the order Characiformes are considered incertae sedis because of a lack of consistent evidence of monophyly, with the genus Astyanax among them. With a cytotaxonomic and evolutionary purpose, we compared the karyotype of two species of Astyanax: Astyanax paranae and Astyanax elachylepis. Conventional cytogenetic analyses revealed 2n = 50 chromosomes for the two species, with interspecific and interpopulation karyotype variations. Heterochromatin was primarily localized in the pericentromeric regions, and it was associated with organized regions of the nucleolus (NORs) and/or telomeric regions in some acrocentric chromosomes. The in situ localization of 18S ribosomal DNA (rDNA) and 5S probes varied among A. paranae populations. In A. elachylepis, only one chromosome pair was stained by the 18S probe and another by the 5S probe, confirming a simple NORs pattern. These results support the utility of chromosome markers in Astyanax taxonomy and reveal the conserved characteristics of the karyotype of A. elachylepis, consisting exclusively of two chromosome arms, and the occurrence of simple homologous and non-syntenic sites for 18S and 5S rDNA in this species.

book reviews ISSN 1948-6596 Lots of good fish in the sea Fishes: A Guide To Their Diversity. Philip A. Hastings, Harold Jack Walker Jr. and Grantly R. Gal- land, 2014, University of California Press. 336pp. £24.95 (Paperback) / $34.99 (eBook) ISBN: 9780520283534 / 9780520959330; http://www.ucpress.edu/ There is a range of excellent guide books out there for the budding non-academic ichthyologist, young student and more wizened academic. The majority however have been developed as field guides, with excellent colour photographs of the species in their natural habitat (where available) or at least with an apt description of their ecology. Hastings et al’s ‘Fishes A Guide to their Diversity’ is different, and has been developed for those stu- dents (and lecturers) that are interested in devel- oping their knowledge of the morphology and tax- onomy of fishes. In this respect, this book is an excellent and exceptionally accessible part of the ‘toolbox of taxonomists’ (Pante et al 2015). A new student in taxonomy (or any new graduate student of ichthyology and morphology), will find a wealth of vital information on how to accurately describe and compare the various mor- phological characteristics that synonymise differ- ent families of fishes. For beginners, however, I would argue that there is utility in using this guide in conjunction with a well-illustrated field guide to provide a full sense of the major colour patterns that help to identify fish groups. More experienced graduate student and early academics can use it a stepping stone to fur- ther their knowledge of the higher level taxonomy of fishes. In this respect, this was the first time I have seen the full oral and pharyngeal morpholo- gy of different fishes provided, which makes this is an excellent resource for examining the morphol- ogy of fishes by way of dissection. The book also makes excellent use of x-rays, with a range of full fish skeletons provided. While this guide may not provide a substan- tial amount of new information for the senior ich- thyologist, Hastings et al have included a much higher diversity of fishes than is usually encom- passed within a guide book. The sheer diversity of deep water fishes, as well as descriptions and pic- tures of several obscure groups that are found in very specific habitats, makes this guide a useful jumping off point for further research into such taxa. While not shying away from using taxonom- ic language, the authors have provided excellent descriptions of each term, as well as clear pictures to illustrate where necessary. In this respect I found the book exceedingly useful – I remember being a young scientist starting out examining the morphology and ecology of small tripterygiid fish- es in New Zealand and spending weeks searching obscure papers to compile a valid list of morpho- logical characteristics (including internal bony structures) that could be used to compare be- tween highly similar species. The authors done the work for us in this guidebook, providing an exten- sive array of morphological characters that can be usefully and easily utilised to compare the mor- phology of different fish species. This book remains strictly within the con- fines of describing the adult form of all fishes listed. There would have been value in also illus- trating and describing the body form, morphology and distinguishing characteristics of the juvenile and larval phases of all the fishes listed. I under- stand why the authors have chosen to restrict themselves to the adult life stage; juveniles have been woefully under-described, and are logistical- ly harder to capture and curate (the same prob- lems also manifest in curating and describing the larval forms of fishes). However, a guide to the diversity of fishes is lacking if it does not provide some description of their non-adult forms. Indeed, it is the larval stage on which the vast majority of research on tropical and temperate fishes has been focused, especially when attempting to un- derstand the connectivity and dispersal of popula- tions. There is an acknowledged dearth of new, well trained and enthusiastic morphologists who can provide the necessary balance to the over- whelmingly use of molecular methods being used to determine the evolutionary relationships of frontiers of biogeography 7.3, 2015 — © 2015 the authors; journal compilation © 2015 The International Biogeography Society

