Comprehensive phylogeny of the family Sparidae (Perciformes: Teleostei) inferred from mitochondrial gene analyses

Morphology and metabolic traits related to swimming performance in Australasian snapper (Chrysophrys auratus) selected for fast growth

Changes in body shape are linked to swimming performance and become relevant for selective breeding programmes in cultured finfish. We studied how the selection for fast growth could affect phenotypes by investigating the relationship between swimming performance and body shape. We also investigated how swimming might affect plasma metabolite concentrations. Critical swimming speed (UCrit), body traits (e.g., BW, body weight; BL, body length; K, condition factor), and plasma lactate and glucose concentrations were evaluated in two cohorts of Australasian snapper (Chrysophrys auratus): one derived from wild broodstock (F1), and the other selected for fast growth (F4). UCrit tests (n = 8) were applied in groups of 10 snapper of similar BW (71.7 g) and BL (14.6 cm). The absolute or relative UCrit values of both cohorts were similar (0.702 m⋅s-1 and 4.795 BL⋅s-1, respectively), despite the F4 cohort displaying a higher K. A positive correlation between K and absolute UCrit (Pearson's r = 0.414) was detected in the F4 cohort, but not in the F1 cohort, which may be linked to differences in body shape. A negative correlation between relative UCrit and body size (Pearson's r between -0.682 and -0.501), but no correlation between absolute UCrit and body size, was displayed in both cohorts. Plasma lactate and glucose concentrations were higher in the F4 cohort at UCrit. Whether a longer selective breeding programme could result in more changes in body shape, potentially affecting swimming performance, should be explored, along with the potential outcomes of the differences in metabolic traits detected.

Mitochondrial Analysis of Sparidae Species to Detect a New DNA Barcoding Marker for Dentex gibbosus to Utilize against Fraud

Dentex gibbosus (Pink dentex) is a fish species of increasing economic interest in the Mediterranean Sea that is consumed both whole and processed. The growing value of this sparid in European markets is responsible for its substitution with fraudulent species. The distinctive morphologic feature of D. gibbosus is the conspicuous hump on the forehead in the older and larger specimens. However, the head is regularly convex in young individuals, requiring high skills and competencies for correct identification. Authentication becomes even more challenging in the case of prepared and processed products. Therefore, the molecular characterization of Pink dentex plays a crucial role in preventing commercial fraud with species substitution. This paper proposes a comparative mitogenome analysis between 19 sparid species of commercial interest as a tool to accurately design species-specific primers targeting a fragment of the NAD2 gene for the identification of D. gibbosus. We successfully detected Pink dentex DNA both using endpoint and real-time PCR. The findings showed the high specificity of the designed primers, demonstrating this a suitable, fast, and cost-effective method that could be used for the unambiguous identification of Pink dentex. This innovative approach for sparid authentication is expected to contribute to seafood traceability, public health assurance, integrity, and the credibility of the seafood industry.

Diversity and structure of sparids external microbiota (Teleostei) and its link with monogenean ectoparasites

Background

Animal-associated microbial communities appear to be key factors in host physiology, ecology, evolution and its interactions with the surrounding environment. Teleost fish have received relatively little attention in the study of surface-associated microbiota. Besides the important role of microbiota in homeostasis and infection prevention, a few recent studies have shown that fish mucus microbiota may interact with and attract some specific parasitic species. However, our understanding of external microbial assemblages, in particular regarding the factors that determine their composition and potential interactions with parasites, is still limited. This is the objective of the present study that focuses on a well-known fish-parasite interaction, involving the Sparidae (Teleostei), and their specific monogenean ectoparasites of the Lamellodiscus genus. We characterized the skin and gill mucus bacterial communities using a 16S rRNA amplicon sequencing, tested how fish ecological traits and host evolutionary history are related to external microbiota, and assessed if some microbial taxa are related to some Lamellodiscus species.

Results

Our results revealed significant differences between skin and gill microbiota in terms of diversity and structure, and that sparids establish and maintain tissue and species-specific bacterial communities despite continuous exposure to water. No phylosymbiosis pattern was detected for either gill or skin microbiota, suggesting that other host-related and environmental factors are a better regulator of host-microbiota interactions. Diversity and structure of external microbiota were explained by host traits: host species, diet and body part. Numerous correlations between the abundance of given bacterial genera and the abundance of given Lamellodiscus species have been found in gill mucus, including species-specific associations. We also found that the external microbiota of the only unparasitized sparid species in this study, Boops boops, harbored significantly more Fusobacteria and three genera, Shewenella, Cetobacterium and Vibrio, compared to the other sparid species, suggesting their potential involvement in preventing monogenean infection.

Conclusions

This study is the first to explore the diversity and structure of skin and gill microbiota from a wild fish family and present novel evidence on the links between gill microbiota and monogenean species in diversity and abundance, paving the way for further studies on understanding host-microbiota-parasite interactions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-022-00180-1.

