Cypriniform Species Research Articles

Annotation and Characterization of the Zacco platypus Genome

The pale chub Zacco platypus (Cypriniformes; Xenocyprididae; Jordan & Evermann, 1902) is widely distributed across freshwater ecosystems in East Asia and has been recognized as a potential model fish species for ecotoxicology and environmental monitoring. Here, a high-quality de novo genome assembly of Z. platypus was constructed through the integration of a combination of long-read Pacific Bioscience (PacBio) sequencing, short-read Illumina sequencing, and Hi-C sequencing technologies. Z. platypus has the smallest genome size compared to other species belonging to the order Cypriniformes. The assembled genome encompasses 41.45% repeat sequences. As shown in other fish, a positive correlation was observed between genome size and the composition of transposable elements (TE) in the genome. Among TEs, a relatively higher rate of DNA transposon was observed, which is a common pattern in the members of the order Cypriniformes. Functional annotation was processed using four representative databases, identifying a core set of 12,907 genes shared among them. Orthologous gene family analysis revealed that Z. platypus has experienced more gene family contraction rather than expansion compared to other Cypriniformes species. Among the uniquely expanded gene families in Z. platypus, detoxification and stress-related gene families were identified, suggesting that this species could represent a promising model for ecotoxicology and environmental monitoring. Taken together, the Z. platypus genome assembly will provide valuable data for omics-based health assessments in aquatic ecosystems, offering further insights into the environmental and ecological facets within this species.

An Empirical Assessment of Diversity in Fish Species: Case Study of Madhubani District, India

Sarisab Pahi Chaur is a wetland sites in the Madhubani district, Bihar has rich fish diversity. The present investigation was undertaken the status of fish diversity and seasonal impacts on them in Sarisab Pahi Chaur of Madhubani, Bihar. A total number of 29 species representing 17 families of 9 orders of class Actinopterygii were identified from Sarisab Pahi Chaur wetland, the various species of order Cypriniformes 49% and Clupeiformes 16% dominated in the wetland followed by order Siluriformes 15%, Perciformes 12%, Channiformes 6%, Symbrachiformes, Beloniformes, Anguilliformes and Mugiliformes respectively. In present investigation species diversity of fishes of Sarisab Pahi Chaur, ranged between the lowest 0.943 June, 2021 and the highest 1.346 May, 2022. Species evenness (J) of fishes of Sarisab Pahi Chaur, varied from the lowest 0.787 July, 2021 and the highest 0.933 March, 2022 during the investigation period. Species richness (d) of fishes of Sarisab Pahi Chaur, varied from the lowest 6.603 June, 2021 and the highest 12.411 May, 2022. The value of Shannon-Wiener diversity, Species richness and the Evenness in different months are the different value which is depends upon the fish density and physico-chemical parameters of water of wetland. The paper takes into account to explore the importance of wild variety in fish seed production and its support in sustainable livelihood development.

Goldfish phenomics reveals commonalities and a lack of universality in the domestication process for ornamentation

Abstract Domestication process effects are manifold, affecting genotype and phenotype, and assumed to be universal in animals by part of the scientific community. While mammals and birds have been thoroughly investigated, from taming to intensive selective breeding, fish domestication remains comparatively unstudied. The most widely bred and traded ornamental fish species worldwide, the goldfish, underwent the effect of long-term artificial selection on differing skeletal and soft tissue modules through ornamental domestication. Here, we provide a global morphological analysis in this emblematic ornamental domesticated fish. We demonstrate that goldfish exhibit unique morphological innovations in whole-body, cranial, and sensory (Weberian ossicles and brain) anatomy compared to their evolutionary clade, highlighting a remarkable morphological disparity within a single species comparable to that of a macroevolutionary radiation. In goldfish, as in the case of dogs and pigeons in their respective evolutionary contexts, the most ornamented varieties are extremes in the occupied morphological space, emphasizing the power of artificial selection for nonadaptive traits. Using 21st century tools on a dataset comprising the 16 main goldfish breeds, 23 wild close relatives, and 39 cypriniform species, we show that Charles Darwin’s expressed wonder at the goldfish is justified. There is a commonality of overall pattern in the morphological differentiation of domesticated forms selected for ornamental purposes, but the singularity of goldfish occupation and extension within (phylo)morphospaces, speaks against a universality in the domestication process.

