RNF213, a new nuclear marker for acanthomorph phylogeny

Elucidating the Mitogenomic Blueprint of Pomadasys perotaei from the Eastern Atlantic: Characterization and Matrilineal Phylogenetic Insights into Haemulid Grunts (Teleostei: Lutjaniformes)

The parrot grunt fish, Pomadasys perotaei, has a limited distribution in the Eastern Atlantic Ocean and is an important species in marine capture fisheries across several West African countries. Despite its ecological and economic significance, the mitogenomic information for this species is lacking. This study utilized next-generation sequencing to generate the de novo mitogenome of P. perotaei from Eastern Atlantic. The resulting mitogenome is 16,691 base pairs and includes 13 protein-coding genes (PCGs), 22 transfer RNAs, two ribosomal RNAs, and an AT-rich control region (CR). Most of the PCGs exhibit nonsynonymous (Ka) and synonymous (Ks) substitution rates of less than '1', indicating strong negative selection across haemulid fishes. The control region of Pomadasys species contains four conserved domains, as seen in other teleost's, with polymorphic nucleotides that can be used to study population structures through the amplification of short mitochondrial gene fragments. Additionally, Bayesian phylogenetic analysis based on PCGs revealed a non-monophyletic clustering pattern of Pomadasys within the haemulid matrilineal tree. Overall, the structural characterization and phylogenetic analysis enhance our understanding of the genetic composition and evolutionary history of Pomadasys species from the Indo-West Pacific and Eastern Atlantic Oceans.

Endemic Radiation of African Moonfish, Selene dorsalis (Gill 1863), in the Eastern Atlantic: Mitogenomic Characterization and Phylogenetic Implications of Carangids (Teleostei: Carangiformes)

This study offers an in-depth analysis of the mitochondrial genome of Selene dorsalis (Gill 1863), a species native to the Eastern Atlantic Ocean. The circular mitochondrial DNA molecule measures 16,541 base pairs and comprises 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and a control region (CR). The nucleotide composition exhibits a notable adenine-thymine (AT) bias, accounting for 53.13%, which aligns with other species in the Carangidae family. Most PCGs initiate with the ATG codon, with the exception of Cytochrome C oxidase subunit I, which starts with GTG. Analysis of relative synonymous codon usage reveals that leucine and serine are the most prevalent amino acids in the mitochondrial genome of S. dorsalis and its congeners (S. vomer and S. setapinnis). All tRNAs display the typical cloverleaf structure, though tRNA Serine (S1) lacks a dihydrouracil arm. Pairwise comparisons of synonymous and nonsynonymous substitutions for all PCGs yielded values below '1', indicating strong purifying selection. The CR spans 847 bp, representing 5.12% of the mitochondrial genome, and is characterized by high AT content (62.81%). It is situated between tRNA-Pro (TGG) and tRNA-Phe (GAA). The CR contains conserved sequence blocks, with CSB-1 being the longest at 22 bp and CSB-D the shortest at 18 bp. Phylogenetic analysis, using Bayesian and Maximum-likelihood trees constructed from concatenated PCGs across 72 species, successfully differentiates S. dorsalis from other carangids. This study also explores how ocean currents and gyres might influence lineage diversification and parapatric speciation of Selene species between the Atlantic and Pacific Oceans. These results highlight the importance of the mitochondrial genome in elucidating the structural organization and evolutionary dynamics of S. dorsalis and its relatives within marine ecosystems.

FishPIE: a universal phylogenetically informative exon markers set for ray-finned fishes

Understanding the evolutionary history of the highly diverse ray-finned fishes has been challenging, and the development of more universal primers for phylogenetic analyses may help overcoming these challenges. We developed FishPIE, a nested PCR primer set of 82 phylogenetically informative exon markers, and tested it on 203 species from 31 orders of Actinopterygii. We combined orthologous sequences of the FishPIE markers obtained from published genomes and transcriptomes and constructed the phylogeny of 710 species belonging to 190 families and 60 orders. The resulting phylogenies had topologies comparable to previous phylogenomic studies. We demonstrated that the FishPIE markers could address phylogenetic questions across broad taxonomic levels. By incorporating the newly sequenced taxa, we were able to shed new light on the phylogeny of the highly diverse Cypriniformes. Thus, FishPIE holds great promise for generating genetic data for broad taxonomic groups and accelerating our understanding of the fish tree of life.

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FishPIE is a nested PCR primer set of 82 markers for fish phylogenetic analysis

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The markers can be broadly applied to all orders of ray-finned fishes

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Their phylogenetic performance is comparable to that of genomic analyses

Phylogenetics of archerfishes (Toxotidae) and evolution of the toxotid shooting apparatus

Archerfishes (Toxotidae) are variously found in the fresh- and brackish-water environments of Asia Pacific and are well known for their ability to shoot water at terrestrial prey. These shots of water are intended to strike their prey and cause it to fall into the water for capture and consumption. While this behavior is well known, there are competing hypotheses (blowpipe vs. pressure tank hypothesis) of how archerfishes shoot and which oral structures are involved. Current understanding of archerfish shooting structures is largely based on two species, Toxotes chatareus and T. jaculatrix. We do not know if all archerfishes possess the same oral structures to shoot water, if anatomical variation is present within these oral structures, or how these features have evolved. Additionally, there is little information on the evolution of the Toxotidae as a whole, with all previous systematic works focusing on the interrelationships of the family. We first investigate the limits of archerfish species using new and previously published genetic data. Our analyses highlight that the current taxonomy of archerfishes does not conform to the relationships we recover. Toxotes mekongensis and T. siamensis are placed in synonymy of T. chatareus, Toxotes carpentariensis is recognized as a species and removed from synonymy of T. chatareus, and the genus Protoxotes is recognized for T. lorentzi based on the results of our analyses. We then take an integrative approach, using a combined analysis of discrete hard- and soft-tissue morphological characters with genetic data, to construct a phylogeny of the Toxotidae. Using the resulting phylogenetic hypothesis, we then characterize the evolutionary history and anatomical variation within the archerfishes. We discuss the variation in the oral structures and the evolution of the mechanism with respect to the interrelationships of archerfishes, and find that the oral structures of archerfishes support the blowpipe hypothesis but soft-tissue oral structures may also play a role in shooting. Finally, by comparing the morphology of archerfishes to their sister group, we find that the Leptobramidae has relevant shooting features in the oral cavity, suggesting that some components of the archerfish shooting mechanism are examples of co-opted or exapted traits.