Yellowfin tuna (Thunnus albacares) is one of the most important economic fishes around the world. In the present study, we determined the complete mitochondrial DNA sequence and organization of T. albacares. The entire mitochondrial genome is a circular-molecule of 16,528 bp in length, which encodes 37 genes in all. These genes comprise 13 protein-coding genes (ATP6 and 8, COI-III, Cytb, ND1-6 and 4 L), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (12S and 16S rRNAs). The complete mitochondrial genome sequence of T. albacares can provide basic information for the studies on molecular taxonomy and conservation genetics of teleost fishes.

When the first Indo-Pacific Fish Conference (IPFC1) was held in Sydney in 1981, there were still many problems in the generic- and species-level taxonomy of all tetraodontiform families except for the recently reviewed Triacanthodidae and Triacanthidae. The period from IPFC1 to IPFC9 (1981−2013) was a time of great progress in the taxonomy and systematics of the Tetraodontiformes: many review and revisional papers have been published for various genera and species, with descriptions of many new taxa occurring mainly on coral reefs and in tropical freshwaters; and cladistic analyses of morphological characters have been performed to clarify phylogenetic relationships of various families and molecular analyses have greatly progressed to provide detailed phylogenetic relationships of families, genera, and even species. The purpose of this paper is to provide a review on developments in the taxonomy and systematics of the Tetraodontiformes, focusing primarily on contributions since 1980 (when James C. Tyler’s monumental work was published) through the period of IPFCs, including pertinent publications before 1980. This paper recognizes 412 extant species in the 10 families of living Tetraodontiformes, with the allocation of species and genera as follows: Triacanthodidae including 23 species in 11 genera, Triacanthidae seven species in four genera, Balistidae 37 species in 12 genera, Monacanthidae 102 species in 27 genera, Aracanidae 13 species in six genera, Ostraciidae 22 species in five genera, Triodontidae monotypic, Tetraodontidae 184 species in 27 genera, Diodontidae 18 species in seven genera, and Molidae five species in three genera. Phylogenetic relationships of the families have been clarified by morphological and molecular analyses and have provided well-supported sister relationships of the families: Triacanthodidae and Triacanthidae, Balistidae and Monacanthidae, and Tetraodontidae and Diodontidae. However, there remain problems with the phylogenetic positions of the Triodontidae and Molidae due to conflicts of differing positions in morphological and molecular studies (e.g., Molidae has been placed differently among molecular studies).

Assessing the taxonomy of fish is important to manage fish populations, regulate fisheries, and remove the exotic invasive species. Automating this process saves valuable resources of time, money, and manpower. Current methods for automatic fish monitoring rely on a human expert to design features necessary for classifying fish into a taxonomy. This paper describes a method using evolution-constructed (ECO) features to automatically find features that can be used to classify fish species. Rather than relying on human experts to build feature sets to tune their parameters, our method uses simulated evolution to construct series of transforms that convert the input signal of raw pixels of fish images into high-quality features or features that are often overlooked by humans. The effectiveness of ECO features is shown on a dataset of four fish species where using fivefold cross validation an average classification rate of 99.4 % is achieved. Although we use four fish species to prove the feasibility, this method can be easily adapted to new fauna and circumstances.