Solving the Myxidium rhodei (Myxozoa) puzzle: insights into its phylogeny and host specificity in Cypriniformes.

Myxidium rhodei Léger, 1905 (Cnidaria: Myxozoa) is a kidney-infecting myxosporean that was originally described from the European bitterling Rhodeus amarus. Subsequently, it has been documented based on spore morphology in more than 40 other cypriniform species, with the roach Rutilus rutilus being the most commonly reported host. This study introduces the first comprehensive data assessment of M. rhodei, conducted through morphological, ecological and molecular methods. The morphological and phylogenetic analyses of SSU rDNA sequences of Myxidium isolates obtained from European bitterling and roach did not support parasite conspecificity from these fish. In fact, the roach-infecting isolates represent three distinct parasite species. The first two, M. rutili n. sp. and M. rutilusi n. sp., are closely related cryptic species clustering with other myxosporeans in the freshwater urinary clade, sharing the same tissue tropism. The third one, M. batuevae n. sp., previously assigned to M. cf. rhodei, clustered in the hepatic biliary clade sister to bitterling-infecting M. rhodei. Our examination of diverse cypriniform fishes, coupled with molecular and morphological analyses, allowed us to untangle the cryptic species nature of M. rhodei and discover the existence of novel species. This underscores the largely undiscovered range of myxozoan diversity and highlights the need to incorporate sequence data in diagnosing novel species.

Swimming under Pressure: The Sub-Lethal Effects of a Pesticide on the Behaviour of Native and Non-Native Cypriniformes Fish

River ecosystems are exposed to a multitude of stressors, including increasing pesticide run-off driven by precipitation and irrigation. Pyrethroids are the fourth major group of insecticides in use worldwide and have extremely negative effects on aquatic fauna. In this study, we aimed to assess the effects of an acute 2 h sub-lethal exposure to different levels of the pyrethroid esfenvalerate on the swimming behaviour of two Cypriniformes species: the native Iberian barbel (Luciobarbus bocagei) and the non-native invasive bleak (Alburnus alburnus). The experimental set-up consisted of previous exposure to three esfenvalerate concentrations (control, 1.2 (low), and 2.0 (high) μg/L) before being stocked in a three-artificial-flume-channel mesocosm for behavioural trials through direct observation. Monitored behaviours included (i) routine activity, (ii) shoal cohesion, and iii) boldness. Significant differences in fish behaviour were detected for the native species (barbel), as individuals spent significantly more time holding position (i.e., resting) in the control (44.9%) than in the high esfenvalerate concentration (25.2%). Concordantly, control barbels were also found to perform more directional changes than the ones exposed to high esfenvalerate concentrations. Behavioural changes were also found for boldness, measured by the proportion of fish attempts to negotiate the upstream ramp, which were significantly higher in the control (37.4%) and in the high concentration (41.5%) compared to the low one (21.1%). Finally, regarding shoal cohesion of the barbel, it was tighter in the control (81.3%) than in the low- (70.5%) and high- (71.1%) esfenvalerate treatments. For the invasive bleak, there were no significant differences in any of the behavioural traits upon previous exposure to an increasing esfenvalerate concentration. This experimental study demonstrated that even short-term exposure to the pyrethroid esfenvalerate was sufficient to alter the behaviour of a native Cypriniformes fish species while not affecting the non-native species. This may confer greater competitive advantages to non-native fish species in the context of global changes.

