Repeatability, Reproducibility, Separative Power and Subjectivity of Different Fish Morphometric Analysis Methods

Freshwater fish scale database

Scales of the ray finned fishes can be used for multiple purposes. Beside others by their specific structure and elemental composition they are usable for age determination and food-web researches. Additionally, just their presence, absence, shape, location, or numbers could provide a reliable taxonomic information. The fish scales show remarkable size variation also, which characteristics provide reliable information about the environmental needs of freshwater fish. But till now this information was not interpretable and comparable in the absence of a sufficiently large and detailed database. In this study we provide a database which can facilitate the further complex comparative studies. Our dataset consists of 2954 scale photos characterising 193 freshwater fish species. All photos have a uniquely identification code showing exactly which species the scale belongs to. In addition to the photos, our database includes a table showing the exact taxonomic classification of the studied species, the average body profile-index, and the relative scale size, as well as the ecological (flow and feeding habitat preferences) and life strategic characteristics (feeding and breeding guild memberships) of each species. The sampled species have diverse origin, covering five biogeographical regions. An average of five adults from each species were selected for sampling. Three-to-four scales were collected from the anterior part of the body between the dorsal fin and the lateral line. The removed scales were cleaned and prepared to microscope slides, and after this process they were photographed or scanned. Our database can be used for both research and educational purposes. A large number of scale photos assigned of species can be an opportunity to create an automatic species identification system. Moreover, the subjectivity in morphometric measurements can be eliminated by analysing the database with artificial intelligence.

New Insights into Geometric Morphometry Applied to Fish Scales for Species Identification

The possibility of quick and cheap recognition of a fish species from a single dermal scale would be interesting in a wide range of contexts. The methods of geometric morphometry appear to be quite promising, although wide studies comparing different approaches are lacking. We aimed to apply two methods of geometric morphometry, landmark-based and outline-based, on a dataset of scales from five different teleost species: Danio rerio, Dicentrarchus labrax, Mullus surmuletus, Sardina pilchardus, and Sparus aurata. For the landmark-based method the R library "geomorph" was used. Some issues about landmark selection and positioning were addressed and, for the first time on fish scales, an approach with both landmarks and semilandmarks was set up. For the outline-based method the R library "Momocs" was used. Despite the relatively low number of scales analyzed (from 11 to 81 for each species), both methods achieved quite good clustering of all the species. In particular, the landmark-based method used here gave generally higher R2 values in testing species clustering than the outline-based method, but it failed to distinguish between a few couples of species; on the other hand, the outline-based method seemed to catch the differences among all the couples except one. Larger datasets have the potential to achieve better results with outline-based geometric morphometry. This latter method, being free from the problem of recognizing and positioning landmarks, is also the most suitable for being automatized in future applications.

Comparing ant morphology measurements from microscope and online AntWeb.org 2D z-stacked images

Unprecedented technological advances in digitization and the steadily expanding open-access digital repositories are yielding new opportunities to quickly and efficiently measure morphological traits without transportation and advanced/expensive microscope machinery. A prime example is the AntWeb.org database, which allows researchers from all over the world to study taxonomic, ecological, or evolutionary questions on the same ant specimens with ease. However, the reproducibility and reliability of morphometric data deduced from AntWeb compared to traditional microscope measurements has not yet been tested. Here, we compared 12 morphological traits of 46 Temnothorax ant specimens measured either directly by stereomicroscope on physical specimens or via the widely used open-access software tpsDig utilizing AntWeb digital images. We employed a complex statistical framework to test several aspects of reproducibility and reliability between the methods. We estimated (i) the agreement between the measurement methods and (ii) the trait value dependence of the agreement, then (iii) compared the coefficients of variation produced by the different methods, and finally, (iv) tested for systematic bias between the methods in a mixed modeling-based statistical framework. The stereomicroscope measurements were extremely precise. Our comparisons showed that agreement between the two methods was exceptionally high, without trait value dependence. Furthermore, the coefficients of variation did not differ between the methods. However, we found systematic bias in eight traits: apart from one trait where software measurements overestimated the microscopic measurements, the former underestimated the latter. Our results shed light on the fact that relying solely on the level of agreement between methods can be highly misleading. In our case, even though the software measurements predicted microscope measurements very well, replacing traditional microscope measurements with software measurements, and especially mixing data collected by the different methods, might result in erroneous conclusions. We provide guidance on the best way to utilize virtual specimens (2D z-stacked images) as a source of morphometric data, emphasizing the method's limitations in certain fields and applications.

