Using DNA barcoding to assess Caribbean reef fish biodiversity: expanding taxonomic and geographic coverage

Marine and freshwater fishes of Alabama: a revised checklist and discussion of taxonomic issues

Checklists are fundamental and important tools for organizing information about biodiversity that provide a basis for conservation and additional scientific research. While Alabama is recognized as an aquatic biodiversity hotspot with the highest native freshwater fish diversity in the contiguous United States, we currently lack an up-to-date list of the states fishes. In particular, much has changed over the past ~20 years regarding our knowledge of fishes from Alabama and the Mobile River Basin, rendering past comprehensive treatments by Mettee et al. (1996) and Boschung and Mayden (2004) out of date. Here, we provide a revised checklist of marine and freshwater fishes known from the coastal and inland waters of Alabama that includes 463 species (335 primarily freshwater fishes, and 128 marine or diadromous fishes) in 35 orders, 78 families, and 176 genera. Extant, extirpated, and extinct species are included, as are putative candidate species. The checklist is based on prior work, searches of the literature and online sources, as well as parsing a large compilation of >140,000 fish records for Alabama and the Mobile River Basin from 37 data providers in the global Fishnet2 database (www.fishnet2.net) and >4000 marine survey records from the SEAMAP database (https://www.gsmfc.org/seamap.php). After editing and quality control checks, the final combined database contained 144,215 collection records, ~95% of which were georeferenced. We discuss the species descriptions, nomenclatural changes, and updates to marine species that account for changes to the state list, and we close with a discussion of ~13 candidate species forms that remain undescribed, which represent outstanding taxonomic issues in need of further research attention.

DNA barcoding of reef-associated fishes of Saint Martin's Island, Northern Bay of Bengal, Bangladesh

This study employs the DNA barcoding approach to make a molecular taxonomic catalog of reef fishes of Saint Martin's Island (SMI), an ecologically critical area (ECA), and Marine Protected Area (MPA) in Bangladesh. DNA barcoding, along with morphological analysis, confirmed 84 reef-associated fish species in SMI belonging to 16 orders, 39 families, and 67 genera. A total of 184 sequences were obtained in this study where 151 sequences (534-604 bp) of 81 species were identified from the COI barcode gene and 33 sequences (609 bp) of 19 species from the 16S rRNA gene region which were submitted to the GenBank and Barcode of Life Data System (BOLD). Among these sequences, 70 sequences of the COI gene and 16 sequences of 16S rRNA gene region from 41 species were submitted for the first time into the GenBank from Bangladesh. For molecular characterization analysis, another 37 sequences of 15 reef fish species of SMI were added from previous studies, making a total of 221 DNA sequences which comprised 179 sequences of 96 species for the COI gene and 42 sequences of 26 species for the 16S rRNA gene region. The COI sequences contain 145 haplotypes with 337 polymorphic sites, and the mean genetic distances within species, genera, and families were calculated as 0.34%, 12.26%, and 19.03%, respectively. On the contrary, 16S rRNA sequences comprised 31 haplotypes with 241 polymorphic sites, and the mean genetic divergences within species, genera, and families were 0.94%, 4.72%, and 12.43%, respectively. This study is a significant contribution to the marine biodiversity of Bangladesh which would facilitate the assessment of species diversity for strategizing management action. It is also an important input to the DNA barcode library of reef fishes of the northern Bay of Bengal.

The newest COI molecular detection of Asian redtail catfish Hemibagrus nemurus (Valenciennes, 1840) in Progo River, Magelang, Central Java, Indonesia

Objective

This study describes the newest deoxyribonucleic acid (DNA) barcoding Asian redtail catfish (Hemibagrus nemurus) in the Progo River, Magelang, Central Java, Indonesia.

Materials and Methods

Ten fish were caught in the Progo River, Magelang, Central Java, Indonesia. The polymerase chain reaction was the molecular diagnosis to detect the sequences of DNA of Cytochrome Oxidase I compared to National Center for Biotechnology Information data (GenBank).

Results

The results showed that the percent identity was not 100% with H. nemurus data from other locations (GenBank), including Indonesia. The closest percent identity was H. nemurus from Java Island (Accession ID: MK312566.1) with 97.6% similarity. The genetic mutation that happened might be due to environmental change (pollution) in the Progo River recently.

Conclusions

This study showed a genetic mutation in H. nemurus from Progo River may be caused by environmental change. Low pollution exposure levels may not be detrimental (lethal) to fish. However, it can affect fish fertility, which leads to population degradation (gene variation). Attention must be increased for fish survival in the future.

A comprehensive DNA barcode inventory of Austria's fish species

Austria is inhabited by more than 80 species of native and non-native freshwater fishes. Despite considerable knowledge about Austrian fish species, the latest Red List of threatened species dates back 15 years and a systematic genetic inventory of Austria's fish species does not exist. To fulfill this deficit, we employed DNA barcoding to generate an up-to-date and comprehensive genetic reference database for Austrian fish species. In total, 639 newly generated cytochrome c oxidase subunit 1 (COI) sequences were added to the 377 existing records from the BOLD data base, to compile a near complete reference dataset. Standard sequence similarity analyses resulted in 83 distinct clusters almost perfectly reflecting the expected number of species in Austria. Mean intraspecific distances of 0.22% were significantly lower than distances to closest relatives, resulting in a pronounced barcoding gap and unique Barcode Index Numbers (BINs) for most of the species. Four cases of BIN sharing were detected, pointing to hybridization and/or recent divergence, whereas in Phoxinus spp., Gobio spp. and Barbatula barbatula intraspecific splits, multiple BINs and consequently cryptic diversity were observed. The overall high identification success and clear genetic separation of most of the species confirms the applicability and accuracy of genetic methods for bio-surveillance. Furthermore, the new DNA barcoding data pinpoints cases of taxonomic uncertainty, which need to be addressed in further detail, to more precisely assort genetic lineages and their local distribution ranges in a new National Red-List.