Ichthyofauna of the Fresh and Brackish Waters of Russia and Adjacent Areas: Annotated List with Taxonomic Comments. 2. Order Cypriniformes, Suborders Catostomoidei, Cobitoidei and Cyprinoidei

This paper is the second part of the “Ichthyofauna of the Fresh and Brackish Waters of Russia and Adjacent Areas: Annotated List with Taxonomic Comments”, which we started in 2022 based on a critical analysis of scientific publications of the last 200 years, and on the data of the author’s research. The current paper includes all currently known fishes of the order Cypriniformes of Russia and adjacent waters, represented by three suborders Catostomoidei, Cobitoidei and Cyprinoidei, comprising ten families, 64 genera and 177 species. The most specious families were the Leuciscidae (59 species/33.3% of all species), Gobionidae (35/19.8%) and Xenocyprididae (23/13.0%), which together represent just over 66% the total cypriniform species. Fourteen of the studied species (24.7% of all cyprinids in Russia) are introduced species, 21 species (11.9%) are endemic; 32 species (18.1%) are recorded from Russia for the first time. In relation to the habitat, 131 species live and breed exclusively in fresh waters, 31 species are of freshwater origin, but can also tolerate slightly brackish waters, ten species are represented by anadromous forms (all with residential populations), and three species are amphidromic, capable of live and reproduce both in brackish water and in freshwater. According to the IUCN criteria, the majority of fish are classified as Least Concern (135 species/76.3%), but two species, Cobitis taurica and Gobio tauricus, are Critically Endangered.

Year-round spawning of three tropical Cypriniformes fishes in Southeast Asia

Present knowledge on spawning seasonality of freshwater fishes in tropical Asia and their relationship with environmental factors remains limited. Three Southeast Asian Cypriniformes fishes, Lobocheilos ovalis, Rasbora argyrotaenia and Tor Tambra, found in rainforest streams in Brunei Darussalam were studied on a monthly basis for a period of 2 years. To assess spawning characteristics, seasonality, gonadosomatic index and reproductive phases were examined from 621 L. ovalis, 507 R. argyrotaenia and 138 T. tambra. This study also examined environmental factors such as rainfall, air temperature, photoperiod and lunar illumination that may influence the timing of spawning of these species. We found that L. ovalis, R. argyrotaenia and T. tambra were reproductively active throughout the year but did not find that spawning in these species were associated with any of the investigated environmental factors. Our study showed that the non-seasonal reproductive ecology found in the tropical cypriniform species is distinctly different from that of temperate cypriniforms, which are known to follow spawning seasonality, suggesting an evolutionary adaptation to ensure their survival in an unstable environment. The reproductive strategy and ecological responses found in the tropical cypriniforms might be shifted in response to climate change scenarios in the future.

Fishery livelihoods and an adaptation to climate change-induced threats at the Bhomra Wetland: a case study through a stakeholder-driven approach

Abstract The main aim of the present study is to assess the present ecological status of Bhomra wetland with respect to the fisheries and associated ecosystem services and to prescribe some climate-smart adaptation technologies in changing climate. The analysis showed increasing temperature (Kendall's tau = 0.60, p<0.05) and decreasing rainfall (Kendall's tau = −0.33, p<0.05) in the studied region over the last two decades. The wetland is dominated by Cypriniformes species followed by Perciformes species. The overall production of the fish (i.e., 32155 kg) from the wetland in 2020 is below the average production of the last 10 year (i.e., 54704 kg). Canonical correspondence analysis reviled a strong correlation (p<0.05) between the fish assemblage and ecological parameters (mainly total alkalinity and available nitrate) of the wetland. Though the species diversity was moderate along with the moderate species richness (i.e., Shannon-Weiner diversity index = 1.581±0.007), the evenness (Simpson evenness index = 0.995±0.001) was high throughout the wetland. The wetland was found suitable for carp culture, but the ecosystem's health has degraded over time. The communication further suggests several climate-resilient strategies for sustainable utilization of wetland ecosystem services and increasing adaptive capacity of the fishers.