Classifying fossil Darwin wasps (Hymenoptera: Ichneumonidae) with geometric morphometrics of fore wings

Linking fossil species to the extant diversity is often a difficult task, and the correct interpretation of character evidence is crucial for assessing their taxonomic placement. Here, we make use of geometric morphometrics of fore wings to help classify five fossil Darwin wasps from the Early Eocene Fur Formation in Denmark into subfamilies and often tribes. We compile a reference dataset with 342 fore wings of nine extant subfamilies and nine relevant fossil species. Since geometric morphometrics was mostly ignored in the past in Darwin wasp classification, the dataset is first used to examine differences and similarities in wing venation among subfamilies. In a next step, we used the reference dataset to inform the classification of the fossil species, which resulted in the description of one new genus and five new species, Crusopimpla weltii sp. nov., Ebriosa flava gen. et sp. nov., Entypoma? duergari sp. nov., Lathrolestes? zlatorog sp. nov., and Triclistus bibori sp. nov., in four different subfamilies. Carefully assessing data quality, we show that the fore wing venation of fossil Darwin wasps is surprisingly suitable to assign them to a subfamily or even lower taxonomic level, especially when used in conjunction with characters from other parts of the body to narrow down a candidate set of potential subfamilies and tribes. Our results not only demonstrate a fast and useful approach to inform fossil classification but provide a basis for future investigations into evolutionary changes in fore wings of ichneumonids. The high informativeness of wing venation for classification furthermore could be harvested for phylogenetic analyses, which are otherwise often hampered by homoplasy in this parasitoid wasp family.

CRISPR/Cas9-Mediated Transgenesis of the Masu Salmon (Oncorhynchus masou) elovl2 Gene Improves n-3 Fatty Acid Content in Channel Catfish (Ictalurus punctatus)

Omega-3 polyunsaturated fatty acids (n-3 PUFAs), particularly eicosapentaenoic acid (EPA, 20:5n-3) and docosahexaenoic acid (DHA, 22:6n-3), play a very important role in human health. Channel catfish (Ictalurus punctatus) is one of the leading freshwater aquaculture species in the USA, but has low levels of EPA and DHA compared to some fish such as salmon. To improve EPA and DHA content, a modification of the n-3 PUFA biosynthetic pathway was achieved through the insertion of an elovl2 transgene isolated from masu salmon (Oncorhynchus masou) driven by a carp β-actin promoter using a two-hit by gRNA and two oligos with a targeting plasmid (2H2OP) CRISPR/Cas9 approach. Integration rate of the transgene was high (37.5%) and detected in twelve different tissues of P₁ transgenic fish with tissue-specific gene expression. Liver and muscle had relative high gene expression (13.4- and 9.2-fold change, respectively). Fatty acid analysis showed DHA content in the muscle from transgenic fish was 1.62-fold higher than in non-transgenic fish (P < 0.05). Additionally, total n-3 PUFAs and omega-6 polyunsaturated fatty acids (n-6 PUFAs) increased to 1.41-fold and 1.50-fold, respectively, suggesting the β-actin-elovl2 transgene improved biosynthesis of PUFAs in channel catfish as a whole. The n-9 fatty acid level decreased in the transgenic fish compared to the control. Morphometric analysis showed that there were significant differences between injected fish with sgRNAs (including positive and negative fish) and sham-injected controls (P < 0.001). Potential off-target effects are likely the major factor responsible for morphological deformities. Optimization of sgRNA design to maximize activity and reduce off-target effects of CRISPR/Cas9 should be examined in future transgenic research, but this research shows a promising first step in the improvement of n-3 PUFAs in channel catfish.