An updated, illustrated inventory of the marine fishes of the US Virgin Islands

The US Virgin Islands (USVI) include St. John and St. Thomas on the Puerto Rican Platform (PRP) and St. Croix, isolated by 2000 m deep water 45 km south of that platform. Previous inventories of the marine fishes of these islands include a comprehensive 2014 checklist of the fishes of St. Croix and a list of the fishes of the PRP produced in 2000. The latter list noted the locations of many records of the plateau's fishes, allowing the construction of a combined inventory for St. John and St. Thomas. Those two islands are treated here as a single faunal unit because they are only 3.5 km apart on a shared shallow shelf with various islets and reefs in between. Here we provide updated information on those two USVI (St. Croix and St. John-Thomas) marine fish faunas. The additions to the St. Croix and St. John-Thomas inventories presented here are based on a combination of information from the two sources indicated above, more recent publications dealing with those faunas, a review of location records on various online sources of biogeographic data, and voucher photographs taken of fishes in the field by authors of this paper and other citizen scientists. This assessment increased the known fauna of St. Croix by 7.5% to 585 species. The inventory for St. John-Thomas increased by 39.9% from 401 species on the 2000 PRP list to 561 with the inclusion of records from other sources. On-site mtDNA (COI) barcodes are available for approximately one-third of the species of the St. John-Thomas fauna, but for only one species collected at St. Croix. A set of underwater photographs of 372 species (34 of them representing the sole record of a species) from St. John-Thomas and of 11 shallow-water species added to the St. Croix fauna is included. These represent occurrence vouchers and also are intended to facilitate future work that builds on the present compendium.

Genetic Structure of the Mangrove Killifish Kryptolebias hermaphroditus Costa, 2011 (Cyprinodontiformes: Aplocheiloidei) Supports A Wide Connection among its Populations

The Kryptolebias marmoratus species group is composed of the only three vertebrate species that lack females. These species present only males and simultaneously hermaphroditic individuals; that are able to reproduce by allogamy, with males, or by autogamy, performing self-fertilization and generating clones of themselves. The proportion of males is variable among those species and even among their populations. Kryptolebias hermaphroditus has the smallest proportion of males. Indeed, no males have been recorded in most known populations. This is a mainly autogamous species, with small populations having a disjunct distribution along the eastern and northern coast of Brazil. Species presenting such adaptations would be expected to have an elevated rate of genetic population structure, reflecting any barriers that obstruct gene flow between populations. Partial sequences of the mitochondrial cytochrome c oxidase I (COI) gene from 335 individuals were sampled to perform a population analysis. Only a single haplotype of COI, widely distributed throughout all the sampled populations, was recovered for K. hermaphroditus. Here we hypothesize that the high degree of communication within populations is probably the main biological feature leading to this pattern.

The critical role of natural history museums in advancing eDNA for biodiversity studies: a case study with Amazonian fishes

Ichthyological surveys have traditionally been conducted using whole-specimen, capture-based sampling with varied but conventional fishing gear. Recently, environmental DNA (eDNA) metabarcoding has emerged as a complementary, and possible alternative, approach to whole-specimen methodologies. In the tropics, where much of the diversity remains undescribed, vast reaches continue unexplored, and anthropogenic activities are constant threats; there have been few eDNA attempts for ichthyological inventories. We tested the discriminatory power of eDNA using MiFish primers with existing public reference libraries and compared this with capture-based methods in two distinct ecosystems in the megadiverse Amazon basin. In our study, eDNA provided an accurate snapshot of the fishes at higher taxonomic levels and corroborated its effectiveness to detect specialized fish assemblages. Some flaws in fish metabarcoding studies are routine issues addressed in natural history museums. Thus, by expanding their archives and adopting a series of initiatives linking collection-based research, training and outreach, natural history museums can enable the effective use of eDNA to survey Earth's hotspots of biodiversity before taxa go extinct. Our project surveying poorly explored rivers and using DNA vouchered archives to build metabarcoding libraries for Neotropical fishes can serve as a model of this protocol.

Molecular systematics of the Awaous banana complex (River gobies; Teleostei: Oxudercidae)

Diadromous fishes can exhibit interesting evolutionary and population-level patterns given their use of freshwater and marine environments as part of their life histories. The River goby genus Awaous are prominent members of riverine ichthyofaunas and occur throughout Atlantic and Pacific slopes of the Americas from the southern United States to Ecuador and Brazil. Here we study the widespread and polymorphic Awaous banana complex to assess phylogeographic patterns and test previous hypotheses that all populations of this species in the Americas belong to the same species. Analysis of sequence data based on the mitochondrial cytochrome oxidase I gene shows multiple clades within the Atlantic and Pacific basins, which correspond to previously described species. Additionally, haplotype analysis demonstrates unique and unconnected networks between these species. Within these clades we document biogeographic patterns that are congruent with results of other co-occurring diadromous species, as well as a novel biogeographic pattern for the region. Our results support the recognition of distinct species of Awaous in the Atlantic (A. banana and A. tajasica) and Pacific (A. transandeanus) basins. These results are concordant with previously established morphological characters permitting the separation of these species.

A new Hyphessobrycon (Characiformes: Characidae) of the Hyphessobrycon heterorhabdus species-group from the lower Amazon basin, Brazil

ABSTRACT A new species of Hyphessobrycon belonging to the Hyphessobrycon heterorhabdus species-group from the lower rio Tapajós, state of Pará, Brazil, is described. The new species is allocated into the Hyphessobrycon heterorhabdus species-group due to its color pattern, composed by an anteriorly well-defined, horizontally elongated humeral blotch that becomes diffuse and blurred posteriorly, where it overlaps with a conspicuous midlateral dark stripe that becomes blurred towards the caudal peduncle and the presence, in living specimens, of a tricolored longitudinal pattern composed by a dorsal red or reddish longitudinal stripe, a middle iridescent, golden or silvery longitudinal stripe, and a more ventrally-lying longitudinal dark pattern composed by the humeral blotch and dark midlateral stripe. It can be distinguished from all other species of the group by possessing humeral blotch with a straight or slightly rounded ventral profile, lacking a ventral expansion present in all other species of the group. The new species is also distinguished from Hyphessobrycon heterorhabdus by a 9.6% genetic distance in the cytochrome c oxidase I gene. The little morphological distinction of the new species when compared with its most similar congener, H. heterorhabdus, indicates that the new species is one of the first truly cryptic fish species described from the Amazon basin.

DNA barcoding of commercially important reef fishes in Weh Island, Aceh, Indonesia

Knowledge on the precise identification of fish resources is critical for sustainable fisheries management. This study employs the DNA barcoding approach to generate a molecular taxonomic catalogue of commercially important reef fishes in the waters of Weh Island (Aceh Province), the most northerly inhabited island in the biodiverse Indonesian Archipelago. The waters not only support artisanal fisheries but also a feeder for the industry in the greater island of Aceh. In total, 230 specimens from 72 species belonging to 32 genera and 17 families were DNA barcoded, representing a major segment of the captured reef fish taxa and a quarter of fish species diversity that had previously been recorded. The sequence read lengths were 639 bp revealing 359 conserved sites, 280 variable sites, 269 parsimony informative and 11 singletons. Our molecular findings paralleled the morphological identification with no evidence of cryptic species or new species discovery. This study is a significant contribution to the fisheries statistics of this area, which would facilitate assessment of species catch composition and hence for strategizing management plans. It is an important input to the DNA barcode library of Indonesian marine fishes and to the global DNA barcode entries in general.