FISH SPECIES DIVERSITY OF KOLLERU LAKE AT RAMSAR OF ELURU DISTRICT ANDHRA PRADESH, INDIA

During the study period we recorded 29 species The sh production plays a signicant role in the human economy. India has vast potential for development of inland sheries. In the present study an attempt has been made to evaluate the physico-chemical characteristic features and sh fauna diversity of Kolleru Lake Eluru District. It proposed to enhancement of sh production in a sub urban perennial water body in Eluru district of Andhra Pradesh. The study was conducted during May 2021 to April 2022. The study revealed that different regions of the tank receive variable precipitation and hence meteorological factors governing the physico-chemical properties of the tank which in turn inuence planktonic diversity and so that all the physico-chemical and biological factors have direct inuence on the sh production. The present study, it observed that all the physico-chemical parameters are at nearly permissible limit at all the 3 identied stations. It is estimated that the sh fauna of Kolleru Lake consists of 29 species belonging to 12 families. Among the collections 10 species of Cypriniformes, order Siluriformes consists of 5 species, Channiformes consists of 05 species, Perciformes 03 species, and Osteoglossiformes 01 species. Therefore, it is suggested that the immediate measures may be to avoid further contamination of this Lake which has been started contaminated due to anthropological activities. Finally it may be concluded that the Kolleru Lake is rich in sh diversity and is still in a position to set a good example of conservation of native sh fauna by the sustainable management practices.

Towards the phylogenetic placement of the enigmatic African genus Prolabeops Schultz, 1941.

The small cyprinid genus Prolabeops Schultz, 1941 is restricted to the Nyong and Sanaga River systems in Cameroon. In the past, the genus had been suggested to be either a member of the Labeoninae, Torinae or the Smiliogastrinae mainly on the basis of morphological similarities, and it is nowadays considered as incertae sedis within the Cypriniformes. This study provides the first attempt to reveal the phylogenetic position of Prolabeops using molecular data. For this purpose, the authors sequenced a large fraction of the mitochondrial genome (c. 13,600 bp), including all mitochondrial protein coding genes, of two Prolabeops melanhypopterus specimens and an additional four Enteromius specimens. The large-scale phylogenetic analysis was based on an alignment including all mitochondrial protein coding genes of 902 specimens representing c. 899 cypriniform species. Prolabeops was clearly recovered within the African Smiliogastrinae, forming a weakly supported clade together with Enteromius jae, Enteromius hulstaerti and Barboides gracilis. The study data underline the urgent need of a thorough taxonomic revision of the small African barbs collectively placed in the genus Enteromius.

Phylogeographic pattern, genetic diversity, and evolutionary history of the enigmatic freshwater fish species Aulopyge huegelii (Actinopterygii: Cyprinidae)

The genus Aulopyge, represented by a single species, the Dalmatian barbelgudgeon, Aulopyge huegelii, is an endemic genus with very restricted distribution range comprising several rivers in southern Croatia and Bosnia and Herzegovina. In this study, molecular genetic analyses based on three molecular markers (one nuclear and two mitochondrial) were performed to confirm the position of Aulopyge within Cyprinidae, obtain data on its evolutionary history, and describe its population genetic structure and diversity. Specimens of A. huegelii were obtained throughout the distribution range. Phylogenetic reconstruction corroborated the independent position of this species and its placement within the Barbinae subfamily. The evolutionary history of A. huegelii started already in the middle Oligocene, whereas intraspecific divergences that left a trace in its current genetic structure and diversity are of much younger origin, starting in the middle Pleistocene. Unlike in other cypriniform species and genera distributed in the Dinaric karst region, there is no significant structuring within A. huegelii, or distribution of haplotypes concordant with the geographic scale. Furthermore, low effective population sizes estimated for most populations and low genetic diversities within them raise strong concerns about the viability and future survival of this endemic species.

