A mitochondrial DNA based phylogeny of weakfish species of the Cynoscion group (Pisces: Sciaenidae)

We infer the phylogeny of fishes in the New World Cynoscion group (Cynoscion, Isopisthus, Macrodon, Atractoscion, Plagioscion) using 1603 bp of DNA sequence data from three mitochondrial genes. With the exception of Plagioscion, whose position was ambiguous, the Cynoscion group is monophyletic. However, several genera examined are not monophyletic. Atlantic and Pacific species of Cynoscion are interspersed in the tree and geminate species pairs are identified. Intergeneric relationships in the group are clarified. Our analysis is the first comprehensive phylogeny for the Cynoscion group based on molecular data and provides a baseline for future comparative studies of this important group.     

Endoskeletal structure in Cheirolepis (Osteichthyes,Actinopterygii), An early ray‐finned fish

As the sister lineage of all other actinopterygians, the Middle to Late Devonian (Eifelian–Frasnian) Cheirolepis occupies a pivotal position in vertebrate phylogeny. Although the dermal skeleton of this taxon has been exhaustively described, very little of its endoskeleton is known, leaving questions of neurocranial and fin evolution in early ray‐finned fishes unresolved. The model for early actinopterygian anatomy has instead been based largely on the Late Devonian (Frasnian) Mimipiscis, preserved in stunning detail from the Gogo Formation of Australia. Here, we present re‐examinations of existing museum specimens through the use of high‐resolution laboratory‐ and synchrotron‐based computed tomography scanning, revealing new details of the neuro‐cranium, hyomandibula and pectoral fin endoskeleton for the Eifelian Cheirolepis trailli. These new data highlight traits considered uncharacteristic of early actinopterygians, including an uninvested dorsal aorta and imperforate propterygium, and corroborate the early divergence of Cheirolepis within actinopterygian phylogeny. These traits represent conspicuous differences between the endoskeletal structure of Cheirolepis and Mimipiscis. Additionally, we describe new aspects of the parasphenoid, vomer and scales, most notably that the scales display peg‐and‐socket articulation and a distinct neck. Collectively, these new data help clarify primitive conditions within ray‐finned fishes, which in turn have important implications for understanding features likely present in the last common ancestor of living osteichthyans.     

GEOGRAPHIC POPULATION STRUCTURE AND SPECIES DIFFERENCES IN MITOCHONDRIAL DNA OF MOUTHBROODING MARINE CATFISHES (ARIIDAE) AND DEMERSAL SPAWNING TOADFISHES (BATRACHOIDIDAE)

Restriction-fragment length polymorphisms in mitochondrial DNA (mtDNA) were used to evaluate population-genetic structure and matriarchal phylogeny in four species of marine fishes that lack a pelagic larval stage: the catfishes Arius felis and Bagre marinus, and the toadfishes Opsanus tau and O. beta. Thirteen informative restriction enzymes were used to assay mtDNAs from 134 specimens collected from Massachusetts to Louisiana. Considerable genotypic diversity was observed in each species. However, major mtDNA phylogenetic assemblages in catfish and toadfish (as identified in Wagner networks and UPGMA phenograms) exhibited contrasting patterns of geographic distribution: in catfish, distinct mtDNA clades were widespread, while such clades in toadfish tended to be geographically localized. By both the criteria of species' ranges and the geographic pattern of intraspecific mtDNA phylogeny, populations of marine catfish in the western Atlantic have had greater historical interconnectedness than have toadfish. Results are also compared to previously published mtDNA data in freshwater and other marine fishes. Although mtDNA differentiation among conspecific populations of continuously distributed marine fishes is usually lower than that among discontinuously distributed freshwater species inhabiting separate drainages, it is apparent that historical biogeographic factors can importantly influence genetic structure in marine as well as freshwater species.     