Two new species of Plectranthias (Teleostei, Serranidae, Anthiadinae) from mesophotic coral ecosystems in the tropical Central Pacific

Two new species of Plectranthias perchlets are described, collected from mesophotic coral ecosystems in French Polynesia and the Republic of the Marshall Islands, in the tropical Central Pacific. Plectranthiaspolygoniussp. nov. was collected at a depth of 105 m in Tahiti, French Polynesia, and 120 m in Maloelap Atoll, Republic of the Marshall Islands. It was also observed in Moorea and Rangiroa (French Polynesia), and at Majuro and Erikub Atolls, Republic of the Marshall Islands. Plectranthiashinanosp. nov. was collected at a depth of 90–98 m in Tahiti, French Polynesia, and observed in Moorea. The barcode fragment of the cytochrome oxidase I gene of Plectranthiaspolygoniussp. nov. does not closely match any published sequence of Plectranthias, with approximately 15% uncorrected divergence from several species. Plectranthiaspolygoniussp. nov. can be distinguished from all of its congeners by coloration and morphology. The barcode fragment of the COI gene of Plectranthiashinanosp. nov. is closest to Plectranthiasbennetti, with 5.4% uncorrected divergence. Plectranthiashinanosp. nov. is also distinguished from all of its congeners by morphology, and a coloration that includes two indistinct black spots along the base of the dorsal-fin, and transparent yellow dorsal and anal fin membranes. With this publication, the genus Plectranthias now comprises 58 valid species, with representatives from tropical to temperate waters of the Atlantic, Pacific, and Indian oceans. These two new discoveries add to the growing body of research highlighting the rich biodiversity of mesophotic ecosystems.

Assessing species diversity of Coral Triangle artisanal fisheries: A DNA barcode reference library for the shore fishes retailed at Ambon harbor (Indonesia)

The Coral Triangle (CT), a region spanning across Indonesia and Philippines, is home to about 4,350 marine fish species and is among the world's most emblematic regions in terms of conservation. Threatened by overfishing and oceans warming, the CT fisheries have faced drastic declines over the last decades. Usually monitored through a biomass-based approach, fisheries trends have rarely been characterized at the species level due to the high number of taxa involved and the difficulty to accurately and routinely identify individuals to the species level. Biomass, however, is a poor proxy of species richness, and automated methods of species identification are required to move beyond biomass-based approaches. Recent meta-analyses have demonstrated that species richness peaks at intermediary levels of biomass. Consequently, preserving biomass is not equal to preserving biodiversity. We present the results of a survey to estimate the shore fish diversity retailed at the harbor of Ambon Island, an island located at the center of the CT that display exceptionally high biomass despite high levels of threat, while building a DNA barcode reference library of CT shore fishes targeted by artisanal fisheries. We sampled 1,187 specimens and successfully barcoded 696 of the 760 selected specimens that represent 202 species. Our results show that DNA barcodes were effective in capturing species boundaries for 96% of the species examined, which opens new perspectives for the routine monitoring of the CT fisheries.

Co-evolution of cleaning and feeding morphology in western Atlantic and eastern Pacific gobies

Cleaning symbioses are mutualistic relationships where cleaners remove and consume ectoparasites from their clients. Cleaning behavior is rare in fishes and is a highly specialized feeding strategy only observed in around 200 species. Cleaner fishes vary in their degree of specialization, ranging from species that clean as juveniles or facultatively as adults, to nearly obligate or dedicated cleaners. Here, we investigate whether these different levels of trophic specialization correspond with similar changes in feeding morphology. Specifically, we model the evolution of cleaning behavior across the family Gobiidae, which contains the most speciose radiation of dedicated and facultative cleaner fishes. We compared the cranial morphology and dentition of cleaners and non-cleaners across the phylogeny of cleaning gobies and found that facultative cleaners independently evolved four times and have converged on an intermediate morphology relative to that of dedicated cleaners and non-cleaning generalists. This is consistent with their more flexible feeding habits. Cleaner gobies also possess a distinct tooth morphology, which suggests they are adapted for scraping parasites off their clients and show little similarity to other cleaner clades. We propose that evolutionary history and pre-adaptation underlie the morphological and ecological diversification of cleaner fishes.

Molecular characterization of nearshore baitfish populations in Bermuda to inform management

Small-bodied marine fishes play an important role in the food web, feeding both larger fishes and seabirds. Often referred to as baitfishes, they concentrate seasonally in coastal areas in large, often heterospecific assemblages that are targeted by both commercial and recreational fishers. Given apparent declines in at least some of Bermuda’s baitfish species over the past 40 years, it is useful to determine the species composition of baitfish assemblages, and how it varies among sites, in order to inform management. Using genetic barcoding of the Cytochrome c oxidase 1 gene (COI), we confirm species identity, assess intraspecific genetic diversity locally, and determine rates of broader genetic connectivity for baitfish assemblages in Bermuda. Species analyzed included Hypoatherina harringtonensis, Anchoa choerostoma, Jenkinsia lamprotaenia, Harengula humeralis, Opisthonema oglinum and Sardinella aurita. Species identification based on molecular barcoding revealed some misidentification of individuals based solely on gross morphological characteristics, with an error rate of 11%, validating the usefulness of this approach. Interestingly, sequence results for the endemic Bermuda anchovy, A. choerostoma, were within 1% similarity to the more broadly distributed big-eye anchovy, A. lamprotaenia, and thus additional analyses are warranted to evaluate the genetic basis for endemism. Estimates of genetic diversity within and among baitfish assemblages in Bermuda were high, indicating high rates of local connectivity among sites for all species. As such, management should consider Bermuda’s baitfish species as single, highly mixed populations. However, with the exception of H. humeralis and the endemic A. choerostoma, significant genetic differentiation and population structure were found when comparing Bermuda’s baitfish populations with those from other regions, suggesting limited gene flow between other regions and Bermuda for these species. Limited regional connectivity has implications for management, as strong genetic divergence suggests that populations in Bermuda are predominantly self-seeding and thus not likely to be replenished from distant populations. These results therefore support precautionary management of baitfish species in Bermuda.