Infirm effect of phylogeny on morphometric features in a cryptic Gobio species complex

Several recent notes prove that taxonomic relations of close relative animal groups (species complexes or cryptic species) can be revealed by the combined use of genetic and morphologic methodologies. At the same time scarce information can be found about how phylogeny, population origin, and sexual dimorphism affect the morphometric features of these species. In our present work, we performed simultaneous phylogenetic and morphological studies on the taxonomically still questionable Carpathian stream dwelling gudgeons (Cyprinidae, Gobio) by using two different methodologies (distance based and geometric morphometry). Our results were in correspondence with the previous findings, showing the presence of three phylogenetically more or less distinct groups in the area. The results of the whole-body geometric and the traditional, distance-based morphometry reflected the extent of phylogenetic differences. While the results of geometric scale morphometry did not correspond with the genetic subdivisions. Results of three way PERMANOVA analyses showed that the phylogenetic effects on morphometry is less considerable as the population origin or the sexual dimorphism at these cyprinid taxa. Our investigation contributed to the better understanding of the taxonomy of fish stocks in the Carpathian Basin, and to their conservation, but additional investigations will be needed to clarify the exact taxonomic position of the gudgeons (’Gobio sp1’) dominating the eastern part of the studied drainage.

Phenotypic plasticity in Barilius vagra (Hamilton, 1822) (Teleostei: Danionidae) from two geographically distinct river basins of Indian Himalaya

Truss-based morphometric analysis was used to examine phenotypic plasticity of Barilius vagra (Hamilton, 1822) inhabiting the tributaries of the Alaknanda (Ganga River basin) and Chenab (Indus River basin), two geographically distinct river basins in the Indian Himalaya. Fourteen landmarks were connected to generate a truss network of 90 parameters on the body of fish. Eighty morphometric traits out of ninety morphometric measurements explained statistically significant difference among six sampling locations of Barilius vagra from streams in the Alaknanda and Chenab basins. Discriminant function analysis revealed 82% of Barilius vagra specimens originally classified into their own groups. 95% of the variance was explained by 13 principal components. Morphometric characters (1–6, 1–13, 2–5, 2–6, 2–14, 3–6, 4–6, 4–14, 6–12, 7–8, 7–9, 10–11, and 13–14) contributed greatly in differentiation of B. vagra populations from different river basins. The Alaknanda basin reflected some mixing within populations, which may be due to common environmental conditions and fish migration in these streams. This study will be helpful in framing site-specific conservation and management strategies, such as net mesh size selection, avoiding overexploitation, stock augmentation and food availability for different fish populations.

Multiple endpoints of polylactic acid biomicroplastic toxicity in adult zebrafish (Danio rerio)

Although the toxicity of conventional microplastic types (i.e., petroleum derivatives) in different organisms is already known, knowledge about the effects of alternative biopolymers on aquatic vertebrates remains incipient. Thus, the aim of the present study is to test the hypothesis that the exposure of adult Danio rerio individuals to this pollutant for 30 days is enough to cause polylactic acid biomicroplastics (BioMPs of PLA) accumulation in their bodies, which leads to behavioral/neurotoxic, biochemical, and morphological changes. Based on our results, PLA BioMPs at concentrations of 2.5 and 5 mg/L accumulated in the liver, brain, gills and carcass of the assessed animals. However, such an accumulation was not able to cause locomotor damages or to trigger anxiety-like behavior in them. On the other hand, it was enough to cause behavioral changes (in shoal) predictive of co-specific social interaction and anti-predatory defensive response deficit likely related to cholinergic changes inferred by increased acetylcholinesterase activity and REDOX imbalance. This imbalance was featured by increased production of reactive species. We observed that the treatments have affected animals' pigmentation pattern. Therefore, our study highlights the toxicological potential of the herein assessed biopolymer, and this finding puts in check the innocuousness of this material, as well as expands our knowledge about how PLA BioMPs can affect the ichthyofauna in freshwater environments.