Developmental Data and Phylogenetic Systematics: Evolution of the Vertebrate Limb

Among the primary contributions of phylogenetic systematicsto the synthesis of developmental biology and evolution arephylogenetic hypotheses. Phylogenetic hypotheses are criticalin interpreting the patterns of evolution of developmental genesand processes, as are morphological data. Using a robust phylogeny,the evolutionary history of individual morphological or developmentalfeatures can be traced and ancestral conditions inferred. Multiplecharacters (e.g., morphological and developmental) can be mappedtogether on the phylogeny, and patterns of character associationcan be quantified and tested for correlation. Using the vertebrate forelimb as an example, I show that bymapping accurate morphological data (homologous skeletal elementsof the vertebrate forelimb) onto a phylogeny, an alternativeinterpretation of Hox gene expression emerges. Teleost fishesand tetrapods may share no homologous skeletal elements in theirforelimbs, and thus similarities and differences in Hox patternsduring limb development must be reinterpreted. Specifically,the presence of the phase III Hox pattern in tetrapods may notbe correlated with digits but rather may simply be the normalexpression pattern of a metapterygium in fishes. This exampleillustrates the rigorous hypotheses that can be developed usingmorphological data and phylogenetic methods. "Creating a general reference system and investigating the relationsthat extend from it to all other possible and necessary systemsin biology is the task of systematics." (Hennig, 1966, p.7)     

The Molecular Evolution of the Vertebrate Trypsinogens

We expand the already large number of known trypsinogen nucleotide and amino acid sequences by presenting additional trypsinogen sequences from the tunicate (Boltenia villosa), the lamprey (Petromyzon marinus), the pufferfish (Fugu rubripes), and the frog (Xenopus laevis). The current array of known trypsinogen sequences now spans the entire vertebrate phylogeny. Phylogenetic analysis is made difficult by the presence of multiple isozymes within species and rates of evolution that vary highly between both species and isozymes. We nevertheless present a Fitch-Margoliash phylogeny constructed from pairwise distances. We employ this phylogeny as a vehicle for speculation on the evolution of the trypsinogen gene family as well as the general modes of evolution of multigene families. Unique attributes of the lamprey and tunicate trypsinogens are noted. Received: 12 July 1997     

Intestinal microbiota composition in fishes is influenced by host ecology and environment

The digestive tracts of vertebrates are colonized by complex assemblages of micro-organisms, collectively called the gut microbiota. Recent studies have revealed important contributions of gut microbiota to vertebrate health and disease, stimulating intense interest in understanding how gut microbial communities are assembled and how they impact host fitness (Sekirov et al. 2010). Although all vertebrates harbour a gut microbiota, current information on microbiota composition and function has been derived primarily from mammals. Comparisons of different mammalian species have revealed intriguing associations between gut microbiota composition and host diet, anatomy and phylogeny (Ley et al. 2008b). However, mammals constitute <10% of all vertebrate species, and it remains unclear whether similar associations exist in more diverse and ancient vertebrate lineages such as fish. In this issue, Sullam et al. (2012) make an important contribution toward identifying factors determining gut microbiota composition in fishes. The authors conducted a detailed meta-analysis of 25 bacterial 16S rRNA gene sequence libraries derived from the intestines of different fish species. To provide a broader context for their analysis, they compared these data sets to a large collection of 16S rRNA gene sequence data sets from diverse free-living and host-associated bacterial communities. Their results suggest that variation in gut microbiota composition in fishes is strongly correlated with species habitat salinity, trophic level and possibly taxonomy. Comparison of data sets from fish intestines and other environments revealed that fish gut microbiota compositions are often similar to those of other animals and contain relatively few free-living environmental bacteria. These results suggest that the gut microbiota composition of fishes is not a simple reflection of the micro-organisms in their local habitat but may result from host-specific selective pressures within the gut (Bevins & Salzman 2011).     