This paper reviews progress in research on taxonomy and systematics of larval marine and estuarine fishes in the Indo-Pacific since the first Indo-Pacific Fish Conference in 1981. In 1981, the literature on development of fish larvae in the vast Indo-Pacific region was sparse, scattered and of very uneven quality. During the intervening 33 years, taxonomy of adult Indo-Pacific fishes has improved greatly, the proceedings of the landmark Ahlstrom Symposium were published, a large number of larval-fish atlases, or identification guides, have been produced, and the quality of descriptions of larval-fish development in journals has greatly increased. This has resulted in a great improvement in our ability to identify Indo-Pacific fish larvae, particularly oceanic taxa. However, much remains to be done, with the large majority of families having <50 % of species with described larvae, and with only a small proportion of species descriptions based on full developmental series of larvae. DNA technology has helped to establish identities of larvae, but only a small proportion of the larvae so identified have been described, so the potential for DNA to advance larval taxonomy is largely untapped. An integrative approach combining genetics and morphology is required. Online publication of descriptions of larval development and of interactive identification guides to larvae is the most efficient way to make such information available and useful to a variety of users. The great potential for larval-fish ontogeny to contribute to the study of phylogeny of marine fishes has been underrealized. The ageing of current larval-fish taxonomists, and the lack of positions for younger replacement researchers, is a major obstacle to further progress.

Mitofish is a database of fish mitochondrial genomes (mitogenomes) that includes powerful and precise de novo annotations for mitogenome sequences. Fish occupy an important position in the evolution of vertebrates and the ecology of the hydrosphere, and mitogenomic sequence data have served as a rich source of information for resolving fish phylogenies and identifying new fish species. The importance of a mitogenomic database continues to grow at a rapid pace as massive amounts of mitogenomic data are generated with the advent of new sequencing technologies. A severe bottleneck seems likely to occur with regard to mitogenome annotation because of the overwhelming pace of data accumulation and the intrinsic difficulties in annotating sequences with degenerating transfer RNA structures, divergent start/stop codons of the coding elements, and the overlapping of adjacent elements. To ease this data backlog, we developed an annotation pipeline named MitoAnnotator. MitoAnnotator automatically annotates a fish mitogenome with a high degree of accuracy in approximately 5 min; thus, it is readily applicable to data sets of dozens of sequences. MitoFish also contains re-annotations of previously sequenced fish mitogenomes, enabling researchers to refer to them when they find annotations that are likely to be erroneous or while conducting comparative mitogenomic analyses. For users who need more information on the taxonomy, habitats, phenotypes, or life cycles of fish, MitoFish provides links to related databases. MitoFish and MitoAnnotator are freely available at http://mitofish.aori.u-tokyo.ac.jp/ (last accessed August 28, 2013); all of the data can be batch downloaded, and the annotation pipeline can be used via a web interface.

We reviewed the taxonomy and systematics research history of freshwater fish in China based on 1 236 taxonomic literature records on Chinese freshwater fish. The research was divided into five research periods according to specific historical events: (1) period by foreign scholars, (2) period with Chinese scholars, (3) period during World War II and Civil War, (4) recovery period and (5) period of rapid development. There were representative studies and innovations in all periods. We also discuss here the characteristics of each period on the basis of literature analysis.

Three new species of Cobitis, C. fasciola sp. nov., C. crassicauda sp. nov. and C. stenocauda sp. nov. are found from the River Xinjiang and the River Le'anjiang, tributaries of Lake Poyang, belonging to the River Yangtze system, Jiangxi Province, China. These cobitid fish are described based on the morphology features such as the pigmentation pattern, shape of lamina circularis, body scales, mouth character and sequences of mitochondrial cytochrome b (cyt b) gene, which can be used for molecular identification and diagnosis of these species. Illustrations of the morphology characters of new species are given, and phylogenetic analysis identifies deoxyribonucleic acid (DNA) lineages closely related to these cobitid fish. Traditional taxonomy of cobitid fish of the subfamily Cobitinae is discussed based on the recent molecular phylogenies of these cobitid fish.