Investigations into the ancestry of the Grape-eye Seabass (Hemilutjanus macrophthalmos) reveal novel limits and relationships for the Acropomatiformes (Teleostei: Percomorpha)

Abstract For 175 years, an unremarkable bass, the Grape-eye Seabass (Hemilutjanus macrophthalmos), has been known from coastal waters in the Eastern Pacific. To date, its phylogenetic placement and classification have been ignored. A preliminary osteological examination of Hemilutjanus hinted that it may have affinities with the Acropomatiformes. To test this hypothesis, we conducted a phylogenetic analysis using UCE and Sanger sequence data to study the placement of Hemilutjanus and the limits and relationships of the Acropomatiformes. We show that Hemilutjanus is a malakichthyid, and our results corroborate earlier studies that have resolved a polyphyletic Polyprionidae; accordingly, we describe Stereolepididae, new family, for Stereolepis. With these revisions, the Acropomatiformes is now composed of the: Acropomatidae; Banjosidae; Bathyclupeidae; Champsodontidae; Creediidae; Dinolestidae; Epigonidae; Glaucosomatidae; Hemerocoetidae; Howellidae; Lateolabracidae; Malakichthyidae; Ostracoberycidae; Pempheridae; Pentacerotidae; Polyprionidae; Scombropidae; Stereolepididae, new family; Symphysanodontidae; Synagropidae; and Schuettea. Finally, using our new hypothesis, we demonstrate that acropomatiforms repeatedly evolved bioluminescence and transitioned between shallow waters and the deep sea.

The Emerging Phylogenetic Perspective on the Evolution of Actinopterygian Fishes

The emergence of a new phylogeny of ray-finned fishes at the turn of the twenty-first century marked a paradigm shift in understanding the evolutionary history of half of living vertebrates. We review how the new ray-finned fish phylogeny radically departs from classical expectations based on morphology. We focus on evolutionary relationships that span the backbone of ray-finned fish phylogeny, from the earliest divergences among teleosts and nonteleosts to the resolution of major lineages of Percomorpha. Throughout, we feature advances gained by the new phylogeny toward a broader understanding of ray-finned fish evolutionary history and the implications for topics that span from the genetics of human health to reconsidering the concept of living fossils. Additionally, we discuss conceptual challenges that involve reconciling taxonomic classification with phylogenetic relationships and propose an alternate higher-level classification for Percomorpha. Our review highlights remaining areas of phylogenetic uncertainty and opportunities for comparative investigations empowered by this new phylogenetic perspective on ray-finned fishes.

Comprehensive phenotypic phylogenetic analysis supports the monophyly of stromateiform fishes (Teleostei: Percomorphacea)

More than half the ray-finned fishes and about one-quarter of all living vertebrates belong to Percomorphacea. Among its 30 orders, Stromateiformes encompass 77 species in 16 genera and six families. Stromateiform monophyly has never been tested using morphology, and it has been rejected by molecular analyses. This comprehensive revision of Stromateiformes includes all its valid genera of all percomorph families previously aligned with the order. We sampled 207 phenotypic characters in 66 terminal taxa representing 14 orders and 46 acanthopterygian families. This dataset significantly surpasses all previous phenotype-based phylogenies of Stromateiformes, which analysed only a fraction of these characters. Stromateiformes is recovered as monophyletic, supported by eight unequivocal synapomorphies. Amarsipidae is the sister group of all other Stromateiformes (= Stromateoidei). Centrolophidae is paraphyletic, with three of its genera allocated into an early-diverging clade and the other four appearing as successive sister groups to a lineage containing the remaining stromateiforms. All other stromateoid families are monophyletic, with the following cladistic arrangement: (Nomeidae (Stromateidae (Tetragonuridae, Ariommatidae))). Our analysis convincingly refutes recent molecular phylogenetic interpretations that fail to recover a monophyletic Stromateiformes. These findings call into question large-scale conclusions of percomorph relationships and trait evolution based solely on molecular data.

Testing the utility of alternative metrics of branch support to address the ancient evolutionary radiation of tunas, stromateoids, and allies (Teleostei: Pelagiaria)

The use of high-throughput sequencing technologies to produce genome-scale datasets was expected to settle some long-standing controversies across the Tree of Life, particularly in areas where short branches occur at deep timescales. Instead, these datasets have often yielded many well-supported but conflicting topologies, and highly variable gene-tree distributions. A variety of branch-support metrics beyond the nonparametric bootstrap are now available to assess how robust a phylogenetic hypothesis may be, as well as new methods to quantify gene-tree discordance. We applied multiple branch support metrics to an ancient group of marine fishes (Teleostei: Pelagiaria) whose interfamilial relationships have proven difficult to resolve due to a rapid accumulation of lineages very early in its history. We analyzed hundreds of loci including published UCE data and newly generated exonic data along with their flanking regions to represent all 16 extant families for more than 150 out of 284 valid species in the group. Branch support was lower for interfamilial relationships (except the SH-like aLRT and aBayes methods) regardless of the type of marker used. Several nodes that were highly supported with bootstrap had very low site and gene-tree concordance, revealing underlying conflict. Despite this conflict, we were able to identify four consistent interfamilial clades, each comprised of two or three families. Combining exons with their flanking regions also produced increased branch lengths in the deep branches of the pelagiarian tree. Our results demonstrate the limitations of employing current metrics of branch support and species-tree estimation when assessing the confidence of ancient evolutionary radiations and emphasize the necessity to embrace alternative measurements to explore phylogenetic uncertainty and discordance in phylogenomic datasets.

Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics

Exon markers have a long history of use in phylogenetics of ray-finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralogues that can mislead phylogenetic analysis. We present seven new probe sets for current target-capture phylogenomic protocols that capture 1,104 exons explicitly filtered for paralogues using gene trees. These seven probe sets span the diversity of teleost fishes, including four sets that target five hyperdiverse percomorph clades which together comprise ca. 17,000 species (Carangaria, Ovalentaria, Eupercaria, and Syngnatharia + Pelagiaria combined). We additionally included probes to capture legacy nuclear exons and mitochondrial markers that have been commonly used in fish phylogenetics (despite some exons being flagged for paralogues) to facilitate integration of old and new molecular phylogenetic matrices. We tested these probes experimentally for 56 fish species (eight species per probe set) and merged new exon-capture sequence data into an existing data matrix of 1,104 exons and 300 ray-finned fish species. We provide an optimized bioinformatics pipeline to assemble exon capture data from raw reads to alignments for downstream analysis. We show that legacy loci with known paralogues are at risk of assembling duplicated sequences with target-capture, but we also assembled many useful orthologous sequences that can be integrated with many PCR-generated matrices. These probe sets are a valuable resource for advancing fish phylogenomics because targeted exons can easily be extracted from increasingly available whole genome and transcriptome data sets, and also may be integrated with existing PCR-based exon and mitochondrial data.

The paleoichthyofauna housed in the Colección Nacional de Paleontología of Universidad Nacional Autónoma de México

Fishes are a paraphyletic group composed by craniates except for the four-limbed clade Tetrapoda. This group was the only vertebrate representative until the Devonian but now comprises almost half of the vertebrate species, dominating nearly all aquatic environments. The fossil record is the key to understand the ancient paleobiodiversity and the patterns that lead the modern fish fauna, and paleontological collections play a fundamental role in providing accommodation, maintenance, and access to the specimens and their respective metadata. Here we present a systematic checklist of fossil fishes housed in the type collection of the Colección Nacional de Paleontología which is located at the Instituto de Geología of Universidad Nacional Autónoma de México. Currently housed in the type collection are 14 chondrichthyan specimens, belonging to two superorders, five orders, seven families, 10 genera, and five nominal species, and 361 osteichthyan specimens, belonging to eight orders, nine families, nine genera, and 26 nominal species. These fossils come from 32 localities and 15 geological units, which range temporally from the Jurassic to the Pleistocene. The paleoichthyofauna housed in the type collection of the Colección Nacional de Paleontología is remarkable for its singularity and reveals new insights about the origin and diversification of many groups of fishes. The recovery and curation of this fossil material indicates that knowledge of Mexican fossil fish diversity and its role in understanding lower vertebrate evolution are just emerging and reaffirms the importance of the biological and paleontological collections to the future biodiversity research.

Flatfish monophyly refereed by the relationship of Psettodes in Carangimorphariae

Background

The monophyly of flatfishes has not been supported in many molecular phylogenetic studies. The monophyly of Pleuronectoidei, which comprises all but one family of flatfishes, is broadly supported. However, the Psettodoidei, comprising the single family Psettodidae, is often found to be most closely related to other carangimorphs based on substantial sequencing efforts and diversely analytical methods. In this study, we examined why this particular result is often obtained.

Results

The mitogenomes of five flatfishes were determined. Select mitogenomes of representative carangimorph species were further employed for phylogenetic and molecular clock analyses. Our phylogenetic results do not fully support Psettodes as a sister group to pleuronectoids or other carangimorphs. And results also supported the evidence of long-branch attraction between Psettodes and the adjacent clades. Two chronograms, derived from Bayesian relaxed-clock methods, suggest that over a short period in the early Paleocene, a series of important evolutionary events occurred in carangimorphs.

Conclusion

Based on insights provided by the molecular clock, we propose the following evolutionary explanation for the difficulty in determining the phylogenetic position of Psettodes: The initial diversification of Psettodes was very close in time to the initial diversification of carangimorphs, and the primary diversification time of pleuronectoids, the other suborder of flatfishes, occurred later than that of some percomorph taxa. Additionally, the clade of Psettodes is long and naked branch, which supports the uncertainty of its phylogenetic placement. Finally, we confirmed the monophyly of flatfishes, which was accepted by most ichthyologists.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4788-5) contains supplementary material, which is available to authorized users.

Multi-gene phylogeny of jacks and pompanos (Carangidae), including placement of monotypic vadigo Campogramma glaycos

In this study, the phylogenetic trees of jacks and pompanos (Carangidae), an ecologically and morphologically diverse, globally distributed fish family, are inferred from a complete, concatenated data set of two mitochondrial (cytochrome c oxidase I, cytochrome b) loci and one nuclear (myosin heavy chain 6) locus. Maximum likelihood and Bayesian inferences are largely congruent and show a clear separation of Carangidae into the four subfamilies: Scomberoidinae, Trachinotinae, Naucratinae and Caranginae. The inclusion of the carangid sister lineages Coryphaenidae (dolphinfishes) and Rachycentridae (cobia), however, render Carangidae paraphyletic. The phylogenetic trees also show with high statistical support that the monotypic vadigo Campogramma glaycos is the sister to all other species within the Naucratinae.

Phylogenetic classification of bony fishes

BACKGROUND

Fish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review of the main criteria used by ichthyologists to define their classifications during the last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, the trend has been to rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with explicit phylogenetic support with arbitrary groupings. Two leading sources in ichthyology frequently used for fish classifications (JS Nelson's volumes of Fishes of the World and W. Eschmeyer's Catalog of Fishes) fail to adopt a global phylogenetic framework despite much recent progress made towards the resolution of the fish Tree of Life. The first explicit phylogenetic classification of bony fishes was published in 2013, based on a comprehensive molecular phylogeny ( www.deepfin.org ). We here update the first version of that classification by incorporating the most recent phylogenetic results.

RESULTS

The updated classification presented here is based on phylogenies inferred using molecular and genomic data for nearly 2000 fishes. A total of 72 orders (and 79 suborders) are recognized in this version, compared with 66 orders in version 1. The phylogeny resolves placement of 410 families, or ~80% of the total of 514 families of bony fishes currently recognized. The ordinal status of 30 percomorph families included in this study, however, remains uncertain (incertae sedis in the series Carangaria, Ovalentaria, or Eupercaria). Comments to support taxonomic decisions and comparisons with conflicting taxonomic groups proposed by others are presented. We also highlight cases were morphological support exist for the groups being classified.