The study of the variability of morphobiological indicators of different size and weight groups of hybrid silver carp (Hypophthalmichthys spp.) as a promising direction of development of the fish processing industry

In water reservoirs, the size and characteristics of fish, in the first place, affect – the composition and clarity of food objects, the number of food competitors and predators, their numbers, industry, and others. Besides, the rate of linear and weight growth are the arteries that determine the value of the species as an object of commercial fishing. The hybrid of silver and bighead carp easily adapts to different growing conditions (from the point of view of the formation of fish-biological indicators), protein in different years depending on feeding conditions, in one reservoir indicators of length and body weight of ribs are inadequate. Evaluating the influence of feeding conditions on the linear growth of the rib, the method of generalized evaluation was used. An indicator equal to the sum of potential fish productivity for phyto-zooplankton was used to characterize the foraging status of a particular condition in a certain period. In terms of the quality of growth indicators, the indicator of the absolute weight of nature with differentiation of farms, age groups, and years was used. The results of the research revealed significant variability in the size and weight characteristics of different groups of silver and bighead carp, which were isolated from ponds and reservoirs. According to the results of experimental studies established for the cultivation of hybrid silver and bighead carp in reservoirs, relatively high rates of linear and weight growth are expected, higher than for similar species, which is provided in the conditions of fish ponds.

Effects of pharmaceutically active compounds (PhACs) on fish body and scale shape in natural waters

Background

In recent years, there are growing concerns about pharmaceutically active compounds (PhACs) in natural ecosystems. These compounds have been found in natural waters and in fish tissues worldwide. Regarding their growing distribution and abundance, it is becoming clear that traditionally used risk assessment methodologies and ecotoxicological studies have limitations in several respects. In our study a new, combined approach of environmental impact assesment of PhACs has been used.

Methods

In this study, the constant watercourses of the suburban region of the Hungarian capital (Budapest) were sampled, and the body shape and scale shape of three fish species (roach Rutilus rutilus, chub Squalius cephalus, gibel carp Carassius gibelio) found in these waters were analyzed, based on landmark-based geometric morphometric methods. Possible connections were made between the differences in body shape and scale shape, and abiotic environmental variables (local- and landscape-scale) and measured PhACs.

Results

Significant connections were found between shape and PhACs concentrations in several cases. Despite the relatively large number of compounds (54) detected, citalopram, propranolol, codeine and trimetazidine significantly affected only fish body and scale shape, based on their concentrations. These four PhACs were shown to be high (citalopram), medium (propranolol and codeine), and low (trimetazidine) risk levels during the environmental risk assessment, which were based on Risk Quotient calculation. Furthermore, seven PhACs (diclofenac, Estrone (E1), tramadol, caffeine 17α-Ethinylestradiol (EE2), 17α-Estradiol (aE2), Estriol (E3)) were also categorized with a high risk level. However, our morphological studies indicated that only citalopram was found to affect fish phenotype amongst the PhACs posing high risk. Therefore, our results revealed that the output of (traditional) environmental/ecological risk assessment based on ecotoxicological data of different aquatic organisms not necessarily show consistency with a “real-life” situation; furthermore, the morphological investigations may also be a good sub-lethal endpoint in ecotoxicological assessments.