Dentex dentex Frauds: Establishment of a New DNA Barcoding Marker

The common dentex (Dentex dentex (Linnaeus, 1758)) is an iconic fish in the Mediterranean diet. Due to its commercial and organoleptic importance, this sparid is highly appreciated in European markets and is often subjected to species substitution frauds. Comparative mitogenomics is a suitable approach for identifying new and effective barcode markers. This study aimed to find a molecular tag useful for unequivocally discriminating the sparid species D. dentex. The comparison of the complete mitochondrial DNA (mtDNA) sequences of 16 sparid species allowed us to highlight the potential of the NAD2 gene for direct identification purposes. Common dentex-specific primers were created and successfully evaluated by end-point and real-rime PCR (Polymerase Chain Reaction) for several fish species, achieving amplification only in the D. dentex. The method proposed in this study appears fast, simple, and inexpensive and requires affordable instrumentation. This approach provides unambiguous results for the common dentex authentication without the sequencing step. The presence/absence assay for D. dentex can be executed in a few hours of lab work. Therefore, national authorities responsible for food safety and traceability could apply and make full use of DNA-testing methods for deterring operators from false seafood declarations.

Lamellodiscus (Monogenea: Diplectanidae) species parasitic on Japanese Acanthopagrus Peters, with proposals of L. chin n. sp. infecting A. sivicolus Akazaki and L. egusai nom. nov. for L. japonicus Ogawa & Egusa, 1978, a junior homonym of L. japonicus Pillai & Pillai, 1974

Lamellodiscus chin n. sp. (Monogenea: Diplectanidae) was described from Acanthopagrus sivicolus Akazaki (Perciformes: Sparidae) in Okinawa-jima Island, Ryukyu Islands based on morphological and molecular data. This new species resembles L. spari and L. elegans in morphologically but differs by its accessory piece curving and widening toward the tip. Three species of Lamellodiscus (L. japonicus Ogawa & Egusa, 1978, L. takitai Ogawa & Egusa, 1978, and L. spari Zhukov, 1970) were recorded from A. schlegelii (Bleeker), and L. japonicus was collected from A. latus (Houttuyn) in the Seto Inland Sea, Japan. I herein propose Lamellodiscus egusai nom. nov. for L. japonicus which is a junior primary homonym of L. japonicus Pillai & Pillai, 1974. Based on the type specimens and newly collected specimens from wild hosts, the type localities of L. japonicus (= L. egusai nom. nov.) and L. takitai are discussed. In addition, a list of nominal species of Japanese diplectanids is provided.

A Rapid Method for the Identification of Fresh and Processed Pagellus erythrinus Species against Frauds

The commercialization of porgies or seabreams of the family Sparidae has greatly increased in the last decade, and some valuable species have become subject to seafood substitution. DNA regions currently used for fish species identification in fresh and processed products belong to the mitochondrial (mt) genes cytochrome b (Cytb), cytochrome c oxidase I (COI), 16S and 12S. However, these markers amplify for fragments with lower divergence within and between some species, failing to provide informative barcodes. We adopted comparative mitogenomics, through the analysis of complete mtDNA sequences, as a compatible approach toward studying new barcoding markers. The intent is to develop a specific and rapid assay for the identification of the common pandora Pagellus erythrinus, a sparid species frequently subject to fraudulent replacement. The genetic diversity analysis (Hamming distance, p-genetic distance, gene-by-gene sequence variability) between 16 sparid mtDNA genomes highlighted the discriminating potential of a 291 bp NAD2 gene fragment. A pair of species-specific primers were successfully designed and tested by end-point and real-time PCR, achieving amplification only in P. erythrinus among several fish species. The use of the NAD2 barcoding marker provides a rapid presence/absence method for the identification of P. erythrinus.

Host Species and Body Site Explain the Variation in the Microbiota Associated to Wild Sympatric Mediterranean Teleost Fishes

Microorganisms are an important component in shaping the evolution of hosts and as such, the study of bacterial communities with molecular techniques is shedding light on the complexity of symbioses between bacteria and vertebrates. Teleost fish are a heterogeneous group that live in a wide variety of habitats, and thus a good model group to investigate symbiotic interactions and their influence on host biology and ecology. Here we describe the microbiota of thirteen teleostean species sharing the same environment in the Mediterranean Sea and compare bacterial communities among different species and body sites (external mucus, skin, gills, and intestine). Our results show that Proteobacteria is the dominant phylum present in fish and water. However, the prevalence of other bacterial taxa differs between fish and the surrounding water. Significant differences in bacterial diversity are observed among fish species and body sites, with higher diversity found in the external mucus. No effect of sampling time nor species individual was found. The identification of indicator bacterial taxa further supports that each body site harbors its own characteristic bacterial community. These results improve current knowledge and understanding of symbiotic relationships among bacteria and their fish hosts in the wild since the majority of previous studies focused on captive individuals.