CONCLUSIONS

This version of the phylogenetic classification of bony fishes is substantially improved, providing resolution for more taxa than previous versions, based on more densely sampled phylogenetic trees. The classification presented in this study represents, unlike any other, the most up-to-date hypothesis of the Tree of Life of fishes.

Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements

Phylogenetics is undergoing a revolution as large-scale molecular datasets reveal unexpected but repeatable rearrangements of clades that were previously thought to be disparate lineages. One of the most unusual clades of fishes that has been found using large-scale molecular datasets is an expanded Syngnathiformes including traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), as well as a diverse set of largely benthic-associated fishes (Callionymoidei, Dactylopteridae, Mullidae, Pegasidae) that were previously dispersed across three orders. The monophyly of this surprising clade of fishes has been upheld by recent studies utilizing both nuclear and mitogenomic data, but the relationships among major lineages within Syngnathiformes remain ambiguous; previous analyses have inconsistent topologies and are plagued by low support at deep divergences between the major lineages. In this study, we use a dataset of ultraconserved elements (UCEs) to conduct the first phylogenomic study of Syngnathiformes. UCEs have been effective markers for resolving deep phylogenetic relationships in fishes and, combined with increased taxon sampling, we expected UCEs to resolve problematic syngnathiform relationships. Overall, UCEs were effective at resolving relationships within Syngnathiformes at a range of evolutionary timescales. We find consistent support for the monophyly of traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), which better agrees with morphological hypotheses than previously published topologies from molecular data. This result was supported by all Bayesian and maximum likelihood analyses, was robust to differences in matrix completeness and potential sources of bias, and was highly supported in coalescent-based analyses in ASTRAL when matrices were filtered to contain the most phylogenetically informative loci. While Bayesian and maximum likelihood analyses found support for a benthic-associated clade (Callionymidae, Dactylopteridae, Mullidae, and Pegasidae) as sister to the long-snouted clade, this result was not replicated in the ASTRAL analyses. The base of our phylogeny is characterized by short internodes separating major syngnathiform lineages and is consistent with the hypothesis of an ancient rapid radiation at the base of Syngnathiformes. Syngnathiformes therefore present an exciting opportunity to study patterns of morphological variation and functional innovation arising from rapid but ancient radiation.

Fin modules: an evolutionary perspective on appendage disparity in basal vertebrates

BACKGROUND

Fishes are extremely speciose and also highly disparate in their fin configurations, more specifically in the number of fins present as well as their structure, shape, and size. How they achieved this remarkable disparity is difficult to explain in the absence of any comprehensive overview of the evolutionary history of fish appendages. Fin modularity could provide an explanation for both the observed disparity in fin configurations and the sequential appearance of new fins. Modularity is considered as an important prerequisite for the evolvability of living systems, enabling individual modules to be optimized without interfering with others. Similarities in developmental patterns between some of the fins already suggest that they form developmental modules during ontogeny. At a macroevolutionary scale, these developmental modules could act as evolutionary units of change and contribute to the disparity in fin configurations. This study addresses fin disparity in a phylogenetic perspective, while focusing on the presence/absence and number of each of the median and paired fins.

RESULTS

Patterns of fin morphological disparity were assessed by mapping fin characters on a new phylogenetic supertree of fish orders. Among agnathans, disparity in fin configurations results from the sequential appearance of novel fins forming various combinations. Both median and paired fins would have appeared first as elongated ribbon-like structures, which were the precursors for more constricted appendages. Among chondrichthyans, disparity in fin configurations relates mostly to median fin losses. Among actinopterygians, fin disparity involves fin losses, the addition of novel fins (e.g., the adipose fin), and coordinated duplications of the dorsal and anal fins. Furthermore, some pairs of fins, notably the dorsal/anal and pectoral/pelvic fins, show non-independence in their character distribution, supporting expectations based on developmental and morphological evidence that these fin pairs form evolutionary modules.

CONCLUSIONS

Our results suggest that the pectoral/pelvic fins and the dorsal/anal fins form two distinct evolutionary modules, and that the latter is nested within a more inclusive median fins module. Because the modularity hypotheses that we are testing are also supported by developmental and variational data, this constitutes a striking example linking developmental, variational, and evolutionary modules.

Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye

Background

Flatfish cranial asymmetry represents one of the most remarkable morphological innovations among vertebrates, and has fueled vigorous debate on the manner and rate at which strikingly divergent phenotypes evolve. A surprising result of many recent molecular phylogenetic studies is the lack of support for flatfish monophyly, where increasingly larger DNA datasets of up to 23 loci have either yielded a weakly supported flatfish clade or indicated the group is polyphyletic. Lack of resolution for flatfish relationships has been attributed to analytical limitations for dealing with processes such as nucleotide non-stationarity and incomplete lineage sorting (ILS). We tackle this phylogenetic problem using a sequence dataset comprising more than 1,000 ultraconserved DNA element (UCE) loci covering 45 carangimorphs, the broader clade containing flatfishes and several other specialized lineages such as remoras, billfishes, and archerfishes.

Results

We present a phylogeny based on UCE loci that unequivocally supports flatfish monophyly and a single origin of asymmetry. We document similar levels of discordance among UCE loci as in previous, smaller molecular datasets. However, relationships among flatfishes and carangimorphs recovered from multilocus concatenated and species tree analyses of our data are robust to the analytical framework applied and size of data matrix used. By integrating the UCE data with a rich fossil record, we find that the most distinctive carangimorph bodyplans arose rapidly during the Paleogene (66.0–23.03 Ma). Flatfish asymmetry, for example, likely evolved over an interval of no more than 2.97 million years.

Conclusions

The longstanding uncertainty in phylogenetic hypotheses for flatfishes and their carangimorph relatives highlights the limitations of smaller molecular datasets when applied to successive, rapid divergences. Here, we recovered significant support for flatfish monophyly and relationships among carangimorphs through analysis of over 1,000 UCE loci. The resulting time-calibrated phylogeny points to phenotypic divergence early within carangimorph history that broadly matches with the predictions of adaptive models of lineage diversification.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0786-x) contains supplementary material, which is available to authorized users.