Genetic and morphological assessment of a vulnerable large catfish, Silonia silondia (Hamilton, 1822), in natural populations from India

Silonia silondia is a commercially important fish distributed in Asian countries, which is under threat due to overexploitation. This study focuses on the morphological analysis and genetic variation of S. silondia individuals, through truss network and sequencing of two mitochondrial regions, respectively, from six wild populations of the Ganga and Mahanadi river systems in India. A total of 38 haplotypes was observed by analysing combined mitochondrial genes (cytochrome b + ATPase 6/8) in 247 individuals of S. silondia collected from six populations. Average haplotype and nucleotide diversities were 0.8508 and 0.00231, respectively. Genetic structure analysis showed the predominant cause of genetic variation to be within populations. The two clades were observed among the haplotypes and time of divergence from their most probable ancestor was estimated to be around 0.3949 mya. Analysis of combined mitochondrial genes in six populations of S. silondia resulted into three management units or genetic stocks. The truss network analysis was carried out by interconnecting 12 landmarks from digital images of specimens to identify phenotypic stocks. Sixty-five truss morphometric variables were analysed for geometric shape variation which revealed morphological divergence in River Son specimens. The present study presents molecular markers and genetic diversity data which can be critical input for conservation and management of differentiated populations and future monitoring of the genetic bottleneck. The morphological shape analysis clearly shows that variation in the insertion of adipose fin is an important parameter influencing the morphological discrimination.

Insect morphometry is reproducible under average investigation standards

Morphometric research is being applied to a growing number and variety of organisms. Discoveries achieved via morphometric approaches are often considered highly transferable, in contrast to the tacit and idiosyncratic interpretation of discrete character states. The reliability of morphometric workflows in insect systematics has never been a subject of focused research, but such studies are sorely needed. In this paper, we assess the reproducibility of morphometric studies of ants where the mode of data collection is a shared routine.We compared datasets generated by eleven independent gaugers, that is, collaborators, who measured 21 continuous morphometric traits on the same pool of individuals according to the same protocol. The gaugers possessed a wide range of morphometric skills, had varying expertise among insect groups, and differed in their facility with measuring equipment. We used intraclass correlation coefficients (ICC) to calculate repeatability and reproducibility values (i.e., intra- and intergauger agreements), and we performed a multivariate permutational multivariate analysis of variance (PERMANOVA) using the Morosita index of dissimilarity with 9,999 iterations.The calculated average measure of intraclass correlation coefficients of different gaugers ranged from R = 0.784 to R = 0.9897 and a significant correlation was found between the repeatability and the morphometric skills of gaugers (p = 0.016). There was no significant association with the magnification of the equipment in the case of these rather small ants. The intergauger agreement, that is the reproducibility, varied between R = 0.872 and R = 0.471 (mean R = 0.690), but all gaugers arrived at the same two-species conclusion. A PERMANOVA test revealed no significant gauger effect on species identity (R 2 = 0.69, p = 0.58).Our findings show that morphometric studies are reproducible when observers follow the standard protocol; hence, morphometric findings are widely transferable and will remain a valuable data source for alpha taxonomy.

A comparison of two methods for estimating measurement repeatability in morphometric studies

Measurement repeatability is often reported in morphometric studies as an index of the contribution of measurement error to trait measurements. However, the common method of remeasuring a mounted specimen fails to capture some components of measurement error and could therefore yield inflated repeatability estimates. Remounting specimens between successive measurements is likely to provide more realistic estimates of repeatability, particularly for structures that are difficult to measure.Using measurements of 22 somatic and genitalic traits of the neriid fly Telostylinus angusticollis, we compared repeatability estimates obtained via remeasurement of a specimen that is mounted once (single-mounted method) versus remeasurement of a specimen that is remounted between measurements (remounted method). We also asked whether the difference in repeatability estimates obtained via the two methods depends on trait size, trait type (somatic vs. genitalic), sclerotization, or sex.Repeatability estimates obtained via the remounted method were lower than estimates obtained via the single-mounted method for each of the 22 traits, and the difference between estimates obtained via the two methods was generally greater for small structures (such as genitalic traits) than for large structures (such as legs and wings). However, the difference between estimates obtained via the two methods did not depend on trait type (genitalic or somatic), tissue type (soft or sclerotized) or sex.Remounting specimens between successive measurements can provide more accurate estimates of measurement repeatability than remeasuring from a single mount, especially for small structures that are difficult to measure.