Cirrhilabruswakanda, a new species of fairy wrasse from mesophotic ecosystems of Zanzibar, Tanzania, Africa (Teleostei, Labridae)

Cirrhilabruswakandasp. nov. is described on the basis of the holotype and four paratypes collected between 50 and 80m depth over low-complexity reef and rubble bottoms at the east coast of Zanzibar, Tanzania, Africa. The new species belongs to a group of fairy wrasses from the western Indian Ocean, sharing a combination of characters that include: short pelvic fins (not or barely reaching anal-fin origin); relatively unmarked dorsal and anal fins; males with a strongly lanceolate caudal fin (except in C.rubrisquamis); both sexes with a pair of prominent facial stripes above and below the orbit; and both sexes with prominent purple scales and osseus elements that persist, and stain purple, respectively, even in preservation. This group of fairy wrasse is part of a larger complex that includes related species from the western Pacific Ocean. In addition to meristic and morphometric comparisons, we also compare mitochondrial DNA sequence data to the aforementioned, putatively related species.

Host DNA integrity within blood meals of hematophagous larval gnathiid isopods (Crustacea, Isopoda, Gnathiidae)

BACKGROUND

Juvenile gnathiid isopods are common ectoparasites of marine fishes. Each of the three juvenile stages briefly attach to a host to obtain a blood meal but spend most of their time living in the substrate, thus making it difficult to determine patterns of host exploitation. Sequencing of host blood meals from wild-caught specimens is a promising tool to determine host identity. Although established protocols for this approach exist, certain challenges must be overcome when samples are subjected to typical field conditions that may contribute to DNA degradation. The goal of this study was to address a key methodological issue associated with molecular-based host identification from free-living, blood-engorged gnathiid isopods-the degradation of host DNA within blood meals. Here we have assessed the length of time host DNA within gnathiid blood meals can remain viable for positive host identification.

METHODS

Juvenile gnathiids were allowed to feed on fish of known species and subsets were preserved at 4-h intervals over 24 h and then every 24 h up to 5 days post-feeding. Host DNA extracted from gnathiid blood meals was sequenced to validate the integrity of host DNA at each time interval. DNA was also extracted from blood meals of wild-fed gnathiids for comparison. Attempts were also made to extract host DNA from metamorphosed juveniles.

RESULTS

Using a cox1 universal fish primer set, known fish host DNA sequences were successfully identified for nearly 100% of third-stage juvenile gnathiid blood meals, digested for up to 5 days post-feeding. For second-stage juveniles, host identification was 100% successful when gnathiids were preserved within 24 h of collection. Fish hosts were positively identified for 69% of sequences from wild-fed gnathiid isopods. Of the 31% of sequences not receiving a ≥ 98 % match to a sequence in GenBank, 25 sequences were of possible invertebrate origin.

CONCLUSIONS

To our knowledge, this is the first study to examine the degradation rate of gnathiid isopod blood meals. Determining the rate at which gnathiids digest their blood meal is an important step in ensuring the successful host identification by DNA-based methods in large field studies.

Fish diversity of the largest deltaic formation in the Americas - a description of the fish fauna of the Parnaíba Delta using DNA Barcoding

Deltas are dynamic and productive systems of enormous ecological significance, encompassing unique and biologically diverse wetland habitats. Here, we present the first data on the molecular diversity of the fish fauna of the Parnaíba Delta, the largest deltaic formation of the Americas. Partial sequences (626 bp) of the mitochondrial COI gene (Cytochrome c oxidase subunit I) were used to barcode 402 individuals, representing 128 species, belonging to 98 genera, 57 families, 17 orders and two classes. The most abundant orders were the Perciformes, Siluriformes, Gobiiformes, and Pleuronectiformes. The Neighbor-Joining (NJ), Bayesian Inference (BI), and BIN analyses produced 103 molecular clusters, while the Automatic Barcode Gap Discovery (ABGD) and Maximum Likelihood (ML) approaches revealed 102 clusters. The mean conspecific, congeneric and confamilial genetic distances were 0.33%, 14.37%, and 18.60%, respectively. Intraspecific divergence ranged from 0.0% to 1.4%, and all species presented barcode gaps, with the exception of two clusters of Cathorops spixii (OTU 96 and OTU 103), which were separated by a low interspecific distance (1.2%), which overlaps the maximum intraspecific genetic distance (1.4%). The barcode data provide new insights into the fish diversity of the Parnaíba Delta, which will be important for the development of further research on this fauna.

Three new species of Chromis (Teleostei, Pomacentridae) from mesophotic coral ecosystems of the Philippines

Three new species of Chromis (Perciformes, Pomacentridae) from the Philippines, collected between 75–150 m depth, are described by a combination of morphological features and their coloration. Chromisguntingsp. n. was found in Batangas and Oriental Mindoro, and differs from its congeners in body depth (2.1–2.2 in SL), and color of adults, light brown, with a silver area on the anterior end and a bilateral black margin along the exterior side of the tail. It is most similar to C.scotochiloptera, with a 5.3% genetic divergence in COI. Chromishangganansp. n. was found around Lubang Island. Body depth (1.9–2.0 in SL) and adult coloration (yellowish with dark black outer margins on dorsal and anal fins) also separate this species from its congeners. It is most similar to C.pembae, with a 2.5% genetic divergence. Chromisbowesisp. n. was found in Batangas, and also differs from its congeners by the combination of body depth (1.5–1.6 in SL), and color of adults (brownish grey in the dorsal side to whitish on the ventral side, with alternating dark and light stripes in the sides of body). It is most similar to C.earina, with a 3.6% genetic divergence in COI.

Prepared for the future: A strong signal of evolution toward the adult benthic niche during the pelagic stage in Labrid fishes

The morphology of organisms reflects a balance between their evolutionary history, functional demands, and biomechanical constraints imposed by the immediate environment. In many fish species, a marked shift in the selection regime is evident when pelagic larvae, which swim and feed in the open ocean, settle in their adult benthic habitat. This shift is particularly dramatic in coral-reef fishes, where the adult habitat is immensely complex. However, whether the adult trophic ecotype affects the morphology of early-life stages is unclear. We measured a suite of 26 functional-morphological traits in the head and body of larvae from an ontogenetic series of 16 labrid species. Using phylogenetic comparative methods, we reconstructed the location of adaptive peaks of larvae whose adults are associated with different trophic ecotypes. We found that the morphospace occupation in these larvae is largely driven by divergent adaptations to the adult benthic habitats. The disparity between adaptive peaks is achieved early and does not monotonically increase with size. Our findings thus refute the notion that larvae rapidly acquire the trophic-specific traits during a metamorphic period immediately prior to settlement. This early specialization might be due to the highly complex musculoskeletal system of the head that cannot be rapidly modified.