Testing the phylogeny of swordtail fishes using split decomposition and spectral analysis

We examine ways of testing for the reliability of inference from biological sequence data using sequences from Xiphophorus fishes and newly implemented methodology for sequence analysis. The approach we take provides one means to examine the fit between model and data for different sequences and hence to evaluate heterogeneity between data sets. In the case of the present study we show D-loop sequences to be a better molecule for studying the phylogeny of Xiphophorus fishes than cytochrome b sequences. The results of the split decomposition and spectral analysis confirm an earlier phylogenetic hypothesis which had been based on maximum parsimony, neighbor-joining, maximum likelihood analyses. Correspondence to: A. Meyer     

Ceratomyxa (Myxozoa: Bivalvulida): Robust taxon or genus of convenience?

The genus Ceratomyxa (Myxozoa: Myxosporea: Bivalvulida) contains parasites that typically infect the gall bladders of marine teleosts. Species of this genus have also been recorded from elasmobranchs, while the best known species (Ceratomyxa shasta) is a systemic pathogen of fresh water salmonid fishes. Here we characterise 10 new species of Ceratomyxa from marine teleosts using morphometric and rDNA sequence data. A phylogeny of all Ceratomyxa species for which ssrDNA sequence is available was estimated by parsimony, maximum likelihood and Bayesian analyses. Mapping host fish taxonomy, geographic locality and morphology onto the phylogenetic tree provided some concordance of these characters to groups of Ceratomyxa species, but in no case was it consistent throughout the inferred phylogeny. The position of C. shasta as a sister species to the Ceratomyxa clade contradicts previous estimates of marine myxozoan phylogeny which suggested C. shasta was an unrelated lineage. Comparative DNA sequence data is available for more than 17% of some 200 described Ceratomyxa species and the genus now represents one of the most cohesive lineages within the Myxozoa. The independent branching of all atypical Ceratomyxa species and Palliatus indecorus, indicates a review of the diagnostic characters and possible division into more genera is warranted when further data are available.     

Evolution of the facial musculature in basal ray-finned fishes

Background

The facial musculature is a remarkable anatomical complex involved in vital activities of fishes, such as food capture and gill ventilation. The evolution of the facial muscles is largely unknown in most major fish lineages, such as the Actinopterygii. This megadiverse group includes all ray-finned fishes and comprises approximately half of the living vertebrate species. The Polypteriformes, Acipenseriformes, Lepisosteiformes, Amiiformes, Elopiformes, and Hiodontiformes occupy basal positions in the actinopterygian phylogeny and a comparative study of their facial musculature is crucial for understanding the cranial evolution of bony fishes (Osteichthyes) as a whole.

Results

The facial musculature of basal actinopterygians is revised, redescribed, and analyzed under an evolutionary perspective. We identified twenty main muscle components ontogenetically and evolutionarily derived from three primordial muscles. Homologies of these components are clarified and serve as basis for the proposition of a standardized and unifying myological terminology for all ray-finned fishes. The evolutionary changes in the facial musculature are optimized on the osteichthyan tree and several new synapomorphies are identified for its largest clades, including the Actinopterygii, Neopterygii, and Teleostei. Myological data alone ambiguously support the monophyly of the Holostei. A newly identified specialization constitutes the first unequivocal morphological synapomorphy for the Elopiformes. The myological survey additionally allowed a reinterpretation of the homologies of ossifications in the upper jaw of acipenseriforms.

Conclusions

The facial musculature proved to be extremely informative for the higher-level phylogeny of bony fishes. These muscles have undergone remarkable changes during the early radiation of ray-finned fishes, with significant implications for the knowledge of the musculoskeletal evolution of both derived actinopterygians and lobe-finned fishes (Sarcopterygii).