Repeated evolution of durophagy during ichthyosaur radiation after mass extinction indicated by hidden dentition

Marine tetrapods quickly diversified and were established as marine top predators after the end-Permian Mass extinction (EPME). Ichthyosaurs were the forerunner of this rapid radiation but the main drivers of the diversification are poorly understood. Cartorhynchus lenticarpus is a basal ichthyosauriform with the least degree of aquatic adaptation, holding a key to identifying such a driver. The unique specimen appeared edentulous based on what was exposed but a CT scanning revealed that the species indeed had rounded teeth that are nearly perpendicular to the jaw rami, and thus completely concealed in lateral view. There are three dental rows per jaw ramus, and the root lacks infoldings of the dentine typical of ichthyopterygians. The well-developed and worn molariform dentition with three tooth rows supports the previous inference that the specimen is not of a juvenile. The premaxilla and the corresponding part of the dentary are edentulous. Molariform dentition evolved three to five times independently within Ichthyosauriformes in the Early and Middle Triassic. Convergent exploitation of hard-shelled invertebrates by different subclades of ichthyosauriforms likely fueled the rapid taxonomic diversification of the group after EPME.

Early development and occurrence patterns of the Pagrinae seabream Argyrops bleekeri (Perciformes: Sparidae): Does early life history have implications for sparid relationships?

The early development and occurrence patterns of Argyrops bleekeri are described based on 87 specimens collected from Nakagusuku Bay on Okinawa Island in southwestern Japan. Larvae and juveniles of the genus Argyrops are distinguished from the other seabreams inhabiting the Western Pacific region by the strength and extent of head spination, body depth, dorsal-fin-ray counts and melanophore patterns. Argyrops bleekeri is easily distinguished from other members of this genus by the presence of a single rudimentary dorsal-fin spine on the first dorsal pterygiophore, melanophore patterns and an allopatric distribution. Argyrops bleekeri larvae [3.3-7.1 mm body length (BL)] and juveniles (6.7-13.0 mm BL) were found in the bay from January to May; nonetheless, they were not collected from the outer bay or in extremely shallow inshore areas such as tidal flats. The results suggest that Argyrops is the most derived red seabream because of its spiny morphology, and it may be a member of an expanding nearshore group of red seabreams, which originally inhabited offshore waters.

A phylogenetic comparative analysis on the evolution of sequential hermaphroditism in seabreams (Teleostei: Sparidae)

The Sparids are an ideal group of fishes in which to study the evolution of sexual systems since they exhibit a great sexual diversity, from gonochorism (separate sexes) to protandrous (male-first) and protogynous (female-first) sequential hermaphroditism (sex change). According to the size-advantage model (SAM), selection should favour sex change when the second sex achieves greater reproductive success at a larger body size than the first sex. Using phylogenetic comparative methods and a sample of 68 sparid species, we show that protogyny and protandry evolve from gonochorism but evolutionary transitions between these two forms of sequential hermaphroditism are unlikely to happen. Using male gonadosomatic index (GSI) as a measure of investment in gametes and proxy for sperm competition, we find that, while gonochoristic and protogynous species support the predictions of SAM, protandrous species do not, as they exhibit higher GSI values than expected even after considering mating systems and spawning modes. We suggest that small males of protandrous species have to invest disproportionally more in sperm production than predicted not only when spawning in aggregations, with high levels of sperm competition, but also when spawning in pairs due to the need to fertilize highly fecund females, much larger than themselves. We propose that this compensatory mechanism, together with Bateman’s principles in sequential hermaphrodites, should be formally incorporated in the SAM.

Genetic relationships and hybridization among three western Atlantic sparid species: sheepshead (Archosargus probatocephalus), sea bream (A. rhomboidalis) and pinfish (Lagodon rhomboides)

Three species of sparids in the western Atlantic, sheepshead (Archosargus probatocephalus), sea bream (A. rhomboidalis), and pinfish (Lagodon rhomboides), share overlapping habitats, spawning seasons, and spawning grounds, providing opportunities for interaction among these species. Three regions of mitochondrial DNA and three nuclear DNA intron sequences were used to construct the genetic relationships among these species. The results showed that these species are closely related, suggesting the presence of soft polytomy with sheepshead and western Atlantic sea bream as sister species. However, western Atlantic sea bream and pinfish are equally divergent from sheepshead. We used a suite of 18 microsatellite markers to verify the occurrence of hybridization, identify the parental types, and evaluate the filial-generation status of 36 individuals morphologically identified as hybrids from the Indian River Lagoon system, in Florida. The 36 putative hybrids were analyzed with a reference group of 172 western Atlantic sea bream, 232 pinfish, and 157 sheepsheads and were all genetically determined to be F1 of sheepshead and western Atlantic sea bream with very little indication or no introgressive hybridization among the 172 reference specimens of western Atlantic sea bream. Hybridization was asymmetric, with western Atlantic sea bream males crossing with sheepshead females. Hybrids were first observed in the Indian River Lagoon in 2005, after the western Atlantic sea bream had become common there, in the 1990s. Their occurrence could be associated with unique features of the Indian River Lagoon that bring the two species together or with recent anthropogenic changes in this system. Further study is needed to determine the causes and long-term effects of the recurrent production of F1 hybrids and the degree of their sterility in the Indian River Lagoon.

Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling

Sparidae (Teleostei: Spariformes) are a family of fish constituted by approximately 150 species with high popularity and commercial value, such as porgies and seabreams. Although the phylogeny of this family has been investigated multiple times, its position among other teleost groups remains ambiguous. Most studies have used a single or few genes to decipher the phylogenetic relationships of sparids. Here, we conducted a thorough phylogenomic analysis using five recently available Sparidae gene-sets and 26 high-quality, genome-predicted teleost proteomes. Our analysis suggested that Tetraodontiformes (puffer fish, sunfish) are the closest relatives to sparids than all other groups used. By analytically comparing this result to our own previous contradicting finding, we show that this discordance is not due to different orthology assignment algorithms; on the contrary, we prove that it is caused by the increased taxon sampling of the present study, outlining the great importance of this aspect in phylogenomic analyses in general.

Sweepstakes reproductive success is absent in a New Zealand snapper (Chrysophrus auratus) population protected from fishing despite "tiny" Ne /N ratios elsewhere

A landmark study published in 2002 estimated a very small N_e /N ratio (around 10^-5 ) in a population of pink snapper (Chrysophrys auratus, Forster, 1801) in the Hauraki Gulf in New Zealand. It epitomized the tiny N_e /N ratios (<10^-3 ) reported in marine species due to the hypothesized operation of sweepstakes reproductive success (SRS). Here we re-evaluate the occurrence of SRS in marine species and the potential effect of fishing on the N_e /N ratio by studying the same species in the same region, but in a population that has been protected from fishing since 1975. We combine empirical, simulation and model-based approaches to estimate N_e (and N_b ) from genotypes of 1,044 adult fish and estimate N using recapture-probabilities. The estimated N_e /N ratio was much larger (0.33, SE: 0.14) than expected. The magnitude of estimates of population-wide variance in individual lifetime reproductive success (10-18) suggested that the sweepstakes effect was negligible in the study population. After evaluating factors that could explain the contrast between studies - experimental design, life history differences, environmental effects and the influence of exploitation on the N_e /N ratio - we conclude that the low N_e of the Hauraki Gulf population is associated with demographic instability in the harvested compared to the protected population despite circumstantial evidence that the 2002 study may have underestimated N_e . This study has broad implications for the prevailing view that reproductive success in the sea is largely driven by chance, and for genetic monitoring of populations using the N_e /N ratio and N_b .

The complete mitochondrial genome of the common pandora Pagellus erythrinus (Perciformes: Sparidae)

The common pandora (Pagellus erythrinus, Linnaeus 1758), one of the most popular sea bream species in the Mediterranean Sea, has high potential for aquaculture development. In this investigation, we analyzed the complete mitochondrial genome of P. erythrinus. The sequence has 16,828 bp in length and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a two non-coding regions (D-loop and L-origin). The overall nucleotide composition is: 27.5% of A, 28.2% of C, 27.5% of T, and 16.8% of G.

The complete mitochondrial genome of the Pink dentex Dentex gibbosus (Perciformes: Sparidae)

The Pink dentex (Dentex gibbosus, Rafinesque 1810) is one of the most commercially important Sparidae species and it is often subjected to fraud. Here, we report the complete mitochondrial genome of D. gibbosus. The mitogenome is 16,771 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding regions. The overall base composition of D. gibbosus mtDNA is: 27.8% for A, 28.60% for C, 16.5% for G, 27.05% for T.

The complete mitochondrial genome of the common dentex, Dentex dentex (perciformes: Sparidae)

The common Dentex (Dentex dentex, Linnaeus 1758) has a significant economic importance and is a highly valued table fish in the Mediterranean region. The paucity of genetic information relating to sparids, despite their growing economic value, provides the impetus for exploring the mitogenomics of this fish group. Here, we sequenced D. dentex complete mitochondrial genome. The sequence is comprised of 16,652 bp and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a 2 non-coding regions (D-loop and L-origin). The overall nucleotide composition is: 27.5% of A, 28.7% of C, 26.9% of T, and 16.9% of G.

Reproductive biology of black seabream Acanthopagrus schlegelii, threadfin porgy Evynnis cardinalis and red pargo Pagrus major in the northern South China Sea with consideration of fishery status and management needs

The reproductive biology of three commercially significant seabream species (family: Sparidae) Acanthopagrus schlegelii, Evynnis cardinalis and Pagrus major, taken from Hong Kong and adjacent northern South China Sea (SCS) waters, were investigated for their sexual patterns, spawning seasons, length at maturity and exploitation in relation to their conservation and management status. Histological analysis showed E. cardinalis and P. major to be functionally gonochoristic, the latter having a bisexual juvenile stage and being a rudimentary hermaphrodite. Acanthopagrus schlegelii is a protandric hermaphrodite. Standard length (L_S ) at 50% sex change for A. schlegelii is 291 mm. L_S at 50% female maturity for E. cardinalis and P. major are 117 and 332 mm, respectively. For all three species, the spawning period falls between November and March. The study highlights geographical differences in reproductive biology among the species and a paucity of fishery or other population-related data. While heavy fishing pressure, life-history characteristics and absence of effective management throughout the geographic ranges of these species make them susceptible to overfishing, they nonetheless appear to be generally more resilient than many other taxa that comprise the multi-species fisheries of the region, possibly due to their relatively rapid sexual maturation and spatial movement patterns. Overall, however, little is known of the biology, fishing history and current fishery status of sparids in general in the northern SCS and the current study is one of the first to examine such aspects of this family in the region and to consider appropriate management options.