Ectodysplasin signalling genes and phenotypic evolution in sculpins (Cottus)

Despite their deeply conserved function among vertebrates, ectodysplasin (Eda) signalling genes are involved in microevolutionary change in humans and sticklebacks. If such a dual role is common, Eda signalling genes constitute hotspots for morphological evolution. Variation in sculpin (Cottus) skin prickling and body shape resembles patterns caused by variation in Eda signalling in sticklebacks. We mapped Eda signalling genes and performed quantitative trait locus mapping in crosses between Cottus rhenanus and Cottus perifretum. A genomic region containing the Eda receptor (Edar) was strongly associated with prickling and contributed to shape. The expression of Edar in developing prickles and skeletal elements in Cottus was confirmed by in situ hybridization. Coding sequence changes between Edar alleles in C. rhenanus and C. perifretum exceeded sequence differentiation in other vertebrates. However, it is likely that additional genetic elements besides coding changes affect the phenotypic variation. Although the phenotype in a natural hybrid lineage between C. rhenanus and C. perifretum resembles C. perifretum, the respective coding Edar alleles are not fully fixed (88.6%). Hence, our results support an involvement of Eda signalling in microevolutionary changes, but imply that the Edar gene is affected by multiple evolutionary processes that vary among freshwater sculpins.

Molecular phylogenetic reconstruction and taxonomic investigation of eelpouts (Cottoidei: Zoarcales) based on Co-1 and Cyt-b mitochondrial genes

The infraorder Zoarcales (Cottoidei), or eelpouts, includes about 400 species of coldwater fishes concentrated mainly in the North Pacific. To date, the molecular phylogenetic methods in combination with morphological data have significantly contributed to understanding the taxonomic composition of this group and made it possible to confirm/refute validity of some families of obscure origin. In spite of the growing amount of new data on taxonomy and evolution of eelpouts, a consideration of the original and independent data is obviously needed to verify the existing knowledge of this taxon. In this study, which is based on concatenated matrix of Co-1 and Cyt-b mitochondrial genes, as well as relying on the samples from seven families and 45 species of eelpouts, we have reconstructed the phylogeny, which is generally consistent with previous inferences. Despite the resolution of the original data matrix is low, we have demonstrated the monophyletic origin of the families Zoarcidae and Anarhichadidae, as well as Neozoarcidae, previously related to Stichaeidae and recently revised Eulophiidae. The polyphyletic patterns amongst some subfamilies in Stichaeidae have been confirmed, whereas Opisthocentrinae and Pholidae seem to constitute a valid family-level taxon. Our results provide new opportunities with respect to taxonomic relationships in the complex and diverse group of eelpouts , whose part in the tree of life is not covered by recently flourishing multilocus phylogeny of teleost fishes. In light of the data obtained, the necessity of more unified and reproducible approaches to resolve the issues of evolution and taxonomy of such a complex group as Zoarcales becomes more evident.

From commensalism to parasitism in Carapidae (Ophidiiformes): heterochronic modes of development?

Phenotypic variations allow a lineage to move into new regions of the adaptive landscape. The purpose of this study is to analyse the life history of the pearlfishes (Carapinae) in a phylogenetic framework and particularly to highlight the evolution of parasite and commensal ways of life. Furthermore, we investigate the skull anatomy of parasites and commensals and discuss the developmental process that would explain the passage from one form to the other. The genus Carapus forms a paraphyletic grouping in contrast to the genus Encheliophis, which forms a monophyletic cluster. The combination of phylogenetic, morphologic and ontogenetic data clearly indicates that parasitic species derive from commensal species and do not constitute an iterative evolution from free-living forms. Although the head morphology of Carapus species differs completely from Encheliophis, C. homei is the sister group of the parasites. Interestingly, morphological characteristics allowing the establishment of the relation between Carapus homei and Encheliophis spp. concern the sound-producing mechanism, which can explain the diversification of the taxon but not the acquisition of the parasite morphotype. Carapus homei already has the sound-producing mechanism typically found in the parasite form but still has a commensal way of life and the corresponding head structure. Moreover, comparisons between the larval and adult Carapini highlight that the adult morphotype "Encheliophis" is obtained by going beyond the adult stage reached by Carapus. The entrance into the new adaptive landscape could have been realised by at least two processes: paedomorphosis and allometric repatterning.

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.

Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment

BACKGROUND

The past decade has witnessed remarkable progress towards resolution of the Tree of Life. However, despite the increased use of genomic scale datasets, some phylogenetic relationships remain difficult to resolve. Here we employ anchored phylogenomics to capture 107 nuclear loci in 29 species of acanthomorph teleost fishes, with 25 of these species sampled from the recently delimited clade Ovalentaria. Previous studies employing multilocus nuclear exon datasets have not been able to resolve the nodes at the base of the Ovalentaria tree with confidence. Here we test whether a phylogenomic approach will provide better support for these nodes, and if not, why this may be.

RESULTS

After using a novel method to account for paralogous loci, we estimated phylogenies with maximum likelihood and species tree methods using DNA sequence alignments of over 80,000 base pairs. Several key relationships within Ovalentaria are well resolved, including 1) the sister taxon relationship between Cichlidae and Pholidichthys, 2) a clade containing blennies, grammas, clingfishes, and jawfishes, and 3) monophyly of Atherinomorpha (topminnows, flyingfishes, and silversides). However, many nodes in the phylogeny associated with the early diversification of Ovalentaria are poorly resolved in several analyses. Through the use of rarefaction curves we show that limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny does not appear to be due to a deficiency of data, as average global node support ceases to increase when only 1/3rd of the sampled loci are used in analyses. Instead this lack of resolution may be driven by model misspecification as a Bayesian mixed model analysis of the amino acid dataset provided good support for parts of the base of the Ovalentaria tree.

CONCLUSIONS

Although it does not appear that the limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny is due to a deficiency of data, it may be that both stochastic and systematic error resulting from model misspecification play a role in the poor resolution at the base of the Ovalentaria tree as a Bayesian approach was able to resolve some of the deeper nodes, where the other methods failed.

Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes

Ultraconserved elements (UCEs) have become popular markers in phylogenomic studies because of their cost effectiveness and their potential to resolve problematic phylogenetic relationships. Although UCE datasets typically contain a much larger number of loci and sites than more traditional datasets of PCR-amplified, single-copy, protein coding genes, a fraction of UCE sites are expected to be part of a nearly invariant core, and the relative performance of UCE datasets versus protein coding gene datasets is poorly understood. Here we use phylogenetic informativeness (PI) to compare the resolving power of multi-locus and UCE datasets in a sample of percomorph fishes with sequenced genomes (genome-enabled). We compare three data sets: UCE core regions, flanking sequence adjacent to the UCE core and a set of ten protein coding genes commonly used in fish systematics. We found the net informativeness of UCE core and flank regions to be roughly ten-fold and 100-fold more informative than that of the protein coding genes. On a per locus basis UCEs and protein coding genes exhibited similar levels of phylogenetic informativeness. Our results suggest that UCEs offer enormous potential for resolving relationships across the percomorph tree of life.

Identification of the notothenioid sister lineage illuminates the biogeographic history of an Antarctic adaptive radiation

BACKGROUND

Antarctic notothenioids are an impressive adaptive radiation. While they share recent common ancestry with several species-depauperate lineages that exhibit a relictual distribution in areas peripheral to the Southern Ocean, an understanding of their evolutionary origins and biogeographic history is limited as the sister lineage of notothenioids remains unidentified. The phylogenetic placement of notothenioids among major lineages of perciform fishes, which include sculpins, rockfishes, sticklebacks, eelpouts, scorpionfishes, perches, groupers and soapfishes, remains unresolved. We investigate the phylogenetic position of notothenioids using DNA sequences of 10 protein coding nuclear genes sampled from more than 650 percomorph species. The biogeographic history of notothenioids is reconstructed using a maximum likelihood method that integrates phylogenetic relationships, estimated divergence times, geographic distributions and paleogeographic history.

RESULTS

Percophis brasiliensis is resolved, with strong node support, as the notothenioid sister lineage. The species is endemic to the subtropical and temperate Atlantic coast of southern South America. Biogeographic reconstructions imply the initial diversification of notothenioids involved the western portion of the East Gondwanan Weddellian Province. The geographic disjunctions among the major lineages of notothenioids show biogeographic and temporal correspondence with the fragmentation of East Gondwana.

CONCLUSIONS

The phylogenetic resolution of Percophis requires a change in the classification of percomorph fishes and provides evidence for a western Weddellian origin of notothenioids. The biogeographic reconstruction highlights the importance of the geographic and climatic isolation of Antarctica in driving the radiation of cold-adapted notothenioids.

The infrabranchial musculature and its bearing on the phylogeny of percomorph fishes (Osteichthyes: Teleostei)

The muscles serving the ventral portion of the gill arches ( = infrabranchial musculature) are poorly known in bony fishes. A comparative analysis of the infrabranchial muscles in the major percomorph lineages reveals a large amount of phylogenetically-relevant information. Characters derived from this anatomical system are identified and discussed in light of current hypotheses of phylogenetic relationships among percomorphs. New evidence supports a sister-group relationship between the Batrachoidiformes and Lophiiformes and between the Callionymoidei and Gobiesocoidei. Investigated data also corroborate the existence of two monophyletic groups, one including the Pristolepididae, Badidae, and Nandidae, and a second clade consisting of all non-amarsipid stromateiforms. New synapomorphies are proposed for the Atherinomorphae, Blenniiformes, Lophiiformes, Scombroidei (including Sphyraenidae), and Gobiiformes. Within the latter order, the Rhyacichthyidae and Odontobutidae are supported as the successive sister families of all remaining gobiiforms. The present analysis further confirms the validity of infrabranchial musculature characters previously proposed to support the grouping of the Mugiliformes with the Atherinomorphae and the monophyly of the Labriformes with the possible inclusion of the Pholidichthyiformes. Interestingly, most hypotheses of relationships supported by the infrabranchial musculature have been advanced by preceding anatomists on the basis of distinct data sources, but were never recovered in recent molecular phylogenies. These conflicts clearly indicate the current unsatisfactory resolution of the higher-level phylogeny of percomorphs.

Mitochondrial genomic investigation of flatfish monophyly

We present the first study to use whole mitochondrial genome sequences to examine phylogenetic affinities of the flatfishes (Pleuronectiformes). Flatfishes have attracted attention in evolutionary biology since the early history of the field because understanding the evolutionary history and patterns of diversification of the group will shed light on the evolution of novel body plans. Because recent molecular studies based primarily on DNA sequences from nuclear loci have yielded conflicting results, it is important to examine phylogenetic signal in different genomes and genome regions. We aligned and analyzed mitochondrial genome sequences from thirty-nine pleuronectiforms including nine that are newly reported here, and sixty-six non-pleuronectiforms (twenty additional clade L taxa [Carangimorpha or Carangimorpharia] and forty-six secondary outgroup taxa). The analyses yield strong support for clade L and weak support for the monophyly of Pleuronectiformes. The suborder Pleuronectoidei receives moderate support, and as with other molecular studies the putatively basal lineage of Pleuronectiformes, the Psettodoidei is frequently not most closely related to other pleuronectiforms. Within the Pleuronectoidei, the basal lineages in the group are poorly resolved, however several flatfish subclades receive consistent support. The affinities of Lepidoblepharon and Citharoides among pleuronectoids are particularly uncertain with these data.

Dispersal capacity predicts both population genetic structure and species richness in reef fishes

Dispersal is a fundamental species characteristic that should directly affect both rates of gene flow among spatially distributed populations and opportunities for speciation. Yet no single trait associated with dispersal has been demonstrated to affect both micro- and macroevolutionary patterns of diversity across a diverse biological assemblage. Here, we examine patterns of genetic differentiation and species richness in reef fishes, an assemblage of over 7,000 species comprising approximately one-third of the extant bony fishes and over one-tenth of living vertebrates. In reef fishes, dispersal occurs primarily during a planktonic larval stage. There are two major reproductive and parental investment syndromes among reef fishes, and the differences between them have implications for dispersal: (1) benthic guarding fishes lay negatively buoyant eggs, typically guarded by the male parent, and from these eggs hatch large, strongly swimming larvae; in contrast, (2) pelagic spawning fishes release small floating eggs directly into the water column, which drift unprotected before small weakly swimming larvae hatch. Using phylogenetic comparative methods, we show that benthic guarders have significantly greater population structure than pelagic spawners and additionally that taxonomic families of benthic guarders are more species rich than families of pelagic spawners. Our findings provide a compelling case for the continuity between micro- and macroevolutionary processes of biological diversification and underscore the importance of dispersal-related traits in influencing the mode and tempo of evolution.