This article investigates the folk taxonomy of four artisanal fisheries communities in Ilhabela/SP. The local folk taxonomy shows how these fishermen identify, name and classify fish resources in the environment exploited by them. Forty-two fishermen from four different local communities of Ilhabela were interviewed through a structured questionnaire and photographs of fish species with occurrence for the southeast region of Brazil. Respondents identified the 24 species listed as 50 generic names and 27 binominal specific names, mainly related to aspects of fish species morphology such as color, shape and size. These fish were classified into eight groups according to local criteria related to the morphology, ecology and fishing forms associated with the capture of species. The morphological aspect was identified as the most used feature by respondents to name and classify local fish, followed by ecological aspects such as behavior, diet and habitat. The comparison of local criteria used for the groups was similar to the scientific taxonomy criteria, showing a detailed local ecological knowledge by this group of fishers.

The taxonomy of deep-sea fishes of India was pioneered by the outstanding works of A.W. Alcock, based on the samples collected during the voyage of the Indian marine survey steamer, HMS ‘Investigator’. Alcock’s publications (1889–1907) are the major detailed work on the deep-sea fauna of Indian waters. Recent studies on deep-sea fishes from the Indian exclusive economic zone has resulted in the description of many new species and new records from Indian waters (Oommen, 1978; Sajeevan et al., 2009; Akhilesh et al., 2010; Bineesh et al., 2010; Kurup et al., 2010; Anderson & Bineesh, 2011).

Up to the present, the genus Leptostichaeus has been considered as belonging to subfamily Lumpeninae. A series of characters was analyzed for family and subfamily diagnostics within the group Stichaeidae. It was found that, in combination of all examined characters, the genus Leptostichaeus is either similar to Azygopterus or occupies an intermediate position between the latter and other members of the family Stichaeidae. The genus Leptostichaeus is transferred into the group Azygopterinae, which is revalidated as a subfamily within the family Stichaeidae.

Taxonomic clarity is a fundamental requirement as it forms the foundation of all other life sciences. In the last decade, chondrichthyan taxonomy has undergone a scientific renaissance with >180 new species formally described. This effort encompasses c. 15% of the global chondrichthyan fauna, which consists of 1185 currently recognized species. The important role of chondrichthyan taxonomy for conservation management has been highlighted in recent years with new species descriptions or taxonomic resolution of a number of threatened species. These include Australian gulper (genus Centrophorus) and speartooth sharks (genus Glyphis) in coastal waters of Australia and Borneo. Closer examination of other wide-ranging species, for which the taxonomy was thought to be stable, has shown that they consist of species complexes, e.g. manta rays (Manta spp.) and spotted eagle rays (the Aetobatus narinari complex), and highlights the need for critical re-examination of other wide-ranging species. Molecular methods have provided another useful tool to taxonomists and they have proven to assist greatly with identifying cryptic species and species complexes. The limitations of particular molecular methods being used need, however, to be carefully considered and there are some concerns about how these are being integrated with classical taxonomy. The fundamental importance of taxonomic nomenclature to life sciences is often poorly understood but striving for nomenclatural stability is a critical component of taxonomy. Similarly, biological collections are an extremely vital asset to both taxonomists and the broader scientific community. These collections are becoming increasingly important due in part to molecular species identification initiatives such as the Barcode of Life which has resulted in a large number of voucher specimens linked to tissue samples being deposited. Biological collections are also proving to be imperative in biodiversity studies as they contain a 'gold mine' of historical collection information important for assessing changes in faunal assemblages. Resources are typically limited for taxonomic research and the ageing taxonomic community is another issue of concern for the future of taxonomy on this important group. Succession planning and better resource allocation will be essential to ensure that this fundamental discipline is maintained into the future.