Parasite communities in two sparid fishes from the western Mediterranean: a comparative analysis based on samples from three localities off the Algerian coast

We provide the first known comparative assessment of metazoan parasite communities in two taxonomically and ecologically related sparids, Boops boops and Spicara maena, that are common in the coastal infralittoral habitats in the Mediterranean. Using abundant data for infracommunities in three localities off the Algerian coasts of the Mediterranean, we tested the general prediction that the phylogenetic proximity of the two hosts, their overlapping geographical distribution and habitat occupation, as well as the similar feeding habits and diet would contribute to a homogenization of their parasite community composition and structure. The regional fauna of parasites of B. boops and S. maena along the Algerian coasts of the western Mediterranean was species-rich (36 species) and dominated by heteroxenous species (27 spp; of these 20 digenean spp.). The phylogenetic relatedness between the two hosts resulted in a large number of shared parasites (56 %, 20 spp.). However, the significant overlap in the parasite faunas of the two sparid hosts and their similar feeding habits and diet did not translate into homogeneous parasite community pattern; a significant differentiation in terms of both, composition and structure, was observed.

Phylogenetic placement of enigmatic percomorph families (Teleostei: Percomorphaceae)

Percomorphs are a large and diverse group of spiny-finned fishes that have come to be known as the "bush at the top" due to their persistent lack of phylogenetic resolution. Recently, the broader Euteleost Tree of Life project (EToL) inferred a well-supported phylogenetic hypothesis that groups the diversity of percomorphs into nine well-supported series (supraordinal groups): Ophidiaria, Batrachoidaria, Gobiaria, Syngnatharia, Pelagiaria, Anabantaria, Carangaria, Ovalentaria, and Eupercaria. The EToL also provided, for the first time, a monophyletic definition of Perciformes - the largest order of vertebrates. Despite significant progress made in accommodating the diversity of percomorph taxa into major clades, some 62 families (most previously placed in "Perciformes", as traditionally defined) were not examined by the EToL. Here, we provide evidence for the phylogenetic affinities of 10 of those 62 families, seven of which have largely remained enigmatic. This expanded taxonomic sampling also provides further support for the nine EToL supraordinal series. We examined sequences from 21 genes previously used by the EToL and added two fast-evolving mitochondrial markers in an attempt to increase resolution within the rapid percomorph radiations. We restricted the taxonomic sampling to 1229 percomorph species, including expanded sampling from recent studies. Results of maximum likelihood analysis revealed that bathyclupeids (Bathyclupeidae), galjoen fishes (Dichistiidae), kelpfishes (Chironemidae), marblefishes (Aplodactylidae), trumpeters (Latridae), barbeled grunters (Hapalogenyidae), slopefishes (Symphysanodontidae), and picarel porgies (formerly Centracanthidae) are members of the series Eupercaria ("new bush at the top"). The picarel porgies and porgies (Sparidae) are now placed in the same family (Sparidae). Our analyses suggest a close affinity between the orders Spariformes (including Lethrinidae, Nemipteridae and Sparidae) and Lobotiformes (including the tripletails or Lobotidae, the barbeled grunters, and tigerperches or Datnioididae), albeit support for this group is low. None of the newly examined families belong in the order Perciformes, as recently defined. Finally, we confirm results from other recent studies that place the Australasian salmons (Arripidae) within Pelagiaria, and the false trevallies (Lactariidae) close to flatfishes, jacks, and trevallies, within Carangaria.

Lamellodiscus aff. euzeti Diamanka, Boudaya, Toguebaye & Pariselle, 2011 (Monogenea: Diplectanidae) from the gills of Cheimerius nufar (Valenciennes) (Pisces: Sparidae) collected in the Arabian Sea, with comments on the distribution, specificity and historical biogeography of Lamellodiscus spp

Specimens of Lamellodiscus Johnston & Tiegs, 1922 (Monogenea: Diplectanidae) were collected from the gills of Cheimerius nufar (Valenciennes) (Sparidae) in the Arabian Sea. All of these parasites belonged to one and the same species, which is morphologically very close to L. euzeti Diamanka, Boudaya, Toguebaye & Pariselle, 2011. A different host, distant locality and small morphological differences compared with the original description of L. euzeti acted as a stimulus for a detailed redescription. The specimens from the Arabian Sea differ slightly in the details of the male copulatory organ (MCO) from the type-specimens of L. euzeti, which were re-examined, and from the respective drawings in its original description. Such differences include a longer inner process of the large element of the accessory piece associated with the proximal part of the copulatory tube, a longer point on the small element of the accessory piece associated with the distal part of the copulatory tube, and the presence of a smooth or slightly folded inner margin of this element rather than structures resembling spines which occur in the type-specimens of L. euzeti. Therefore, the present specimens infecting C. nufar in the Indo-Pacific may represent a different, but morphologically very similar species to the Atlantic form L. euzeti; consequently, they are recognised here as Lamellodiscus aff. euzeti. This form belongs to the 'ignoratus s. str.' subgroup of the genus. The composition of this subgroup is redefined to comprise 17 species, including L. corallinus Paperna, 1965 but excluding L. acanthopagri Roubal, 1981, and the morphology of the MCO of representatives of this group is clarified. A link between the diversity of Lamellodiscus species and the ancestral origin of present-day sparid species in the Tethys Sea is suggested. It is shown that Lamellodiscus spp. exhibit rather high levels of specificity to their hosts, since half of them parasitise only a single host species and c.90% infect closely related host species. Comparison of the levels of host-specificity of the species of this genus with other narrowly specific genera of the Dactylogyridea revealed that their estimations are comparable. The possibility of intra-host speciation within Lamellodiscus is discussed. It is shown that a co-evolutionary model is more discernible if it includes data on the occurrence of morphologically similar species from different regions and host taxa.