Completely mitochondrial genome of Neolissochilus heterostomus

In this study, we determined the complete mitochondrial genome of Neolissochilus heterostomus. The genome is 16,585 bp in length, including 2 ribosomal RNA genes, 13 proteins-coding genes, 22 transfer RNA genes, and two non-coding control regions. Sequence analysis showed that the overall base composition of N. heterostomus is T 24.8%, C 27.7%, A 31.7%, and G 15.8%. The sequence is a slight A + T bias of 56.5%, which is similar to other fishes. We describe a phylogenetic analysis of 16 species of Cypriniformes based on the complete mitochondrial genome, and the result showed that N. stracheyi is most closely related to N. heterostomus. This mitogenome sequence data would play an important role in the investigation of phylogenetic relationship of the Cyprinidae.

Vertebrate prey composition analysis of the Pallas’s cat (Otocolobus manul) in the Gongga Mountain Nature Reserve, based on fecal DNA

Abstract Diet analysis is essential to fully understanding the biology of a species and its function within the ecosystem, and is also key in identifying food web interactions and the population dynamics of predators and prey. There is currently little information on the diet of small to mid-sized carnivores due to their elusive behavior. We used a DNA-based method to analyze the vertebrate prey of the Pallas’s cat (Otocolobus manul) in the Gongga Mountain Nature Reserve of southwestern China, a global biodiversity hotspot region. We confirmed 14 scat samples containing the Pallas’s cat DNA from 100 small carnivore scats collected at altitudes between 3200 and 4900 m, and then performed polymerase chain reaction (PCR) amplifications using primers targeting the vertebrate mitochondrial 12S rRNA gene with a blocking oligonucleotide specific to the predator sequence. We identified a total of 18 prey taxa, including nine mammals, eight birds and one fish. Our results show that pikas (in 79% of the scats) and birds (in 50% of the scats) are the predominant prey consumed by the Pallas’s cat in our investigation area. The most important finding in our study is that Cypriniformes species were found in the Pallas’s cat’s diet, exhibiting dietary diversification consistent with the accessible fauna of the surrounding environment. In order to increase the detectability of both typical and rare vertebrate prey items, we constructed a blocking primer to inhibit the amplification of the Pallas’s cat DNA.

Polymorphism of MHC class IIB in an acheilognathid species, Rhodeus sinensis shaped by historical selection and recombination

BackgroundRhodeus sinensis is a bitterling species occurring throughout the numerous freshwater systems on the East Asia. Here, we analyzed the diversity of the MHC class IIB (DAB) genes from this species, which may offer meaningful insights into evolutionary processes in this species as well as other bitterlings.ResultsUsing cDNA and gDNA samples from 50 individuals, we discovered classical 140 allelic sequences that could be allocated into either DAB1 (Rhsi-DAB1) or DAB3 (Rhsi-DAB3). DAB sequences completely lacking the intron, but identical or similar to Rhsi-DAB1, were also discovered from our gDNA samples, and this intron loss likely originated from the retrotransposition events of processed mDNA. The β1 domain was the most polymorphic in both Rhsi-DAB1 and -DAB3. Putative peptide biding residues (PBRs) in Rhsi-DAB1, but not in Rhsi-DAB3, exhibited a significant dN/dS, presumably indicating that different selection pressures have acted on those two DABs. Recombination between different alleles seemed to have contributed to the increase of diversity in Rhsi-DABs. Upon phylogenetic analysis, Rhsi-DAB1 and -DAB3 formed independent clusters. Several alleles from other species of Cypriniformes were embedded in the clade of Rhsi-DAB1, whereas Rhsi-DAB3 clustered with alleles from the wider range of taxa (Cyprinodontiformes), indicating that these two Rhsi-DABs have taken different historical paths.ConclusionsA great deal of MHC class IIB allelic diversity was found in R. sinensis, and gene duplication, selection and recombination may have contributed to this diversity. Based on our data, it is presumed that such historical processes have commonly or differently acted on the polymorphism of Rhsi-DAB1 and -DAB3.