Assignment of Gilthead Seabream Sparus aurata to Its Origin through Scale Shape and Microchemistry Composition: Management Implications for Aquaculture Escapees

This study tests the suitability of the gilthead seabream scales as a proxy for origin selection in wild and anthropogenically pressured environments. Scale morphology and microchemistry were used to discriminate the habitat selection of two wild, farmed and wild farm-associated populations where landmark and outline-based scale morphometrics, trace-element chemistry and scale microstructure characteristics were analysed. The morphometric techniques successfully differentiated between the farmed and wild origin scale phenotypes. Reduced discrimination sensitivity between the wild and wild farm-associated origin was, however, reported. The discrimination based on microchemistry (B, Ba, Mn, K, Sr and Zn) classified the scales with high accuracy according to their origin (wild vs. farmed vs. wild farm-associated) and sampling locations, thus proving itself as a powerful tool in provenance study of gilthead seabream. Disparity in scale microstructure characteristics accounted for radii, circuli and inter-circulus spacing, hence unveiling the differences in growth and environmental conditions between the wild and farmed fish. In brief, scale shape was found to be a potent exploration tool for farmed fish identification, whereas scale microchemistry yielded a good resolution in identifying gilthead seabream membership among different habitats. Considering the importance of this species in aquaculture and fisheries throughout the Mediterranean, more research is needed to assess the usefulness of scales as nonlethal biogeochemical tags.

Intraspecific variation and structuring of phenotype in a lake-dwelling species are driven by lake size and elevation

The fragmented, heterogeneous and relatively depauperate ecosystems of recently glaciated lakes present contrasting ecological opportunities for resident fish. Across a species, local adaptation may induce diverse and distinct phenotypic responses to various selection pressures. We tested for intraspecific phenotypic structuring by population in a common native lake-dwelling fish species across a medium-scale geographic region with considerable variation in lake types. We investigated potential lake-characteristic drivers of trophic morphology. Using geometric morphometric techniques, we quantified the head shapes of 759 adult brown trout (Salmo trutta L.) from 28 lakes and reservoirs across Scotland. Multivariate statistical analyses showed that almost all populations differed from one another. Trout from larger and deeper lakes had deeper, but shorter heads, and smaller eyes. Higher elevation lakes were associated with fish with shorter heads and jaws. Within-population shape variation also differed by population, and was positively correlated with lake surface area and depth. Trout within reservoirs differed subtly from those in natural lakes, having larger eyes, shorter jaws and greater variability. This study documents an extraordinary morphological variation between and within populations of brown trout, and demonstrates the role of the extrinsic environment in driving phenotypic structuring over a medium-scale and varied geographic area.

Phenotypic plasticity under desert environment constraints: mandible variation in the dwarf fat-tailed jerboa, Pygeretmus pumilio (Rodentia: Dipodidae)

Arid areas have a comparatively narrow range of habitat types, with restricted variation in environmental parameters, leaving narrow boundaries for phenotypic variation to correlate with ecological variables. To test this presumption, we explored variation in size and shape of the mandible in the dwarf fat-tailed jerboa (Pygeretmus pumilio (Kerr, 1792)) under the constraints of a rigorous desert environment. Size varied significantly and predictably with geographic position and demonstrated a strong, nonlinear longitudinal pattern. Moreover, size was associated with several other climatic variables but not with soil properties or with proxies for primary productivity. Our results suggest that for rodents exposed to rapid and extreme changes, larger size may have multiple advantages, notably in maintaining euthermia during cold nights and efficient water metabolism under aridity stress, in accumulating fat reserves for hibernation, and in digging deeper burrows, better protected from surface extremes. Shape varied clinally along the longitudinal transect, and the pattern was affected more by temperature than by precipitation. We conclude that the success of dwarf fat-tailed jerboa in occupying an extensive geographic range relies on their ability to meet environmental heterogeneity through cohesive and diverse responses, including physiology, behaviour, life-history traits, and morphological plasticity.