The complete mitochondrial genome of the gilthead seabream Sparus aurata L. (Sparidae)

The complete mitochondrial genome of the gilthead seabream Sparus aurata Linnaeus 1758, one of the world's most important mariculture species, was sequenced using next generation sequencing technology. The genome sequence is comprised of 16,652 bp exhibiting the canonical vertebrate mitochondria gene order. Regions of gene overlap, tRNA length, as well as start and stop codon were similar to those observed in other Sparidae. Phylogenetic reconstructions based on mitochondrial protein coding genes corroborate the view that Sparidae is paraphyletic and includes Centracanthidae.

Review of the Acanthopagrus latus complex (Perciformes: Sparidae) with descriptions of three new species from the Indo-West Pacific Ocean

Acanthopagrus latus, long considered a single valid Indo-West Pacific Ocean species, characterized by having yellow pelvic, anal and caudal fins, is reviewed and separated into A. latus (east Asian shelf) and Acanthopagrus longispinnis (Bengal Bay), and three new species: Acanthopagrus morrisoni sp. nov. (north-western Australia), Acanthopagrus arabicus sp. nov. [Middle East (except for the Red Sea) to coasts of Iran and Pakistan, and western Indian coast] and Acanthopagrus sheim sp. nov. (The Gulf). Although A. latus as redefined considerably varies in morphology and colouration, it can be recognized as a discrete east Asian endemic, with the following nominal species being junior synonyms: Chrysophrys auripes, Chrysophrys xanthopoda, Chrysophrys rubroptera and Sparus chrysopterus. Chrysophrys novaecaledoniae, known only from the holotype (type locality: Nouméa, New Caledonia), is a questionable junior synonym of A. latus, the lack of subsequent collections suggesting that the type locality is erroneous. Acanthopagrus longispinnis is differentiated from the other species in the complex by consistently having 12 dorsal-fin spines and a much larger second anal-fin spine, 21-26% (mean 23%) of standard length (LS ) (v. 14-24%, mean 18-21% in the other four species). Acanthopagrus morrisoni sp. nov. has the entire caudal fin yellow with a wide black posterior margin (persisting in preserved specimens) and consistently 3 ½ scale rows between the fifth dorsal-fin spine base and the lateral line. Acanthopagrus sheim sp. nov. has the pelvic, anal and lower caudal fins vivid yellow, with two (rarely three) small black blotches on the lower inter-radial membranes between the spinous and soft dorsal-fin rays. Acanthopagrus arabicus sp. nov. consistently has 4 ½ scale rows between the fifth dorsal-fin spine base and the lateral line, whereas A. latus always has black streaks proximally on the inter-radial membranes between the yellow anal-fin rays. A neotype and lectotye, respectively, are designated for A. latus and A. longispinnis. The p-distance (net nucleotide substitutions per site) of partial mitochondrial 16s ribosomal RNA genes (538 bp) among the above species (except A. longispinnis) and three other congeners (Acanthopagrus berda, Acanthopagrus pacificus and Acanthopagrus bifasciatus) strongly indicates that each is a distinct species. A key is provided for the 20 species of Acanthopagrus currently known from the Indo-West Pacific Ocean.

Phylogenetic perspectives on the evolution of functional hermaphroditism in teleost fishes