     

Otolith shape lends support to the sensory drive hypothesis in rockfishes

The sensory drive hypothesis proposes that environmental factors affect both signalling dynamics and the evolution of signals and receivers. Sound detection and equilibrium in marine fishes are senses dependent on the sagittae otoliths, whose morphological variability appears intrinsically linked to the environment. The aim of this study was to understand if and which environmental factors could be conditioning the evolution of this sensory structure, therefore lending support to the sensory drive hypothesis. Thus, we analysed the otolith shape of 42 rockfish species (Sebastes spp.) to test the potential associations with the phylogeny, biological (age), ecological (feeding habit and depth distribution) and biogeographical factors. The results showed strong differences in the otolith shapes of some species, noticeably influenced by ecological and biogeographical factors. Moreover, otolith shape was clearly conditioned by phylogeny, but with a strong environmental effect, cautioning about the use of this structure for the systematics of rockfishes or other marine fishes. However, our most relevant finding is that the data supported the sensory drive hypothesis as a force promoting the radiation of the genus Sebastes. This hypothesis holds that adaptive divergence in communication has significant influence relative to other life history traits. It has already been established in Sebastes for visual characters and organs; our results showed that it applies to otolith transformations as well (despite the clear influence of feeding and depth), expanding the scope of the hypothesis to other sensory structures.     

The biogeography and phylogeny of schizothoracine fishes (Schizopygopsis) in the Qinghai‐Tibetan Plateau

Freshwater fish belonging to the genus Schizopygopsis are widespread in drainages throughout the Qinghai‐Tibetan Plateau and, thus, a model group with which to investigate how paleo‐drainage changes linked to historical uplifting within the Qinghai‐Tibetan Plateau influence speciation. To date, the phylogenetic and taxonomic relationships within Schizopygopsis remain controversial. In this study, we constructed a comprehensive molecular phylogeny of Schizopygopsis based on six mitochondrial gene sequences. We compared the taxonomic relationships revealed by this phylogeny with those obtained from morphological data. We also used this phylogeny to assess the extent to which the evolution of Schizopygopsis has been driven by paleo‐drainage changes linked to uplifting of the Qinghai‐Tibetan Plateau. Results indicated that all Schizopygopsis taxa formed a monophyletic group comprising five major clades, which were inconsistent with the taxonomic relationships based on morphology for this group. Our results also strongly supported the validity of S. anteroventris and S. microcephalus as distinct species within Schizopygopsis. Molecular calibrations showed that species within the middle Yangtze species diverged earlier (~4.5 Mya) than species within the Indus River (~3.0 Mya), the Mekong River (~2.8 Mya) and the Tsangpo + Salween rivers (~2.5 Mya). The most recent evolutionary splits occurred among species from the upper and lower Yangtze River, the Yellow River and the Qiadam Basin at about 1.8 to 0.3 Mya. Our molecular evidence and use of the molecular clock calibration have allowed us to associate speciation events within the genus Schizopygopsis to the formation and separation of paleo‐drainage connections caused by tectonic events during the uplifting of the Qinghai‐Tibetan Plateau (~4.5 Mya). This work underlines the dominant role of vicariance in shaping the evolutionary history of the genus Schizopygopsis. Further research using multiple loci and more extensive sampling will reveal a more complete picture of the phylogenetic relationships and biogeography of Schizopygopsis fishes.     

Molecular phylogeny of Potamotrygonocotyle (Monogenea,Monocotylidae) challenges the validity of some of its species

Fehlauer‐Ale, K. H. & Littlewood, D. T. J. (2011). Molecular phylogeny of Potamotrygonocotyle (Monogenea, Monocotylidae) challenges the validity of some of its species. —Zoologica Scripta, 40, 638–658. The marine‐derived stingrays Potamotrygonidae are the only chondrichthyans landlocked to freshwaters of Central and South America. The family includes approximately 22 described species organized in four genera widely distributed across the main Atlantic and Caribbean continental drainages. Investigations into the parasite fauna of potamotrygonids have mainly focused on cestodes, with a few studies addressing the biodiversity of monogeneans. Potamotrygonocotyle (Monogenea, Monocotylidae) is composed of 12 species, exclusively found in the gills of species of Potamotrygonidae. This study presents molecular phylogenetic analyses of this group of monogeneans distributed throughout La Plata and Amazonas basins, with the purpose of readdressing the phylogeny of Monocotylidae based on 28S rDNA sequences and of unravelling the phylogeny of its species using data from mitochondrial gene cytochrome c oxidase subunit I and nuclear gene internal transcribed spacer 1. The phylogenetic status of the five tested monocotylid subfamilies and most of their internal relationships are concordant with the results of a previous study, and the monophyletic status of Potamotrygonocotyle based on molecular data is corroborated for the first time. However, the placement of the genus within Monocotylidae is not resolved, as its sister‐group relationship with Neoheterocotyle and Troglocephalus is uncertain. Investigations into the relationships within Potamotrygonocotyle support the monophyletic status of nine nominal species and suggest the existence of cryptic lineages for the remaining three. Molecular analyses reveal distinct sister‐groups relationships in comparison with a previously published phylogeny for the genus based on morphological data. Finally, the surveys of this study expand the known distribution range of some members of Potamotrygonocotyle.     