The systematics and taxonomy of poeciliid fishes (guppies and allies) remain poorly understood despite the relative importance of these species as model systems in the biological sciences. This study focuses on testing the monophyly of the nominal poeciliine tribe Heterandriini and the genus Heterandria, through examination of the morphological characters on which the current classification is based. These characters include aspects of body shape (morphometrics), scale and fin-ray counts (meristics), pigmentation, the cephalic laterosensory system, and osteological features of the neurocranium, oral jaws and suspensorium, branchial basket, pectoral girdle, and the gonopodium and its supports. A Maximum Parsimony analysis was conducted of 150 characters coded for 56 poeciliid and outgroup species, including 22 of 45 heterandriin species (from the accounted in Parenti &amp; Rauchenberger, 1989), or seven of nine heterandriin species (from the accounted in Lucinda &amp; Reis, 2005). Multistate characters were analyzed as both unordered and ordered, and iterative a posteriori weighting was used to improve tree resolution. Tree topologies obtained from these analyses support the monophyly of the Middle American species of "Heterandria," which based on available phylogenetic information, are herein reassigned to the genus Pseudoxiphophorus. None of the characters used in previous studies to characterize the nominal taxon Heterandriini are found to be unambiguously diagnostic. Some of these characters are shared with species in other poeciliid tribes, and others are reversed within the Heterandriini. These results support the hypothesis that Pseudoxiphophorus is monophyletic, and that this clade is not the closest relative of H. formosa (the type species) from southeastern North America. Available morphological data are not sufficient to assess the phylogenetic relationships of H. formosa with respect to other members of the Heterandriini. The results further suggest that most tribe-level taxa of the Poeciliinae are not monophyletic, and that further work remains to resolve the evolutionary relationships of this group.

With the goal of contributing to the taxonomy and systematics of the Neotropical cichlid fishes of the genus Symphysodon, we analyzed 336 individuals from 24 localities throughout the entire distributional range of the genus. We analyzed variation at 13 nuclear microsatellite markers, and subjected the data to Bayesian analysis of genetic structure. The results indicate that Symphysodon is composed of four genetic groups: group PURPLE—phenotype Heckel and abacaxi; group GREEN—phenotype green; group RED—phenotype blue and brown; and group PINK—populations of Xingú and Cametá. Although the phenotypes blue and brown are predominantly biological group RED, they also have substantial contributions from other biological groups, and the patterns of admixture of the two phenotypes are different. The two phenotypes are further characterized by distinct and divergent mtDNA haplotype groups, and show differences in mean habitat use measured as pH and conductivity. Differences in mean habitat use is also observed between most other biological groups. We therefore conclude that Symphysodon comprises five evolutionary significant units: Symphysodon discus (Heckel and abacaxi phenotypes), S. aequifasciatus (brown phenotype), S. tarzoo (green phenotype), Symphysodon sp. 1 (blue phenotype) and Symphysodon sp. 2 (Xingú group).

Robert (Bob) McDowall died in Christchurch, New Zealand on 20 February 2011 after a short illness. Bob was a widely published author and an acknowledged world authority on the taxonomy and biogeography of freshwater fishes. In a preface to Bob’s recent magnum opus on the osteology of the galaxiids and allied genera (McDowall and Burridge 2011), the series editor, Peter Bartsch called him “a complete zoologist” and listed his knowledge and experience ranged from “taxonomy, biogeography and systematics to reproductive biology, behaviour, ecology, evolution, fisheries and conservation biology”. So, how did this talented and productive fisheries scientist come to acquire a profound knowledge of not only the freshwater fish fauna of New Zealand but of the southern hemisphere? Bob was born on 15 September 1939 in Palmerston North in 1939, the second youngest in a family of five. Bob attended Victoria University of Wellington (1958–62), completing an M. Sc. in zoology. As a young scientist, Bob recognised he had available to him a virtually unstudied fish fauna, the native freshwater fishes of New Zealand. The fauna is sparse (~ 40 species) and characterised by a high degree of diadromy. Bob soon realised that this fauna offered an opportunity to “explore pattern and process, cause and effect, evolution and biogeography, in a way that would have been much more difficult in areas with more speciose faunas” (McDowall 2010). One of the earliest papers he wrote on the origins of the New Zealand freshwater fish fauna (McDowall 1964) was probably instrumental in his gaining the opportunity to study at the Museum of Comparative Zoology, Harvard University USA (1965–68) where he was exposed to the teachings of the likes of Ernst Mayr, P J Darlington, Giles Mead, Alfred Romer and other luminaries of that era. His Ph. D. was on the systematics and phylogeny of the New Zealand galaxiids. The family Galaxiidae comprises a group of southern hemisphere fishes whose wide geographic range and the diversity of habitats they have colonised are somewhat akin to the northern hemisphere salmonids. The galaxiids were destined to become a major research focus for Bob. Upon completion of his doctorate and return to New Zealand, Bob was instructed to commence research on the diet of brown trout, Salmo trutta, something he regarded of much lesser importance than understanding the ecology of native species. With a dogmatism that often characterised his dealings with authority, he ignored this directive and established an extensive field Environ Biol Fish DOI 10.1007/s10641-011-9877-0