Hermaphroditism is taxonomically widespread among teleost fishes and takes on many forms including simultaneous, protogynous, and protandrous hermaphroditism, bidirectional sex change, and androdioecy. The proximate mechanisms that influence the timing, incidence, and forms of hermaphroditism in fishes are supported by numerous theoretical and empirical studies on their mating systems and sexual patterns, but few have examined aspects of sex-allocation theory or the evolution of hermaphroditism for this group within a strict phylogenetic context. Fortunately, species-level phylogenetic reconstructions of the evolutionary history of many lineages of fishes have emerged, providing opportunities for understanding fine-scale evolutionary pathways and transformations of sex allocation. Examinations of several families of fishes with adequate data on phylogeny, patterns of sex allocation, mating systems, and with some form of hermaphroditism reveal that the evolution and expression of protogyny and other forms of sex allocation show little evidence of phylogenetic inertia within specific lineages but rather are associated with particular mating systems in accordance with prevalent theories about sex allocation. Transformations from protogyny to gonochorism in groupers (Epinephelidae), seabasses (Serranidae), and wrasses and parrotfishes (Labridae) are associated with equivalent transformations in the structure of mating groups from spawning of pairs to group spawning and related increases in sperm competition. Similarly, patterns of protandry, androdioecy, simultaneous hermaphroditism, and bidirectional sex change in other lineages (Aulopiformes, Gobiidae, and Pomacentridae) match well with particular mating systems in accordance with sex-allocation theory. Unlike other animals and plants, we did not find evidence that transitions between hermaphroditism and gonochorism required functional intermediates. Two instances in which our general conclusions might not hold include the expression of protandry in the Sparidae and the distribution of simultaneous hermaphroditism. In the Sparidae, the association of hypothesized mating systems and patterns of sex allocation were not always consistent with the size-advantage model (SAM), in that certain protandric sparids show evidence of intense sperm competition that should favor the expression of gonochorism. In the other case, simultaneous hermaphroditism does not occur in some groups of monogamous fishes, which are similar in ecology to the hermaphroditic serranines, suggesting that this form of sex allocation may be more limited by phylogenetic inertia. Overall, this work strongly supports sexual lability within teleost fishes and confirms evolutionary theories of sex allocation in this group of vertebrates.

Estimating the rate of irreversibility in protein evolution

Whether or not evolutionary change is inherently irreversible remains a controversial topic. Some examples of evolutionary irreversibility are known; however, this question has not been comprehensively addressed at the molecular level. Here, we use data from 221 human genes with known pathogenic mutations to estimate the rate of irreversibility in protein evolution. For these genes, we reconstruct ancestral amino acid sequences along the mammalian phylogeny and identify ancestral amino acid states that match known pathogenic mutations. Such cases represent inherent evolutionary irreversibility because, at the present moment, reversals to these ancestral amino acid states are impossible for the human lineage. We estimate that approximately 10% of all amino acid substitutions along the mammalian phylogeny are irreversible, such that a return to the ancestral amino acid state would lead to a pathogenic phenotype. For a subset of 51 genes with high rates of irreversibility, as much as 40% of all amino acid evolution was estimated to be irreversible. Because pathogenic phenotypes do not resemble ancestral phenotypes, the molecular nature of the high rate of irreversibility in proteins is best explained by evolution with a high prevalence of compensatory, epistatic interactions between amino acid sites. Under such mode of protein evolution, once an amino acid substitution is fixed, the probability of its reversal declines as the protein sequence accumulates changes that affect the phenotypic manifestation of the ancestral state. The prevalence of epistasis in evolution indicates that the observed high rate of irreversibility in protein evolution is an inherent property of protein structure and function.

The ligand specificity of the G-protein-coupled receptor GPR34

Lyso-PS (lyso-phosphatidylserine) has been shown to activate the G(i/o)-protein-coupled receptor GPR34. Since in vitro and in vivo studies provided controversial results in assigning lyso-PS as the endogenous agonist for GPR34, we investigated the evolutionary conservation of agonist specificity in more detail. Except for some fish GPR34 subtypes, lyso-PS has no or very weak agonistic activity at most vertebrate GPR34 orthologues investigated. Using chimaeras we identified single positions in the second extracellular loop and the transmembrane helix 5 of carp subtype 2a that, if transferred to the human orthologue, enabled lyso-PS to activate the human GPR34. Significant improvement of agonist efficacy by changing only a few positions strongly argues against the hypothesis that nature optimized GPR34 as the receptor for lyso-PS. Phylogenetic analysis revealed several positions in some fish GPR34 orthologues which are under positive selection. These structural changes may indicate functional specification of these orthologues which can explain the species- and subtype-specific pharmacology of lyso-PS. Furthermore, we identified aminoethyl-carbamoyl ATP as an antagonist of carp GPR34, indicating ligand promiscuity with non-lipid compounds. The results of the present study suggest that lyso-PS has only a random agonistic activity at some GPR34 orthologues and the search for the endogenous agonist should consider additional chemical entities.

A phylogenetic perspective on the evolution of Mediterranean teleost fishes

The Mediterranean Sea is a highly diverse, highly studied, and highly impacted biogeographic region, yet no phylogenetic reconstruction of fish diversity in this area has been published to date. Here, we infer the timing and geographic origins of Mediterranean teleost species diversity using nucleotide sequences collected from GenBank. We assembled a DNA supermatrix composed of four mitochondrial genes (12S ribosomal DNA, 16S ribosomal DNA, cytochrome c oxidase subunit I and cytochrome b) and two nuclear genes (rhodopsin and recombination activating gene I), including 62% of Mediterranean teleost species plus 9 outgroups. Maximum likelihood and Bayesian phylogenetic and dating analyses were calibrated using 20 fossil constraints. An additional 124 species were grafted onto the chronogram according to their taxonomic affinity, checking for the effects of taxonomic coverage in subsequent diversification analyses. We then interpreted the time-line of teleost diversification in light of Mediterranean historical biogeography, distinguishing non-endemic natives, endemics and exotic species. Results show that the major Mediterranean orders are of Cretaceous origin, specifically ∼100–80 Mya, and most Perciformes families originated 80–50 Mya. Two important clade origin events were detected. The first at 100–80 Mya, affected native and exotic species, and reflects a global diversification period at a time when the Mediterranean Sea did not yet exist. The second occurred during the last 50 Mya, and is noticeable among endemic and native species, but not among exotic species. This period corresponds to isolation of the Mediterranean from Indo-Pacific waters before the Messinian salinity crisis. The Mediterranean fish fauna illustrates well the assembly of regional faunas through origination and immigration, where dispersal and isolation have shaped the emergence of a biodiversity hotspot.