Phylogenetic relationships of Middle American cichlids (Cichlidae, Heroini) based on combined evidence from nuclear genes, mtDNA, and morphology

Heroine cichlids are the second largest and very diverse tribe of Neotropical cichlids, and the only cichlid group that inhabits Mesoamerica. The taxonomy of heroines is complex because monophyly of most genera has never been demonstrated, and many species groups are without applicable generic names after their removal from the catch-all genus Cichlasoma (sensu Regan, 1905). Hence, a robust phylogeny for the group is largely wanting. A rather complete heroine phylogeny based on cytb sequence data is available [Concheiro Pérez, G.A., Říčan O., Ortí G., Bermingham, E., Doadrio, I., Zardoya, R. 2007. Phylogeny and biogeography of 91 species of heroine cichlids (Teleostei: Cichlidae) based on sequences of the cytochrome b gene. Mol. Phylogenet. Evol. 43, 91–110], and in the present study, we have added and analyzed independent data sets (nuclear and morphological) to further confirm and strengthen the cytb-phylogenetic hypothesis. We have analyzed a combined cytb-nuclear (RAG1 and two S7 introns) data set of 48 species representing main heroine lineages to achieve further resolution of heroine higher taxonomic levels and a combined cytb-morphological data set of 92 species to stabilize generic taxonomy. The recovered phylogenies supported the circumamazonian—CAM—Heroini (sensu Concheiro Peréz et al., 2007) as a monophyletic group, that could be divided into six main clades: (1) australoheroines (the southernmost heroine genus Australoheros), (2) nandopsines (the Antillean genus Nandopsis), (3) caquetaines (including the north western Amazonian genera Caquetaia and Heroina), (4) astatheroines (including Astatheros, Herotilapia and Rocio), (5) amphilophines (including Amphilophus and related genera), and (6) herichthyines (including Herichthyis and related genera). Nuclear and mitochondrial data partitions arrived at highly congruent topologies. Suprageneric relationships were influenced mainly by the nuclear signal, as well as the most basal phylogenetic position of Australoheros within CAM heroines. The new phylogeny of the tribe Heroini provides robust framework to stabilize the taxonomy of the group and for future comparative studies on these morphologically and ecologically diverse freshwater fishes. Morphology was mostly informative at the genus level and aid in determining the monophyly and composition of heroine genera. Upon acceptance of all putative genera, as recovered in this study, the Heroini would be with 35 genera the most genus-rich clade of Neotropical cichlids.     

Variation in rod spectral sensitivity of fishes is best predicted by habitat and depth

Rod spectral sensitivity data (λ_max), measured by microspectrophotometry, were compiled for 403 species of ray-finned fishes in order to examine four hypothesized predictors of rod spectral sensitivity (depth, habitat, diet and temperature). From this database, a subset of species that were known to be adults and available on a published phylogeny (n = 210) were included in analysis, indicating rod λ_max values averaging 503 nm and ranging from 477 to 541 nm. Linear models that corrected for phylogenetic relatedness showed that variation in rod sensitivity was best predicted by habitat and depth, with shorter wavelength λ_max values occurring in fishes found offshore or in the deep sea. Neither diet, nor the interaction of diet and habitat, had significant explanatory power. Although temperature significantly correlated with rod sensitivity, in that fishes in temperate latitudes had longer wavelength rod λ_max values than those in tropical latitudes, sampling inequity and other confounds require the role of the temperature to be studied further. Together, these findings indicate that fish rod λ_max is influenced by several ecological factors, suggesting that selection can act on even small differences in fish spectral sensitivity.     