Wiley et al. (2011) begin their critique of our paper (Mooi &amp; Gill, 2010) with an assertion: “we need to make itclear that the foundation of their arguments rests not on scientific rigor, but rather on opinions about the re-classification of fishes using molecular data. This bias is the reason that they only targeted researchers who proposed changes in the higher-level taxonomy of fishes using phylogenetic hypotheses based on DNA sequence data (Miya et al. 2007, Smith &amp; Craig 2007, Thacker 2009). In criticizing these studies, they do not suggest any alternative relationships or provide any counter evidence to the proposed relationships.” And on page 8, they apparently read our thoughts (aside from the title, none of the words in quotations was written by us in that context) and concluded: “Mooi &amp; Gill entitled their paper “A crisis in fish systematics” because they long for the days when “real” ichthyologists found “meaningful” characters and “true” relationships.” Finally (p. 9), they contend that “Mooi &amp; Gill’s various studies are usually focused on Johnson &amp; Patterson’s (1993: 555) “disparate twigs of the [percomorph] tree,” whereas the explicit studies they criticize are large-scale and taxon rich datasets that have not otherwise been analyzed in Percomorpha.”

The Desventuradas Islands (San Felix and San Ambrosio) and Juan Fernandez Archipelago (Robinson Crusoe and Alejandro Selkirk) are oceanic islands of volcanic origin located in the southeastern Pacific off Chile. Based on new material collected since 1997, revision of the R/V Anton Bruun expeditions collections, and a taxonomic update, the coastal fish fauna of Juan Fernandez Archipelago and Desventuradas Islands found a total of 52 species, with 41 and 43 species, respectively. The number of coastal fish species recorded herein as endemic for Juan Fernandez is only five (12,2%) and three species are new records (Gymnothorax cf. obesus, Gnathophis sp., Suezichthys sp). The Desventuradas Islands have only two endemic species (4,6%) and four species are new records (Scorpaenodes englerti, Maxillicosta reticulata, Suezichthys sp., Aseraggodes bahamondei). The reduced number of endemic species for the Juan Fernandez Islands as compared with previous accounts (15 species) is the result that more species were found to be endemic to both islands groups (22 species = 42,3% all coastal fishes), suggesting these two island groups should be considered a single biogeographic unit. The eastern extension of the Indo West Pacific Region to include the Nazca Ridge, Desventuradas and Juan Fernandez Islands is supported herein. The zoogeographical affinities between Desventuradas and western Pacific Islands (Easter Island to Australia), includes 16 species, adding five new species to previous lists. Relationships of three genera indicate a Western Pacific origin with one or more dispersal events to the Desventuradas and Juan Fernandez Islands. Another seven genera, with relatively few species and restricted distribution, may have this same pattern. Only one phylogenetic study indicates a continental origin with a westward dispersal (Odontesthes), however another three genera may have this same pattern of dispersal.

Taxonomy of Small-sized Cichlid Fishes in the Shell-bed Area of Lake Tanganyika