DNA barcoding and morphological taxonomy: identification of lanternfish (Myctophidae) larvae in the Gulf of Mexico

Accurate identification of fish larval stages is complicated and time-consuming due to the lack of diagnostic morphological characters, especially during early developmental stages. The distribution of lanternfish (Myctophidae) has been described based on the morphological identification of adult stages. Larvae of only a few species of Myctophidae have been described, and the description is not always precise. In this study, larvae were collected and morphologically identified as Diaphus mollis, Hygophum hygomii, H. reinhardtii, H. taaningi, Myctophum obtusirostre and M. selenops. The DNA barcode region of the mitochondrial cytochrome oxidase I gene (COI) was determined for all larvae. The COI sequences matched reference barcodes available in GenBank for 14 of the identified larvae. The remaining COI sequences matched reference barcodes for different species of Myctophidae including Centrobranchus nigroocellatus, Diogenichthys atlanticus and Lepidophanes guentheri. This effort demonstrated the importance of integrated morphological and molecular analysis of species diversity and distribution of the Myctophidae in the Gulf of México.

Tosanoidesaphrodite, a new species from mesophotic coral ecosystems of St. Paul's Rocks, Mid Atlantic Ridge (Perciformes, Serranidae, Anthiadinae)

During a recent expedition to St. Paul's Rocks, Atlantic Ocean, a distinctive and previously unknown species of Anthiadinae was collected at a depth of 120 m. A genetic analysis indicated the undescribed species is a member of the genus Tosanoides, which was only known to occur in the Pacific Ocean. This new taxon is distinguishable from all other Tosanoides species by the following combination of characters: soft dorsal fin rays 15-16; anal fin rays 9; ventral scale rows 9-10; last dorsal spine the longest (instead first through fourth). Here Tosanoidesaphrodite sp. n. is described and illustrated, only known from St. Paul's Rocks.

DNA barcoding for identification of fish species in the Taiwan Strait

DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene in the mitochondrial genome is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding reference database of fishes in the Taiwan Strait and evaluate the applicability of using the COI gene for the identification of fish at the species level. A total of 284 mitochondrial COI barcode sequences were obtained from 85 genera, 38 families and 12 orders of fishes. The mean length of the sequences was 655 base pairs. The average Kimura two parameter (K2P) distances within species, genera, families, orders and classes were 0.21%, 6.50%, 23.70% and 25.60%, respectively. The mean interspecific distance was 31-fold higher than the mean intraspecific distance. The K2P neighbor-joining trees based on the sequence generally clustered species in accordance with their taxonomic classifications. High efficiency of species identification was demonstrated in the present study by DNA barcoding, and we conclude that COI sequencing can be used to identify fish species.

Plectranthiasahiahiata, a new species of perchlet from a mesophotic ecosystem at Rapa Nui (Easter Island) (Teleostei, Serranidae, Anthiadinae)

A new species of the perchlet genus Plectranthias is herein described from a single specimen found at Rapa Nui (Easter Island) in the South Pacific. Plectranthiasahiahiata sp. n. was collected at a depth of 83 m in a mesophotic coral ecosystem at Rapa Nui. The main difference between Plectranthiasahiahiata and other members of the genus is higher fin-ray counts (X, 18 dorsal; 18 pectoral) and its distinctive coloration. Compared to the three other known eastern South Pacific species, P.ahiahiata has more dorsal-fin rays, more pectoral-fin rays, fewer tubed lateral-line scales, fewer gill rakers, a longer head relative to SL, a very short first dorsal spine relative to SL, and a short third anal spine relative to SL. Plectranthiasahiahiata is distinguished from western Pacific species, by having more dorsal- and pectoral-fin rays. The closest relative based on genetic divergence (with 12.3% uncorrected divergence in the mitochondrial COI gene) is Plectranthiaswinniensis, a widely distributed species, suggesting important links between Rapa Nui and western Pacific islands. This new species adds to the high endemism of the Rapa Nui ichthyofauna, and is further evidence of the importance of mesophotic reefs as unique communities.

Roa rumsfeldi, a new butterflyfish (Teleostei, Chaetodontidae) from mesophotic coral ecosystems of the Philippines

A new species of the butterflyfish genus Roa is herein described from the Verde Island Passage in the Philippines, West Pacific Ocean. Roarumsfeldisp. n. was found on mesophotic coral ecosystems at Puerto Galera and Batangas, and sampled through technical mixed-gas rebreather diving at 100–130 m depth. This represents the fifth known species of Roa. The main differences between Roarumsfeldisp. n. and its congeners are the lower number of pored scales in the lateral line, longer snout, longer caudal peduncle, shorter caudal fin, pelvic fin color (dark first spine vs. white in all other Roa), and genetics (8.4% divergence from its closest relative Roamodesta in the mitochondrial COI gene). Roa spp. are usually seen in pairs, but the two specimens we collected were solitary individuals. We have kept one of the specimens alive in the California Academy of Sciences’ Twilight Zone exhibit for more than one year, where it thrives and is feeding on a variety of dried and fresh food.

Developing an Apicomplexan DNA Barcoding System to Detect Blood Parasites of Small Coral Reef Fishes

Apicomplexan parasites are obligate parasites of many species of vertebrates. To date, there is very limited understanding of these parasites in the most-diverse group of vertebrates, actinopterygian fishes. While DNA barcoding targeting the eukaryotic 18S small subunit rRNA gene sequence has been useful in identifying apicomplexans in tetrapods, identification of apicomplexans infecting fishes has relied solely on morphological identification by microscopy. In this study, a DNA barcoding method was developed that targets the 18S rRNA gene primers for identifying apicomplexans parasitizing certain actinopterygian fishes. A lead primer set was selected showing no cross-reactivity to the overwhelming abundant host DNA and successfully confirmed 37 of the 41 (90.2%) microscopically verified parasitized fish blood samples analyzed in this study. Furthermore, this DNA barcoding method identified 4 additional samples that screened negative for parasitemia, suggesting this molecular method may provide improved sensitivity over morphological characterization by microscopy. In addition, this PCR screening method for fish apicomplexans, using Whatman FTA preserved DNA, was tested in efforts leading to a more simplified field collection, transport, and sample storage method as well as a streamlining sample processing important for DNA barcoding of large sample sets.