Discordant mitochondrial and nuclear gene phylogenies in emydid turtles: implications for speciation and conservation

Do phylogenies and branch lengths based on mitochondrial DNA (mtDNA) provide a reasonable approximation to those based on multiple nuclear loci? In the present study, we show widespread discordance between phylogenies based on mtDNA (two genes) and nuclear DNA (nucDNA; six loci) in a phylogenetic analysis of the turtle family Emydidae. We also find an unusual type of discordance involving the unexpected homogeneity of mtDNA sequences across species within genera. Of the 36 clades in the combined nucDNA phylogeny, 24 are contradicted by the mtDNA phylogeny, and six are strongly contested by each data set. Two genera (Graptemys, Pseudemys) show remarkably low mtDNA divergence among species, whereas the combined nuclear data show deep divergences and (for Pseudemys) strongly supported clades. These latter results suggest that the mitochondrial data alone are highly misleading about the rate of speciation in these genera and also about the species status of endangered Graptemys and Pseudemys species. In addition, despite a strongly supported phylogeny from the combined nuclear genes, we find extensive discordance between this tree and individual nuclear gene trees. Overall, the results obtained illustrate the potential dangers of making inferences about phylogeny, speciation, divergence times, and conservation from mtDNA data alone (or even from single nuclear genes), and suggest the benefits of using large numbers of unlinked nuclear loci. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 445–461.     

Gelatinous zooplankton (ctenophores,salps and medusae): an important food resource of fishes in the temperate SW Atlantic Ocean

This study quantifies the occurrence of gelatinous zooplankton in the stomach contents of fishes from the southwest Atlantic Ocean (33°–55°S). More than 69,000 fish stomachs belonging to 107 species were examined. A total of 39 fishes were documented as consumers of gelatinous zooplankton, 23 of which were newly discovered. Three gelatinous organism consumption categories are recognized: (1) very frequent consumers (10 species, six of which were exclusive); frequent consumers (five species); and occasional consumers (26 species). Three types of gelatinous prey (ctenophores, salps and medusae) were found in the stomach contents of fishes. Ctenophores were consumed at high levels across almost the entire continental shelves of Argentina and Uruguay. Salps were frequent prey on the slope and southern shelf. In contrast, medusae were consumed in coastal areas, slopes and the southern shelf. Classification methods (group average sorting of the Bray–Curtis similarity measures based on log (X?+?1)-transformed percentage data) determined six areas where fishes predated on gelatinous organisms. SIMPER (similarity percentages) analysis determined which fishes contributed more to the consumption of gelatinous organisms. Results revealed that two fish species (Stromateus brasiliensis and Squalus acanthias) had high gelatinous zooplankton predation rates throughout the entire study area, while another six species (Patagonotothen ramsayi, Helicolenus dactylopterus lahillei, Macrourus holotrachys, Merluccius hubbsi, Schroederichthys bivius, and Macruronus magellanicus), while widely distributed, seemed to have specific areas where consumption occurred. This study not only provides new knowledge about the importance of gelatinous zooplankton in the diet of numerous fishes, but might also be valuable for planning and managing local fisheries.     