Biometric and genetic differences in kelabau ( Osteochilus spp.) as revealed using cytochrome c oxidase subunit 1

Background: Kelabau ( Osteochilus spp.) is a freshwater fish commonly found in the rivers of Riau, Indonesia. Researchers believe that these are Osteochilus kelabau; however, accurate taxonomic determination of these fish in Riau waters has not been made. The purpose of this study was to facilitate the identification of the kelabau based on its morphology and genetics using biometric and cytochrome c oxidase subunit 1 ( CO1) analyses, respectively. Methods: Fish samples were collected from the Siak, Kampar and Rokan rivers in Riau Province, Indonesia. The DNA of 90 fish was extracted from the caudal fins using a DNA extraction kit, after which it was amplified using primers Fish-F1 and Fish-R1. Sequencing was conducted by Applied Biosystems Macrogen Korea, and the DNA sequences were then edited and aligned using MEGA v. 7. All samples were BLAST-searched for identification using the National Center for Biotechnology Information and BOLD System. Phylogenetic trees were constructed, and the similarity index was calculated using accession numbers AP011385.1 and KC631202.1 in GenBank. Results: Analysis of the consensus barcode sequence for 86 species revealed a high percentage of barcode matches (96%-97% in GenBank and 96.6%-96.76% in the BOLD System). The nucleotide distance between groups of kelabau from the different rivers based on the Kimura 2-parameter model gave the following results: 0.05% between groups from the Siak and Kampar rivers, 0.09% between those from the Siak and Rokan rivers and 0.05% between those from the Kampar and Rokan rivers. The nucleotide distance between the groups in the Siak (0.09%), Kampar (0.00%) and Rokan (0.10%) Rivers indicated that the kelabau in those rivers were related to each other. Conclusions: Based on the results of the research data using CO1 and biometric analyses, the kelabau were confirmed to be O. melanopleurus.

Biometric and genetic differences in kelabau ( Osteochilus spp.) as revealed using cytochrome c oxidase subunit 1

Background: Kelabau ( Osteochilus spp.) is a freshwater fish commonly found in the rivers of Riau, Indonesia. Researchers believe that these are Osteochilus kelabau; however, accurate taxonomic determination of these fish in Riau waters has not been made. The purpose of this study was to facilitate the identification of the kelabau based on its morphology and genetics using biometric and cytochrome c oxidase subunit 1 ( CO1) analyses, respectively. Methods: Fish samples were collected from the Siak, Kampar and Rokan rivers in Riau Province, Indonesia. The DNA of 90 fish was extracted from the caudal fins using a DNA extraction kit, after which it was amplified using primers Fish-F1 and Fish-R1. Sequencing was conducted by Applied Biosystems Macrogen Korea, and the DNA sequences were then edited and aligned using MEGA v. 7. All samples were BLAST-searched for identification using the National Center for Biotechnology Information and BOLD System. Phylogenetic trees were constructed, and similarity index was calculated using accession numbers AP011385.1 and KC631202.1 in GenBank. Results: Analysis of the consensus barcode sequence for 86 species revealed a high percentage of barcode matches (96%-97% in GenBank and 96.6%-96.76% in the BOLD System). The nucleotide distance between groups of kelabau from the different rivers based on the Kimura 2-parameter model gave the following results: 0.05% between groups from the Siak and Kampar rivers, 0.09% between those from the Siak and Rokan rivers and 0.05% between those from the Kampar and Rokan rivers. The nucleotide distance between the groups in the Siak (0.09%), Kampar (0.00%) and Rokan (0.10%) Rivers indicated that the kelabau in those rivers were related to each other. Conclusions: Based on the results of the research data using CO1 and biometric analyses, the kelabau were confirmed to be O. melanopleurus.