Phylogeography of freshwater fish Puntius sophore in India

Phylogeography and evolutionary history of the freshwater species are poorly known. We document the phylogeography of widely distributed Puntius sophore using cytochrome oxidase subunit I (COI) gene of 650 bp. In the present study, we used 61 individual sequences from known geographic locations across India whereas data are lacking from other parts of its distribution range. Total 20 haplotypes with the intra-species sequence divergence ranging from 0.004 to 0.025 were observed and they were split into two major clades (North and Northeastern to Central India). Two distant geographic (North and Northeastern to Central India) regions shared haplotype suggesting ancient river connectivity or introduction of species from Northeast and Central India. Overall nucleotide and haplotype diversities were 0.00971 and 0.915. The Tajima's D and Fu's Fs values were found negative but non-significant thus rejecting the population expansion model followed by the multimodal mode of mismatch distribution. Bayesian skyline plots from both the clade showed steady population history over time; and start of decline in recent years in the clade B (∼1000-1500 years). The present finding is in support to the 'Satpura hypothesis' proposed to explain species movement patterns from Southeast Asian countries to Indian subcontinent, seconded by P. sophore showing high genetic diversity within Northern India clade (high genetic splits) because of presence of high river network in comparison to other parts of the country.

A new deep-reef scorpionfish (Teleostei, Scorpaenidae, Scorpaenodes) from the southern Caribbean with comments on depth distributions and relationships of western Atlantic members of the genus

A new species of scorpionfish, Scorpaenodesbarrybrowni Pitassy & Baldwin, sp. n. which is described, was collected during submersible diving in the southern Caribbean as part of the

Smithsonian’s Deep Reef Observation Project

(DROP). It differs from the other two western Atlantic species of the genus, Scorpaenodescaribbaeus and Scorpaenodestredecimspinosus, in various features, including its color pattern, having an incomplete lateral line comprising 8–10 pored scales, tending to be more elongate, usually having the 11^th–12^th pectoral-fin rays elongate, and by 20–23% divergence in the

cytochrome c oxidase I

(COI) DNA barcode sequences. It further differs from one or the other of those species in head spination and in numbers of soft dorsal-fin rays, pectoral-fin rays, and precaudal + caudal vertebrae. Inhabiting depths of 95–160 m, the new species is the deepest western Atlantic member of the genus (Scorpaenodescaribbaeus occurs at depths < 35 m and Scorpaenodestredecimspinosus from 7 to 82 m). DNA barcode data do not rigorously resolve relationships among the ten species of the genus for which those data are available.

Integrative taxonomy supports new candidate fish species in a poorly studied neotropical region: the Jequitinhonha River Basin

Molecular identification through DNA barcoding has been proposed as a way to standardize a global biodiversity identification system using a partial sequence of the mitochondrial COI gene. We applied an integrative approach using DNA barcoding and traditional morphology-based bioassessment to identify fish from a neotropical region possessing low taxonomic knowledge: the Jequitinhonha River Basin (Southeastern Brazil). The Jequitinhonha River Basin (JRB) has a high rate of endemism and is considered an area of high priority for fish conservation, with estimates indicating the presence of around 110 native and non-indigenous species. DNA barcodes were obtained from 260 individuals belonging to 52 species distributed among 35 genera, 21 families and 6 orders, including threatened and rare species such as Rhamdia jequitinhonha and Steindachneridion amblyurum. The mean Kimura two-parameter genetic distances within species, genera and families were: 0.44, 12.16 and 20.58 %, respectively. Mean intraspecific genetic variation ranged from 0 to 11.43 %, and high values (>2 %) were recovered for five species. Species with a deep intraspecific distance, possibly flagging overlooked taxa, were detected within the genus Pimelodella. Fifteen species, only identified to the genus level, had unique BINs, with a nearest neighbor distance over 2 % and therefore, potential new candidate species supported by DNA barcoding. The integrative taxonomy approach using DNA barcoding and traditional taxonomy may be a remedy to taxonomy impediment, accelerating species identification by flagging potential new candidate species and to adequately conserve the megadiverse neotropical ichthyofauna.

DNA barcoding and evaluation of genetic diversity in Cyprinidae fish in the midstream of the Yangtze River

The Yangtze River is the longest river in China and is divided into upstream and mid-downstream regions by the Three Gorges (the natural barriers of the Yangtze River), resulting in a complex distribution of fish. Dramatic changes to habitat environments may ultimately threaten fish survival; thus, it is necessary to evaluate the genetic diversity and propose protective measures. Species identification is the most significant task in many fields of biological research and in conservation efforts. DNA barcoding, which constitutes the analysis of a short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) sequence, has been widely used for species identification. In this study, we collected 561 COI barcode sequences from 35 fish from the midstream of the Yangtze River. The intraspecific distances of all species were below 2% (with the exception of Acheilognathus macropterus and Hemibarbus maculatus). Nevertheless, all species could be unambiguously identified from the trees, barcoding gaps and taxonomic resolution ratio values. Furthermore, the COI barcode diversity was found to be low (≤0.5%), with the exception of H. maculatus (0.87%), A. macropterus (2.02%) and Saurogobio dabryi (0.82%). No or few shared haplotypes were detected between the upstream and downstream populations for ten species with overall nucleotide diversities greater than 0.00%, which indicated the likelihood of significant population genetic structuring. Our analyses indicated that DNA barcoding is an effective tool for the identification of cyprinidae fish in the midstream of the Yangtze River. It is vital that some protective measures be taken immediately because of the low COI barcode diversity.

Role of DNA barcoding in marine biodiversity assessment and conservation: An update

More than two third area of our planet is covered by oceans and assessment of marine biodiversity is a challenging task. With the increasing global population, there is a tendency to exploit marine resources for food, energy and other requirements. This puts pressure on the fragile marine environment and necessitates sustainable conservation efforts. Marine species identification using traditional taxonomical methods is often burdened with taxonomic controversies. Here we discuss the comparatively new concept of DNA barcoding and its significance in marine perspective. This molecular technique can be useful in the assessment of cryptic species which is widespread in marine environment and linking the different life cycle stages to the adult which is difficult to accomplish in the marine ecosystem. Other advantages of DNA barcoding include authentication and safety assessment of seafood, wildlife forensics, conservation genetics and detection of invasive alien species (IAS). Global DNA barcoding efforts in the marine habitat include MarBOL, CeDAMar, CMarZ, SHARK-BOL, etc. An overview on DNA barcoding of different marine groups ranging from the microbes to mammals is revealed. In conjugation with newer and faster techniques like high-throughput sequencing, DNA barcoding can serve as an effective modern tool in marine biodiversity assessment and conservation.