Genomic approaches with natural fish populations

Natural populations v. inbred stocks provide a much richer resource for identifying the effects of nucleotide substitutions because natural populations have greater polymorphism. Additionally, natural populations offer an advantage over most common research organisms because they are subject to natural selection, and analyses of these adaptations can be used to identify biologically important changes. Among fishes, these analyses are enhanced by having a wide diversity of species (>28 000 species, more than any other group of vertebrates) living in a huge range of environments (from below freezing to > 46° C, in fresh water to salinities >40 ppt.). Moreover, fishes exhibit many different life‐history and reproductive strategies and have many different phenotypes and social structures. Although fishes provide numerous advantages over other vertebrate models, there is still a dearth of available genomic tools for fishes. Fishes make up approximately half of all known vertebrate species, yet <0·2% of fish species have significant genomic resources. Nonetheless, genomic approaches with fishes have provided some of the first measures of individual variation in gene expression and insights into environmental and ecological adaptations. Thus, genomic approaches with natural fish populations have the potential to revolutionize fundamental studies of diverse fish species that offer myriad ecological and evolutionary questions.     

Venom evolution widespread in fishes: a phylogenetic road map for the bioprospecting of piscine venoms

Knowledge of evolutionary relationships or phylogeny allows for effective predictions about the unstudied characteristics of species. These include the presence and biological activity of an organism's venoms. To date, most venom bioprospecting has focused on snakes, resulting in six stroke and cancer treatment drugs that are nearing U.S. Food and Drug Administration review. Fishes, however, with thousands of venoms, represent an untapped resource of natural products. The first step involved in the efficient bioprospecting of these compounds is a phylogeny of venomous fishes. Here, we show the results of such an analysis and provide the first explicit suborder-level phylogeny for spiny-rayed fishes. The results, based on approximately 1.1 million aligned base pairs, suggest that, in contrast to previous estimates of 200 venomous fishes, >1,200 fishes in 12 clades should be presumed venomous. This assertion was corroborated by a detailed anatomical study examining potentially venomous structures in >100 species. The results of these studies not only alter our view of the diversity of venomous fishes, now representing >50% of venomous vertebrates, but also provide the predictive phylogeny or "road map" for the efficient search for potential pharmacological agents or physiological tools from the unexplored fish venoms.     

Genetic differentiation between two sympatric morphs of the blind Iran cave barb Iranocypris typhlops

The phylogenetic relationship between two sympatric morphotypes of the Iran cave barb Iranocypris typhlops, and Garra rufa, was investigated by sequencing the cytochrome c oxidase I (coI) region (788 bp) providing the first molecular evidence of their phylogeny. Consistent with their morphological differences, the mean genetic distance between the two forms of I. typhlops was significantly higher than generally reported for intraspecific divergence in freshwater fishes. They were phylogenetically closer to G. rufa than to any other species.     

Molecular systematics of threadfin breams and relatives (Teleostei,Nemipteridae)

Threadfin breams and relatives of the family Nemipteridae comprise 69 currently recognized species in five genera. They are found in the tropical and subtropical Indo‐West Pacific and most are commercially important. Using recently developed molecule‐based approaches exploiting DNA sequence variation among species/specimens, this study reconstructed a comprehensive phylogeny of the Nemipteridae, examined the validity of species and explored the cryptic diversity of the family, and tested previous phylogenetic hypotheses. A combined data set (105 taxa from 41 morphospecies) with newly determined sequences from two nuclear genes (RAG1 and RH) and one mitochondrial gene (COI), and a data set with only COI gene sequences (329 newly obtained plus 328 from public databases from a total of 53 morphospecies) were used in the phylogenetic analysis. The latter was further used for species delimitation analyses with two different tools to explore species diversity. Our phylogenetic results showed that all the currently recognized genera were monophyletic. The monotypic genus Scaevius is the sister group of Pentapodus and they together are sister to Nemipterus. These three genera combined to form the sister group of the clade comprising Parascolopsis and Scolopsis. The validity of most of the examined species was confirmed except in some cases. The combined evidence from the results of different analyses revealed a gap in our existing knowledge of species diversity in the Nemipteridae. We found several currently recognized species contain multiple separately evolving metapopulation lineages within species; some lineages should be considered as new species for further assignment. Finally, some problematic sequences deposited in public databases (probably due to misidentification) were also revised in this study to improve the accuracy for prospective DNA barcoding work on nemipterid fishes.