Mitogenomic circumscription of a novel percomorph fish clade mainly comprising "Syngnathoidei" (Teleostei)

Percomorpha, comprising about 60% of modern teleost fishes, has been described as the "(unresolved) bush at the top" of the tree, with its intrarelationships still being ambiguous owing to huge diversity (>15,000 species). Recent molecular phylogenetic studies based on extensive taxon and character sampling, however, have revealed a number of unexpected clades of Percomorpha, and one of which is composed of Syngnathoidei (seahorses, pipefishes, and their relatives) plus several groups distributed across three different orders. To circumscribe the clade more definitely, we sampled several candidate taxa with reference to the previous studies and newly determined whole mitochondrial genome (mitogenome) sequences for 16 percomorph species across syngnathoids, dactylopterids, and their putatively closely-related fishes (Mullidae, Callionymoidei, Malacanthidae). Unambiguously aligned sequences (13,872 bp) from those 16 species plus 78 percomorphs and two outgroups (total 96 species) were subjected to partitioned Bayesian and maximum likelihood analyses. The resulting trees revealed a highly supported clade comprising seven families in Syngnathoidei (Gasterosteiformes), Dactylopteridae (Scorpaeniformes), Mullidae in Percoidei and two families in Callionymoidei (Perciformes). We herein proposed to call this clade "Syngnathiformes" following the latest nuclear DNA studies with some revisions on the included families.

Evaluating the effects of non-neutral molecular markers on phylogeny inference

Nucleotide substitution models used in molecular phylogenetics do not account for nucleotide sequences evolving under selection, yet selection is rarely tested for. If non-neutral markers violate these models (i.e. non-independence of sites), it is expected that their reconstructed topologies be incongruent with those inferred from neutral ones and conclusions made from those phylogenies should be reexamined. Using rhodopsin as a phylogenetic marker has recently been called into question for exactly this reason. Rhodopsin is assumed to have evolved under strong positive selection for organisms that inhabit similar aquatic environments, making it unsuitable for the phylogenetics of aquatic organisms, but it is unclear what the effects of non-neutrality on phylogeny estimation are. To evaluate potential incongruence of neutral versus non-neutral markers, and the notion that rhodopsin should not be used in the molecular phylogenetics of fishes, a molecular dataset of 78 acanthomorph taxa and sequences from four nuclear, protein coding loci (including rhodopsin), were examined. Only one marker was found to be neutral while the remaining tests, for all other loci, rejected the null hypothesis of neutrality. To evaluate the possible effect(s) of positively versus negatively selected sites, the three non-neutral markers were analyzed to determine the presence of positively and negatively selected codons. To determine congruence in topology among ML trees inferred by individual neutral and non-neutral markers, as well as the combined (concatenated) dataset, tree, comparisons of distances among trees and hypothesis (topology) testing were carried out. Results of the tree distance metrics and topology testing support the notion that neutrality alone does not determine congruence in topology, and those data that are inferred to have evolved under selection should not necessarily be excluded. In addition, the number of sites inferred to have evolved under positive selection does not predict congruence with other markers or the topology inferred with the concatenated dataset.

Are flatfishes (Pleuronectiformes) monophyletic?

All extant species of flatfish (order Pleuronectiformes) are thought to descend from a common ancestor, and therefore to represent a monophyletic group. This hypothesis is based largely on the dramatic bilateral asymmetry and associated ocular migration characteristics of all flatfish. Yet, molecular-based phylogenetic studies have been inconclusive on this premise. Support for flatfish monophyly has varied with differences in taxonomic and gene region sampling schemes. Notably, the genus Psettodes has been found to be more related to non-flatfishes than to other flatfishes in many recent studies. The polyphyletic nature of the Pleuronectiformes is often inferred to be the result of weak historical signal and/or artifact of phylogenetic inference due to a bias in the data. In this study, we address the question of pleuronectiform monophyly with a broad set of markers (from six phylogenetically informative nuclear loci) and inference methods designed to limit the influence of phylogenetic artifacts. Concomitant with a character-rich analytical strategy, an extensive taxonomic sampling of flatfish and potential close relatives is used to increase power and resolution. Results of our analyses are most consistent with a non-monophyletic Pleuronectiformes with Psettodes always being excluded. A fossil-calibrated Bayesian relaxed clock analysis estimates the age of Pleuronectoidei to be 73 Ma, and the time to most recent common ancestor of Pleuronectoidei, Psettodes, and other relative taxa to be 77 Ma. The ages are much older than the records of any fossil pleuronectiform currently recognized. We discuss our findings in the context of the available morphological evidence and discuss the compatibility of our molecular hypothesis with morphological data regarding extinct and extant flatfish forms.

Contribution to the study of acoustic communication in two Belgian river bullheads (Cottus rhenanus and C. perifretum) with further insight into the sound-producing mechanism

BACKGROUND

The freshwater sculpins (genus Cottus) are small, bottom-living fishes widely distributed in North America and Europe. The taxonomy of European species has remained unresolved for a long time due to the overlap of morphological characters. Sound production has already been documented in some cottid representatives, with sounds being involved in courtship and agonistic interactions. Although the movements associated with sound production have been observed, the underlying mechanism remains incomplete. Here, we focus on two closely related species from Belgium: C. rhenanus and C. perifretum. This study aims 1) to record and to compare acoustic communication in both species, 2) to give further insight into the sound-producing mechanism and 3) to look for new morphological traits allowing species differentiation.