Pempheris gasparinii, a new species of sweeper fish from Trindade Island, southwestern Atlantic (Teleostei, Pempheridae)

Pempherisgaspariniisp. n. is described from five specimens, 59.1–68.0 mm in standard length. It is only known to occur in the shallow reefs of Trindade Island, 1200 km east of the Brazilian coast, in the southwestern Atlantic. Pempherisgasparinii is the third recognized species of Pempheris in the Atlantic Ocean. This new species is morphologically similar to its close relative, Pempherispoeyi, differing by the number of lateral-line scales (51–54 in Pempherisgasparinii vs. 47–49 in Pempherispoeyi), scales below lateral line (10–11 vs. 9), circumpeduncular scales (11–12 vs. 13), head and caudal peduncle lengths (2.7–3.3 vs 3.5–4.0 in head length). Moreover, Pempherisgasparinii shows a 4% genetic divergence from Pempherispoeyi at the cytochrome oxidase I locus (COI), consistent with a lineage split at the beginning of the Pleistocene. This new species represents the 12^th endemic fish species from Trindade Island.

Looking back on a decade of barcoding crustaceans

Species identification represents a pivotal component for large-scale biodiversity studies and conservation planning but represents a challenge for many taxa when using morphological traits only. Consequently, alternative identification methods based on molecular markers have been proposed. In this context, DNA barcoding has become a popular and accepted method for the identification of unknown animals across all life stages by comparison to a reference library. In this review we examine the progress of barcoding studies for the Crustacea using the Web of Science data base from 2003 to 2014. All references were classified in terms of taxonomy covered, subject area (identification/library, genetic variability, species descriptions, phylogenetics, methods, pseudogenes/numts), habitat, geographical area, authors, journals, citations, and the use of the Barcode of Life Data Systems (BOLD). Our analysis revealed a total number of 164 barcoding studies for crustaceans with a preference for malacostracan crustaceans, in particular Decapoda, and for building reference libraries in order to identify organisms. So far, BOLD did not establish itself as a popular informatics platform among carcinologists although it offers many advantages for standardized data storage, analyses and publication.

A new, mesophotic Coryphopterus goby (Teleostei, Gobiidae) from the southern Caribbean, with comments on relationships and depth distributions within the genus

A new species of western Atlantic Coryphopterus is described from mesophotic depths off Curaçao, southern Caribbean. Coryphopteruscurasubsp. n., is similar to Coryphopterusdicrus in, among other features, having two prominent pigment spots of roughly equal intensity on the pectoral-fin base, the pelvic fins fused to form a disk, and no pelvic frenum. The two species can be differentiated by body depth (shallower in Coryphopteruscurasub at origin of dorsal fin and caudal peduncle); differences in the pigmentation on the head, trunk, and basicaudal region; and usually by total number of rays (spinous plus soft) in the second dorsal fin (10–11, usually 11, in Coryphopteruscurasub, 10 in Coryphopterusdicrus). Coryphopteruscurasub differs from other Coryphopterus species that have a prominent pigment spot on the lower portion of the pectoral-fin base (Coryphopteruspunctipectophorus and Coryphopterusvenezuelae) in, among other features, lacking a pelvic frenum. Coryphopteruscurasub was collected between 70 and 80 m, the deepest depth range known for the genus. Collections of Coryphopterusvenezuelae at depths of 65–69 m extend the depth range of that species by approximately 50 m. Mitochondrial cytochrome c oxidase subunit I (COI) data corroborate the recognition of Coryphopteruscurasub as a distinct species but do not rigorously resolve its relationships within the genus. A revised key to the western Atlantic species of Coryphopterus is presented.

Genetic identification of bucktooth parrotfish Sparisoma radians (Valenciennes, 1840) (Labridae, Scarinae) by chromosomal and molecular markers

Parrotfishes (Labridae, Scarinae) comprise a large marine fish group of difficult identification, particularly during juvenile phase when the typical morphology and coloration of adults are absent. Therefore, the goal of this study was to test cytogenetic markers and DNA barcoding in the identification of bucktooth parrtotfish Sparisoma radians from the northeastern coast of Brazil. Sequencing of cytochrome c oxidase subunit I (COI) confirmed all studied samples as S. radians, and all showed high similarity (99-100%) with Caribbean populations. The karyotype of this species was divergent from most marine Perciformes, being composed of 2n = 46 chromosomes. These consisted of a large number of metacentric and submetacentric pairs with small amounts of heterochromatin and GC-rich single nucleolar organizer regions (NORs) not syntenic to 5S rDNA clusters. These are the first data about DNA barcoding in parrotfish from the Brazilian province and the first refined chromosomal analysis in Scarinae, providing useful data to a reliable genetic identification of S. radians.

Connectivity across the Caribbean Sea: DNA barcoding and morphology unite an enigmatic fish larva from the Florida straits with a new species of sea bass from deep reefs off Curaçao

Integrative taxonomy, in which multiple disciplines are combined to address questions related to biological species diversity, is a valuable tool for identifying pelagic marine fish larvae and recognizing the existence of new fish species. Here we combine data from DNA barcoding, comparative morphology, and analysis of color patterns to identify an unusual fish larva from the Florida Straits and demonstrate that it is the pelagic larval phase of a previously undescribed species of Liopropoma sea bass from deep reefs off Curaçao, southern Caribbean. The larva is unique among larvae of the teleost family Serranidae, Tribe Liopropomini, in having seven elongate dorsal-fin spines. Adults of the new species are similar to the golden bass, Liopropoma aberrans, with which they have been confused, but they are distinct genetically and morphologically. The new species differs from all other western Atlantic liopropomins in having IX, 11 dorsal-fin rays and in having a unique color pattern–most notably the predominance of yellow pigment on the dorsal portion of the trunk, a pale to white body ventrally, and yellow spots scattered across both the dorsal and ventral portions of the trunk. Exploration of deep reefs to 300 m using a manned submersible off Curaçao is resulting in the discovery of numerous new fish species, improving our genetic databases, and greatly enhancing our understanding of deep-reef fish diversity in the southern Caribbean. Oh the mother and child reunion is only a moment away. Paul Simon.

The covert world of fish biofluorescence: a phylogenetically widespread and phenotypically variable phenomenon

The discovery of fluorescent proteins has revolutionized experimental biology. Whereas the majority of fluorescent proteins have been identified from cnidarians, recently several fluorescent proteins have been isolated across the animal tree of life. Here we show that biofluorescence is not only phylogenetically widespread, but is also phenotypically variable across both cartilaginous and bony fishes, highlighting its evolutionary history and the possibility for discovery of numerous novel fluorescent proteins. Fish biofluorescence is especially common and morphologically variable in cryptically patterned coral-reef lineages. We identified 16 orders, 50 families, 105 genera, and more than 180 species of biofluorescent fishes. We have also reconstructed our current understanding of the phylogenetic distribution of biofluorescence for ray-finned fishes. The presence of yellow long-pass intraocular filters in many biofluorescent fish lineages and the substantive color vision capabilities of coral-reef fishes suggest that they are capable of detecting fluoresced light. We present species-specific emission patterns among closely related species, indicating that biofluorescence potentially functions in intraspecific communication and evidence that fluorescence can be used for camouflage. This research provides insight into the distribution, evolution, and phenotypic variability of biofluorescence in marine lineages and examines the role this variation may play.