High-throughput microsatellite marker development in two sparid species and verification of their transferability in the family Sparidae

Recently, 454 sequencing has emerged as a popular method for isolating microsatellites owing to cost-effectiveness and time saving. In this study, repeat-enriched libraries from two southern African endemic sparids (Pachymetopon blochii and Lithognathus lithognathus) were 454 GS-FLX sequenced. From these, 7370 sequences containing repeats (SCRs) were identified. A brief survey of 23 studies showed a significant difference between the number of SCRs when enrichment was performed first before 454 sequencing. We designed primers for 302 unique fragments containing more than five repeat units and suitable flanking regions. A fraction (<11%) of these loci were characterized with 18 polymorphic microsatellite loci (nine in each of the focal species) being described. Sanger sequencing of alleles confirmed that size variation was because of differences in the number of tandem repeats. However, a case of homoplasy and sequencing errors in the 454 sequencing were identified. These newly developed and four previously isolated loci were successfully used to identify polymorphic markers in nine other economically important species, representative of sparid diversity. The combination of newly developed markers with data from previous sparid cross-species studies showed a significant negative correlation between genetic divergence to focal species and microsatellite transferability. The high level of transferability we described (48% amplification success and 32% polymorphism) suggests that the 302 microsatellite loci identified represent an excellent resource for future studies on sparids. Microsatellite marker development should commonly include tests of transferability to reduce costs and increase feasibility of population genetics studies in nonmodel organisms.

Resolution of the Acanthopagrus black seabream complex based on mitochondrial and amplified fragment-length polymorphism analyses

In this study, DNA analyses were employed to verify the identity of six morphologically similar species that occur in the coastal waters of Taiwan: the black seabream complex (Acanthopagrus latus, Acanthopagrus schlegelii, Acanthopagrus sivicolus, Acanthopagrus taiwanensis, Acanthopagrus chinshira and Acanthopagrus pacificus). Amplified fragment-length polymorphism (AFLP) analyses clearly distinguished the same six species that are morphologically diagnosable based on subtle differences in scale counts and anal-fin colouration. In contrast, mitochondrial DNA analyses based on cytochrome b gene sequences did not distinguish individuals of A. schlegelii and A. sivicolus, reflecting either historical introgression or recent speciation and incomplete sorting of their mitochondrial lineages. Phylogenetic relationships among these six north-west Pacific Ocean species of Acanthopagrus analysed using AFLP data were consistent with scale rows above the lateral line (TRac), sperm ultrastructure and geographical distribution. The study provides molecular tools for future research relevant to improved management of these resources, and an increased understanding of the evolutionary history of this radiation.

Lamellodiscus euzeti n. sp. (Monogenea:Diplectanidae), a parasite from Dentex canariensis and D. gibbosus (Teleostei:Sparidae) in the Atlantic Ocean and Mediterranean Sea

Lamellodiscus euzeti n. sp. (Monogenea: Diplectanidae) is described from the gills of two sparid fishes, Dentex canariensis (Steindachner) off Senegal and Ivory Coast and D. gibbosus (Rafinesque) off Senegal and Tunisia. The new species belongs to the “ignoratus” group, characterized by a lamellodisc with complete lamellae, a “lyre” shaped male copulatory organ type, and the “ignoratus” sensu stricto subgroup, characterized by a haptor with simple lateral dorsal bars. Lamellodiscus euzeti n. sp can be distinguished from all the congeneric species of the “ignoratus” subgroup by the presence of a prominent protuberance at the base of the curved part of the simple piece of the male copulatory organ (MCO), a large bulb at the base of the bifurcated piece of the MCO and the presence of 5-6 spines in the distal portion of the axial branch of the bifurcated piece of the MCO. Specificity and biogeography of Lamellodiscus species from sparid fishes are discussed.

Discrimination of two picarel species Spicara flexuosa and Spicara maena (Pisces: Centracanthidae) based on mitochondrial DNA sequences

A DNA methodology based on PCR and sequencing analysis of the mtDNA 16S rRNA gene was developed for the discrimination of picarel Spicara flexuosa and blotched picarel Spicara maena (Pisces: Centracanthidae). The molecular results indicated that there is a clear discrimination between the two species, as all the individuals of S. flexuosa revealed the same 16S rDNA haplotype while the S. maena haplotype differs in 15 distinct nucleotides.