Zebrafish Mutants Carrying Leptin a (lepa) Gene Deficiency Display Obesity, Anxiety, Less Aggression and Fear, and Circadian Rhythm and Color Preference Dysregulation

Leptin, a hormone secreted by peripheral adipose tissues, regulates the appetite in animals. Recently, evidence has shown that leptin also plays roles in behavioral response in addition to controlling appetite. In this study, we examined the potential function of leptin on non-appetite behaviors in zebrafish model. By using genome editing tool of Transcription activator-like effector nuclease (TALEN), we successfully knocked out leptin a (lepa) gene by deleting 4 bp within coding region to create a premature-translation stop. Morphological and appetite analysis showed the lepa KO fish display a phenotype with obese, good appetite and elevation of Agouti-related peptide (AgRP) and Ghrelin hormones, consistent with the canonical function of leptin in controlling food intake. By multiple behavior endpoint analyses, including novel tank, mirror biting, predator avoidance, social interaction, shoaling, circadian rhythm, and color preference assay, we found the lepa KO fish display an anxiogenic phenotype showing hyperactivity with rapid swimming, less freezing time, less fear to predator, loose shoaling area forming, and circadian rhythm and color preference dysregulations. Using biochemical assays, melatonin, norepinephrine, acetylcholine and serotonin levels in the brain were found to be significantly reduced in lepa KO fish, while the levels of dopamine, glycine and cortisol in the brain were significantly elevated. In addition, the brain ROS level was elevated, and the anti-oxidative enzyme catalase level was reduced. Taken together, by performing loss-of-function multiple behavior endpoint testing and biochemical analysis, we provide strong evidence for a critical role of lepa gene in modulating anxiety, aggression, fear, and circadian rhythm behaviors in zebrafish for the first time.

Geometric Morphometrics as a Tool to Evaluate Teratogenic Effects in Zebrafish (Danio rerio)

Geometric morphometrics allows for the characterization of shape using Cartesian geometric coordinates rather than linear or volumetric measurements, which are dependent upon size and are insufficient to capture geometric shape. By using landmarks on specimens, variations in position, orientation and scale between specimens can be removed to better compare variations in shape. This method has primarily been used in the fields of evolutionary biology and taxonomy. Here we describe how geometric morphometrics can be used to delineate variations in shape caused by teratogenic compounds in zebrafish.

Mayfly and fish species identification and sex determination in bleak (Alburnus alburnus) by MALDI-TOF mass spectrometry

Besides food quality control of fish or cephalopods, the novel mass spectrometry (MS) approaches could be effective and beneficial methods for the investigation of biodiversity in ecological research. Our aims were to verify the applicability of MALDI-TOF MS in the rapid identification of closely related species, and to further develop it for sex determination in phenotypically similar fish focusing on the low mass range. For MALDI-TOF MS spectra analysis, ClinProTools software was applied, but our observed classification was also confirmed by Self Organizing Map. For verifying the wide applicability of the method, brains from invertebrate and vertebrate species were used in order to detect the species related markers from two mayflies and eight fish as well as sex-related markers within bleak. Seven Ephemera larvae and sixty-one fish species related markers were observed and nineteen sex-related markers were identified in bleak. Similar patterns were observed between the individuals within one species. In contrast, there were markedly diverse patterns between the different species and sexes visualized by SOMs. Two different Ephemera species and male or female fish were identified with 100% accuracy. The various fish species were classified into 8 species with a high level of accuracy (96.2%). Based on MS data, dendrogram was generated from different fish species by using ClinProTools software. This MS-based dendrogram shows relatively high correspondence with the phylogenetic relationships of both the studied species and orders. In summary, MALDI-TOF MS provides a cheap, reliable, sensitive and fast identification tool for researchers in the case of closely related species using mass spectra acquired in a low mass range to define specific molecular profiles. Moreover, we presented evidence for the first time for determination of sex within one fish species by using this method. We conclude that it is a powerful tool that can revolutionize ecological and environmental research.