RESULTS

Both Cottus species produce multiple-pulsed agonistic sounds using a similar acoustic pattern: the first interpulse duration is always longer, making the first pulse unit distinct from the others. Recording sound production and hearing abilities showed a clear relationship between the sound spectra and auditory thresholds in both species: the peak frequencies of calls are around 150 Hz, which corresponds to their best hearing sensitivity. However, it appears that these fishes could not hear acoustic signals produced by conspecifics in their noisy habitat considering their hearing threshold expressed as sound pressure (~ 125 dB re 1 μPa). High-speed video recordings highlighted that each sound is produced during a complete back and forth movement of the pectoral girdle.

CONCLUSIONS

Both Cottus species use an acoustic pattern that remained conserved during species diversification. Surprisingly, calls do not seem to have a communicative function. On the other hand, fish could detect substrate vibrations resulting from movements carried out during sound production. Similarities in temporal and spectral characteristics also suggest that both species share a common sound-producing mechanism, likely based on pectoral girdle vibrations. From a morphological point of view, only the shape of the spinelike scales covering the body allows species differentiation.

Parasites as biological tags of fish stocks: a meta-analysis of their discriminatory power

The use of parasites as biological tags to discriminate among marine fish stocks has become a widely accepted method in fisheries management. Here, we first link this approach to its unstated ecological foundation, the decay in the similarity of the species composition of assemblages as a function of increasing distance between them, a phenomenon almost universal in nature. We explain how distance decay of similarity can influence the use of parasites as biological tags. Then, we perform a meta-analysis of 61 uses of parasites as tags of marine fish populations in multivariate discriminant analyses, obtained from 29 articles. Our main finding is that across all studies, the observed overall probability of correct classification of fish based on parasite data was about 71%. This corresponds to a two-fold improvement over the rate of correct classification expected by chance alone, and the average effect size (Zr = 0·463) computed from the original values was also indicative of a medium-to-large effect. However, none of the moderator variables included in the meta-analysis had a significant effect on the proportion of correct classification; these moderators included the total number of fish sampled, the number of parasite species used in the discriminant analysis, the number of localities from which fish were sampled, the minimum and maximum distance between any pair of sampling localities, etc. Therefore, there are no clear-cut situations in which the use of parasites as tags is more useful than others. Finally, we provide recommendations for the future usage of parasites as tags for stock discrimination, to ensure that future applications of the method achieve statistical rigour and a high discriminatory power.

Phylogeny and biogeography of a shallow water fish clade (Teleostei: Blenniiformes)

BACKGROUND

The Blenniiformes comprises six families, 151 genera and nearly 900 species of small teleost fishes closely associated with coastal benthic habitats. They provide an unparalleled opportunity for studying marine biogeography because they include the globally distributed families Tripterygiidae (triplefin blennies) and Blenniidae (combtooth blennies), the temperate Clinidae (kelp blennies), and three largely Neotropical families (Labrisomidae, Chaenopsidae, and Dactyloscopidae). However, interpretation of these distributional patterns has been hindered by largely unresolved inter-familial relationships and the lack of evidence of monophyly of the Labrisomidae.

RESULTS

We explored the phylogenetic relationships of the Blenniiformes based on one mitochondrial (COI) and four nuclear (TMO-4C4, RAG1, Rhodopsin, and Histone H3) loci for 150 blenniiform species, and representative outgroups (Gobiesocidae, Opistognathidae and Grammatidae). According to the consensus of Bayesian Inference, Maximum Likelihood, and Maximum Parsimony analyses, the monophyly of the Blenniiformes and the Tripterygiidae, Blenniidae, Clinidae, and Dactyloscopidae is supported. The Tripterygiidae is the sister group of all other blennies, and the Blenniidae is the sister group of the remaining blennies. The monophyly of the Labrisomidae is supported with the exclusion of the Cryptotremini and inclusion of Stathmonotus, and we elevate two subgenera of Labrisomus to establish a monophyletic classification within the family. The monophyly of the Chaenopsidae is supported with the exclusion of Stathmonotus (placed in the Stathmonotini) and Neoclinus and Mccoskerichthys (placed in the Neoclinini). The origin of the Blenniiformes was estimated in the present-day IndoPacific region, corresponding to the Tethys Sea approximately 60.3 mya. A largely Neotropical lineage including the Labrisomidae, Chaenopsidae and Dactyloscopidae (node IV) evolved around 37.6 mya when the Neotropics were increasingly separated from the IndoPacific, but well before the closure of the Tethys Sea.

CONCLUSIONS

Relationships recovered in this study are similar to those of earlier analyses within the Clinidae and Chaenopsidae, and partially similar within the Blenniidae, but tripterygiid relationships remain poorly resolved. We present the first comprehensive phylogenetic hypothesis for a monophyletic Labrisomidae with five tribes (Labrisomini, Mnierpini, Paraclinini, Stathmonotini and Starksiini). Global distributions of blenny genera included in our analysis support the evolution of a largely Neotropical clade whose closest relatives (clinids and cryptotremines) are temperate in distribution.

Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families

Uncertainties surrounding the evolutionary origin of the epipelagic fish family Scombridae (tunas and mackerels) are symptomatic of the difficulties in resolving suprafamilial relationships within Percomorpha, a hyperdiverse teleost radiation that contains approximately 17,000 species placed in 13 ill-defined orders and 269 families. Here we find that scombrids share a common ancestry with 14 families based on (i) bioinformatic analyses using partial mitochondrial and nuclear gene sequences from all percomorphs deposited in GenBank (10,733 sequences) and (ii) subsequent mitogenomic analysis based on 57 species from those targeted 15 families and 67 outgroup taxa. Morphological heterogeneity among these 15 families is so extraordinary that they have been placed in six different perciform suborders. However, members of the 15 families are either coastal or oceanic pelagic in their ecology with diverse modes of life, suggesting that they represent a previously undetected adaptive radiation in the pelagic realm. Time-calibrated phylogenies imply that scombrids originated from a deep-ocean ancestor and began to radiate after the end-Cretaceous when large predatory epipelagic fishes were selective victims of the Cretaceous-Paleogene mass extinction. We name this clade of open-ocean fishes containing Scombridae “Pelagia” in reference to the common habitat preference that links the 15 families.