Design of mini-barcode for catfishes for assessment of archival biodiversity

Recovery of DNA barcode sequences is often challenging from the archived specimens. However, short fragments of DNA may be recovered, which would significantly improve many unresolved taxonomic conflicts. Here, we designed a mini-barcode for catfishes comprising several species and many cryptic taxa. We analysed a data set of 3048 publicly available COI barcode sequences representing 547 worldwide catfish species and performed 152 628 interspecies comparisons. A significantly more positively correlated interspecies distance was detected with transversion (0.78, P < 0.001) than with transition (0.70, P < 0.001). This suggested that transversions were better diagnostics for species identification. In the aligned data set, two transversion-rich fragments (53 bp and 119 bp) were identified. Transition/transversion bias value was 1.04 in 53-bp fragment, 1.23 in 119-bp fragment and 1.50 in full-length barcode. The interspecies distance with full-length barcode was 0.212 ± 0.037, while that with 53-bp and 119-bp fragments was 0.325 ± 0.039 and 0.218 ± 0.045, respectively. Survey of 53-bp fragment showed a possibility of only 1144 barcodes, while that of 119-bp fragment showed >4 million barcodes. Thus, the 119-bp fragment is a viable mini-barcode for catfishes comprising >3000 extant species. Experiment with 82 archived catfishes showed successful recovery of this mini-barcode using the designed primer. The mini-barcode sequences showed species-specific similarity in the range of 98-100% with the global database. Therefore, survey of a transversion-rich fragment within the full-length barcode would be an ideal approach of mini-barcode design for biodiversity assessment.

The phylogenetic significance of colour patterns in marine teleost larvae

Ichthyologists, natural-history artists, and tropical-fish aquarists have described, illustrated, or photographed colour patterns in adult marine fishes for centuries, but colour patterns in marine fish larvae have largely been neglected. Yet the pelagic larval stages of many marine fishes exhibit subtle to striking, ephemeral patterns of chromatophores that warrant investigation into their potential taxonomic and phylogenetic significance. Colour patterns in larvae of over 200 species of marine teleosts, primarily from the western Caribbean, were examined from digital colour photographs, and their potential utility in elucidating evolutionary relationships at various taxonomic levels was assessed. Larvae of relatively few basal marine teleosts exhibit erythrophores, xanthophores, or iridophores (i.e. nonmelanistic chromatophores), but one or more of those types of chromatophores are visible in larvae of many basal marine neoteleosts and nearly all marine percomorphs. Whether or not the presence of nonmelanistic chromatophores in pelagic marine larvae diagnoses any major teleost taxonomic group cannot be determined based on the preliminary survey conducted, but there is a trend toward increased colour from elopomorphs to percomorphs. Within percomorphs, patterns of nonmelanistic chromatophores may help resolve or contribute evidence to existing hypotheses of relationships at multiple levels of classification. Mugilid and some beloniform larvae share a unique ontogenetic transformation of colour pattern that lends support to the hypothesis of a close relationship between them. Larvae of some tetraodontiforms and lophiiforms are strikingly similar in having the trunk enclosed in an inflated sac covered with xanthophores, a character that may help resolve the relationships of these enigmatic taxa. Colour patterns in percomorph larvae also appear to diagnose certain groups at the interfamilial, familial, intergeneric, and generic levels. Slight differences in generic colour patterns, including whether the pattern comprises xanthophores or erythrophores, often distinguish species. The homology, ontogeny, and possible functional significance of colour patterns in larvae are discussed. Considerably more investigation of larval colour patterns in marine teleosts is needed to assess fully their value in phylogenetic reconstruction.

Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna?

BACKGROUND

The megadiverse Neotropical freshwater ichthyofauna is the richest in the world with approximately 6,000 recognized species. Interestingly, they are distributed among only 17 orders, and almost 80% of them belong to only three orders: Characiformes, Siluriformes and Perciformes. Moreover, evidence based on molecular data has shown that most of the diversification of the Neotropical ichthyofauna occurred recently. These characteristics make the taxonomy and identification of this fauna a great challenge, even when using molecular approaches. In this context, the present study aimed to test the effectiveness of the barcoding methodology (COI gene) to identify the mega diverse freshwater fish fauna from the Neotropical region. For this purpose, 254 species of fishes were analyzed from the Upper Parana River basin, an area representative of the larger Neotropical region.

RESULTS

Of the 254 species analyzed, 252 were correctly identified by their barcode sequences (99.2%). The main K2P intra- and inter-specific genetic divergence values (0.3% and 6.8%, respectively) were relatively low compared with similar values reported in the literature, reflecting the higher number of closely related species belonging to a few higher taxa and their recent radiation. Moreover, for 84 pairs of species that showed low levels of genetic divergence (<2%), application of a complementary character-based nucleotide diagnostic approach proved useful in discriminating them. Additionally, 14 species displayed high intra-specific genetic divergence (>2%), pointing to at least 23 strong candidates for new species.

CONCLUSIONS

Our study is the first to examine a large number of freshwater fish species from the Neotropical area, including a large number of closely related species. The results confirmed the efficacy of the barcoding methodology to identify a recently radiated, megadiverse fauna, discriminating 99.2% of the analyzed species. The power of the barcode sequences to identify species, even with low interspecific divergence, gives us an idea of the distribution of inter-specific genetic divergence in these megadiverse fauna. The results also revealed hidden genetic divergences suggestive of reproductive isolation and putative cryptic speciation in some species (23 candidates for new species). Finally, our study constituted an important contribution to the international Barcoding of Life (iBOL.org) project, providing barcode sequences for use in identification of these species by experts and non-experts, and allowing them to be available for use in other applications.

Advancing nematode barcoding: a primer cocktail for the cytochrome c oxidase subunit I gene from vertebrate parasitic nematodes

Although nematodes are one of the most diverse metazoan phyla, species identification through morphology is difficult. Several genetic markers have been used for their identification, but most do not provide species-level resolution in all groups, and those that do lack primer sets effective across the phylum, precluding high-throughput processing. This study describes a cocktail of three novel primer pairs that overcome this limitation by recovering cytochrome c oxidase I (COI) barcodes from diverse nematode lineages parasitic on vertebrates, including members of three orders and eight families. Its effectiveness across a broad range of nematodes enables high-throughput processing.