First record of Trichodina centrostrigeata Basson, Van As & Paperna, 1983 (Ciliophora: Trichodinidae) from Oreochromis niloticus (Linnaeus, 1758) cultured in southeastern Mexico

Nile tilapia Oreochromis niloticus is one of the most economically important freshwater fish cultivated worldwide. Despite its importance and being one of the cichlid fish most studied from a parasitological point of view in Mexico, there are few studies about the ectoparasite protozoa that infect them. In this study, a total of 240 juvenile individuals of O. niloticus from an experimental culture (in Tabasco, Mexico) were examined to detect the presence of trichodinid parasites. Trichodinid parasites were impregnated with silver nitrate and stained with Harris´ hematoxylin solution for taxonomic evaluation. A disc-shaped trichodinid with a body diameter of 38 ± 3.3 μm adhesive disc diameter of 34 ± 3.3 μm and a denticulate ring diameter of 19 ± 2.1 μm was found. Trichodina centrostrigeata has been previously reported having specificity for cypriniform species, but in the present study, the Nile tilapia was reported as a new fish host and southeastern Mexico as a new geographical distribution for this parasite.

Convergent evolution of locomotor morphology but not performance in gymnotiform swimmers.

Convergent evolution of a novel locomotor strategy implies that a fitness benefit may be associated with the new gait. Opportunities to study this phenomenon are often constrained by a lack of transitional taxa, but teleost fishes offer examples of extant species across such evolutionary shifts in gait. For instance, one species from Osteoglossiformes and the entire order of Gymnotiformes independently evolved a novel gait, gymnotiform locomotion, where thrust is produced by the undulation of an elongate anal fin. Here, we investigate whether this convergence in gait is also associated with similarities in shape, burst swimming abilities, and/or steady-swimming energetics. Specifically, we measured body and fin morphology of fish within Gymnotiformes and Osteoglossiformes, along with closely related Siluriformes and Cypriniformes, to examine the link between gymnotiform locomotion and morphology in a phylogenetic context. Second, we tested the burst swimming capabilities and oxygen consumption during endurance swimming of a subset of the same gymnotiform, osteoglossiform, and cypriniform species, including "transitional" Osteoglossiformes that exhibit intermediate gaits, to determine whether the evolution of this specialized gait is associated with a change in either of these performance metrics. Our results suggest that convergence on the gymnotiform gait is associated with morphological convergence, but does not constrain a fish's maximum sprinting speeds or their energetic demands during steady swimming.

The complex trophic anatomy of silver carp, Hypophthalmichthys molitrix, highlighting a novel type of epibranchial organ

Hypophthalmichthys molitrix, silver carp, is an invasive Asian carp that has become increasingly widespread and ecologically destructive within the upper Mississippi River Basin. Its complex trophic anatomy may help explain the apparent efficiency with which they consume phytoplankton, outcompeting native filter feeders. This cypriniform species is characterized by trophic synapomorphies that include a palatal organ, loss of upper pharyngeal jaws, and a hypertrophied lower pharyngeal jaw. However, in silver carp these structures have become greatly modified and diverge from the more basal condition that characterizes species such as goldfish. The trophic apparatus of silver carp is composed of discrete structures that are functionally coupled: filtering plates, paired epibranchial organs (EBO), a modified palatal organ composed of large muscular folds that interdigitate with the filtering plates, and hypertrophied lower pharyngeal jaws and teeth. The filtering plates fill a significant portion of the buccal cavity, especially since the distal parts of these filtering plates make up a key component of the EBOs. EBOs, food aggregating structures found in many teleosts, are thought to have independently evolved at least six times. Ranging in complexity from small slits on the dorsal wall of the pharyngeal cavity to exceedingly intricate spiraling structures, EBOs are morphologically diverse among filter-feeding fishes. Despite this morphological diversity and broad taxonomic distribution, little is known regarding the functional anatomy of the EBO. Moreover, the EBO in silver carp is distinct from the organs previously described in other species, being created by four independent pharyngeal involutions (instead of the more typical one or two) that form spiral-shaped pharyngeal tubes surrounded by circumferential muscle. On each side of the head greatly hypertrophied hyomandibulae and opercles are connected to the anterior cartilaginous caps of the bilateral EBOs via enlarged muscles. Given that these fish are pump filter feeders we hypothesize that the opercula may compress and expand the EBOs during pumping causing food to be moved posteriorly toward the pharyngeal jaws.

Direct and indirect effects of predatory young‐of‐year fishes in a dryland river food web

Summary Young‐of‐year (YOY) fishes are sometimes numerically dominant vertebrate consumers in many large river systems, but their effects as predators are not as well understood as those of adult fishes. We predicted that YOY fishes influence community composition and abundance of invertebrate prey. Predation effects could be especially important in recruitment‐driven dryland river systems, where YOY fishes seasonally comprise a large portion of overall fish biomass. We conducted a mesocosm experiment to quantify effects of YOY fishes on trophic dynamics and interactions with environmental factors in a dryland river food web. We manipulated presence of YOY fishes (an assemblage of cypriniform species) and supplemental allochthonous carbon (LEAF treatments) in 24 mesocosms, and measured invertebrate abundance and diversity over 6 weeks. Experimental conditions mimicked a seasonal river drying regime that occurs during YOY fish growth. Seasonal drying in the Rio Grande frequently results in isolated pools with altered habitat complexity and riparian connectivity. Fishes exerted direct top‐down control of invertebrate assemblage composition through differential prey selection, and indirect control mediated by non‐lethal responses of invertebrates to predatory fishes. We observed enhanced water clarity in LEAF treatments associated with greater prey selectivity in fishes, presumably through enhanced visual feeding. Stable isotope analysis (C and N) was used to measure indirect impacts of YOY fishes on invertebrate prey items. YOY fishes caused a significant decrease in “isotopic niche breadth” among invertebrate taxa, suggesting that fish predators limit foraging opportunities for these consumers. However, allochthonous carbon sources were predominant in invertebrate diets in all LEAF treatments, suggesting consumer access to more biologically available autochthonous production is limited by factors other than fish predation. Although the roles of abiotic drivers and adult fishes in determining food web structure have received more attention, our results indicate that YOY fishes exert biologically relevant top‐down control of invertebrate assemblage composition and trophic complexity in dryland river ecosystems against a backdrop of substantial changes in carbon availability and abiotic conditions (e.g. water quality and habitat volume) over the growing season.

Design of character-based DNA barcode motif for species identification: A computational approach and its validation in fishes.

The DNA barcodes are generally interpreted using distance-based and character-based methods. The former uses clustering of comparable groups, based on the relative genetic distance, while the latter is based on the presence or absence of discrete nucleotide substitutions. The distance-based approach has a limitation in defining a universal species boundary across the taxa as the rate of mtDNA evolution is not constant throughout the taxa. However, character-based approach more accurately defines this using a unique set of nucleotide characters. The character-based analysis of full-length barcode has some inherent limitations, like sequencing of the full-length barcode, use of a sparse-data matrix and lack of a uniform diagnostic position for each group. A short continuous stretch of a fragment can be used to resolve the limitations. Here, we observe that a 154-bp fragment, from the transversion-rich domain of 1367 COI barcode sequences can successfully delimit species in the three most diverse orders of freshwater fishes. This fragment is used to design species-specific barcode motifs for 109 species by the character-based method, which successfully identifies the correct species using a pattern-matching program. The motifs also correctly identify geographically isolated population of the Cypriniformes species. Further, this region is validated as a species-specific mini-barcode for freshwater fishes by successful PCR amplification and sequencing of the motif (154bp) using the designed primers. We anticipate that use of such motifs will enhance the diagnostic power of DNA barcode, and the mini-barcode approach will greatly benefit the field-based system of rapid species identification.

Papers supported by the All Cypriniformes Species Inventory Project (ACSII) and the Asian Society of Ichthyologists including those presented at the Asian Fish Biodiversity Conference in Penang, Malaysia, 11–14 January 2014 (Table of contents)

Papers supported by the All Cypriniformes Species Inventory Project (ACSII) and the Asian Society of Ichthyologists including those presented at the Asian Fish Biodiversity Conference in Penang, Malaysia, 11–14 January 2014 (Table of contents)